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diff --git a/README-hacking.md b/README-hacking.md index ad44d3c..6d02976 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -1,8 +1,8 @@ Maneage: managing data lineage ============================== -Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2020-2025 Raul Infante-Sainz <infantesainz@gmail.com>\ +Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2020-2026 Raul Infante-Sainz <infantesainz@gmail.com>\ See the end of the file for license conditions. Maneage is a **fully working template** for doing reproducible research (or @@ -174,82 +174,179 @@ Published works using Maneage The list below shows some of the works that have already been published with (earlier versions of) Maneage, and some that have been recently -submitted for peer review. The previous version of Maneage was called -"Reproducible paper template", with a separate git tree. Maneage is -evolving rapidly, so some details will differ between the different -versions. The more recent papers will tend to be the most useful as good -working examples. - +submitted for peer review. Maneage is evolving rapidly, so some details +will differ between the different versions. The more recent papers will +tend to be the most useful as good working examples if you are just +starting. + +In the list below, by clicking on the paper's publication year, you will be +taken to the paper's indexed page on the [SciX Digital +Library](https://scixplorer.org) (successor to the [NASA +ADS](https://ui.adsabs.harvard.edu)) which contains further bibliographic +information like title, DOI and etc, in a unified format (independent of +which journal the paper is published in). + + - Eskandarlou et + al. ([2026](https://scixplorer.org/abs/2026arXiv260322166E), A&A + accepted; + arXiv:[2603.22166](https://arxiv.org/abs/2510.2603.22166)). The + project's version controlled source is on + [Gitlab](https://gitlab.com/sepideh.esk/alba), necessary software, + outputs and backup of history are available at + [zenodo.17674805](http://doi.org/10.5281/zenodo.17674805); and the + archived git history is available at + [swh:1:dir:7c203a565ec6ef40d8419dbdf70e8639b78f4b99](https://archive.softwareheritage.org/swh:1:dir:7c203a565ec6ef40d8419dbdf70e8639b78f4b99;origin=https://gitlab.com/Sepideh.Esk/alba;visit=swh:1:snp:adc584ff3540ea3151de6ebc8462805e8818b1f4;anchor=swh:1:rev:f9d0f9cb25c80415107c962cc53d369a650e9b82). + - Eskandarlou et + al. ([2026](https://scixplorer.org/abs/2026A%26A...705A..67E), A&A, + Volume 705, id.A67, 14 pp; + arXiv:[2510.12940](https://arxiv.org/abs/2510.12940)). The project's + version controlled source is on + [Gitlab](https://gitlab.com/sepideh.esk/psf-j-plus), necessary software, + outputs and backup of history are available at + [zenodo.17348653](http://doi.org/10.5281/zenodo.17348653); and the + archived git history is available at + [swh:1:dir:fc95ed9ad173de6fa64690e3d71ab041c630f32c](https://archive.softwareheritage.org/swh:1:dir:fc95ed9ad173de6fa64690e3d71ab041c630f32c;origin=https://gitlab.com/Sepideh.Esk/psf-j-plus;visit=swh:1:snp:31bb4550902f7902a0a65d0674106271de776d3e;anchor=swh:1:rev:4860c70d6285a60300e429889e8637e98568a915). + - Saremi et al. ([2025](https://scixplorer.org/abs/2025A%26A...701A.116S), + A&A, Volume 701, id.A116, 18 pp.; + arXiv:[2508.02780](https://arxiv.org/abs/2508.02780)). The project's + version controlled source is on + [Gitlab](https://gitlab.com/nasim-projects/pipeline), necessary + software, outputs and backup of history are available at + [zenodo.16152699](https://doi.org/10.5281/zenodo.16152699); and the + archived git history is available at + [swh:1:dir:b3657cfb6053fd976695bd63c15cb99e5095648a](https://archive.softwareheritage.org/swh:1:dir:b3657cfb6053fd976695bd63c15cb99e5095648a;origin=https://gitlab.com/nasim-projects/pipeline;visit=swh:1:snp:ab7c6f0b9999f42d77154103c1bc082fa23b325c;anchor=swh:1:rev:afeb282c01983cba2a11eb4b2f25d5a40d35c164). + - Eskandarlou & Akhlaghi + ([2024](https://scixplorer.org/abs/2024RNAAS...8..168E), RNAAS, Volume + 8, Issue 6, id.168; + arXiv:[2406.14619](https://arxiv.org/abs/2406.14619)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `polar-plot` + branch). Necessary software, outputs and backup of history are available + at [zenodo.11403643](https://doi.org/10.5281/zenodo.11403643); and the + archived git history is available at + [swh:1:dir:4e09bf85f9f87336fa55920bf67e7bcf6d58bbd5](https://archive.softwareheritage.org/swh:1:dir:4e09bf85f9f87336fa55920bf67e7bcf6d58bbd5;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:557ee1a90de465659659ecc46df0c5ce29d0bb61;anchor=swh:1:rev:375e12e52080006be6a28e10980e79ef54d13d1d). + - Infante-Sainz et + al. ([2024](https://scixplorer.org/abs/2024RNAAS...8...22I), RNAAS, + Volume 8, Issue 1, id.22; + arXiv:[2401.05303](https://arxiv.org/abs/2401.05303)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `radial-profile` + branch). Necessary software, outputs and backup of history are available + at [zenodo.10124582](https://doi.org/10.5281/zenodo.10124582); and the + archived git history is available at + [swh:1:dir:d5029e066916cb64f0d95d20eb88294acc78b2b1](https://archive.softwareheritage.org/swh:1:dir:d5029e066916cb64f0d95d20eb88294acc78b2b1;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:b065324c2ef3b48bc26e8f30e48102a1abd2052f;anchor=swh:1:rev:61764447b16da44538e5ddbf7fb69937ba138e81). + - Infante-Sainz & Akhlaghi + ([2024](https://scixplorer.org/abs/2024RNAAS...8...10I), RNAAS, Volume + 8, Issue 1, id.10; + arXiv:[2401.03814](https://arxiv.org/abs/2401.03814)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `color-faint-gray` + branch). Necessary software, outputs and backup of history are available + at [zenodo.10058165](https://doi.org/10.5281/zenodo.10058165); and the + archived git history is available at + [swh:1:dir:1064a48d4bb58d6684c3df33c6633a04d4141d2d](https://archive.softwareheritage.org/swh:1:dir:1064a48d4bb58d6684c3df33c6633a04d4141d2d;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:a083ff647c571f895d1ccc9f7432fa1b9a1d03a8;anchor=swh:1:rev:ff77b619daa50b05ddd83206d979d1f8a53d040b). + - Peper, Roukema & Bolejko + ([2023](https://scixplorer.org/abs/2023MNRAS.525...91P), MNRAS, 525, 91, + DOI:10.1093/mnras/stad2246, + arXiv:[2304.00591](https://arxiv.org/abs/2304.00591)): The live version + of the controlled source is [at + Codeberg](https://codeberg.org/mpeper/lensing); the main input + dataset, a software snapshot, the software tarballs, the project outputs + and editing history are available at + [zenodo.8103985](https://zenodo.org/record/8103985); and the archived + git history is available at + [swh:1:dir:f57fd0e254bcb976c1ab34b6c9c9708e891f7914](https://archive.softwareheritage.org/swh:1:dir:f57fd0e254bcb976c1ab34b6c9c9708e891f7914;origin=https://codeberg.org/mpeper/lensing;visit=swh:1:snp:984413c49bb02ee0eec88c3ac01614808d57beb7;anchor=swh:1:rev:185c36f1b6263588526be3881078626869041882). + - Eskandarlou et + al. ([2023](https://scixplorer.org/abs/2023RNAAS...7..269E), RNAAS, + Volume 7, Issue 12, id.269; + arXiv:[2312.04263](https://arxiv.org/abs/2312.04263)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `zeropoint` + branch). Necessary software, outputs and backup of history are available + at [zenodo.10256845](https://doi.org/10.5281/zenodo.10256845); and the + archived git history is available at + [swh:1:dir:8b2d1f63be96de3de03aa3e2bb68fa7fa52df56f](https://archive.softwareheritage.org/swh:1:dir:8b2d1f63be96de3de03aa3e2bb68fa7fa52df56f;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:e37e226bab517eef24d854467682b2fcf5d7dc32;anchor=swh:1:rev:ea682783d83707c0e1d114a5de74a100be9f545d). + - Akhlaghi ([2023](https://scixplorer.org/abs/2023RNAAS...7..211A), RNAAS), Volume 7, Issue + 10, id.211; arXiv:[2310.15006](https://arxiv.org/abs/2310.15006)). The + project's version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the + `pointing-simulate` branch). - Borkowska & Roukema - ([2022](https://ui.adsabs.harvard.edu/abs/2021arXiv211214174B), MNRAS - Submitted, arXiv:2112.14174): The live version of the controlled source - is [at Codeberg](https://codeberg.org/boud/gevcurvtest); the main input + ([2022](https://scixplorer.org/abs/2022CQGra..39u5007B), Classical and + Quantum Gravity, Volume 39, Issue 21, id.215007, 29 pp; + arXiv:[2112.14174](https://arxiv.org/abs/2112.14174)): The live version + of the controlled source is [at + Codeberg](https://codeberg.org/boud/gevcurvtest); the main input dataset, a software snapshot, the software tarballs, the project outputs and editing history are available at [zenodo.5806027](https://doi.org/10.5281/zenodo.5806027); and the - archived git history is available at [swh:1:rev:54398b720ddbac269ede30bf1e27fe27f07567f7](https://archive.softwareheritage.org/browse/revision/54398b720ddbac269ede30bf1e27fe27f07567f7). - - - Peper & Roukema - ([2021](https://ui.adsabs.harvard.edu/abs/2021MNRAS.505.1223P), MNRAS, - 505, 1223, DOI:10.1093/mnras/stab1342, arXiv:2010.03742): The live - version of the controlled source is [at + archived git history is available at + [swh:1:rev:54398b720ddbac269ede30bf1e27fe27f07567f7](https://archive.softwareheritage.org/browse/revision/54398b720ddbac269ede30bf1e27fe27f07567f7). + - Peper & Roukema ([2021](https://scixplorer.org/abs/2021MNRAS.505.1223P), + MNRAS, 505, 1223; arXiv:[2010.03742](https://arxiv.org/abs/2010.03742)): + The live version of the controlled source is [at Codeberg](https://codeberg.org/boud/elaphrocentre); the main input dataset, a software snapshot, the software tarballs, the project outputs and editing history are available at [zenodo.4699702](https://zenodo.org/record/4699702); and the archived git history is available at [swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e](https://archive.softwareheritage.org/swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e). - - - Roukema ([2021](https://ui.adsabs.harvard.edu/abs/2021PeerJ...911856R), - PeerJ, 9:e11856, arXiv:2007.11779): The live version of the controlled - source is [at Codeberg](https://codeberg.org/boud/subpoisson); the main - input dataset, a software snapshot, the software tarballs, the project - outputs and editing history are available at + - Roukema ([2021](https://scixplorer.org/abs/2021PeerJ...911856R), PeerJ, + Vol. 9, article id. e11856; + arXiv:[2007.11779](https://arxiv.org/abs/2007.11779)): The live version + of the controlled source is [at + Codeberg](https://codeberg.org/boud/subpoisson); the main input dataset, + a software snapshot, the software tarballs, the project outputs and + editing history are available at [zenodo.4765705](https://zenodo.org/record/4765705); and the archived git history is available at [swh:1:rev:72242ca8eade9659031ea00394a30e0cc5cc1c37](https://archive.softwareheritage.org/swh:1:rev:72242ca8eade9659031ea00394a30e0cc5cc1c37). - - - Akhlaghi et - al. ([2021](https://ui.adsabs.harvard.edu/abs/2021CSE....23c..82A), - CiSE, 23(3), 82 DOI:10.1109/MCSE.2021.3072860 arXiv:2006.03018): The - project's version controlled source is [on + - Akhlaghi et al. ([2021](https://scixplorer.org/abs/2021CSE....23c..82A), + CiSE, 23(3), 82; arXiv:[2006.03018](https://arxiv.org/abs/2006.03018)): + The project's version controlled source is [on Gitlab](https://gitlab.com/makhlaghi/maneage-paper), necessary software, outputs and backup of history are available at [zenodo.3872248](https://doi.org/10.5281/zenodo.3872248); and the archived git history is available at [swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717](https://archive.softwareheritage.org/swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717). - - Infante-Sainz et - al. ([2020](https://ui.adsabs.harvard.edu/abs/2020MNRAS.491.5317I), - MNRAS, 491, 5317): The version controlled project source is available - [on GitLab](https://gitlab.com/infantesainz/sdss-extended-psfs-paper) - and is also archived on Zenodo with all the necessary software tarballs: + al. ([2020](https://scixplorer.org/abs/2020MNRAS.491.5317I), MNRAS, 491, + 5317; arXiv:[1911.01430](https://arxiv.org/abs/1911.01430)): The version + controlled project source is available [on + GitLab](https://gitlab.com/infantesainz/sdss-extended-psfs-paper) and is + also archived on Zenodo with all the necessary software tarballs: [zenodo.3524937](https://zenodo.org/record/3524937). - - - Akhlaghi ([2019](https://arxiv.org/abs/1909.11230), IAU Symposium - 355). The version controlled project source is available - [on GitLab](https://gitlab.com/makhlaghi/iau-symposium-355) and is also + - Akhlaghi ([2019](https://scixplorer.org/abs/2019arXiv190911230A), IAU + Symposium 355; + arXiv:[1909.11230](https://arxiv.org/abs/1909.11230)). The version + controlled project source is available [on + GitLab](https://gitlab.com/makhlaghi/iau-symposium-355) and is also archived on Zenodo with all the necessary software tarballs: [zenodo.3408481](https://doi.org/10.5281/zenodo.3408481). +The items below were the precursors to Maneage. In other words, the work to +have reproducible results in the items below lead to what is now +Maneage. They are therefore much less complete than what Maneage is today, +but are important from a historical perspective. - Section 7.3 of Bacon et - al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A - 608, A1): The version controlled project source is available [on + al. ([2017](https://scixplorer.org/abs/2017A%26A...608A...1B), A&A 608, + A1; arXiv:[1710.03002](https://arxiv.org/abs/1710.03002)): The version + controlled project source is available [on GitLab](https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes) and a snapshot of the project along with all the necessary input datasets and outputs is available in [zenodo.1164774](https://doi.org/10.5281/zenodo.1164774). - - Section 4 of Bacon et - al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A, - 608, A1): The version controlled project is available [on + al. ([2017](https://scixplorer.org/abs/2017A%26A...608A...1B), A&A, 608, + A1; arXiv:[1710.03002](https://arxiv.org/abs/1710.03002)): The version + controlled project is available [on GitLab](https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry) and a snapshot of the project along with all the necessary input datasets is available in [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746). - - Akhlaghi & Ichikawa - ([2015](http://adsabs.harvard.edu/abs/2015ApJS..220....1A), ApJS, 220, - 1): The version controlled project is available [on + ([2015](https://scixplorer.org/abs/2015ApJS..220....1A), ApJS, 220, 1; + arXiv:[1505.01664](https://arxiv.org/abs/1505.01664)): The version + controlled project is available [on GitLab](https://gitlab.com/makhlaghi/NoiseChisel-paper). This is the very first (and much less mature!) incarnation of Maneage: the history of Maneage started more than two years after this paper was @@ -482,26 +579,25 @@ project files. However, file dates are important in the current design of Maneage: Make checks the dates of the prerequisite files and target files to see if the target should be re-built. -To fix this problem, for Maneage we use a forked version of -[Metastore](https://github.com/mohammad-akhlaghi/metastore). Metastore use -a binary database file (which is called `.file-metadata`) to keep the -modification dates of all the files under version control. This file is -also under version control, but is hidden (because it shouldn't be modified -by hand). During the project's configuration, Maneage installs to Git hooks -to run Metastore 1) before making a commit to update its database with the -file dates in a branch, and 2) after doing a checkout, to reset the -file-dates after the checkout is complete and re-set the file dates back to -what they were. +This is relevant, for example, in the `analysis/` side of calculations when +a rule in a `reproduce/analysis/make/SOMETHING.mk` is dependent on +`reproduce/analysis/conf/SOMETHING.conf` (where `SOMETHING` is one of the +science pipeline steps that you have prepared). Switching back and forth +between git branches will update the timestamp on `SOMETHING.conf`, +incorrectly implying, according to the Make rules, that a rule in +SOMETHING.mk has to be run again. -In practice, Metastore should work almost fully invisibly within your -project. The only place you might notice its presence is that you'll see -`.file-metadata` in the list of modified/staged files (commonly after -merging your branches). Since its a binary file, Git also won't show you -the changed contents. In a merge, you can simply accept any changes with -`git add -u`. But if Git is telling you that it has changed without a merge -(for example if you started a commit, but canceled it in the middle), you -can just do `git checkout .file-metadata` and set it back to its original -state. +To address this problem, you can use the `touch` command to backdate the +timestamp of files that you want to be considered to be old. For example +with the command below: + +```shell +$ touch --date=2000-01-01 reproduce/analysis/conf/SOMETHING.conf +$ ls -l reproduce/analysis/conf/SOMETHING.conf # to check +``` + +You may want to use a date that is obviously (to you) fake, so that you +don't accidentally believe the date later on. @@ -580,7 +676,47 @@ First custom commit $ pwd # Just to confirm where you are. ``` - 2. **Prepare to build project**: The `./project configure` command of the + 2. The final job of Maneage is to create your paper's PDF. By default it + uses a custom LaTeX style that resembles that of the Astrophysical + Journal (because the precusor of Maneage was for [Akhlaghi & Ichikawa + 2015](https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A)). The + journal you plan to submit your paper to will have its own separate + style. So it is best that you start your project by writing in the + desired style. We have already customized Maneage for the official + styles of some journals. To find them, run `git branch -r | grep + journal`. If your planned journal is one of them, you can take the + following steps to start your project based on that journal's style. If + it is not in these, you can ignore this step for now and customize the + style later (you can model based on these branchs). In the commands + below, we'll assume you want to prepare for the Astronomy and + Astrophysics journal (A&A). + + ```shell + $ git checkout -b journal origin-maneage/journal-a-and-a + $ git log -1 --oneline | awk '{print $1}' # To keep the commit hash + $ git rebase -i main # See description below + ``` + + In the first text editor that opens after the last command, change all + (except the first) `pick`s into `squash`, then save the change and + close the editor. In case there is no conflict, the second editor will + be pre-filled with all the commit messages in that branch. You do not + need those, so you can delete everything and write a commit message + like the following: `A&A journal (commit XXXXX of Maneage's + journal-a-and-a branch)`. Just replace the `XXXXX` with the output of + the second command above. The commit hash is important to be stored + here since it allows you to later check if any updates have been made + in that branch in the future. After completing the git rebase operation + (last command above), run the following commands below to put the new + commit in your `main` branch (and continue working based on that). + + ```shell + $ git checkout main + $ git merge journal + $ git branch -D journal + ``` + + 3. **Prepare to build project**: The `./project configure` command of the next step will build the different software packages within the "build" directory (that you will specify). Nothing else on your system will be touched. However, since it takes long, it is useful to see @@ -600,7 +736,7 @@ First custom commit $ ./project --check-config ``` - 3. **Test Maneage**: Before making any changes, it is important to test it + 4. **Test Maneage**: Before making any changes, it is important to test it and see if everything works properly with the commands below. If there is any problem in the `./project configure` or `./project make` steps, please contact us to fix the problem before continuing. Since the @@ -618,7 +754,7 @@ First custom commit # Open 'paper.pdf' and see if everything is ok. ``` - 4. **Setup the remote**: You can use any [hosting + 5. **Setup the remote**: You can use any [hosting facility](https://en.wikipedia.org/wiki/Comparison_of_source_code_hosting_facilities) that supports Git to keep an online copy of your project's version controlled history. We recommend [GitLab](https://gitlab.com) because @@ -646,7 +782,7 @@ First custom commit git push origin maneage # Push 'maneage' branch to 'origin' (no tracking). ``` - 5. **Title**, **short description** and **author**: You can start adding + 6. **Title**, **short description** and **author**: You can start adding your name (with your possible coauthors) and tentative abstract in `paper.tex`. You should see the relevant place in the preamble (prior to `\begin{document}`. Just note that some core project metadata like @@ -659,7 +795,7 @@ First custom commit specific journal's style), please feel free to use it your own methods after finishing this checklist and doing your first commit. - 6. **Delete dummy parts**: Maneage contains some parts that are only for + 7. **Delete dummy parts**: Maneage contains some parts that are only for the initial/test run, mainly as a demonstration of important steps, which you can use as a reference to use in your own project. But they not for any real analysis, so you should remove these parts as @@ -712,7 +848,7 @@ First custom commit $ ./project make ``` - 7. **Ignore changes in some Maneage files**: One of the main advantages of + 8. **Ignore changes in some Maneage files**: One of the main advantages of Maneage is that you can later update your infra-structure by merging your `main` branch with the `maneage` branch. This is good for many low-level features that you will likely never modify yourself. But it @@ -744,7 +880,7 @@ First custom commit $ git add .gitattributes ``` - 8. **Copyright and License notice**: It is necessary that _all_ the + 9. **Copyright and License notice**: It is necessary that _all_ the "copyright-able" files in your project (those larger than 10 lines) have a copyright and license notice. Please take a moment to look at several existing files to see a few examples. The copyright notice is @@ -762,11 +898,11 @@ First custom commit and generally, all the files you modified in the previous step. ``` - Copyright (C) 2018-2025 Existing Name <existing@email.address> - Copyright (C) 2025-2025 YOUR NAME <YOUR@EMAIL.ADDRESS> + Copyright (C) 2018-2026 Existing Name <existing@email.address> + Copyright (C) 2026-2026 YOUR NAME <YOUR@EMAIL.ADDRESS> ``` - 9. **Configure Git for fist time**: If this is the first time you are + 10. **Configure Git for fist time**: If this is the first time you are running Git on this system, then you have to configure it with some basic information in order to have essential information in the commit messages (ignore this step if you have already done it). Git will @@ -780,7 +916,7 @@ First custom commit $ git config --global core.editor nano ``` - 10. **Your first commit**: You have already made some small and basic + 11. **Your first commit**: You have already made some small and basic changes in the steps above and you are in your project's `main` branch. So, you can officially make your first commit in your project's history and push it. But before that, you need to make sure @@ -799,7 +935,7 @@ First custom commit $ git push # Push your commit to your remote. ``` - 11. **Read the publication checklist**: The publication checklist below is + 12. **Read the publication checklist**: The publication checklist below is very similar to this one, but for the final phase of your project. For now, you don't have to do any of its steps, but reading it will give you good insight into the later stages of your project. If you already @@ -809,7 +945,7 @@ First custom commit Making it much easier to complete that checklist when you are ready for submission. - 12. **Start your exciting research**: You are now ready to add flesh and + 13. **Start your exciting research**: You are now ready to add flesh and blood to this raw skeleton by further modifying and adding your exciting research steps. You can use the "published works" section in the introduction (above) as some fully working models to learn @@ -993,7 +1129,7 @@ $ git status # Just for a check above) with the classification `both modified:`. Open one of these files with your favorite text editor and correct the conflict (placed in between `<<<<<<<`, `=======` and `>>>>>>>`). Once all conflicts in a file are -remoted, the file will be automatically removed from the "Unmerged paths" +removed, the file will be automatically removed from the "Unmerged paths" of `git status`. So run `git status` after correcting the conflicts of each file just to make sure things are clean. TIP: If you want the changes in one file to be only from a special branch (`maneage` or `main`, completely @@ -1319,6 +1455,50 @@ future. are public). If not, you can mention that everything is ready for such a submission after acceptance. + * Some journals (like the "Astronomy and Astrophysics" journal) + require that only a single LaTeX file be submitted without any + commens (along with all the figures). In other words, they do not + want any sub-directories: only a single LaTeX file, one `.bbl` file + and one PDF per figure. Here is how you can do this: + ```shell + # If you don't already have 'latexpand' in your OS, install it: + $ tlmgr install latexpand + + # Unpack the tarball and make a directory for a single-LaTeX source. + $ tar -xf maneaged-XXXXXXX.tar.gz + $ cd maneaged-XXXXXXX.tar.gz + $ mkdir one-latex + + ## The '--empty-comments' and subsequent call to AWK (that removes + ## lines starting with '%') is because we need the lines ending in a + ## '%' for some LaTeX macros). + $ latexpand paper.tex --output=one-latex/paper-0.tex \ + --empty-comments + $ awk '!/^%/' one-latex/paper-0.tex > one-latex/paper.tex + $ rm one-latex/paper-0.tex + + ## Copy the other necessary files (if you are using specific journal + ## style files, also copy them). + $ cp paper.bbl one-latex/ + $ cp tex/tikz/*.pdf one-latex/ + + ## Correct the location of the images. + $ sed -i -e's|tex/tikz/|./|' one-latex/paper.tex + ``` + + * You can confirm the contents of the `one-latex` directory made + above by running `pdflatex paper` inside that directory. Your + operating system's LaTeX may not have all the necessary packages, + in that case run `tlmgr install XXXXX` (where `XXXXX` is the + value of `texlive-packages` in + `reproduce/software/config/texlive-packages.conf`. Afterwards, + clean up all the temporary files with this command: + ```shell + $ rm *.log *.aux *.auxlock *.bcf *.out *.xml + ``` + + * Upload the contents of this `one-latex` directory to the journal. + - **Future versions**: Both Zenodo and arXiv allow uploading new versions after your first publication. So it is recommended to put more recent versions of your published projects later (for example after applying @@ -1678,6 +1858,41 @@ for the benefit of others. +Maneage Development Workflow +============================ + +Maneage users can only use it by developing it, therefore Maneage is a very +unique software: the boundary between a user and developer is very blurry +by design/philosophy. We hope that all users can contribute to the +`maneage` branch for project-agnostic bugs/features that they fix/add. In +this section, the development workflow is described: + + - At any point that you find a bug or want to share a fix, anyone is + welcome to open a "Bug" or "Task" on GNU Savannah (which is the main + project management interface of Maneage). In case the submitter already + has a commit to merge, they can fork Maneage (similar to [this forking + tutorial](https://www.gnu.org/software/gnuastro/manual/html_node/Forking-tutorial.html)) + and share their commit in the Savannah post. + + - The review of bugs and merge requests will happen at the earliest + possible time for the maintainer. At this point, the maintainer will + create a new development branch over the `maneage` branch in a + development repository (not the main Maneage repository) and all + separate merge requests will be rebased over that branch. Finally, all + the commits in that branch will be `squash`ed into a single commit that + will be merged over the `maneage` branch. Of course, every contributor + will be acknowledged in the squashed commit for their contribution. + + - The `squash`ing into a single commit is intentionally done because the + `maneage` branch is shared between all projects that use Maneage and + we do not want to introduce complexity in their history by preserving + all the various development commits that were done before the + merge. + + - After the merge, the development branch may be deleted from the + development repository: any historically relevant point that you find + when making a commit should be written as comments within the source + (to be preserved during the squash) and not in the commit message. @@ -1,7 +1,7 @@ Reproducible source for XXXXXXXXXXXXXXXXX ------------------------------------------------------------------------- -Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This is the reproducible project source for the paper titled "**XXX XXXXX @@ -1,4 +1,4 @@ -%% Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% See the end of the file for license conditions. \documentclass[10pt, twocolumn]{article} @@ -3,8 +3,8 @@ # High-level script to manage the project. # Run './project --help' for a description of how to use it. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/bash/download-multi-try.sh b/reproduce/analysis/bash/download-multi-try.sh index bea88d5..16950b5 100755 --- a/reproduce/analysis/bash/download-multi-try.sh +++ b/reproduce/analysis/bash/download-multi-try.sh @@ -31,7 +31,7 @@ # reason, you don't want to use a lock file, set the 'lockfile' name to # 'nolock'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf index 5860806..7373503 100644 --- a/reproduce/analysis/config/INPUTS.conf +++ b/reproduce/analysis/config/INPUTS.conf @@ -105,7 +105,7 @@ # also called '%' (if your local copy of the input dataset and the only # repository names are the same, be sure to set '%' accordingly). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf index ba8c960..80eb60a 100644 --- a/reproduce/analysis/config/delete-me-squared-num.conf +++ b/reproduce/analysis/config/delete-me-squared-num.conf @@ -1,6 +1,6 @@ # Number of samples in the demonstration analysis (to be deleted). # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf index 1ab7de1..4c95c2f 100644 --- a/reproduce/analysis/config/metadata.conf +++ b/reproduce/analysis/config/metadata.conf @@ -15,7 +15,7 @@ # and the copyright license name and standard link to the fully copyright # license. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf index 7821306..e0400d3 100644 --- a/reproduce/analysis/config/pdf-build.conf +++ b/reproduce/analysis/config/pdf-build.conf @@ -12,7 +12,7 @@ # LaTeX. Otherwise, a notice will just printed that, no PDF will be # created. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf index 031085d..09cca90 100644 --- a/reproduce/analysis/config/verify-outputs.conf +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,6 +1,6 @@ # To enable verification of output datasets set this variable to 'yes'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index a20abc6..1377395 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -1,6 +1,6 @@ # Dummy Makefile to create a random dataset for plotting. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 5150373..7aefd3f 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -1,6 +1,6 @@ # Project initialization. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -265,16 +265,8 @@ clean: # executing 'build'. rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf -# Delete all the built outputs except the dependency programs. We'll -# use Bash's extended options builtin ('shopt') to enable "extended -# glob" (for listing of files). It allows extended features like -# ignoring the listing of a file with '!()' that we are using -# afterwards. - shopt -s extglob - rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex) - rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir)) - rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/* - rm -rf $(badir)/preparation-done.mk +# Delete the full 'badir' (containing all analysis outputs). + rm -rf $(badir) distclean: clean # Without cleaning the Git hooks, we won't be able to easily commit @@ -329,12 +321,11 @@ $(project-package-contents): paper.pdf | $(texdir) paper.tex > $$dir/paper.tex # Copy ONLY the version-controlled files in 'reproduce' and -# 'tex/src'. This is important because files like 'LOCAL.conf' (in -# 'reproduce/software/config') should not be archived, they contain -# information about the host computer and are irrelevant for -# others. Also some project authors may have temporary files here -# that are not under version control and thus shouldn't be archived -# (although this is bad practice, but that is up to the user). +# 'tex/src'. This is important because the git commit hash goes in +# the tarball name (should correspond to it) and some project authors +# may have temporary files here that are not under version control +# and thus shouldn't be archived (although this is bad practice, but +# that is up to the user). # # To keep the sub-directory structure, we are packaging the files # with Tar, piping it, and unpacking it in the archive directory. So @@ -362,17 +353,20 @@ $(project-package-contents): paper.pdf | $(texdir) rm -rf $$dir/tex/build/build* # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or -# PGFPlots was used to generate them), copy them too. +# PGFPlots was used to generate them), copy them too. Note that in +# the main project source, 'tex/tikz' is just a symbolic link to +# 'tex/build/tikz'. But inside the tarball we do not want to have +# symbolic links and they should be independent. if ls tex/tikz/*.pdf &> /dev/null; then cp tex/tikz/*.pdf $$dir/tex/tikz fi # When submitting to places like arXiv, they will just run LaTeX once -# and won't run 'biber'. So we need to also keep the '.bbl' file into -# the distributing tarball. However, BibLaTeX is particularly -# sensitive to versioning (a '.bbl' file has to be read by the same -# BibLaTeX version that created it). This is hard to do with -# non-up-to-date places like arXiv. Therefore, we thus just copy the +# and won't run 'biber' or 'biblatex'. So we need to also keep the +# '.bbl' file into the distributing tarball. However, BibLaTeX is +# particularly sensitive to versioning (a '.bbl' file has to be read +# by the same BibLaTeX version that created it). This is hard to do +# with non-up-to-date places like arXiv. Therefore, we just copy the # whole of BibLaTeX's source (the version we are using) into the top # tarball directory. In this way, arXiv's LaTeX engine will use the # same BibLaTeX version to interpret the '.bbl' file. TIP: you can diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index b1b794c..c218cdd 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -1,6 +1,6 @@ # Build the final PDF paper/report. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -19,6 +19,21 @@ +# Software info in TeX +# -------------------- +# +# The information of the installed software is placed in the +# '.build/software' directory (which the TeX build should not depend +# on). Therefore, we should copy those macros here in the LaTeX build +# directory, so the TeX directory is completely independent from each +# other. +$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex + cp $(bsdir)/config/*.tex $(mtexdir)/ + + + + + # LaTeX macros for paper # ---------------------- # @@ -40,19 +55,36 @@ # Note that if you don't want the final PDF and just want the processing # and file outputs, you can give any value other than 'yes' to # 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'. -$(mtexdir)/project.tex: $(mtexdir)/verify.tex +$(mtexdir)/project.tex: $(mtexdir)/verify.tex $(mtexdir)/dependencies.tex # If no PDF is requested, or if LaTeX isn't available, don't continue # to building the final PDF. Otherwise, merge all the TeX macros into # one for building the PDF. - @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then + @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; + then # Put a LaTeX input command for all the necessary macro files. -# 'hardware-parameters.tex' is created in 'configure.sh'. +# Note that 'hardware-parameters.tex' is created in 'configure.sh' +# (which is why it is first in the list). projecttex=$(mtexdir)/project.tex rm -f $$projecttex - for t in $(subst paper,,$(makesrc)) hardware-parameters; do - echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex + for t in hardware-parameters $(subst paper,,$(makesrc)); do + +# Only add the macro file to 'project.tex' if the macro file is +# not empty. Empty macro files are not a bug in Maneage alone: 1) +# the processing of a sub-Makefile may not need to produce any +# written macro for the PDF, and that is perfectly fine. 2) LaTeX +# can also '\input' an empty file. However, it is important for +# for publication servers (like arXiv) that do not allow +# uploading empty files. Therefore, when 'project.tex' contains +# empty files, such severs will not be able compile the PDF +# because the file name is mentioned in 'project.tex', but cannot +# be found in the uploaded files. + tfile=tex/build/macros/$$t.tex + if [ -s $$tfile ]; then + echo "\input{$$tfile}" >> $$projecttex + fi + done # Possibly highlight the '\new' parts of the text. @@ -110,21 +142,6 @@ tikzdir:=$(texbdir)/tikz -# Software info in TeX -# -------------------- -# -# The information of the installed software is placed in the -# '.build/software' directory (which the TeX build should not depend -# on). Therefore, we should copy those macros here in the LaTeX build -# directory, so the TeX directory is completely independent from each -# other. -$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex - cp $(bsdir)/config/*.tex $(mtexdir)/ - - - - - # The bibliography # ---------------- # @@ -137,8 +154,7 @@ $(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex # recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't # been modified, we don't want to re-build the bibliography, only the final # PDF. -$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ - | $(mtexdir)/project.tex +$(texbdir)/paper.bbl: tex/src/references.tex | $(mtexdir)/project.tex # If '$(mtexdir)/project.tex' is empty, don't build PDF. @macros=$$(cat $(mtexdir)/project.tex) @@ -164,9 +180,9 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ # for details. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper fi @@ -198,9 +214,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # option '-shell-escape'. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex # Come back to the top project directory and copy the built PDF diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index ffb2a3c..352fd00 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -1,6 +1,6 @@ # Basic preparations, called by './project make'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index e87aed8..7286ca6 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -1,6 +1,6 @@ # Top-level Makefile (first to be loaded). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index d2d1c14..8d1c2e0 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -4,7 +4,7 @@ # are not included here. Please see that file for thorough comments on each # step. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index c74f8ca..91c4b77 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -1,6 +1,6 @@ # Verify the project outputs before building the paper. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -138,11 +138,44 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex) # Verify TeX macros (the values that go into the PDF text). for m in $(verify-check); do - file=$(mtexdir)/$$m.tex - if [ $$m == delete-me ]; then s=711e2f7fa1f16ecbeeb3df6bcb4ec705 - else echo; echo "'$$m' not recognized."; exit 1 + +# Set the macro file name, make sure it exists (the user may have +# forgot to create it in the respective sub-Makefile). + tfile=$(mtexdir)/$$m.tex + if ! [ -f $$tfile ]; then + printf "$$tfile: ERROR: does not exist! If you do not " + printf "(currently) plan macros to be added to the final " + printf "PDF from that sub-Makefile, do the following to " + printf "avoid this error: put a 'touch \$$@' as the recipe " + printf "of the '\$$(mtexdir)/$$m.tex' target (at the bottom " + printf "of 'reproduce/analysis/make/$$m.mk'). If you later " + printf "decide to define macros there, simply replace the " + printf "temporary 'touch \$$@' command with the command(s) " + printf "to prepare/write the macro (see 'initialize.mk' " + printf "as an example)\n"; + exit 1 fi - $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp) + +# Check the hash for this file and verify it. + case $$m in + delete-me) s=711e2f7fa1f16ecbeeb3df6bcb4ec705;; + *) # This file's hash is not in the list above. + +# If the file is empty, we can skip it (with the 'continue' +# command). Otherwise, the user should be informed with an +# error. + if [ -s $$tfile ]; then + printf "$$tfile: ERROR: please add the hash of this " + printf "macro file to the list of hashes above this " + printf "error message (in " + printf "'reproduce/analysis/make/verify.mk')\n"; exit 1 + else + continue + fi + ;; + esac + $(call verify-txt-no-comments-no-space, $$tfile, $$s, $@.tmp) + done # Move temporary file to final target. diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex index 5697885..3c012cf 100644 --- a/reproduce/software/bibtex/astrometrynet.tex +++ b/reproduce/software/bibtex/astrometrynet.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex index 3df1aa1..aa9d162 100644 --- a/reproduce/software/bibtex/astropy.tex +++ b/reproduce/software/bibtex/astropy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/corner.tex b/reproduce/software/bibtex/corner.tex index fd7ea76..164adda 100644 --- a/reproduce/software/bibtex/corner.tex +++ b/reproduce/software/bibtex/corner.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex index 311072d..0c761ce 100644 --- a/reproduce/software/bibtex/cython.tex +++ b/reproduce/software/bibtex/cython.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex index 15c5c62..f5f4069 100644 --- a/reproduce/software/bibtex/fftw.tex +++ b/reproduce/software/bibtex/fftw.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/galsim.tex b/reproduce/software/bibtex/galsim.tex index bbfdec1..c3cd7d6 100644 --- a/reproduce/software/bibtex/galsim.tex +++ b/reproduce/software/bibtex/galsim.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/gnuastro.tex b/reproduce/software/bibtex/gnuastro.tex index 7d56e3e..8f97305 100644 --- a/reproduce/software/bibtex/gnuastro.tex +++ b/reproduce/software/bibtex/gnuastro.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex index afdd6a6..6063722 100644 --- a/reproduce/software/bibtex/healpix.tex +++ b/reproduce/software/bibtex/healpix.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex index 1d5270b..a1f8b4d 100644 --- a/reproduce/software/bibtex/imfit.tex +++ b/reproduce/software/bibtex/imfit.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/kiwisolver.tex b/reproduce/software/bibtex/kiwisolver.tex index 47d3f56..62df2a2 100644 --- a/reproduce/software/bibtex/kiwisolver.tex +++ b/reproduce/software/bibtex/kiwisolver.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2025-2025 Boud Roukema <boud@cosmo.torun.pl> +%% Copyright (C) 2025-2026 Boud Roukema <boud@cosmo.torun.pl> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex index ec7bab4..68d648a 100644 --- a/reproduce/software/bibtex/matplotlib.tex +++ b/reproduce/software/bibtex/matplotlib.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex index 83510dd..b973248 100644 --- a/reproduce/software/bibtex/missfits.tex +++ b/reproduce/software/bibtex/missfits.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2020-2025 Surena Fatemi <surena.fatemi@ipm.ir> +%% Copyright (C) 2020-2026 Surena Fatemi <surena.fatemi@ipm.ir> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex index 10e0e74..6125251 100644 --- a/reproduce/software/bibtex/mpi4py.tex +++ b/reproduce/software/bibtex/mpi4py.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex index fb017c4..8955d3d 100644 --- a/reproduce/software/bibtex/numpy.tex +++ b/reproduce/software/bibtex/numpy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/parallel.tex b/reproduce/software/bibtex/parallel.tex new file mode 100644 index 0000000..1ba1018 --- /dev/null +++ b/reproduce/software/bibtex/parallel.tex @@ -0,0 +1,15 @@ +%% Copyright (C) 2026-2026 Boud Roukema <boud@cosmo.torun.pl> +%% +%% Copying and distribution of this file, with or without modification, +%% are permitted in any medium without royalty provided the copyright +%% notice and this notice are preserved. This file is offered as-is, +%% without any warranty. + +@ARTICLE{parallel, + author = {{Tange}, Ole}, + title = "{GNU Parallel 20260322, https://doi.org/10.5281/zenodo.19321428}", + journal = {Zenodo.19321428}, + year = 2026, + month = mar, + doi = {10.5281/zenodo.19321428}, +} diff --git a/reproduce/software/bibtex/r-cran.tex b/reproduce/software/bibtex/r-cran.tex index c58eeeb..f17fc3a 100644 --- a/reproduce/software/bibtex/r-cran.tex +++ b/reproduce/software/bibtex/r-cran.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2022-2025 Boud Roukema <boud@cosmo.torun.pl> -%% Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2022-2026 Boud Roukema <boud@cosmo.torun.pl> +%% Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex index b5c4da9..271a09e 100644 --- a/reproduce/software/bibtex/scamp.tex +++ b/reproduce/software/bibtex/scamp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex index 1296393..0574891 100644 --- a/reproduce/software/bibtex/scipy.tex +++ b/reproduce/software/bibtex/scipy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex index 818f04a..33ec1e8 100644 --- a/reproduce/software/bibtex/sextractor.tex +++ b/reproduce/software/bibtex/sextractor.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sip_tpv.tex b/reproduce/software/bibtex/sip_tpv.tex index 0d52e33..d9b7cdd 100644 --- a/reproduce/software/bibtex/sip_tpv.tex +++ b/reproduce/software/bibtex/sip_tpv.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex index e0989f9..813942d 100644 --- a/reproduce/software/bibtex/swarp.tex +++ b/reproduce/software/bibtex/swarp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sympy.tex b/reproduce/software/bibtex/sympy.tex index 01e481b..18e4254 100644 --- a/reproduce/software/bibtex/sympy.tex +++ b/reproduce/software/bibtex/sympy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex index caf1500..00d8195 100644 --- a/reproduce/software/bibtex/tides.tex +++ b/reproduce/software/bibtex/tides.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index e60f344..7d45d06 100644 --- a/reproduce/software/config/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in @@ -3,7 +3,7 @@ # This is just a template for the './project configure' script to fill # in. Please don't make any change to this file. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -31,8 +31,9 @@ DEPENDENCIES-DIR = @ddir@ # Other local settings (compiler, downloader and user). SYS_CPATH = @sys_cpath@ -DOWNLOADER = @downloader@ GROUP-NAME = @groupname@ +DOWNLOADER = @downloader@ +SYS_LIBRARY_SH_PATH = @sys_library_sh_path@ diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf index 716fd41..51791a5 100644 --- a/reproduce/software/config/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -1,7 +1,7 @@ # Necessary high-level software to build in this project. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -42,5 +42,7 @@ top-level-programs = gnuastro top-level-python = # R libraries/modules -# [For developers 2022-01-02: 'r-cran-cowplot r-cran-gridExtra' for all] +# +# As of 2022-01-02: to have all of the R packages, select 'r-cran-cowplot +# r-cran-gridExtra'. top-level-r-cran = diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 89738ce..9e1c437 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -1,8 +1,8 @@ # sha512 checksums of all the necessary software tarballs. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -15,43 +15,42 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = 52fa7d14e5f05d7b1b5f64ca110388db119fd6b8d4cc25011e0e25848491507e610259091c56f3ca7a7688ee2547f8a98de2005626b35c29558e71f28e29b848 -binutils-checksum = efbc5957bd22804a860261886598778347e82f9cbc0728d21d26748b7296e34328fdc16252868169594a001a301babbcd0964d9c508523736bc79cac2aff8efc +bash-checksum = b905e107403ceb25ad92f26ab71d6a7f12b1cadbcb27de9f5fefa7da31e96de0be281f8095170ed36e3fc22237dcfc252ff674925e6123638f6a3e11f3c5ecfd +binutils-checksum = ad7bbebc0c4e537c15d7537027246e2c1c0d355efcd6a369c7ef91c6491ec6a6e9af24c60b7df7508213abeedbd2e53c41549889073ac1f629b0746b78ee894b bzip2-checksum = 929cb1b2d0db8a505e2bafe3ce2c893c8f132dd617c0110e86e19f116b570a85de3c8a635483b530456fc8f8b6698c8190d21313e47607f442807b10489ac86e certpem-checksum = 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Not all packages will use all sections so you # should leave out sections that your package does not use. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index f0e040e..26c992f 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -3,7 +3,7 @@ # is irrelevant). Note that this is not a to be read as a variable but will # be parsed as a list. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh index deae01b..e2c7bb7 100755 --- a/reproduce/software/config/software_acknowledge_context.sh +++ b/reproduce/software/config/software_acknowledge_context.sh @@ -10,8 +10,8 @@ # your project to make a smoothly readable English text. Afterwards, please # feel free to modify them as you wish. # -# Copyright (C) 2021-2025 Boud Roukema <boud@cosmo.torun.pl> -# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index e68a771..7210fd5 100644 --- a/reproduce/software/config/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf @@ -4,8 +4,8 @@ # name to this variable (you can check in 'ctan.org' to find the official # name). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2022-2025 Boud Roukema <boud@astro.uni.torun.pl> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2026 Boud Roukema <boud@astro.uni.torun.pl> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf index 0babd69..56f1129 100644 --- a/reproduce/software/config/texlive.conf +++ b/reproduce/software/config/texlive.conf @@ -2,7 +2,7 @@ # # installdir: Install directory # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 8bf7b23..f976930 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -3,8 +3,8 @@ # If un-commented the URLs of this file will be used. Otherwise default # servers (primarily on 'zenodo.org') will be checked for the tarball. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2020-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -25,7 +25,7 @@ #curl-url = https://curl.haxx.se/download #dash-url = http://gondor.apana.org.au/~herbert/dash/files #diffutils-url = http://ftp.gnu.org/gnu/diffutils -#file-url = ftp://ftp.astron.com/pub/file +#file-url = http://ftp.astron.com/pub/file #findutils-url = http://ftp.gnu.org/gnu/findutils #flock-url = https://github.com/discoteq/flock/releases #gawk-url = http://ftp.gnu.org/gnu/gawk @@ -35,12 +35,12 @@ #gmp-url = https://gmplib.org/download/gmp #grep-url = http://ftp.gnu.org/gnu/grep #gzip-url = http://akhlaghi.org/src -#isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure +#isl-url = http://gcc.gnu.org/pub/gcc/infrastructure #less-url = http://www.greenwoodsoftware.com/less/ #libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv #libtool-url = http://ftp.gnu.org/gnu/libtool #libunistring-url = http://ftp.gnu.org/gnu/libunistring -#libxml2-url = ftp://xmlsoft.org/libxml2 +#libxml2-url = https://download.gnome.org/sources/libxml2 #lzip-url = https://download.savannah.gnu.org/releases/lzip/ #m4-url = http://akhlaghi.org/maneage-software #make-url = http://akhlaghi.org/src @@ -52,7 +52,6 @@ #patchelf-url = https://github.com/NixOS/patchelf/releases/download/$(patchelf-version) #perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}')) #pkgconfig-url = http://pkg-config.freedesktop.org/releases -#podlators-url = https://www.eyrie.org/~eagle/software/podlators/ #readline-url = http://ftp.gnu.org/gnu/readline #sed-url = http://ftp.gnu.org/gnu/sed #tar-url = http://ftp.gnu.org/gnu/tar @@ -94,6 +93,9 @@ #expat-url = https://github.com/libexpat/libexpat/releases #fftw-url = https://fftw.org #flex-url = https://github.com/westes/flex/files/981163 +#framel: 2025-05-23 from https://software.igwn.org/lscsoft/source/framel-8.47.3.tar.xz; +# see also https://git.ligo.org/virgo/virgoapp/Fr +#framel-url = https://software.igwn.org/lscsoft/source #freetype-url = https://download.savannah.gnu.org/releases/freetype #gdb-url = http://ftp.gnu.org/gnu/gdb #ghostscript-url = https://www.ghostscript.com/releases/gsdnld.html @@ -140,13 +142,16 @@ #scamp-url = http://akhlaghi.org/maneage-software #scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download #sextractor-url = http://akhlaghi.org/maneage-software +#sqlite-url - https://sqlite.org #swarp-url = https://www.astromatic.net/download/swarp #swig-url = https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version) +#tcltk-defaults - 2025-05-24 - repacked from Debian/testing https://packages.debian.org/source/testing/tcltk-defaults #tides-url = http://akhlaghi.org/maneage-software +#tzdb-url = https://www.iana.org/time-zones #util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.40 #valgrind-url = https://sourceware.org/pub/valgrind #vim-url = ftp://ftp.vim.org/pub/vim/unix -#wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib +#wcslib-url = https://www.atnf.csiro.au/computing/software/wcs/wcslib-releases #xlsxio-url = https://github.com/brechtsanders/xlsxio/archive #yaml-url = pyyaml.org/download/libyaml @@ -195,8 +200,10 @@ # But be sure to send us a link to the tarball so we upload it to Maneage's # backup servers. #astropy-url = https://files.pythonhosted.org/packages/45/12/a1c582b3f9df5e2680eae0ed82c8057ae06d6130a1f7a5c0770fa899737e +#astropy-healpix-url = https://files.pythonhosted.org/packages/5c/8a/dfd71e4db13706383ca2cea0b2831eb10da2c286d4494f183f80fc03cbc2 #astropy-iers-data-url = https://files.pythonhosted.org/packages/a1/4d/b9511aba29d4330437497166a7049ab9bac53e344c54e44a35390724ca37 #contourpy-url = https://files.pythonhosted.org/packages/25/c2/fc7193cc5383637ff390a712e88e4ded0452c9fbcf84abe3de5ea3df1866 +#cosmodesi-mpytools = https://github.com/cosmodesi/mpytools/archive #cppy-url = https://files.pythonhosted.org/packages/45/ed/b35645a1b285bce356f30cc0fe77a042375c385660ccd61e0cdc4c1f7c44 #cycler-url = https://files.pythonhosted.org/packages/a9/95/a3dbbb5028f35eafb79008e7522a75244477d2838f38cbb722248dabc2a8 #cython-url = https://files.pythonhosted.org/packages/5a/25/886e197c97a4b8e254173002cdc141441e878ff29aaa7d9ba560cd6e4866 @@ -205,7 +212,9 @@ #flit-core-url = https://files.pythonhosted.org/packages/bc/18/b9b81cab2b8f63e6e7f72e1ba2766a0454fcd563e7a77b8299cb917ba805 #fonttools-url = https://files.pythonhosted.org/packages/1c/8c/9ffa2a555af0e5e5d0e2ed7fdd8c9bef474ed676995bb4c57c9cd0014248 #gpep517-url = https://files.pythonhosted.org/packages/1c/53/e6ad6aa7036d62ac009986e1e5180465353344afd958ddc8ac15e3b632bc +#healpy-url = https://files.pythonhosted.org/packages/a4/db/4d1e7fcd429151edb1e2c6d10365f86de217097e276c0b44dbc197028d21 #kiwisolver-url = https://files.pythonhosted.org/packages/82/59/7c91426a8ac292e1cdd53a63b6d9439abd573c875c3f92c146767dd33faf +#ligo-skymap-url = https://files.pythonhosted.org/packages/f5/f5/fa82a88c104a9d1fcf863e05a56b213b512db05bc72b5c4f1c7c7d3bc118 #matplotlib-url = https://files.pythonhosted.org/packages/68/dd/fa2e1a45fce2d09f4aea3cee169760e672c8262325aa5796c49d543dc7e6 #meson-url = https://files.pythonhosted.org/packages/02/98/bbcaf6caaaa0510a68834f119ac793a8abade6ff827fc2791eeb6f8b4a66 #meson-python-url = https://files.pythonhosted.org/packages/67/66/91d242ea8dd1729addd36069318ba2cd03874872764f316c3bb51b633ed2 diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 166e8ff..3e4ec9a 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -1,8 +1,8 @@ # Versions of the various dependencies # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -17,38 +17,35 @@ # -------------------------------------------------------------- # # CLASS:BASIC (important identifier for 'awk'; don't modify this line) -binutils-version = 2.43.1 +bash-version = 5.3.9 +binutils-version = 2.45.1 bison-version = 3.8.2 -coreutils-version = 9.6 -curl-version = 8.11.1 -dash-version = 0.5.12 -diffutils-version = 3.10 -file-version = 5.46 +coreutils-version = 9.11 +curl-version = 8.17.0 +diffutils-version = 3.12 findutils-version = 4.10.0 flock-version = 0.4.0 -gawk-version = 5.3.1 -gcc-version = 14.2.0 -gettext-version = 0.23.1 -git-version = 2.48.1 -gmp-version = 6.3.0 -grep-version = 3.11 -gzip-version = 1.13 +gawk-version = 5.3.2 +gettext-version = 1.0 +git-version = 2.52.0 +grep-version = 3.12 +gzip-version = 1.14 help2man-version = 1.49.3 isl-version = 0.27 -less-version = 668 +less-version = 685 libiconv-version = 1.18 libtool-version = 2.5.4 -libunistring-version = 1.3 -libxml2-version = 2.13.5 +libunistring-version = 1.4.2 +libxml2-version = 2.15.1 lzip-version = 1.25 +m4-version = 1.4.21 make-version = 4.4.1 mpc-version = 1.3.1 -mpfr-version = 4.2.1 -nano-version = 8.3 -openssl-version = 3.4.0 -perl-version = 5.40.1 -podlators-version = 6.0.2 -readline-version = 8.2.13 +mpfr-version = 4.2.2 +nano-version = 9.0 +openssl-version = 3.6.0 +perl-version = 5.42.0 +readline-version = 8.3.3 sed-version = 4.9 tar-version = 1.35 texinfo-version = 7.2 @@ -56,7 +53,6 @@ unzip-version = 6.0 wget-version = 1.25.0 which-version = 2.23 xz-version = 5.6.3 -zip-version = 3.0 zlib-version = 1.3.1 # Version-dependent build @@ -86,20 +82,37 @@ certpem-version = 2025-02-10 # supported. patchelf-version = 0.13 +# Dash +# ---- +# +# Dash 0.5.13.1 causes the build of pkg-config to put the building of +# Maneage within apptainer to go into the background! Forcing the user to +# run 'fg' to continue the build. When updating to a later version, be +# careful about this: that it does not cause this issue. +dash-version = 0.5.12 + # Not working with C23 # -------------------- # # As of GCC 15.1, the default C standard has been changed from C17 to C23 # and the following software cannot be built with C23. So we have added -# '-std=c17' to the CFLAGS environment variable in their build rules. After -# updating their version (and if you have GCC 15.1 or later) first remove -# '-std=c17' and then try the build. If it works, move the software back up -# to the main list before the commit. +# '-std=$(GNU_STD_OLD)' to the CFLAGS environment variable in their build +# rules. A test is done in 'configure.sh' to see if the host compiler has +# 'gnu17' and if not, to use 'gnu99'. After updating a package's version +# (and if you have GCC 15.1 or later) first remove '-std=$(GNU_STD_OLD)' +# and then try the build. If it works, move the software package back up to +# the main list before making a commit. +gmp-version = 6.3.0 +file-version = 5.46 ncurses-version = 6.5 -bash-version = 5.2.37 -m4-version = 1.4.19 pkgconfig-version = 0.29.2 +# GCC +# --- +# +# There is a version-specific 'sed -e' fix for a bug in this version of GCC +# that should no longer be necessary in future versions. +gcc-version = 15.2.0 @@ -123,21 +136,23 @@ automake-version = 1.17 boost-version = 1.87.0 cairo-version = 1.16.0 cdsclient-version = 3.84 -cfitsio-version = 4.5.0 +cfitsio-version = 4.6.3 cmake-version = 3.31.5 eigen-version = 3.4.0 emacs-version = 28.1 expat-version = 2.6.4 fftw-version = 3.3.10 flex-version = 2.6.4-410-74a89fd +framel-version = 8.47.3 freetype-version = 2.13.3 gdb-version = 11.1 ghostscript-fonts-gnu-version = 6.0 ghostscript-fonts-std-version = 8.11 -ghostscript-version = 10.04.0 -gnuastro-version = 0.23 +ghostscript-version = 10.06.0 +gnuastro-version = 0.24 gperf-version = 3.1 gsl-version = 2.8 +healpix-version = 3.83-2024Nov13 icu-version = 70.1 imagemagick-version = 7.1.0-13 imfit-version = 1.6.1 @@ -151,14 +166,17 @@ libpaper-version = 1.1.29 libpng-version = 1.6.46 libtiff-version = 4.7.0 libtirpc-version = 1.2.6 +metaio-version = 8.5.0-a5da19d metastore-version = 1.1.2-23-fa9170b missfits-version = 2.8.0 -ninjabuild-version = 1.12.1 +ninjabuild-version = 1.13.2 openblas-version = 0.3.29 -openmpi-version = 4.1.1 +openmpi-version = 5.0.10 openssh-version = 8.0p1 +parallel-version = 20260322 patch-version = 2.7.6 pcre-version = 8.44 +pcre2-version = 10.45 pixman-version = 0.40.0 plplot-version = 5.15.0 r-cran-version = 4.1.2 @@ -166,15 +184,19 @@ rpcsvc-proto-version = 1.4 scamp-version = 2.10.0 scons-version = 3.0.5 sextractor-version = 2.25.0 +sqlite-version = 3.53.0 swarp-version = 2.41.5 -swig-version = 4.0.2 +swig-version = 4.3.1 +tcl-version = 9.1a1 tides-version = 2.0 -util-linux-version = 2.40.4 +tk-version = 9.1a1 +tzdb-version = 2026a +util-linux-version = 2.41.3 valgrind-version = 3.18.1 -vim-version = 9.0 -wcslib-version = 8.4 +wcslib-version = 8.5 xlsxio-version = 0.2.21 yaml-version = 0.2.5 +zip-version = 3.0-15 # Xorg packages fontconfig-version = 2.16.0 @@ -192,8 +214,12 @@ xcb-proto-version = 1.17.0 xorgproto-version = 2024.1 xtrans-version = 1.5.2 -# Version-dependent build -# ----------------------- +# Not working with C23 (similar to same topic in basic): future versions +# may have fixed this problem, so when updating, first remove '-std=gnu17' +# and if it builds without crashing, put this back in the normal list. +vim-version = 9.0 + +# Version is in the build recipe lapack-version = 3.8.0 libgit2-version = 1.9.0 @@ -213,6 +239,17 @@ minizip-version = $(zlib-version) # version 1.12.0. hdf5-version = 1.13.1 +# The lalsuite tarball within Maneage is based on the upstream commit +# 678514ed of 21 May 2025 of https://git.ligo.org/lscsoft/lalsuite. But +# instead of being a 950 Mb '.tar.gz' file including the '.git/' directory +# (or a 320 Mb '.tar.gz' file without the '.git/' directory), our tarball +# is a 25 Mb '.tar.lz' file (a factor of 30 to 10 times smaller). The main +# difference (apart from the extra compression provided by lzip) is that +# this light tarball does not include the big test data files. A +# description of how this tarball was made and what files have been removed +# is in the 'README-Maneage-LightWeight.md' file that is within the +# tarball. +lalsuite-version = v7.26-15-g1e4c5e5080 @@ -227,74 +264,77 @@ hdf5-version = 1.13.1 # URL in 'reproduce/software/make/python.mk'. # # CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line) -asn1crypto-version = 0.24.0 -asteval-version = 0.9.16 -astropy-version = 7.0.1 +astropy-healpix-version = 1.1.2 astropy-iers-data-version = 0.2025.2.24.0.34.4 +astropy-version = 7.1.0 beautifulsoup4-version = 4.10.0 -beniget-version = 0.4.1 -certifi-version = 2018.11.29 cffi-version = 1.15.0 -chardet-version = 3.0.4 +colorama-version = 0.4.6 contourpy-version = 1.3.1 -corner-version = 2.0.1 +cosmodesi-mpytools-version = 1.0.0-04369fc9 cppy-version = 1.3.1 cycler-version = 0.12.1 cython-version = 3.0.12 -eigency-version = 1.77 -emcee-version = 3.0.1 -entrypoints-version = 0.3 -esutil-version = 0.6.9 +exceptiongroup-version = 1.3.0 extension-helpers-version = 1.2.0 features-version = 0.5.12 flake8-version = 3.7.8 flit-core-version = 3.11.0 +flit-scm-version = 1.7.0 fonttools-version = 4.56.0 -future-version = 0.18.1 galsim-version = 2.3.5 -gast-version = 0.5.3 gpep517-version = 16 h5py-version = 2.10.0 +hatch-vcs-version = 0.5.0 +hatchling-version = 1.27.0 +healpy-version = 1.18.1 html5lib-version = 1.0.1 -idna-version = 2.8 -jeepney-version = 0.4 +igwn-ligolw-version = 2.1.0 +igwn-segments-version = 2.1.0 +iniconfig-version = 2.1.0 jinja2-version = 3.0.3 +joblib-version = 1.5.0 kiwisolver-version = 1.4.8 +ligo-skymap-version = 2.4.0 lmfit-version = 0.9.14 +lscsoft-glue-version = 4.1.0 lsstdesccoord-version = 1.2.0 -markupsafe-version = 2.0.1 -meson-version = 1.7.0 meson-python-version = 0.17.1 -mpi4py-version = 3.1.3 -mpmath-version = 1.1.0 +meson-version = 1.7.0 +mpi4py-version = 4.0.3 +networkx-version = 3.5 numpy-version = 2.2.3 packaging-version = 24.2 -pexpect-version = 4.7.0 +pandas-version = 2.2.3 +pathspec-version = 0.12.1 pillow-version = 11.1.0 pip-version = 19.0.2 -ply-version = 3.11 +pluggy-version = 1.6.0 pybind11-version = 2.13.6 -pycodestyle-version = 2.5.0 -pycparser-version = 2.19 pyerfa-version = 2.0.1.5 -pyflakes-version = 2.1.1 -pyproject-metadata-version = 0.9.0 +pyfftw-version = 0.15.1 +pygments-version = 2.19.2 pyparsing-version = 3.2.1 -pypkgconfig-version = 1.5.1 +pyproject-metadata-version = 0.9.0 +pytest-version = 8.4.1 python-dateutil-version = 2.9.0.post0 python-installer-version = 0.7.0 +python3-fitsio-version = 1.3.0 pythran-version = 0.11.0 +pytz-version = 2025.2 pyyaml-version = 6.0.2 requests-version = 2.21.0 -setuptools-version = 75.8.0 +scikit-base-version = 0.12.2 +scikit-learn-version = 1.6.1 setuptools-scm-version = 8.2.0 +setuptools-version = 80.8.0 sip_tpv-version = 1.1 six-version = 1.17.0 -soupsieve-version = 1.8 sympy-version = 1.4 -uncertainties-version = 3.1.6 -urllib3-version = 1.24.1 -webencodings-version = 0.5.1 +threadpoolctl-version = 3.6.0 +tqdm-version = 4.67.1 +trove-classifiers-version = 2025.5.9.12 +versioneer-version = 0.29 wheel-version = 0.45.1 # Matplotlib and Scipy are big packages that may have difficulty resolving @@ -304,26 +344,11 @@ scipy-version = 1.15.2 # CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line) -# Special Python modules: -# -# Healpy: When any Python module is requested, healpix will also build its -# Python module Healpy. -# -# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting -# it here. When future versions fix the problem, we'll un-comment it again. -#healpy-version = xxxxx - -# Problematic software that are currently ignored: - -# Healpix 3.80 has different installation scheme that is not yet -# implemented here, and unfortunately healpix 3.50 has conflicts with -# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring -# it. -#healpix-version = 3.50 +# Problematic software that is currently ignored: # Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731), # so it and its dependencies are being ignored: 'cryptography', and thus @@ -335,6 +360,34 @@ semantic-version-version = 2.10.0 #keyring-version = 18.0.0 #astroquery-version = 0.4 +# Not yet adated to the GPEP517 build method: +#asn1crypto-version = 0.24.0 +#asteval-version = 0.9.16 +#beniget-version = 0.4.1 +#certifi-version = 2018.11.29 +#chardet-version = 3.0.4 +#corner-version = 2.0.1 +#eigency-version = 1.77 +#emcee-version = 3.0.1 +#entrypoints-version = 0.3 +#esutil-version = 0.6.9 +#future-version = 0.18.1 +#gast-version = 0.5.3 +#idna-version = 2.8 +#jeepney-version = 0.4 +#markupsafe-version = 2.0.1 +#mpmath-version = 1.1.0 +#pexpect-version = 4.7.0 +#ply-version = 3.11 +#pycodestyle-version = 2.5.0 +#pycparser-version = 2.19 +#pyflakes-version = 2.1.1 +#pypkgconfig-version = 1.5.1 +#soupsieve-version = 1.8 +#uncertainties-version = 3.1.6 +#urllib3-version = 1.24.1 +#webencodings-version = 0.5.1 + diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md index 00afef4..0d1464d 100644 --- a/reproduce/software/make/README.md +++ b/reproduce/software/make/README.md @@ -1,7 +1,7 @@ Software building instructions ------------------------------ -Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This directory contains Makefiles that are called by the high-level diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk index 6e7d415..a20f558 100644 --- a/reproduce/software/make/atlas-multiple.mk +++ b/reproduce/software/make/atlas-multiple.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk index 2b68677..79f5b42 100644 --- a/reproduce/software/make/atlas-single.mk +++ b/reproduce/software/make/atlas-single.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 4b18c29..92fa8f0 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -21,9 +21,9 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -105,12 +105,13 @@ endif export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings) # This is the "basic" tools where we are relying on the host operating -# system, but are slowly populating our basic software envirnoment. To run -# (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here, -# we'll first tell the programs to look into any possible pre-defined -# 'LD_LIBRARY_PATH', then we'll add our own newly installed libraries. We -# will also make sure that there is no "current directory" in it (by -# removing a starting or trailing ':' and any occurance of '::'. +# system, but are slowly populating our basic software envirnoment. So +# here, we are also appending the host's 'LD_LIBRARY_PATH' to Maneage's +# installed library path. It is just important to keep Maneage's library +# directories first so when something has been built, the newly built +# software use (link-with) Maneage's libraries, not the host's. We will +# also make sure that there is no "current directory" in it (by removing a +# starting or trailing ':' and any occurance of '::'). # # But first: in case LD_LIBRARY_PATH is empty, give it the default value of # $(sys_library_sh_path) (which was the location of the libraries needed by @@ -120,7 +121,7 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings) ifeq ($(strip $(LD_LIBRARY_PATH)),) export LD_LIBRARY_PATH=$(sys_library_sh_path) endif -export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \ +export LD_LIBRARY_PATH := $(shell echo $(ildir):$(LD_LIBRARY_PATH) \ | sed -e's/::/:/g' -e's/^://' -e's/:$$//') # RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is @@ -253,6 +254,23 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \ # systems) $(call makelink,ldd) +# zic: On some systems like Debian GNU/Linux, 'zic' may be in +# '/usr/sbin' and is available to users. But it is not normally in +# the 'PATH' of a non-root user. This is because the executables +# there are normally system-level commands, and most are executable +# only by the root user. + $(call makelink,zic) + if [ "x$$(command -v zic)" = x ]; then + zicfullpath=$$(PATH=$${PATH}:/usr/sbin command -v zic) + if [ "x$${zicfullpath}" = x ]; then + printf "Warning: 'zic' not found. You may need it for" + printf " higher-level packages such as 'tzdb'. Install" + printf " 'zic' if needed.\n" + else + ln -sf $$(realpath $${zicfullpath}) $(ibdir)/zic + fi + fi + # We want this to be empty (so it doesn't interefere with the other # files in 'ibidir'. touch $@ @@ -344,24 +362,22 @@ $(ibidir)/zlib-$(zlib-version): | $(ibdir) $(ildir) $(lockdir) echo "Zlib $(zlib-version)" > $@ # GNU Tar: When built statically, tar gives a segmentation fault on -# unpacking Bash. So we'll build it dynamically. Note that technically, zip -# and unzip aren't dependencies of Tar, but for a clean build, we'll set -# Tar to be the last compression-related software (the first-set of -# software to be built). +# unpacking Bash. So we'll build it dynamically. $(ibidir)/tar-$(tar-version): \ $(ibidir)/xz-$(xz-version) \ $(ibidir)/gzip-$(gzip-version) \ $(ibidir)/zlib-$(zlib-version) \ $(ibidir)/bzip2-$(bzip2-version) -# Since all later programs depend on Tar, the configuration will hit -# a bottleneck here: only making Tar. So its more efficient to built -# it on multiple threads (even when the user's Make doesn't pass down -# the number of threads). +# About the onfigurations: nls and iconv were creating problems with +# the dependencies on MacOs and are not relevant in the context of +# Maneage, hence, they are disabled. $(call unsafe-config) tarball=tar-$(tar-version).tar.lz $(call import-source, $(tar-url), $(tar-checksum)) - $(call gbuild, tar-$(tar-version), , , -j$(numthreads) V=1) + $(call gbuild, tar-$(tar-version), , \ + --disable-nls am_cv_func_iconv=no, \ + -j$(numthreads) V=1) echo "GNU Tar $(tar-version)" > $@ @@ -378,8 +394,8 @@ $(ibidir)/tar-$(tar-version): \ # Patchelf is necessary for some software on GNU/Linux systems, its job is # to manually insert RPATH into the dynamically-linked executable. Since # all the other software depend on Pathelf, to avoid manually repeating as -# a prerequisite (and forgetting in others causing bugs), we'll put it as a -# dependancy of 'tar'. +# a prerequisite (and forgetting in others causing bugs), it is installed +# in this phase (right after 'tar'). $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version) tarball=patchelf-$(patchelf-version).tar.lz $(call import-source, $(patchelf-url), $(patchelf-checksum)) @@ -390,7 +406,47 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version) echo "PatchELF $(patchelf-version)" > $@ fi +$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version) + +# Download the tarball. + tarball=pkg-config-$(pkgconfig-version).tar.lz + $(call import-source, $(pkgconfig-url), $(pkgconfig-checksum)) + +# An existing 'libiconv' can cause a conflict with 'pkg-config' (this +# is why 'libiconv' depends on 'pkg-config'). On a clean build, +# 'pkg-config' is built first. But when we don't have a clean build +# (and 'libiconv' exists) there will be a problem. So before +# re-building 'pkg-config', we'll remove any installation of +# 'libiconv'. + rm -f $(ildir)/libiconv* $(idir)/include/iconv.h +# Some Mac OS systems may have a version of the GNU C Compiler (GCC) +# installed that doesn't support some necessary features of building +# Glib (as part of pkg-config), so we will disable pkg-config's +# internal Glib for Mac systems, and to be further safe, we'll make +# sure it will use LLVM's Clang. +# +# On macOS systems, to ensure that Clang can build pkg-config, take +# the following steps: +# 1. Install the latest Glib via Homebrew: +# brew install glib +# 2. Set these environment variables before configuring Maneage: +# export GLIB_CFLAGS=$(pkg-config --cflags glib-2.0) +# export GLIB_LIBS=$(pkg-config --libs glib-2.0) +# 3. Ensure PKG_CONFIG_PATH includes Homebrew's pkgconfig: +# export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig:$PKG_CONFIG_PATH + if [ x$(on_mac_os) = xyes ]; then + extra_pkgconf="" + export compiler="CC=clang" + else + export compiler="" + extra_pkgconf="--with-internal-glib" + fi + export CFLAGS="-std=$(std_c_old) $$CFLAGS" + $(call gbuild, pkg-config-$(pkgconfig-version), static, \ + $$compiler $$extra_pkgconf \ + --with-pc-path=$(ildir)/pkgconfig, V=1) + echo "pkg-config $(pkgconfig-version)" > $@ @@ -410,7 +466,10 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version) # function (for tilde expansion). The first can be disabled with # '--disable-load', but unfortunately I don't know any way to fix the # second. So, we'll have to build it dynamically for now. -$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) \ + $(ibidir)/pkg-config-$(pkgconfig-version) + +# Prepare the input. tarball=ncurses-$(ncurses-version).tar.lz $(call import-source, $(ncurses-url), $(ncurses-checksum)) @@ -426,12 +485,18 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk* # Standard build process. - export CFLAGS="-std=gnu17 $$CFLAGS" + export CFLAGS="-std=$(std_c_old) $$CFLAGS" $(call gbuild, ncurses-$(ncurses-version), static, \ - --with-shared --enable-rpath --without-normal \ - --without-debug --with-cxx-binding \ - --with-cxx-shared --enable-widec --enable-pc-files \ - --with-pkg-config=$(ildir)/pkgconfig, -j$(numthreads)) + --with-shared \ + --enable-rpath \ + --enable-widec \ + --without-debug \ + --without-normal \ + --enable-pc-files \ + --with-cxx-shared \ + --with-cxx-binding \ + --with-pkg-config=$(ildir)/pkgconfig, \ + -j$(numthreads)) # Unfortunately there are many problems with 'ncurses' using "normal" # (or 8-bit) characters. The standard way that will work is to build @@ -540,6 +605,7 @@ $(ibidir)/readline-$(readline-version): \ # pname=bash50-$(printf "%03d" $i); \ # wget http://ftp.gnu.org/gnu/bash/bash-5.0-patches/$pname -O ../$pname;\ # patch -p0 -i ../$pname; \ +# rm ../$pname; \ # done # $ cd .. # $ mv bash-5.0 bash-5.0.$number @@ -565,10 +631,10 @@ $(ibidir)/bash-$(bash-version): \ if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link" else stopt="" fi; - export CFLAGS="$$CFLAGS -std=gnu17 \ + export CFLAGS="$$CFLAGS \ -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \ -DSTANDARD_UTILS_PATH='\"$(ibdir)\"' \ - -DSYS_BASHRC='\"$(BASH_ENV)\"' " + -DSYS_BASHRC='\"$(BASH_ENV)\"'" $(call gbuild, bash-$(bash-version),, $$stopt \ --with-installed-readline=$(ildir) \ --with-curses=yes, \ @@ -585,9 +651,6 @@ $(ibidir)/bash-$(bash-version): \ # shell. By convention, 'sh' is just a symbolic link to the preferred # shell executable. So we'll define '$(ibdir)/sh' as a symbolic link # to the Bash that we just built and installed. -# -# Just to be sure that the installation step above went well, before -# making the link, we'll see if the file actually exists there. ln -fs $(ibdir)/bash $(ibdir)/sh echo "GNU Bash $(bash-version)" > $@ @@ -600,6 +663,7 @@ $(ibidir)/bash-$(bash-version): \ + # Level 4: Most other programs # ---------------------------- @@ -613,15 +677,21 @@ perl-conflddlflags = else perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS" endif -$(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/perl-$(perl-version): $(ibidir)/tar-$(tar-version) + +# Import tarball. tarball=perl-$(perl-version).tar.lz $(call import-source, $(perl-url), $(perl-checksum)) + +# Extract the version strings. major_version=$$(echo $(perl-version) \ | sed -e's/\./ /g' \ | awk '{printf("%d", $$1)}') base_version=$$(echo $(perl-version) \ | sed -e's/\./ /g' \ | awk '{printf("%d.%d", $$1, $$2)}') + +# Unpack, build and install. cd $(ddir) rm -rf perl-$(perl-version) tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions @@ -632,15 +702,15 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) -Duseshrplib \ -Dprefix=$(idir) \ -Dvendorprefix=$(idir) \ - -Dprivlib=$(idir)/share/perl$$major_version/core_perl \ - -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \ - -Dsitelib=$(idir)/share/perl$$major_version/site_perl \ - -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/site_perl \ - -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \ - -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \ - -Dscriptdir=$(idir)/bin/core_perl \ - -Dsitescript=$(idir)/bin/site_perl \ - -Dvendorscript=$(idir)/bin/vendor_perl \ + -Dprivlib=$(idir)/share/perl$$major_version/perl-core \ + -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/perl-core \ + -Dsitelib=$(idir)/share/perl$$major_version/perl-site \ + -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/perl-site \ + -Dvendorlib=$(idir)/share/perl$$major_version/perl-vendor \ + -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/perl-vendor \ + -Dscriptdir=$(idir)/bin/perl-core \ + -Dsitescript=$(idir)/bin/perl-site \ + -Dvendorscript=$(idir)/bin/perl-vendor \ -Dinc_version_list=none \ -Dman1ext=1perl \ -Dman3ext=3perl \ @@ -651,7 +721,14 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) make install cd .. rm -rf perl-$(perl-version) - cd $$topdir + +# Symbolic links to necessary Perl programs (that Perl installs in +# the 'perl-core' directory. + ln -sf $(ibdir)/perl-core/xsubpp $(ibdir)/xsubpp + ln -sf $(ibdir)/perl-core/pod2man $(ibdir)/pod2man + ln -sf $(ibdir)/perl-core/pod2text $(ibdir)/pod2text + +# Final target. echo "Perl $(perl-version)" > $@ @@ -720,29 +797,6 @@ $(ibidir)/coreutils-$(coreutils-version): \ rm -rf coreutils-$(coreutils-version) echo "GNU Coreutils $(coreutils-version)" > $@ -# Podlators -# -# POD is short for "Plain Old Documentation", that is the format used in -# Perl's documentation. Podlators provies two executables pod2man and -# pod2text convert this into the roff format (used in man pages) or pod2 It -# is used by some software like OpenSSL to create their man pages. -$(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version) - tarball=podlators-$(podlators-version).tar.lz - $(call import-source, $(podlators-url), $(podlators-checksum)) - cd $(ddir) - rm -rf podlators-$(podlators-version) - tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions - cd podlators-$(podlators-version) - $(shsrcdir)/prep-source.sh $(ibdir) - perl Makefile.PL - make - make install - ln -sf $(ibdir)/site_perl/pod2man $(ibdir)/pod2man - ln -sf $(ibdir)/site_perl/pod2text $(ibdir)/pod2text - cd .. - rm -rf podlators-$(podlators-version) - echo "podlators $(podlators-version)" > $@ - # OpenSSL # # Until we find a nice and generic way to create an updated CA file in the @@ -750,8 +804,9 @@ $(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version) # along with the other tarballs. $(idir)/etc:; mkdir $@ $(idir)/etc/ssl: | $(idir)/etc; mkdir $@ -$(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \ - | $(idir)/etc/ssl +$(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \ + $(ibidir)/patchelf-$(patchelf-version) \ + | $(idir)/etc/ssl # First download the certificates and copy them into the # installation directory. @@ -907,7 +962,7 @@ $(ibidir)/diffutils-$(diffutils-version): \ echo "GNU Diffutils $(diffutils-version)" > $@ $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version) - export CFLAGS="-std=c99 $$CFLAGS" + export CFLAGS="-std=$(std_c_old) $$CFLAGS" tarball=file-$(file-version).tar.lz $(call import-source, $(file-url), $(file-checksum)) $(call gbuild, file-$(file-version), static, \ @@ -959,6 +1014,8 @@ $(ibidir)/help2man-$(help2man-version): \ $(call gbuild, help2man-$(help2man-version), static, ,V=1) echo "Help2man $(Help2man-version)" > $@ +# Even though libiconv does not use pkg-config, pkg-config conflicts with +# it, see the comments in pkg-config for more. $(ibidir)/libiconv-$(libiconv-version): \ $(ibidir)/pkg-config-$(pkgconfig-version) tarball=libiconv-$(libiconv-version).tar.lz @@ -974,12 +1031,14 @@ $(ibidir)/libunistring-$(libunistring-version): \ -j$(numthreads)) echo "GNU libunistring $(libunistring-version)" > $@ -$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/tar-$(tar-version) # The libxml2 tarball also contains Python bindings which are built # and installed to a system directory by default. If you don't need # the Python bindings, the easiest solution is to compile without # Python support: './configure --without-python'. If you really need -# the Python bindings, use '--with-python-install-dir=DIR' instead. +# its Python bindings: +# 1. Add the Python dependency. +# 2. Add the '--with-python-install-dir=DIR' configure option. tarball=libxml2-$(libxml2-version).tar.lz $(call import-source, $(libxml2-url), $(libxml2-checksum)) $(call gbuild, libxml2-$(libxml2-version), static, \ @@ -1018,7 +1077,7 @@ $(ibidir)/gmp-$(gmp-version): \ $(ibidir)/coreutils-$(coreutils-version) tarball=gmp-$(gmp-version).tar.lz $(call import-source, $(gmp-url), $(gmp-checksum)) - export CFLAGS="-std=gnu17 $$CFLAGS" + export CFLAGS="-std=$(std_c_old) $$CFLAGS" $(call gbuild, gmp-$(gmp-version), static, \ --enable-cxx --enable-fat, \ -j$(numthreads)) @@ -1065,10 +1124,6 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) -j$(numthreads) V=1) echo "GNU Grep $(grep-version)" > $@ -# M4 doesn't depend on PatchELF, but just to be consistent with the -# levels/phases introduced here (where the compressors are level 1, -# PatchELF is level 2, and ...), we'll set it as a dependency. -# # The '--with-syscmd-shell' is used as the default shell and if not given, # 'm4' will use '/bin/sh' (which is not under Maneage control and can cause # problems in 'high-level.mk' because it closes off the system's @@ -1076,10 +1131,9 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) # library, the high-level programs will not be built). We are setting this # default shell to Dash because M4 is built before our own Bash. Recall # that Dash is built before we enter this Makefile. -$(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/m4-$(m4-version): $(ibidir)/libiconv-$(libiconv-version) tarball=m4-$(m4-version).tar.lz $(call import-source, $(m4-url), $(m4-checksum)) - export CFLAGS="-std=gnu17 $$CFLAGS" $(call gbuild, m4-$(m4-version), static, \ --with-syscmd-shell=$(ibdir)/dash, \ -j$(numthreads) V=1) @@ -1091,33 +1145,6 @@ $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version) $(call gbuild, mpfr-$(mpfr-version), static) echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@ -$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version) - -# Download the tarball. - tarball=pkg-config-$(pkgconfig-version).tar.lz - $(call import-source, $(pkgconfig-url), $(pkgconfig-checksum)) - -# An existing 'libiconv' can cause a conflict with 'pkg-config', this -# is why 'libiconv' depends on 'pkg-config'. On a clean build, -# 'pkg-config' is built first. But when we don't have a clean build -# (and 'libiconv' exists) there will be a problem. So before -# re-building 'pkg-config', we'll remove any installation of -# 'libiconv'. - rm -f $(ildir)/libiconv* $(idir)/include/iconv.h - -# Some Mac OS systems may have a version of the GNU C Compiler (GCC) -# installed that doesn't support some necessary features of building -# Glib (as part of pkg-config). So to be safe, for Mac systems, we'll -# make sure it will use LLVM's Clang. - if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang" - else export compiler="" - fi - export CFLAGS="-std=gnu17 $$CFLAGS" - $(call gbuild, pkg-config-$(pkgconfig-version), static, \ - $$compiler --with-internal-glib \ - --with-pc-path=$(ildir)/pkgconfig, V=1) - echo "pkg-config $(pkgconfig-version)" > $@ - $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version) tarball=sed-$(sed-version).tar.lz $(call import-source, $(sed-url), $(sed-checksum)) @@ -1225,6 +1252,7 @@ $(ibidir)/binutils-$(binutils-version): \ $(call makelink,ld) $(call makelink,nm) $(call makelink,ps) + $(call makelink,lipo) $(call makelink,strip) $(call makelink,ranlib) echo "" > $@ @@ -1448,6 +1476,14 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \ -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp +# Bug in GCC 15.2.0 using glibc 2.43 (see [1]) as fixed in [2]. +# [1] https://patchwork.ozlabs.org/project/gcc/patch/e1679277-d7c9-49aa-8365-a8dca082d9bd@web.de +# [2] https://github.com/johnny-mnemonic/toolchain-autobuilds/commit/9585fdfc + sed -e's|char \*q = strchr (p + 1,|const char \*q = strchr (p + 1,|' \ + libgomp/affinity-fmt.c > affinity-fmt-tmp.c + mv affinity-fmt-tmp.c libgomp/affinity-fmt.c + + # Set the build directory for the processing. mkdir build cd build diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index 463fbbf..984d0bf 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -3,7 +3,7 @@ # imported into 'basic.mk' and 'high-level.mk'. They should be activated # with Make's 'Call' function. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 67ca8b6..d059544 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -438,6 +438,23 @@ $(ibidir)/cfitsio-$(cfitsio-version): tar cf $$customtar cfitsio-$(cfitsio-version) cd $$topdir +# Add SSE2 optimization only when we are on a Linux kernel or using +# macOS on an Intel CPU. + arch=$$(uname -m) + unames=$$(uname -s) + if [ "$$unames" = "Linux" ]; then + confopts="$$confopts --enable-sse2" + elif [ "$$unames" = "Darwin" ] && [ "$$arch" = "x86_64" ]; then + confopts="$$confopts --enable-sse2" + fi + +# On macOS, system libraries (e.g., libSystem) are inside the SDK, +# not standard paths. 'xcrun' provides the correct SDK path; use $$ +# so it is evaluated by the shell (not Make). + if [ $(on_mac_os) = yes ]; then + export SDKROOT=$$(xcrun --show-sdk-path) + fi + # Continue the standard build on the customized tarball. Note that # with the installation of CFITSIO, 'fpack' and 'funpack' are not # installed by default. Because of that, they are added explicity. @@ -446,7 +463,10 @@ $(ibidir)/cfitsio-$(cfitsio-version): # specific 'shared' target for the building of the shared libraries. export gbuild_tar=$(ddir)/$$customtar $(call gbuild, cfitsio-$(cfitsio-version), , \ - --enable-sse2 --enable-reentrant \ + $$confopts \ + --disable-curl \ + --disable-fortran \ + --enable-reentrant \ --with-bzip2=$(idir), , \ make fpack funpack) rm $$customtar @@ -505,36 +525,62 @@ $(ibidir)/expat-$(expat-version): $(call gbuild, expat-$(expat-version), static) echo "Expat $(expat-version)" > $@ +# FFTW manual customizations: +# +# - To activate the OpenMPI features of FFTW, add OpenMPI as a dependency +# of FFTW: the necessary flags are automatically added if OpenMPI was +# installed before FFTW. +# +# - There are Intel-specific optimizations that can be enabled by adding +# the following two options to 'opts' +# +# --enable-avx --enable-sse2 +# +# However, they cause crashes on non-Intel processors (has been confirmed +# in ARM's aarch64). So in the generic scenario they are +# removed. Checking how these optimizations affect the numerical accuracy +# of the result (and thus optionally adding them for Intel-based +# processors) should be studied before they are optionally added for +# Intel-based CPUs (and ignored for others). $(ibidir)/fftw-$(fftw-version): # Prepare the source tarball. tarball=fftw-$(fftw-version).tar.lz $(call import-source, $(fftw-url), $(fftw-checksum)) -# FFTW's single and double precision libraries must be built -# independently: for the the single-precision library, we need to add -# the '--enable-float' option. We will build this first, then the -# default double-precision library. -# -# There are Intel-specific optimizations that can be enabled by -# adding the following two options to 'confop' -# -# --enable-avx --enable-sse2 -# -# However, they cause crashs on non-Intel processors (has been -# confirmed in ARM's aarch64). So in the generic scenario they are -# removed. Checking how these optimizations affect the numeric -# accuracy of the result (and thus optionally adding them for -# Intel-based processors) should be studied before they are -# optionally added for Intel-based CPUs (and ignored for others). - confop="--enable-shared --enable-threads" - $(call gbuild, fftw-$(fftw-version), static, \ - $$confop --enable-float) - $(call gbuild, fftw-$(fftw-version), static, \ - $$confop) - cp $(dtexdir)/fftw.tex $(ictdir)/ +# Specific customizations: you can add the options mentioned above +# after the 'if' statements, for example: "opts=$$opts EXTRA". + opts="--enable-shared --enable-threads" + if [ x$(on_mac_os) = xyes ]; then opts="$$opts --disable-fortran" + else + if [ -f $(ibidir)/openmpi-$(openmpi-version) ]; then + opts="$$opts --enable-openmp --enable-mpi" + fi + fi + +# FFTW's single, double and long-double precision libraries must be +# built separately (fully independent builds and installs). + $(call gbuild, fftw-$(fftw-version), static, $$opts) + $(call gbuild, fftw-$(fftw-version), static, $$opts \ + --enable-float) + $(call gbuild, fftw-$(fftw-version), static, $$opts \ + --enable-long-double) + cp -pv $(dtexdir)/fftw.tex $(ictdir)/ echo "FFTW $(fftw-version) \citep{fftw}" > $@ +# 2026-02-20 'framel' is needed by the python package lalsuite, which is +# needed by ligo-skymap; currently the compile of 'framel' 8.49.0 fails with +# +# error: initialization of 'void (*)(void)' from incompatible +# pointer type 'void (*)(int, char *)' [-Wincompatible-pointer-types] +# +# Hints: try using gcc -std=gnu99 or -std=gnu11 (default is -std=gnu17). +$(ibidir)/framel-$(framel-version): $(ibidir)/cmake-$(cmake-version) + tarball=framel-$(framel-version).tar.lz + $(call import-source, $(framel-url), $(framel-checksum)) + $(call cbuild, framel-$(framel-version), static) + echo "Framel $(framel-version)" > $@ + $(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version) # As of version 2.13.2, FreeType doesn't account for the 'SHELL' # environment variable. The issue has been reported to the @@ -571,64 +617,114 @@ $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version) echo "HDF5 library $(hdf5-version)" > $@ # HEALPix includes the source of its C, C++, Python (and several other -# languages) libraries within one tarball. We will include the Python -# installation only when any other Python module is requested (in -# 'TARGETS.conf'). +# languages) libraries within one tarball. However, we do not build the +# python version here; instead we provide 'healpy' as a separate package; +# see 'python.mk' for the build rule. # # Note that the default './configure' script is an interactive script which # is hard to automate. So we need to go into the 'autotools' directory of # the 'C' and 'cxx' directories and configure the GNU Build System (with # 'autoreconf', which uses 'autoconf' and 'automake') to easily build the # HEALPix C/C++ libraries in batch mode. -ifeq ($(strip $(targets-python)),) -healpix-python-dep = -else -healpix-python-dep = $(ipydir)/matplotlib-$(matplotlib-version) \ - $(ipydir)/astropy-$(astropy-version) -endif -$(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \ +$(ibidir)/healpix-$(healpix-version): \ $(ibidir)/cfitsio-$(cfitsio-version) \ $(ibidir)/autoconf-$(autoconf-version) \ $(ibidir)/automake-$(automake-version) + +# Import the tarball. tarball=healpix-$(healpix-version).tar.lz $(call import-source, $(healpix-url), $(healpix-checksum)) - if [ x"$(healpix-python-dep)" = x ]; then - pycommand1="echo no-healpy-because-no-other-python" - pycommand2="echo no-healpy-because-no-other-python" - else - pycommand1="python setup.py build" - pycommand2="python setup.py install" - fi - rm -rf $(ddir)/Healpix_$(healpix-version) + +# Setup the build directory + rm -rf $(ddir)/healpix-$(healpix-version) topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions - cd Healpix_$(healpix-version) + cd healpix-$(healpix-version) $(shsrcdir)/prep-source.sh $(ibdir) - cd src/C/autotools + +# Compile and install libsharp: + cd src/common_libraries/libsharp autoreconf --install ./configure --prefix=$(idir) make V=1 -j$(numthreads) SHELL=$(ibdir)/bash make install - cd ../../cxx/autotools/ + +# Compile and install the C version: + cd ../../C/autotools + printf "\n\nDEBUG ONLY\n\n"; /bin/pwd; printf "\nGUBED\n\n\n" + autoreconf --install + ./configure --prefix=$(idir) + make V=1 -j$(numthreads) SHELL=$(ibdir)/bash + make install + +# Compile and install the C++ version: + cd ../../cxx/ + printf "\n\nDEBUG.BBBB ONLY\n\n"; /bin/pwd; printf "\nBBB.GUBED\n\n\n" autoreconf --install ./configure --prefix=$(idir) # With CFITSIO 4.0, the 'CFITSIO_VERSION' macro has three -# components. But this version of Healpix doesn't yet account for -# this. +# components. But this (which?) version of Healpix doesn't yet +# account for this. sed -i -e's/CFITSIO_VERSION/fitsversion/' cxxsupport/fitshandle.cc # Continue with the building. make V=1 -j$(numthreads) SHELL=$(ibdir)/bash make install - cd ../../healpy - $$pycommand1 - $$pycommand2 + +# Finalize the build cd $$topdir - rm -rf $(ddir)/Healpix_$(healpix-version) + rm -rf $(ddir)/healpix-$(healpix-version) cp $(dtexdir)/healpix.tex $(ictdir)/ echo "HEALPix $(healpix-version) \citep{healpix}" > $@ +# 2025-05-24 The build rules here for 'lalsuite' include git initialisation +# with a dummy commit of all the source files since this is required for an +# install unless the .git/ directory (currently 650 Mb) is included in the +# tarball. Our lalsuite tarball also has many big data test files removed, +# since these are unlikely to be needed in typically astronomy usage; this +# brings the .tar.lz file down to 25 Mb from the default of about 950 Mb +# (tar.gz) or 740 Mb (tar.lz). +# +# If you need to do full gravitational wave work with 'lalsuite', then you +# should provide an alternative tarball and edit the three files +# reproduce/software/config/{versions,checksums,urls}.conf in order to use +# your preferred tarball. +$(ipydir)/lalsuite-$(lalsuite-version): \ + $(ibidir)/automake-$(automake-version) \ + $(ibidir)/swig-$(swig-version) \ + $(ibidir)/metaio-$(metaio-version) \ + $(ibidir)/framel-$(framel-version) \ + $(ipydir)/astropy-$(astropy-version) \ + $(ipydir)/igwn-segments-$(igwn-segments-version) \ + $(ipydir)/lscsoft-glue-$(lscsoft-glue-version) \ + $(ipydir)/python-dateutil-$(python-dateutil-version) + tarball=lalsuite-$(lalsuite-version).tar.lz + $(call import-source, $(lalsuite-url), \ + $(lalsuite-checksum)) + +# First: build from source as if it's a C source only. + cd $(ddir) + unpackdir=lalsuite-$(lalsuite-version) + rm -rf $$unpackdir + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) + +# A git commit is needed to generate version-control files; the +# strings in these will be rather arbitrary and should be ignored. + git init && git add . + git commit -a --no-edit -m "Dummy commit" \ + --author "Tarball <tar@ball.only>" + autoreconf + ./configure --prefix="$(idir)" --enable-swig-python + make + make install + +# Clean up and build final tarball + cd $(ddir); rm -fr $$unpackdir + echo "LALSuite $(lalsuite-version)" > $@ + $(ibidir)/libbsd-$(libbsd-version): $(ibidir)/libmd-$(libmd-version) tarball=libbsd-$(libbsd-version).tar.lz $(call import-source, $(libbsd-url), $(libbsd-checksum)) @@ -731,7 +827,8 @@ $(ibidir)/libtiff-$(libtiff-version): $(ibidir)/libjpeg-$(libjpeg-version) $(call gbuild, libtiff-$(libtiff-version), static, \ --disable-jbig \ --disable-webp \ - --disable-zstd) + --disable-zstd \ + --disable-libdeflate ) echo "Libtiff $(libtiff-version)" > $@ $(ibidir)/libtirpc-$(libtirpc-version): @@ -839,9 +936,52 @@ $(ibidir)/ninjabuild-$(ninjabuild-version): $(ibidir)/cmake-$(cmake-version) echo "Ninja build system $(ninjabuild-version)" > $@ $(ibidir)/openblas-$(openblas-version): + +# Import the tarball. tarball=openblas-$(openblas-version).tar.lz $(call import-source, $(openblas-url), $(openblas-checksum)) - if [ x$(on_mac_os) = xyes ]; then export CC=clang; fi + +# If 'gcc' is actually a symbolic link to 'clang', then print the +# following message to guide the user on how to prepare their +# environment. + if $$CC --version | grep clang &> /dev/null; then + +# Print message. + echo; echo + printf "*********************************************\n" + printf "OpenBlas could not be installed with Clang!\n\n" + printf "In order to install OpenBLAS, GCC and Gfortran are " + printf "needed. You can take the following steps to fix " + printf "this:\n\n" + printf "1. Install GCC with Homebrew.\n" + printf "2. Get the full path of 'gcc', 'g++', and 'gfortran' " + printf "(for example with 'which gcc').\n" + printf "3. Comment the 'exit 1' and un-comment (and edit) the " + printf "'export's that are below this message (in the " + printf "'openblas' rule of " + printf "'reproduce/software/make/high-level.mk', within the " + printf "'openblas' rule):\n\n" + printf " exit 1\n" + printf " #export CC=/opt/homebrew/bin/gcc-XX\n" + printf " #export CXX=/opt/homebrew/bin/g++-XX\n" + printf " #export FC=/opt/homebrew/bin/gfortran-XX\n\n" + printf " with the lines:\n\n" + printf " #exit 1\n" + printf " export CC=/opt/homebrew/bin/gcc-15\n" + printf " export CXX=/opt/homebrew/bin/g++-15\n" + printf " export FC=/opt/homebrew/bin/gfortran-15\n\n" + printf "5. Re-configure Maneage.\n" + printf "*********************************************\n" + echo; echo + +# Parts to modify when the message above is printed. + exit 1 + #export CC=/opt/homebrew/bin/gcc-XX + #export CXX=/opt/homebrew/bin/g++-XX + #export FC=/opt/homebrew/bin/gfortran-XX + fi + +# Do the build. cd $(ddir) tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions cd openblas-$(openblas-version) @@ -908,6 +1048,209 @@ $(ibidir)/tides-$(tides-version): cp $(dtexdir)/tides.tex $(ictdir)/ echo "TIDES $(tides-version) \citep{tides}" > $@ +$(ibidir)/sqlite-$(sqlite-version): $(ibidir)/tcl-$(tcl-version) + tarball=sqlite-$(sqlite-version).tar.lz + $(call import-source, $(sqlite-url), $(sqlite-checksum)) + $(call gbuild, sqlite-$(sqlite-version),, \ + --enable-all --enable-static --enable-shared) + echo "Sqlite $(sqlite-version)" > $@ + +$(ibidir)/tcl-$(tcl-version): $(ibidir)/zlib-$(zlib-version) \ + $(ibidir)/tzdb-$(tzdb-version) + +# If both the tcl and tk packages are needed, then they must be built +# together, with identical version numbers. Thus, for simplicity in +# the build system, whether or not we build only tcl, or both tcl and +# tk, we must check that the versions are identical. + if [ "x$(tcl-version)" != "x$(tk-version)" ]; then + printf "Error: This build system requires identical tcl and " + printf "tk versions to be selected **even if** tk is not " + printf "going to be built. However, tcl-version=$(tcl-version) " + printf "while tk-version=$(tk-version)\n" + exit 1 + fi + +# Prepare the input tarball. + tarball=tcl-$(tcl-version).tar.lz + $(call import-source, $(tcl-url), $(tcl-checksum)) + +# Setup the build directory + cd $(ddir) + unpackdir_tcl=tcl-$(tcl-version) + rm -rf $${unpackdir_tcl} + +# Install TCL + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd - # return to the top maneage directory + cd $(ddir)/$${unpackdir_tcl}/unix + $(shsrcdir)/prep-source.sh $(ibdir) + ./configure --prefix="$(idir)" + make -j$(numthreads) + make install + cd - # return to the top maneage directory + +# Setup the 'tclsh' symbolic link. + maj_min_version=$$(printf $(tcl-version)| \ + sed -e "s;^\([0-9]*\.[0-9]*\).*\';\1;") + printf "Will symlink tclsh$${maj_min_version} as tclsh ...\n" + cd $(ibdir) + rm -fv tclsh && ln -sv tclsh$${maj_min_version} tclsh + cd - + cd $(ddir) + +# Finalize. + if (printf "$$unpackdir_tcl" | grep "[a-z][a-z]"); then \ + rm -fr $$unpackdir_tcl + fi + echo "Tcl $(tcl-version)" > $(ibidir)/tcl-$(tcl-version) + + +# The tk library needs the X11 library for building GUIs, and should not +# normally be needed for a non-interactive project. However, GUIs built +# with tk might be convenient during development of a project, since visual +# checks within the maneage shell may be useful. +# +# We need to rebuild tcl temporarily in the temporary build area in order +# to build tk. However, we want the tk target to be dependent on tcl as a +# prerequisite to avoid the possibility of parallel builds that risk +# conflicting within the build area because of duplicate use of the same +# tcl package directory after untarring the archive. +$(ibidir)/tk-$(tk-version): $(ibidir)/zip-$(zip-version) \ + $(ibidir)/tcl-$(tcl-version) \ + $(ibidir)/libx11-$(libx11-version) \ + +# Prepare the tarball. + tarball=tk-$(tk-version).tar.lz + $(call import-source, $(tk-url), $(tk-checksum)) + +# If both the tcl and tk packages are needed, then they must be built +# together, with identical version numbers. Thus, for simplicity in +# the build system, whether or not we build only tcl, or both tcl and +# tk, we must check that the versions are identical. + if [ "x$(tcl-version)" != "x$(tk-version)" ]; then + printf "Error: This build system requires identical tcl and " + printf "tk versions to be selected **even if** tk is not " + printf "going to be built. However, tcl-version=$(tcl-version) " + printf "while tk-version=$(tk-version)\n" + exit 1 + fi + +# Make sure no temporary directory exists. + cd $(ddir) + unpackdir=tk-$(tk-version) + if (printf "$$unpackdir" | grep "[a-z][a-z]"); then + rm -rf $$unpackdir + fi + +# Install TK: zipfs is being disabled because of the problem with +# installing zip (see the comments above zip). + cd $(ddir) + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd $$unpackdir/unix + $(shsrcdir)/prep-source.sh $(ibdir) + ./configure --prefix="$(idir)" --with-tcl=$(ildir) + make -j$(numthreads) + make install + +# Finalize. + cd $(ddir) + if (printf "$$unpackdir" | grep "[a-z][a-z]"); then \ + rm -fr $$unpackdir; fi + echo "Tk $(tk-version)" > $(ibidir)/tk-$(tk-version) + + + +# WARNING: Dependence on glibc: tzdb (time zone data base) uses the 'zic' +# program from the GNU C library. Until Maneage builds its own glibc, it is +# imported from the host operating system in the 'low-level-links' step of +# 'basic.mk'. +$(ibidir)/tzdb-$(tzdb-version): + +# Import the tarball + tarball=tzdb-$(tzdb-version).tar.lz + $(call import-source, $(tzdb-url), $(tzdb-checksum)) + +# Unpack the tarball. + cd $(ddir) + unpackdir=tzdb-$(tzdb-version) + rm -rf $$unpackdir + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd $$unpackdir + +# Make necessary corrections. + TZGEN=$(strip $(ddir))/$$unpackdir/tzgen + printf "\n\n\n_____TZGEN=$${TZGEN}_____\n\n\n" + make AWK=gawk BACKWARD="backward" PACKRATDATA=backzone \ + PACKRATLIST=zone.tab VERSION_DEPS= tzdata.zi leapseconds + +# Build the timezone data +# +# The '-b fat' option was created in glibc by around 2020, when +# '-b slim' became the default. Allowing the default of '-b slim' +# could potentially lead to a #Y2038 bug [3]. +# +# Some other hacks are also needed for older glibc. +# +# [1] https://mm.icann.org/pipermail/tz-announce/2020-October/000059.html +# [2] https://github.com/stub42/pytz/issues/48 +# [3] https://en.wikipedia.org/wiki/Year_2038_problem + BFAT_OPTION=$$(if (zic -b fat 2>/dev/null); then \ + printf "%sb fat" "-"; else printf ""; fi) + if [ "x$${BFAT_OPTION}" = "x" ]; then \ + sed -e 's/Sa\([^a-zA-Z]\)/Sat\1/g' \ + -e 's/Su\([^a-zA-Z]\)/Sun\1/g' \ + -e 's/^\(.\|..\) Sat/\1 Sa/' \ + -e "s/lastSu\'/lastSun/" tzdata.zi \ + | grep -v "^L" \ + > tzdata.zi.3letter.days + zic $${BFAT_OPTION} -d $${TZGEN} -L /dev/null \ + tzdata.zi.3letter.days + zic $${BFAT_OPTION} -d $${TZGEN}/right -L leapseconds \ + tzdata.zi.3letter.days + else + zic $${BFAT_OPTION} -d $${TZGEN} -L /dev/null tzdata.zi + zic $${BFAT_OPTION} -d $${TZGEN}/right -L leapseconds \ + tzdata.zi + fi + +# Replace hardlinks by symlinks + if [ "x$${BFAT_OPTION}" = "x" ]; then + +# Older method of creating symbolic links: + grep '^L ' $(ddir)/$$unpackdir/tzdata.zi \ + | while read L target name ; do + absolute_name="$${TZGEN}/$$name" + relative_target=$$(realpath -m -s \ + --relative-to="$${absolute_name%/*}" \ + "$${TZGEN}/$$target") + maybe_newdir=$$(printf $$name | sed -e "s;/[^/]*\';;") + mkdir -p $${TZGEN}/$${maybe_newdir} + mkdir -p $${TZGEN}/right/$${maybe_newdir} + ln -sf "$$relative_target" "$${TZGEN}/$$name" + ln -sf "$$relative_target" "$${TZGEN}/right/$$name" + done + + else + +# More recent (2025-05-25) method of creating symbolic links: + grep '^L ' $(ddir)/$$unpackdir/tzdata.zi \ + | while read L target name ; do + absolute_name="$${TZGEN}/$$name" + relative_target=$$(realpath -m -s \ + --relative-to="$${absolute_name%/*}" \ + "$${TZGEN}/$$target") + ln -sf "$$relative_target" "$${TZGEN}/$$name" + ln -sf "$$relative_target" "$${TZGEN}/right/$$name" + done + fi + +# Generate a posixrules file (with a UTC timezone) and install. + ln -s Etc/UTC $${TZGEN}/posixrules + mkdir -p $(idir)/share/zoneinfo + cp -rv $${TZGEN}/* $(idir)/share/zoneinfo/ + cd $(ddir); rm -rf $$unpackdir + echo "IANA Time Zone Database (tzdb) $(tzdb-version)" > $@ + $(ibidir)/valgrind-$(valgrind-version): tarball=valgrind-$(valgrind-version).tar.lz $(call import-source, $(valgrind-url), $(valgrind-checksum)) @@ -963,7 +1306,19 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) tarball=wcslib-$(wcslib-version).tar.lz $(call import-source, $(wcslib-url), $(wcslib-checksum)) +# macOS arm64 fix: reserve extra space in binary headers so +# install_name_tool (called bellow, after installation) can safely +# update library paths. Without this, we get the following error: +# "larger updated load commands do not fit". SDKROOT is also +# necessary for system libraries. + if [ x$(on_mac_os) = xyes ]; then + sdk=$$(xcrun --show-sdk-path) + LDFLAGS="$$LDFLAGS -isysroot $$sdk" + export LDFLAGS="$$LDFLAGS -Wl,-headerpad_max_install_names" + fi + # Build WCSLIB while disabling some features: +# # - Fortran is disabled because as of May 2023, on macOS systems # where we do not install GCC (and thus a standard 'gfortran'), the # LLVM Fortran compiler is not complete and will cause a crash. If @@ -972,11 +1327,18 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) # systems. Hopefully some time in the future, GCC will also be # install-able on macOS within Maneage or LLVM's 'gfortran' will # also be complete and will not cause a crash. +# # - PGPLOT is disabled because it has many manual steps in its # installation. Therefore, we currently do not build PGPlots in # Maneage. Once (if) it is added, we can remove '--without-pgplot'. +# +# - Flex is disabled because we have not made it a prerequisite for +# the 'wcslib' target, and we don't want the behaviour to differ +# between host OSes that may or may not have 'flex', or may have +# different versions of 'flex'. $(call gbuild, wcslib-$(wcslib-version), , \ LIBS="-pthread -lcurl -lm" \ + --disable-flex \ --without-pgplot \ --disable-fortran \ --with-cfitsiolib=$(ildir) \ @@ -1186,6 +1548,13 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ tarball=ghostscript-$(ghostscript-version).tar.lz $(call import-source, $(ghostscript-url), $(ghostscript-checksum)) +# On macOS we use the system compiler and linker. The system linker +# there doesn't support '--copy-dt-needed-entries', while the one on +# Linux crashes if we remove it. So we only activate it on macOS. + if [ x$(on_mac_os) = xno ]; then + export LDFLAGS="$$LDFLAGS -Wl,--copy-dt-needed-entries" + fi + # Unpack it and configure Ghostscript. The option # '-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library from being # required at compile time. @@ -1193,13 +1562,12 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions cd ghostscript-$(ghostscript-version) $(shsrcdir)/prep-source.sh $(ibdir) - ./configure --prefix=$(idir) \ - --disable-cups \ + ./configure --disable-cups \ + --prefix=$(idir) \ --enable-dynamic \ --disable-compile-inits \ - --disable-hidden-visibility \ - CFLAGS="-DPNG_ARM_NEON_OPT=0" \ - LDFLAGS=-Wl,--copy-dt-needed-entries + --disable-hidden-visibility \ + CFLAGS="-DPNG_ARM_NEON_OPT=0" # Build and install the program and the shared libraries. make V=1 -j$(numthreads) @@ -1224,18 +1592,61 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ rm -rf ghostscript-$(ghostscript-version) echo "GPL Ghostscript $(ghostscript-version)" > $@ +# Gnuastro can optionally depend on libgit2, but it is not included as a +# dependency here for the two reasons below. If you would like to have it, +# add it as a dependency (its build instruction and dependencies are here +# already), then remove the '--without-libgit2' configure option) and also +# comment the following two generic configuration lines: 'outfitsnocommit' +# and 'outfitsnoconfig'. +# - Within Maneage, we have everything under Git already and users are +# expected to include the version in all their products. +# - libgit2 can only be built with CMake (which takes extremely long to +# compile: possibly even longer than GCC!). +# - Maneage is often run on HPCs that can have network connections +# between the storage and processer and the necessary libgit2 +# operations on every created file can have a performance impact. $(ibidir)/gnuastro-$(gnuastro-version): \ $(ibidir)/gsl-$(gsl-version) \ $(ibidir)/wcslib-$(wcslib-version) \ $(ibidir)/libjpeg-$(libjpeg-version) \ $(ibidir)/libtiff-$(libtiff-version) \ - $(ibidir)/libgit2-$(libgit2-version) \ $(ibidir)/ghostscript-$(ghostscript-version) + +# Generic installation. tarball=gnuastro-$(gnuastro-version).tar.lz $(call import-source, $(gnuastro-url), $(gnuastro-checksum)) - $(call gbuild, gnuastro-$(gnuastro-version), static, , \ - -j$(numthreads)) + $(call gbuild, gnuastro-$(gnuastro-version), static, \ + --without-libgit2, -j$(numthreads)) cp $(dtexdir)/gnuastro.tex $(ictdir)/ + +# Generally, besides the Git commit, we are also disabling the +# default mode of printing any type of metadata and versions of +# dependencies in output headers (through the installation-wide +# configuration file). This is done because within a large pipeline, +# Gnuastro is used to create many intermediate files (that are +# deleted shortly after being created) and it is not worth the +# overhread to keep this information in those intermediate products: +# it is the pipeline's responsibility to put them in the final +# outputs. We recommend to use the Gnuastro Fits program's keyword +# writing options to add as much contextual metadata on your final +# products as possible. Some tips: +# - The creation date is not good (because it is not reproducible +# and will make simple validation hard). The project's Commit +# should be used instead. +# - Define a keyword to keep the public URL of the repository of +# the Maneage'd project. In this way, a person who gets your +# final product can easily check that for all the information +# (including software versions and configuration options). + gconf=$(idir)/etc/gnuastro/gnuastro.conf + echo "" >> $$gconf + echo "# Maneage specific (see Gnuastro build rule for details)." \ + >> $$gconf + echo " outfitsnocommit = 1" >> $$gconf + echo " outfitsnoconfig = 1" >> $$gconf + echo " outfitsnodate = 1" >> $$gconf + echo " outfitsnoversions = 1" >> $$gconf + +# Final target. echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@ $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version) @@ -1353,6 +1764,16 @@ $(ibidir)/imfit-$(imfit-version): \ rm -rf $$unpackdir echo "Imfit $(imfit-version) \citep{imfit2015}" > $@ +# This is the LIGO lscsoft package 'metaio' [1] (to be distinguished from +# some other packages with the same name). +# +# [1] https://git.ligo.org/lscsoft/metaio +$(ibidir)/metaio-$(metaio-version): + tarball=metaio-$(metaio-version).tar.lz + $(call import-source, $(metaio-url), $(metaio-checksum)) + $(call gbuild, metaio-$(metaio-version), static) + echo "Lscsoft Metaio $(metaio-version)" > $@ + # Minizip 1.x is actually distributed within zlib. It doesn't have its own # independent tarball. So we need a custom build, which include the GNU # Autotools (Autoconf and Automake). Note that Minizip 2.x isn't like this @@ -1459,6 +1880,25 @@ $(ibidir)/netpbm-$(netpbm-version): \ rm -rf $$unpackdir echo "Netpbm $(netpbm-version)" > $@ +$(ibidir)/parallel-$(parallel-version): + +# Prepare the tarball and build it. + tarball=parallel-$(parallel-version).tar.lz + $(call import-source, $(parallel-url), $(parallel-checksum)) + $(call gbuild, parallel-$(parallel-version), static) + +# GNU Parallel requires the users to acknowledge that they will cite +# it. Otherwise, it prints a warning on every run: reminding the user +# to cite it. In Maneage, we make sure that all software that request +# citation are cited automatically, so there is no need for a +# Maneager to get this warning and we can automatically ensure the +# developer that it will be cited. + echo "will cite" | $(ibdir)/parallel --citation + +# Copy the BibTeX source of the citation and finish. + cp -pv $(dtexdir)/parallel.tex $(ictdir)/ + echo "GNU Parallel $(parallel-version) \citep{parallel}" > $@ + $(ibidir)/patch-$(patch-version): tarball=patch-$(patch-version).tar.gz $(call import-source, $(patch-url), $(patch-checksum)) @@ -1477,6 +1917,13 @@ $(ibidir)/pcre-$(pcre-version): , V=1 -j$(numthreads)) echo "Perl Compatible Regular Expressions $(pcre-version)" > $@ +$(ibidir)/pcre2-$(pcre2-version): + tarball=pcre2-$(pcre2-version).tar.lz + $(call import-source, $(pcre2-url), $(pcre2-checksum)) + $(call gbuild, pcre2-$(pcre2-version), static) + echo "Perl Compatible Regular Expressions 2 $(pcre2-version)" > $@ + + # On macOS 12.3 Monterey with AppleClang 13.1.6.13160021, Plplot 5.15.0 # needs the 'finite' function of 'math.h' which has been deprecated in # macOS. By manually adding "#define finite isfinite" in 'math.h' like @@ -1643,15 +2090,13 @@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version) cp $(dtexdir)/swarp.tex $(ictdir)/ echo "SWarp $(swarp-version) \citep{swarp}" > $@ -$(ibidir)/swig-$(swig-version): - -# Option --without-pcre was a suggestion once the configure step was -# tried and it failed. It was not recommended but it works! pcr is a -# dependency of swig +$(ibidir)/swig-$(swig-version): \ + $(ibidir)/pcre2-$(pcre2-version) +# Not disabling pcre, since PCRE is needed for lalsuite (python). tarball=swig-$(swig-version).tar.lz $(call import-source, $(swig-url), $(swig-checksum)) $(call gbuild, swig-$(swig-version), static, \ - --without-pcre --without-tcl) + --without-tcl) echo "Swig $(swig-version)" > $@ # The disables: @@ -1718,8 +2163,19 @@ $(ibidir)/util-linux-$(util-linux-version): \ # manually by commenting the relevant files in the # 'configure.ac'. sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \ + -e's|UL_BUILD_INIT(\[bits\], \[yes\])|UL_BUILD_INIT(\[bits\], \[no\])|' \ -i configure.ac +# 'autogen.sh' checks for dependencies, but 'flex' (that is not built +# in Maneage) is not needed when compiling from tarball (see: +# https://github.com/util-linux/util-linux/pull/2531#issuecomment-1798020594) + sed -i '/flex/d' autogen.sh + ./autogen.sh + +# The 'autogen.sh' call resets the 'SHELL' (that was corrected in +# 'prep-source.sh') to '/bin/sh'. Therefore, we need to correct it. + sed -i -e's|SHELL = /bin/sh|SHELL = $(SHELL)|' po/Makefile.in.in + # Having updated 'configure.ac', we need to re-generate the # './configure' script with 'autoreconf' (which is part of Autoconf # and needs Automake; hence why they are dependencies. @@ -1729,7 +2185,6 @@ $(ibidir)/util-linux-$(util-linux-version): \ export CONFIG_SHELL=$(ibdir)/bash ./configure --prefix=$(idircustom)/util-linux \ --disable-dependency-tracking \ - --enable-libmount-support-mtab \ --disable-silent-rules \ --disable-liblastlog2 \ --disable-mountpoint \ @@ -1808,6 +2263,7 @@ $(ibidir)/vim-$(vim-version): unpackdir=vim-$(vim-version) cd $(ddir)/$$unpackdir $(shsrcdir)/prep-source.sh $(ibdir) + export CFLAGS="-std=gnu17 $$CFLAGS" ./configure --prefix=$(idir) \ --disable-canberra \ --enable-multibyte \ @@ -1833,16 +2289,28 @@ $(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version) BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) echo "Unzip $(unzip-version)" > $@ -$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version) +$(ibidir)/zip-$(zip-version): + +# Prepare the tarball and build directory. tarball=zip-$(zip-version).tar.lz $(call import-source, $(zip-url), $(zip-checksum)) - $(call gbuild, zip-$(zip-version), static,, \ - -f unix/Makefile generic \ - CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ - -f unix/Makefile generic \ - BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) - echo "Zip $(zip-version)" > $@ +# Unpack and go into the directory. + export LDFLAGS="$$LDFLAGS -static" + cd $(ddir) + rm -fr zip-$(zip-version)/ + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd zip-$(zip-version)/ + +# Build and install + make SHELL=$(ibdir)/bash -f unix/Makefile generic + make SHELL=$(ibdir)/bash install -f unix/Makefile \ + generic BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 + +# Go back to the top build directory, clean up and finalize. + cd $(ddir) + rm -rf zip-$(zip-version)/ + echo "Zip $(zip-version)" > $@ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index c994e3f..6153f0a 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -83,7 +83,11 @@ $(ibidir)/libffi-$(libffi-version): fi echo "Libffi $(libffi-version)" > $@ -$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) +# 2025-05-26 '--with-system-ffi' seems to be obsolete +# TODO: For a recommended list of dependencies, see +# https://github.com/pyenv/pyenv/wiki#suggested-build-environment +$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) \ + $(ibidir)/sqlite-$(sqlite-version) # Download the source. tarball=python-$(python-version).tar.lz @@ -346,12 +350,27 @@ $(ipydir)/astropy-$(astropy-version): \ rm -fv $(idir)/bin/fits{diff,check,header,info,2bitmap} rm -fv $(idir)/bin/{samp_hub,showtable,volint,wcslint} +# Uncomment the 'export' command below only when building from a git +# tarball, e.g. for testing if a bug still occurs: +# export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_ASTROPY=7.2.0.87 + # Do the basic build. $(call pybuild, tar -xf, astropy-$(astropy-version),,, \ GPEP517) cp -pv $(dtexdir)/astropy.tex $(ictdir)/ echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@ +$(ipydir)/astropy-healpix-$(astropy-healpix-version): \ + $(ipydir)/extension-helpers-$(extension-helpers-version) \ + $(ipydir)/numpy-$(numpy-version) + tarball=astropy-healpix-$(astropy-healpix-version).tar.lz + $(call import-source, $(astropy-healpix-url), \ + $(astropy-healpix-checksum)) + $(call pybuild, tar -xf, \ + astropy-healpix-$(astropy-healpix-version),,, \ + GPEP517) + echo "Astropy-healpix $(astropy-healpix-version)" > $@ + $(ipydir)/astropy-iers-data-$(astropy-iers-data-version): \ $(ipydir)/setuptools-$(setuptools-version) tarball=astropy-iers-data-$(astropy-iers-data-version).tar.lz @@ -360,7 +379,7 @@ $(ipydir)/astropy-iers-data-$(astropy-iers-data-version): \ $(call pybuild, tar -xf, \ astropy-iers-data-$(astropy-iers-data-version),,, \ GPEP517) - echo "Astropy-Iers-Data $(astropy-iers-data-version)" > $@ + echo "Astropy-IERS-data $(astropy-iers-data-version)" > $@ $(ipydir)/beautifulsoup4-$(beautifulsoup4-version): \ $(ipydir)/soupsieve-$(soupsieve-version) @@ -400,6 +419,13 @@ $(ipydir)/chardet-$(chardet-version): \ $(call pybuild, tar -xf, chardet-$(chardet-version), , \ Chardet $(chardet-version)) +$(ipydir)/colorama-$(colorama-version): \ + $(ipydir)/hatchling-$(hatchling-version) + tarball=colorama-$(colorama-version).tar.lz + $(call import-source, $(colorama-url), $(colorama-checksum)) + $(call pybuild, tar -xf, \ + colorama-$(colorama-version),,, GPEP517) + $(ipydir)/contourpy-$(contourpy-version): \ $(ipydir)/pybind11-$(pybind11-version) \ $(ipydir)/meson-python-$(meson-python-version) @@ -417,6 +443,15 @@ $(ipydir)/corner-$(corner-version): $(ipydir)/matplotlib-$(matplotlib-version) cp $(dtexdir)/corner.tex $(ictdir)/ echo "Corner $(corner-version) \citep{corner}" > $@ +$(ipydir)/cosmodesi-mpytools-$(cosmodesi-mpytools-version): \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/scipy-$(scipy-version) + tarball=cosmodesi-mpytools-$(cosmodesi-mpytools-version).tar.lz + $(call import-source, $(cosmodesi-mpytools-url), $(cosmodesi-mpytools-checksum)) + $(call pybuild, tar -xf, cosmodesi-mpytools-$(cosmodesi-mpytools-version), , \ + Cosmodesi-mpytools $(cosmodesi-mpytools-version), GPEP517) + echo "Cosmodesi-mpytools $(cosmodesi-mpytools-version)" > $@ + $(ipydir)/cppy-$(cppy-version): \ $(ipydir)/setuptools-scm-$(setuptools-scm-version) tarball=cppy-$(cppy-version).tar.lz @@ -482,6 +517,15 @@ $(ipydir)/entrypoints-$(entrypoints-version): \ $(call pybuild, tar -xf, entrypoints-$(entrypoints-version), , \ EntryPoints $(entrypoints-version)) +$(ipydir)/exceptiongroup-$(exceptiongroup-version): \ + $(ipydir)/setuptools-$(setuptools-version) \ + $(ipydir)/flit-scm-$(flit-scm-version) + tarball=exceptiongroup-$(exceptiongroup-version).tar.lz + $(call import-source, $(exceptiongroup-url), $(exceptiongroup-checksum)) + $(call pybuild, tar -xf, exceptiongroup-$(exceptiongroup-version), , \ + Exceptiongroup $(exceptiongroup-version), GPEP517) + + $(ipydir)/extension-helpers-$(extension-helpers-version): \ $(ipydir)/setuptools-scm-$(setuptools-scm-version) tarball=extension-helpers-$(extension-helpers-version).tar.lz @@ -507,6 +551,16 @@ $(ipydir)/flit-core-$(flit-core-version): \ $(call pybuild, tar -xf, flit-core-$(flit-core-version), , \ Flit-core $(flit-core-version), GPEP517) + +$(ipydir)/flit-scm-$(flit-scm-version): \ + $(ipydir)/flit-core-$(flit-core-version) \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) + tarball=flit-scm-$(flit-scm-version).tar.lz + $(call import-source, $(flit-scm-url), $(flit-scm-checksum)) + $(call pybuild, tar -xf, flit-scm-$(flit-scm-version), , \ + flit-scm $(flit-scm-version), GPEP517) + + # Although cython is not an obligatory prerequisite of fonttools, we force # it as a prerequisite for reproducibility; otherwise build parallelism may # lead to some builds with and some builds without cython, depending on how @@ -558,6 +612,23 @@ $(ipydir)/gpep517-$(gpep517-version): \ BOOT_GPEP517) echo "gpep517 $(gpep517-version)" > $@ +$(ipydir)/hatchling-$(hatchling-version): \ + $(ipydir)/packaging-$(packaging-version) \ + $(ipydir)/pathspec-$(pathspec-version) \ + $(ipydir)/pluggy-$(pluggy-version) \ + $(ipydir)/trove-classifiers-$(trove-classifiers-version) + tarball=hatchling-$(hatchling-version).tar.lz + $(call import-source, $(hatchling-url), $(hatchling-checksum)) + $(call pybuild, tar -xf, \ + hatchling-$(hatchling-version),,, GPEP517) + +$(ipydir)/hatch-vcs-$(hatch-vcs-version): \ + $(ipydir)/hatchling-$(hatchling-version) + tarball=hatch-vcs-$(hatch-vcs-version).tar.lz + $(call import-source, $(hatch-vcs-url), $(hatch-vcs-checksum)) + $(call pybuild, tar -xf, hatch-vcs-$(hatch-vcs-version), , \ + Hatch-vcs $(hatch-vcs-version), GPEP517) + $(ipydir)/h5py-$(h5py-version): \ $(ipydir)/six-$(six-version) \ $(ibidir)/hdf5-$(hdf5-version) \ @@ -572,15 +643,38 @@ $(ipydir)/h5py-$(h5py-version): \ $(call pybuild, tar -xf, h5py-$(h5py-version), , \ h5py $(h5py-version)) -# 'healpy' is actually installed as part of the HEALPix package. It will be -# installed with its C/C++ libraries if any other Python library is -# requested with HEALPix. So actually calling for 'healpix' (when 'healpix' -# is requested) is not necessary. But some users might not know about this -# and just ask for 'healpy'. To avoid confusion in such cases, we'll just -# set 'healpy' to be dependent on 'healpix' and not download any tarball -# for it, or write anything in the final target. -$(ipydir)/healpy-$(healpy-version): $(ibidir)/healpix-$(healpix-version) - touch $@ +# As of 2025-05-20, there are at least three python healpix packages at +# pypi.org, with versions: +# +# https://pypi.org/project/healpy 1.18.1 +# https://pypi.org/project/healpix 2024.2 +# https://pypi.org/project/astropy-healpix 1.1.2 +# +# Maneage provides both 'healpy' and 'astropy-healpix', independently. We +# ignore pypix 'healpix', whose name risks confusion with the C/C++/fortran +# version of healpix. +# +# For simplicity and error tracing, you should best install either healpy +# or astropy-healpix, not both. For example, astropy_healpix/healpy.py has +# an interface to provide 'healpy' type function names. However, it may be +# possible to use both if your python imports avoid namespace clashes. See +# the documentation and source code of the respective packages to study how +# they relate to one another. +# +# The 'healpy' package requires the C/C++ 'healpix' package to be built +# in order to use the shared 'libsharp' library. +$(ipydir)/healpy-$(healpy-version): \ + $(ibidir)/healpix-$(healpix-version) \ + $(ipydir)/matplotlib-$(matplotlib-version) \ + $(ipydir)/scipy-$(scipy-version) + tarball=healpy-$(healpy-version).tar.lz + $(call import-source, $(healpy-url), \ + $(healpy-checksum)) + $(call pybuild, tar -xf, \ + healpy-$(healpy-version),,, \ + GPEP517) + echo "Healpy $(healpy-version)" > $@ + $(ipydir)/html5lib-$(html5lib-version): \ $(ipydir)/six-$(six-version) \ @@ -612,6 +706,13 @@ $(ipydir)/jinja2-$(jinja2-version): $(ipydir)/markupsafe-$(markupsafe-version) $(call pybuild, tar -xf, jinja2-$(jinja2-version), , \ Jinja2 $(jinja2-version)) +$(ipydir)/joblib-$(joblib-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=joblib-$(joblib-version).tar.lz + $(call import-source, $(joblib-url), $(joblib-checksum)) + $(call pybuild, tar -xf, \ + joblib-$(joblib-version),,, GPEP517) + $(ipydir)/keyring-$(keyring-version): \ $(ipydir)/entrypoints-$(entrypoints-version) \ $(ipydir)/secretstorage-$(secretstorage-version) \ @@ -631,6 +732,48 @@ $(ipydir)/kiwisolver-$(kiwisolver-version): \ cp -pv $(dtexdir)/kiwisolver.tex $(ictdir)/ echo "Kiwisolver $(kiwisolver-version) \citep{cassowary2001}" > $@ +# 2025-05-21: As of Feb 2025, it appears the lscsoft group is not maintaining +# python-ligo-lw and ligo-segments; the LIGO Computing Group forked these +# to igwn-ligolw and igwn-segments, respectively [1]. +# [1] https://github.com/ahnitz/ligo-segments/issues/1 +$(ipydir)/igwn-segments-$(igwn-segments-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=igwn-segments-$(igwn-segments-version).tar.lz + $(call import-source, $(igwn-segments-url), $(igwn-segments-checksum)) + $(call pybuild, tar -xf, \ + igwn-segments-$(igwn-segments-version),, \ + Igwn-segments $(igwn-segments-version), GPEP517) + + +$(ipydir)/iniconfig-$(iniconfig-version): \ + $(ipydir)/hatch-vcs-$(hatch-vcs-version) + tarball=iniconfig-$(iniconfig-version).tar.lz + $(call import-source, $(iniconfig-url), $(iniconfig-checksum)) + $(call pybuild, tar -xf, iniconfig-$(iniconfig-version), , \ + Iniconfig $(iniconfig-version), GPEP517) + +# Upstream this is called ligo.skymap with a full stop '.'; we replace it +# by a hyphen '-' to reduce the chance of regex errors. +# +# 2025-05-19 Warning: this might have some undetected dependencies. +$(ipydir)/ligo-skymap-$(ligo-skymap-version): \ + $(ibidir)/gsl-$(gsl-version) \ + $(ipydir)/tqdm-$(tqdm-version) \ + $(ibidir)/sqlite-$(sqlite3-version) \ + $(ipydir)/astropy-$(astropy-version) \ + $(ipydir)/lalsuite-$(lalsuite-version) \ + $(ipydir)/igwn-ligolw-$(igwn-ligolw-version) \ + $(ipydir)/igwn-segments-$(igwn-segments-version) \ + $(ipydir)/astropy-healpix-$(astropy-healpix-version) + tarball=ligo-skymap-$(ligo-skymap-version).tar.lz + $(call import-source, $(ligo-skymap-url), \ + $(ligo-skymap-checksum)) + $(call pybuild, tar -xf, \ + ligo-skymap-$(ligo-skymap-version),,, \ + GPEP517) + echo "ligo-skymap $(ligo-skymap-version)" > $@ + + $(ipydir)/lmfit-$(lmfit-version): \ $(ipydir)/six-$(six-version) \ $(ipydir)/scipy-$(scipy-version) \ @@ -644,6 +787,14 @@ $(ipydir)/lmfit-$(lmfit-version): \ $(call pybuild, tar -xf, lmfit-$(lmfit-version), , \ LMFIT $(lmfit-version)) +$(ipydir)/lscsoft-glue-$(lscsoft-glue-version): \ + $(ipydir)/gpep517-$(gpep517-version) \ + $(ipydir)/python-installer-$(python-installer-version) + tarball=lscsoft-glue-$(lscsoft-glue-version).tar.lz + $(call import-source, $(lscsoft-glue-url), $(lscsoft-glue-checksum)) + $(call pybuild, tar -xf, \ + lscsoft-glue-$(lscsoft-glue-version),,, GPEP517) + $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \ $(ipydir)/cffi-$(cffi-version) \ $(ipydir)/numpy-$(numpy-version) \ @@ -661,11 +812,19 @@ $(ipydir)/markupsafe-$(markupsafe-version): \ $(call pybuild, tar -xf, markupsafe-$(markupsafe-version), , \ MarkupSafe $(markupsafe-version)) +# As of 2026-04-19: Matplotlib needs internet to download and build its +# custom versions of 'freetype' and 'qhull'. The proposed option to 'python +# -m pip instsall' in [1] for using system libraries was tested, but did +# not work in this setup (our 'pybuild' uses 'python -m gpep517 +# install-from-source', not 'pip'). +# +# [1] https://matplotlib.org/stable/install/dependencies.html $(ipydir)/matplotlib-$(matplotlib-version): \ $(itidir)/texlive \ $(ipydir)/numpy-$(numpy-version) \ $(ipydir)/cycler-$(cycler-version) \ $(ipydir)/pillow-$(pillow-version) \ + $(ibidir)/freetype-$(freetype-version) \ $(ipydir)/fonttools-$(fonttools-version) \ $(ipydir)/contourpy-$(contourpy-version) \ $(ipydir)/kiwisolver-$(kiwisolver-version) \ @@ -706,12 +865,11 @@ $(ipydir)/meson-python-$(meson-python-version): \ echo "Meson-Python $(meson-python-version)" > $@ $(ipydir)/mpi4py-$(mpi4py-version): \ - $(ipydir)/gpep517-$(gpep517-version) \ $(ibidir)/openmpi-$(openmpi-version) \ - $(ipydir)/python-installer-$(python-installer-version) + $(ipydir)/cython-$(cython-version) tarball=mpi4py-$(mpi4py-version).tar.lz $(call import-source, $(mpi4py-url), $(mpi4py-checksum)) - $(call pybuild, tar -xf, mpi4py-$(mpi4py-version)) + $(call pybuild, tar -xf, mpi4py-$(mpi4py-version),,, GPEP517) cp $(dtexdir)/mpi4py.tex $(ictdir)/ echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@ @@ -723,8 +881,17 @@ $(ipydir)/mpmath-$(mpmath-version): \ $(call pybuild, tar -xf, mpmath-$(mpmath-version), , \ mpmath $(mpmath-version)) -# Until 2025-02-22: we had 'export CFLAGS="--std=c99 $$CFLAGS"' before -# calling pybuild; but that doesn't seem to be necessary. +$(ipydir)/networkx-$(networkx-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=networkx-$(networkx-version).tar.lz + $(call import-source, $(networkx-url), $(networkx-checksum)) + $(call pybuild, tar -xf, \ + networkx-$(networkx-version),,, \ + GPEP517) + echo "networkx $(networkx-version)" > $@ + +# Numpy's MacOS builds using Xcode prior to 26.3 needed the following flags +# added to 'LDFLAGS': '-undefined dynamic_lookup -bundle'. $(ipydir)/numpy-$(numpy-version): \ $(ipydir)/cython-$(cython-version) \ $(ibidir)/openblas-$(openblas-version) \ @@ -732,9 +899,6 @@ $(ipydir)/numpy-$(numpy-version): \ $(ipydir)/meson-python-$(meson-python-version) tarball=numpy-$(numpy-version).tar.lz $(call import-source, $(numpy-url), $(numpy-checksum)) - if [ x$(on_mac_os) = xyes ]; then - export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle" - fi conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" $(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \ Numpy $(numpy-version), GPEP517) @@ -748,6 +912,23 @@ $(ipydir)/packaging-$(packaging-version): \ $(call pybuild, tar -xf, packaging-$(packaging-version), , \ Packaging $(packaging-version), GPEP517) +$(ipydir)/pandas-$(pandas-version): \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/versioneer-$(versioneer-version) \ + $(ipydir)/pytz-$(pytz-version) + tarball=pandas-$(pandas-version).tar.lz + $(call import-source, $(pandas-url), $(pandas-checksum)) + $(call pybuild, tar -xf, pandas-$(pandas-version), , \ + Pandas $(pandas-version), GPEP517) + echo "pandas $(pandas-version)" > $@ + +$(ipydir)/pathspec-$(pathspec-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=pathspec-$(pathspec-version).tar.lz + $(call import-source, $(pathspec-url), $(pathspec-checksum)) + $(call pybuild, tar -xf, \ + pathspec-$(pathspec-version),,, GPEP517) + $(ipydir)/pexpect-$(pexpect-version): \ $(ipydir)/gpep517-$(gpep517-version) \ $(ipydir)/python-installer-$(python-installer-version) @@ -773,6 +954,13 @@ $(ipydir)/pillow-$(pillow-version): $(ibidir)/libjpeg-$(libjpeg-version) \ # $(call pybuild, tar -xf, pip-$(pip-version), , \ # PiP $(pip-version)) +$(ipydir)/pluggy-$(pluggy-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=pluggy-$(pluggy-version).tar.lz + $(call import-source, $(pluggy-url), $(pluggy-checksum)) + $(call pybuild, tar -xf, \ + pluggy-$(pluggy-version),,, GPEP517) + $(ipydir)/ply-$(ply-version): \ $(ipydir)/gpep517-$(gpep517-version) \ $(ipydir)/python-installer-$(python-installer-version) @@ -828,6 +1016,13 @@ $(ipydir)/pyflakes-$(pyflakes-version): \ $(call pybuild, tar -xf, pyflakes-$(pyflakes-version), , \ pyflakes $(pyflakes-version)) +$(ipydir)/pygments-$(pygments-version): \ + $(ipydir)/hatchling-$(hatchling-version) + tarball=pygments-$(pygments-version).tar.lz + $(call import-source, $(pygments-url), $(pygments-checksum)) + $(call pybuild, tar -xf, pygments-$(pygments-version), , \ + Pygments $(pygments-version), GPEP517) + $(ipydir)/pyparsing-$(pyparsing-version): \ $(ipydir)/gpep517-$(gpep517-version) \ $(ipydir)/flit-core-$(flit-core-version) \ @@ -854,8 +1049,26 @@ $(ipydir)/pyproject-metadata-$(pyproject-metadata-version): \ $(call pybuild, tar -xf, \ pyproject-metadata-$(pyproject-metadata-version),,, GPEP517) + +$(ipydir)/pytest-$(pytest-version): \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) \ + $(ipydir)/colorama-$(colorama-version) \ + $(ipydir)/exceptiongroup-$(exceptiongroup-version) \ + $(ipydir)/iniconfig-$(iniconfig-version) \ + $(ipydir)/packaging-$(packaging-version) \ + $(ipydir)/pluggy-$(pluggy-version) \ + $(ipydir)/pygments-$(pygments-version) + tarball=pytest-$(pytest-version).tar.lz + $(call import-source, $(pytest-url), $(pytest-checksum)) + $(call pybuild, tar -xf, \ + pytest-$(pytest-version),,, \ + GPEP517) + echo "pytest $(pytest-version)" > $@ + + $(ipydir)/python-dateutil-$(python-dateutil-version): \ - $(ipydir)/setuptools-scm-$(setuptools-scm-version) + $(ipydir)/setuptools-scm-$(setuptools-scm-version) \ + $(ipydir)/six-$(six-version) tarball=python-dateutil-$(python-dateutil-version).tar.lz $(call import-source, $(python-dateutil-url), $(python-dateutil-checksum)) $(call pybuild, tar -xf, python-dateutil-$(python-dateutil-version), , \ @@ -885,6 +1098,37 @@ $(ipydir)/python-installer-$(python-installer-version): \ BOOT_INSTALLER) echo "Python-installer $(python-installer-version)" > $@ +# 2025-05-21: As of Feb 2025, it appears the lscsoft group is not maintaining +# python-ligo-lw and ligo-segments; the LIGO Computing Group forked these +# to igwn-ligolw and igwn-segments, respectively [1]. +# [1] https://github.com/ahnitz/ligo-segments/issues/1 +$(ipydir)/igwn-ligolw-$(igwn-ligolw-version): \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) + tarball=igwn-ligolw-$(igwn-ligolw-version).tar.lz + $(call import-source, $(igwn-ligolw-url), \ + $(igwn-ligolw-checksum)) + $(call pybuild, tar -xf, \ + igwn-ligolw-$(igwn-ligolw-version),,, \ + GPEP517) + echo "igwn-ligolw $(igwn-ligolw-version)" > $@ + +$(ipydir)/pyfftw-$(pyfftw-version): $(ipydir)/numpy-$(numpy-version) \ + $(ibidir)/fftw-$(fftw-version) + tarball=pyfftw-$(pyfftw-version).tar.lz + $(call import-source, $(pyfftw-url), $(pyfftw-checksum)) + $(call pybuild, tar -xf, pyfftw-$(pyfftw-version), , \ + Pyfftw $(pyfftw-version), GPEP517) + + +# Called 'fitsio' in pypi.org: https://pypi.org/project/fitsio +$(ipydir)/python3-fitsio-$(python3-fitsio-version): \ + $(ibidir)/patch-$(patch-version) \ + $(ipydir)/numpy-$(numpy-version) + tarball=python3-fitsio-$(python3-fitsio-version).tar.lz + $(call import-source, $(python3-fitsio-url), $(python3-fitsio-checksum)) + $(call pybuild, tar -xf, python3-fitsio-$(python3-fitsio-version), , \ + Python3 Fitsio $(python3-fitsio-version), GPEP517) + $(ipydir)/pythran-$(pythran-version): \ $(ipydir)/ply-$(ply-version) \ $(ipydir)/gast-$(gast-version) \ @@ -904,6 +1148,13 @@ $(ipydir)/pyyaml-$(pyyaml-version): \ $(call pybuild, tar -xf, pyyaml-$(pyyaml-version), , \ PyYAML $(pyyaml-version), GPEP517) +$(ipydir)/pytz-$(pytz-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=pytz-$(pytz-version).tar.lz + $(call import-source, $(pytz-url), $(pytz-checksum)) + $(call pybuild, tar -xf, pytz-$(pytz-version), , \ + Pytz $(pytz-version), GPEP517) + $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(ipydir)/numpy-$(numpy-version) \ $(ipydir)/certifi-$(certifi-version) \ @@ -914,41 +1165,39 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(call pybuild, tar -xf, requests-$(requests-version), , \ Requests $(requests-version)) -# 'pythran' is disabled in the build of Scipy because of complications it -# caused on some systems. We explicitly disable it using a preprocessor -# directive. 'Pythran' can in principle speed up compilation of scientific -# software [1][2]. +# Scipy building notes: +# +# 1. 'pythran' is disabled in the build of Scipy because of complications +# it caused on some systems. 'Pythran' can in principle speed up +# compilation of scientific software [1][2]. We explicitly disable it by +# modifying the source. Technically it should also be possible to pass +# the following option to the gpep517 build recipes with correct +# escaping of single and double quotes, but this has not tried as of +# 2025-02-25. +# --config-json='{"setup-args":"-Duse-pythran=false"}' +# +# 2. Scipy's MacOS builds using Xcode prior to 26.3 needed the following +# flags added to 'LDFLAGS': '-undefined dynamic_lookup -bundle'. +# # [1] https://pythran.readthedocs.io/en/latest -# [2] https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html +# [2] https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html#use-of-pythran $(ipydir)/scipy-$(scipy-version): \ $(ipydir)/numpy-$(numpy-version) \ $(ipydir)/pybind11-$(pybind11-version) + +# Import the tarball. tarball=scipy-$(scipy-version).tar.lz $(call import-source, $(scipy-url), $(scipy-checksum)) - if [ x$(on_mac_os) = xyes ]; then - export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle" - else -# Same question as for 'numpy': why '-shared'? This obstructs -# the meson build. -# export LDFLAGS="$(LDFLAGS) -shared" - : - fi - conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" -# Disable pythran: see -# https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html#use-of-pythran -# export SCIPY_USE_PYTHRAN=0 # deprecated(?) -# Option 1: Hack the source: +# Disable pythran (see above). pyhook_before() { mv -iv meson.options meson.options.orig; \ sed -e 's/\(use-pythran.*value: *\)true/\1false/' \ meson.options.orig > meson.options } -# Option 2: pass the string -# --config-json='{"setup-args": "-Duse-pythran=false"}' -# to gpep517 with correct escaping of single and double quotes. -# Not tried as of 2025-02-25. +# Build Scipy. + conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" $(call pybuild, tar -xf, scipy-$(scipy-version),$$conf,, GPEP517) cp $(dtexdir)/scipy.tex $(ictdir)/ echo "Scipy $(scipy-version) \citep{scipy2020}" > $@ @@ -1003,6 +1252,26 @@ $(ipydir)/sip_tpv-$(sip_tpv-version): \ cp $(dtexdir)/sip_tpv.tex $(ictdir)/ echo "sip_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@ +$(ipydir)/scikit-base-$(scikit-base-version): \ + $(ipydir)/gpep517-$(gpep517-version) \ + $(ipydir)/python-installer-$(python-installer-version) + tarball=scikit-base-$(scikit-base-version).tar.lz + $(call import-source, $(scikit-base-url), $(scikit-base-checksum)) + $(call pybuild, tar -xf, scikit-base-$(scikit-base-version), , \ + Scikit-base $(scikit-base-version), GPEP517) + echo "scikit-base $(scikit-base-version)" > $@ + +$(ipydir)/scikit-learn-$(scikit-learn-version): \ + $(ipydir)/joblib-$(joblib-version) \ + $(ipydir)/threadpoolctl-$(threadpoolctl-version) \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/scipy-$(scipy-version) + tarball=scikit-learn-$(scikit-learn-version).tar.lz + $(call import-source, $(scikit-learn-url), $(scikit-learn-checksum)) + $(call pybuild, tar -xf, scikit-learn-$(scikit-learn-version), , \ + Scikit-learn $(scikit-learn-version), GPEP517) + echo "scikit-learn $(scikit-learn-version)" > $@ + $(ipydir)/six-$(six-version): \ $(ipydir)/setuptools-$(setuptools-version) tarball=six-$(six-version).tar.lz @@ -1026,6 +1295,29 @@ $(ipydir)/sympy-$(sympy-version): $(ipydir)/mpmath-$(mpmath-version) cp $(dtexdir)/sympy.tex $(ictdir)/ echo "SymPy $(sympy-version) \citep{sympy}" > $@ +$(ipydir)/threadpoolctl-$(threadpoolctl-version): \ + $(ipydir)/flit-core-$(flit-core-version) + tarball=threadpoolctl-$(threadpoolctl-version).tar.lz + $(call import-source, $(threadpoolctl-url), $(threadpoolctl-checksum)) + $(call pybuild, tar -xf, threadpoolctl-$(threadpoolctl-version), , \ + threadpoolctl $(threadpoolctl-version), GPEP517) + echo "threadpoolctl $(threadpoolctl-version)" > $@ + +$(ipydir)/tqdm-$(tqdm-version): \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) + tarball=tqdm-$(tqdm-version).tar.lz + $(call import-source, $(tqdm-url), $(tqdm-checksum)) + $(call pybuild, tar -xf, \ + tqdm-$(tqdm-version),, \ + Tqdm $(tqdm-version), GPEP517) + +$(ipydir)/trove-classifiers-$(trove-classifiers-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=trove-classifiers-$(trove-classifiers-version).tar.lz + $(call import-source, $(trove-classifiers-url), $(trove-classifiers-checksum)) + $(call pybuild, tar -xf, \ + trove-classifiers-$(trove-classifiers-version),,, GPEP517) + $(ipydir)/uncertainties-$(uncertainties-version): $(ipydir)/numpy-$(numpy-version) tarball=uncertainties-$(uncertainties-version).tar.lz $(call import-source, $(uncertainties-url), $(uncertainties-checksum)) @@ -1040,6 +1332,13 @@ $(ipydir)/urllib3-$(urllib3-version): \ $(call pybuild, tar -xf, urllib3-$(urllib3-version), , \ Urllib3 $(urllib3-version)) +$(ipydir)/versioneer-$(versioneer-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=versioneer-$(versioneer-version).tar.lz + $(call import-source, $(versioneer-url), $(versioneer-checksum)) + $(call pybuild, tar -xf, versioneer-$(versioneer-version), , \ + Versioneer $(versioneer-version), GPEP517) + $(ipydir)/webencodings-$(webencodings-version): \ $(ipydir)/setuptools-$(setuptools-version) \ $(ipydir)/setuptools-scm-$(setuptools-scm-version) diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk index 7c86c23..7a09915 100644 --- a/reproduce/software/make/r-cran.mk +++ b/reproduce/software/make/r-cran.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2022-2025 Boud Roukema <boud@cosmo.torun.pl> -# Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2026 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk index 864c32a..33847f3 100644 --- a/reproduce/software/make/xorg.mk +++ b/reproduce/software/make/xorg.mk @@ -14,8 +14,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -120,6 +120,7 @@ $(ibidir)/fontconfig-$(fontconfig-version): \ $(ibidir)/libxml2-$(libxml2-version) \ $(ibidir)/freetype-$(freetype-version) \ $(ibidir)/util-linux-$(util-linux-version) + # Import the source. tarball=fontconfig-$(fontconfig-version).tar.lz $(call import-source, $(fontconfig-url), $(fontconfig-checksum)) diff --git a/reproduce/software/shell/apptainer-README.md b/reproduce/software/shell/apptainer-README.md index a7826ec..d2a14c8 100644 --- a/reproduce/software/shell/apptainer-README.md +++ b/reproduce/software/shell/apptainer-README.md @@ -1,7 +1,7 @@ # Maneage'd projects in Apptainer -Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>\ +Copyright (C) 2025-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es>\ See the end of the file for license conditions. For an introduction on containers, see the "Building in containers" section @@ -47,7 +47,7 @@ software environment) to easily move it from one computer to another. project. This file is necessary for future runs of your project within the container. - 3. To execute your project remote the `--build-only` and use `./run.sh` to + 3. To execute your project remove the `--build-only` and use `./run.sh` to execute it. If you want to enter your Maneage'd project shell, add the `--project-shell` option to the call inside `./run.sh`. diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh index c581ade..8760db6 100755 --- a/reproduce/software/shell/apptainer.sh +++ b/reproduce/software/shell/apptainer.sh @@ -41,8 +41,8 @@ # # Known problems: # -# Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es> +# Copyright (C) 2025-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -71,14 +71,14 @@ set -e # Default option values +sif="" jobs=0 quiet=0 source_dir= build_only= -base_name="" +base_sif="" shm_size=20gb scriptname="$0" -project_name="" project_shell=0 container_shell=0 base_os=debian:stable-slim @@ -97,9 +97,9 @@ Top-level script to build and run a Maneage'd project within Apptainer. --source-dir=STR Directory of source code (default: 'pwd -P'). Apptainer images + --sif=STR Project's apptainer image (a '.sif' file). --base-os=STR Base OS name (default: '$base_os'). - --base-name=STR Base OS apptainer image (a '.sif' file). - --project-name=STR Project's apptainer image (a '.sif' file). + --base-sif=STR Base OS apptainer image (a '.sif' file). Interactive shell --project-shell Open the project's shell within the container. @@ -155,10 +155,12 @@ do --source-dir=*) source_dir="${1#*=}"; check_v "$1" "$source_dir"; shift;; # Container options. - --base-name) base_name="$2"; check_v "$1" "$base_name"; shift;shift;; - --base-name=*) base_name="${1#*=}"; check_v "$1" "$base_name"; shift;; - --project-name) project_name="$2"; check_v "$1" "$project_name"; shift;shift;; - --project-name=*) project_name="${1#*=}"; check_v "$1" "$project_name"; shift;; + --sif) sif="$2"; check_v "$1" "$sif"; shift;shift;; + --sif=*) sif="${1#*=}"; check_v "$1" "$sif"; shift;; + --base-os) base_os="$2"; check_v "$1" "$base_os"; shift;shift;; + --base-os=*) base_os="${1#*=}"; check_v "$1" "$base_os"; shift;; + --base-sif) base_sif="$2"; check_v "$1" "$base_sif"; shift;shift;; + --base-sif=*) base_sif="${1#*=}"; check_v "$1" "$base_sif"; shift;; # Interactive shell. --project-shell) project_shell=1; shift;; @@ -193,21 +195,22 @@ done # # Make sure that the build directory is given and that it exists. if [ x$build_dir = x ]; then - printf "$scriptname: '--build-dir' not provided, this is the location " - printf "that all built analysis files will be kept on the host OS\n" + printf "$scriptname: '--build-dir' not provided, this is the " + printf "location that all built analysis files will be kept on " + printf "the host OS\n" exit 1; else if ! [ -d $build_dir ]; then - printf "$scriptname: '$build_dir' (value to '--build-dir') doesn't " - printf "exist\n" + printf "$scriptname: '$build_dir' (value to '--build-dir') " + printf "doesn't exist\n" exit 1; fi fi # Set the default project and base-OS image names (inside the build # directory). -if [ x"$base_name" = x ]; then base_name=$build_dir/maneage-base.sif; fi -if [ x"$project_name" = x ]; then project_name=$build_dir/maneaged.sif; fi +if [ x"$base_sif" = x ]; then base_sif=$build_dir/maneage-base.sif; fi +if [ x"$sif" = x ]; then sif=$build_dir/maneaged.sif; fi @@ -278,9 +281,9 @@ fi # # Build the base operating system using Maneage's './project configure' # step. -if [ -f $project_name ]; then +if [ -f $sif ]; then if [ $quiet = 0 ]; then - printf "$scriptname: info: project's image ('$project_name') " + printf "$scriptname: info: project's image ('$sif') " printf "already exists and will be used. If you want to build a " printf "new project image, give a new name to '--project-name'. " printf "To remove this message run with '--quiet'\n" @@ -289,12 +292,13 @@ else # Build the basic definition, with just Debian-slim with minimal # necessary tools. - if [ -f $base_name ]; then + if [ -f $base_sif ]; then if [ $quiet = 0 ]; then - printf "$scriptname: info: base OS docker image ('$base_name') " - printf "already exists and will be used. If you want to build a " - printf "new base OS image, give a new name to '--base-name'. " - printf "To remove this message run with '--quiet'\n" + printf "$scriptname: info: base OS apptainer image " + printf "('$base_sif') already exists and will be used. " + printf "If you want to build a new base OS image, give " + printf "a new name to '--base-sif'. To remove this " + printf "message run with '--quiet'\n" fi else @@ -308,7 +312,7 @@ From: $base_os EOF # Build the base operating system container and delete the # temporary definition file. - apptainer build $base_name $base_def + apptainer build $base_sif $base_def rm $base_def fi @@ -329,7 +333,7 @@ EOF maneage_def=$build_dir/maneage.def cat <<EOF > $maneage_def Bootstrap: localimage -From: $base_name +From: $base_sif %setup mkdir -p \${APPTAINER_ROOTFS}/home/maneager/input @@ -361,7 +365,7 @@ From: $base_name else \\ printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\ printf "to 'maneage_apptainer_stat' environment variable) "; \\ - printf "is not recognized: should be either 'shell' or 'run'"; \\ + printf "is not recognized: should be either 'shell' or 'run'\n"; \\ exit 1; \\ fi; \\ else \\ @@ -384,7 +388,7 @@ EOF $software_dir_mnt \ --ignore-fakeroot-command \ \ - $project_name \ + $sif \ $maneage_def # Clean up. @@ -396,7 +400,7 @@ fi if ! [ x"$build_only" = x ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: Maneaged project has been configured " - printf "successfully in the '$project_name' image" + printf "successfully in the '$sif' image\n" fi exit 0 fi @@ -418,7 +422,7 @@ else fi # Build the hostname from the name of the SIF file of the project name. -hstname=$(echo "$project_name" \ +hstname=$(echo "$sif" \ | awk 'BEGIN{FS="/"}{print $NF}' \ | sed -e's|.sif$||') @@ -453,4 +457,4 @@ apptainer $aopt \ --hostname $hstname \ --cwd /home/maneager/source \ \ - $project_name + $sif diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh index 6bbd774..d88b84a 100755 --- a/reproduce/software/shell/bashrc.sh +++ b/reproduce/software/shell/bashrc.sh @@ -34,7 +34,7 @@ # shell'). # # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 4887816..3e0163e 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -2,9 +2,9 @@ # # Necessary preparations/configurations for the reproducible project. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -228,7 +228,7 @@ empty_build_tmp() { # accidentally delete the whole root partition (or a least the '/home' # partition of the user). if ! [ x"$( ls -A $tmpblddir )" = x ]; then - rm -r "$tmpblddir"/* + rm -rf "$tmpblddir"/* fi rm -r "$tmpblddir" } @@ -378,7 +378,11 @@ if [ $built_container = 0 ]; then # between Intel or Apple M1 CPUs. Here we disinguish between Apple # M1 or others. maccputype=$(sysctl -n machdep.cpu.brand_string) - if [ x"$maccputype" = x"Apple M1" ]; then + if [ x"$maccputype" = x"Apple M1" ] \ + || [ x"$maccputype" = x"Apple M2" ] \ + || [ x"$maccputype" = x"Apple M3" ] \ + || [ x"$maccputype" = x"Apple M4" ] \ + || [ x"$maccputype" = x"Apple M5" ] ; then address_size_physical=$(sysctl -n machdep.cpu.thread_count) address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) else @@ -781,6 +785,25 @@ fi +# Older C standard versions +# ------------------------- +# +# Some basic packages require an old standard of C compilation; for their +# list, see the 'Not working with C23' list in '../config/versions.conf'. +# Here, we first try 'gnu17', but if that fails on the host compiler, we +# fall back to 'gnu99'. +if [ $built_container = 0 ]; then + printf "int main(void){; return 0;}\n" > $testsource + if gcc -std=gnu17 $testsource -o $testprog 2> /dev/null; then + std_c_old="gnu17" + else std_c_old="gnu99" + fi + rm $testsource $testprog +fi + + + + # Fortran compiler # ---------------- # @@ -856,33 +879,6 @@ fi -# See if the linker accepts -Wl,-rpath-link -# ----------------------------------------- -# -# '-rpath-link' is used to write the information of the linked shared -# library into the shared object (library or program). But some versions of -# LLVM's linker don't accept it an can cause problems. -# -# IMPORTANT NOTE: This test has to be done **AFTER** the definition of -# 'instdir', otherwise, it is going to be used as an empty string. -if [ $built_container = 0 ]; then - cat > $testsource <<EOF -#include <stdio.h> -#include <stdlib.h> -int main(void) {return EXIT_SUCCESS;} -EOF - if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null \ - > /dev/null; then - export rpath_command="-Wl,-rpath-link=$instdir/lib" - else - export rpath_command="" - fi - - # Delete the temporary directory for compiler checking. - rm -f $testprog $testsource - rm -r $compilertestdir - elapsed_time_from_prev_step compiler-rpath -fi @@ -1146,6 +1142,20 @@ EOF echo " ** Please select another directory." echo "" else + # Set the '.build' and '.local' symbolic links (and delete + # possibly existing symbolic links). These commands are also + # present in the top-level 'project' script, but they are only + # invoked when '--build-dir' is called. When it is not called + # (the user wants to insert the directories interactively: the + # scenario here), the links need to be created from + # scratch. Furthermore, in case the given directory to + # '--build-dir' has problems (fails to pass the sanity checks + # above), the symbolic links also need to be recreated. + rm -f .build .local + ln -s $bdir .build + ln -s $bdir/software/installed .local + + # Inform the user echo " -- Build directory set to ($instring): '$bdir'" fi done @@ -1396,6 +1406,55 @@ elapsed_time_from_prev_step downloader +# Libraries necessary for the system's shell +# ------------------------------------------ +# +# In some cases (mostly the programs that Maneage doesn't yet build by +# itself), the programs may call the system's shell, not Maneage's +# shell. After we close-off the system environment from Maneage, this will +# cause a crash! To avoid such cases, we need to find the locations of the +# libraries that the shell needs and temporarily add them to the library +# search path. +# +# About the 'grep -v "(0x[^)]*)"' term (from bug 66847, see [1]): On some +# systems [2], the output of 'ldd /bin/sh' includes a line for the vDSO [3] +# that is different to the formats that are assumed, prior to this commit, +# by the algorithm in 'configure.sh' when evaluating the variable +# 'sys_library_sh_path'. This leads to a fatal syntax error in (at least) +# 'ncurses', because the option using 'sys_library_sh_path' contains an +# unquoted RAM address in parentheses. Even if the address were quoted, it +# would still be incorrect. This 'grep' command excludes candidate host +# path strings that look like RAM addresses to address the problem. +# +# [1] https://savannah.nongnu.org/bugs/index.php?66847 +# [2] https://stackoverflow.com/questions/34428037/how-to-interpret-the-output-of-the-ldd-program +# [3] man vdso +if [ $built_container = 0 ]; then + if [ x"$on_mac_os" = xyes ]; then + sys_library_sh_path=$(otool -L /bin/sh \ + | awk '/\/lib/{print $1}' \ + | sed 's#/[^/]*$##' \ + | sort \ + | uniq \ + | awk '{if (NR==1) printf "%s", $1; \ + else printf ":%s", $1}') + else + sys_library_sh_path=$(ldd /bin/sh \ + | awk '{if($3!="") print $3}' \ + | sed 's#/[^/]*$##' \ + | grep -v "(0x[^)]*)" \ + | sort \ + | uniq \ + | awk '{if (NR==1) printf "%s", $1; \ + else printf ":%s", $1}') + fi + elapsed_time_from_prev_step sys-library-sh-path +fi + + + + + # When no local configuration existed, write the parameters into the local # configuration file. sdir=$bdir/software @@ -1415,6 +1474,7 @@ if [ $rewritelconfig = yes ]; then -e's|@sys_cpath[@]|'"$sys_cpath"'|' \ -e's|@downloader[@]|'"$downloader"'|' \ -e's|@groupname[@]|'"$maneage_group_name"'|' \ + -e's|@sys_library_sh_path[@]|'"$sys_library_sh_path"'|' \ $lconfin >> $lconf fi elapsed_time_from_prev_step LOCAL-write @@ -1486,6 +1546,41 @@ fi +# See if the linker accepts -Wl,-rpath-link +# ----------------------------------------- +# +# '-rpath-link' is used to write the information of the linked shared +# library into the shared object (library or program). But some versions of +# LLVM's linker don't accept it an can cause problems. +# +# IMPORTANT NOTE: This test has to be done **AFTER** the definition of +# 'instdir'. Otherwise, the rpath-link value set within rpath_command in +# the case of a successful test compile (if $CC ...) will be "/lib", +# i.e. the host system root /lib directory, instead of the maneage library +# directory. +if [ $built_container = 0 ]; then + cat > $testsource <<EOF +#include <stdio.h> +#include <stdlib.h> +int main(void) {return EXIT_SUCCESS;} +EOF + if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null \ + > /dev/null; then + export rpath_command="-Wl,-rpath-link=$instdir/lib" + else + export rpath_command="" + fi + + # Delete the temporary directory for compiler checking. + rm -f $testprog $testsource + rm -r $compilertestdir + elapsed_time_from_prev_step compiler-rpath +fi + + + + + # Software building directory (possibly in RAM) # --------------------------------------------- # @@ -1666,53 +1761,6 @@ fi -# Libraries necessary for the system's shell -# ------------------------------------------ -# -# In some cases (mostly the programs that Maneage doesn't yet build by -# itself), the programs may call the system's shell, not Maneage's -# shell. After we close-off the system environment from Maneage, this will -# cause a crash! To avoid such cases, we need to find the locations of the -# libraries that the shell needs and temporarily add them to the library -# search path. -# -# About the 'grep -v "(0x[^)]*)"' term (from bug 66847, see [1]): On some -# systems [2], the output of 'ldd /bin/sh' includes a line for the vDSO [3] -# that is different to the formats that are assumed, prior to this commit, -# by the algorithm in 'configure.sh' when evaluating the variable -# 'sys_library_sh_path'. This leads to a fatal syntax error in (at least) -# 'ncurses', because the option using 'sys_library_sh_path' contains an -# unquoted RAM address in parentheses. Even if the address were quoted, it -# would still be incorrect. This 'grep command excludes candidate host path -# strings that look like RAM addresses to address the problem. -# -# [1] https://savannah.nongnu.org/bugs/index.php?66847 -# [2] https://stackoverflow.com/questions/34428037/how-to-interpret-the-output-of-the-ldd-program -# [3] man vdso -if [ $built_container = 0 ]; then - if [ x"$on_mac_os" = xyes ]; then - sys_library_sh_path=$(otool -L /bin/sh \ - | awk '/\/lib/{print $1}' \ - | sed 's#/[^/]*$##' \ - | sort \ - | uniq \ - | awk '{if (NR==1) printf "%s", $1; \ - else printf ":%s", $1}') - else - sys_library_sh_path=$(ldd /bin/sh \ - | awk '{if($3!="") print $3}' \ - | sed 's#/[^/]*$##' \ - | grep -v "(0x[^)]*)" \ - | sort \ - | uniq \ - | awk '{if (NR==1) printf "%s", $1; \ - else printf ":%s", $1}') - fi - elapsed_time_from_prev_step sys-library-sh-path -fi - - - # Find Zenodo URL for software downloading # ---------------------------------------- @@ -1816,6 +1864,7 @@ if [ $quiet = 0 ]; then echo "Building/validating software: basic"; fi numthreads=$numthreads \ needs_ldl=$needs_ldl \ on_mac_os=$on_mac_os \ + std_c_old=$std_c_old \ host_cc=$host_cc \ -j$numthreads elapsed_time_from_prev_step make-software-basic @@ -1874,9 +1923,10 @@ ______________________________________________________ !!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! TeX Live couldn't be installed during the configuration (probably because -there were downloading problems). TeX Live is only necessary in making the -final PDF (which is only done after all the analysis has been complete). It -is not used at all during the analysis. +there were downloading problems, or you used the '--offline' option). TeX +Live is only necessary in making the final PDF (which is only done after +all the analysis has been complete). It is not used at all during the +analysis. Therefore, if you don't need the final PDF, and just want to do the analysis, you can safely ignore this warning and continue. diff --git a/reproduce/software/shell/docker-README.md b/reproduce/software/shell/docker-README.md index d651e22..dd46f4f 100644 --- a/reproduce/software/shell/docker-README.md +++ b/reproduce/software/shell/docker-README.md @@ -1,6 +1,6 @@ # Maneage'd projects in Docker -Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. For an introduction on containers, see the "Building in containers" section @@ -35,28 +35,25 @@ software environment) to easily move it from one computer to another. systemctl start docker ``` - 2. Using your favorite text editor, create a `run.sh` in your top Maneage - directory (as described in the comments at the start of the `docker.sh` - script in this directory). Just activate `--build-only` on the first - run so it doesn't go onto doing the analysis and just sets up the - software environment. Set the respective directory(s) based on your - filesystem (the software directory is optional). The `run.sh` file name - is already in `.gitignore` (because it contains local directories), so - Git will ignore it and it won't be committed by mistake. + 2. At the start of the `docker.sh` script in this directory, you can see + the necessary command to run. Just activate `--build-only` on the first + run so it doesn't go onto doing the analysis (that can be done at any + later time). Set the respective directory(s) based on your filesystem + (the software directory is optional). You can put the command in a + `run.sh` at the top of the project (it is already in `.gitignore`: + because it contains local directories). 3. After the setup is complete, remove the `--build-only` and run the command below to confirm that `maneage-base` (the OS of the container) and `maneaged` (your project's full Maneage'd environment) images are available. If you want different names for these images, add the - `--project-name` and `--base-name` options to the `docker.sh` call. + `--project-name` and `--base-name` options to the `docker.sh` call. You + can see the list of available images with this command: ```shell docker image list ``` - 4. You are now ready to do your analysis by removing the `--build-only` - option. - diff --git a/reproduce/software/shell/docker.sh b/reproduce/software/shell/docker.sh index 714c75f..5cd8f11 100755 --- a/reproduce/software/shell/docker.sh +++ b/reproduce/software/shell/docker.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/usr/bin/env bash # # Create a Docker container from an existing image of the built software # environment, but with the source, data and build (analysis) directories @@ -47,7 +47,7 @@ # clipped, log limit 2MiB reached]" message. We need to find a way to # fix this (so nothing gets clipped: useful for debugging). # -# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -409,22 +409,25 @@ else # that the user gave there. mkdir $tmp_dir/$tsdir cp -r "$software_dir"/* $tmp_dir/$tsdir/ - printf " --mount=type=bind,source=$tsdir,target=$dts \x5C\n" >> $df + printf " --mount=type=bind,source=$tsdir,target=$dts \x5C\n" \ + >> $df fi # Construct the rest of the 'RUN' command. printf " cp -r $dsr /home/maneager/source; \x5C\n" >> $df printf " cd /home/maneager/source; \x5C\n" >> $df - printf " ./project configure --jobs=$jobs \x5C\n" >> $df + printf " ./project configure \x5C\n" >> $df + printf " --no-pause \x5C\n" >> $df + printf " --jobs=$jobs \x5C\n" >> $df printf " --build-dir=$intbuild \x5C\n" >> $df printf " --input-dir=/home/maneager/input \x5C\n" >> $df - printf " --software-dir=$dts; \x5C\n" >> $df + printf " --software-dir=$dts; \x5C\n" >> $df - # We are deleting the '.build/software/tarballs' directory because this - # directory is not relevant for the analysis of the project. But in - # case any tarball was downloaded, it will consume space within the - # container. - printf " rm -rf .build/software/tarballs; \x5C\n" >> $df + # We are deleting the contents of the '.build/software/tarballs' + # directory (tarballs of the sources of the software) because they are + # not relevant to the execution of the project and will consume space + # within the container. + printf " rm -rf .build/software/tarballs/*; \x5C\n" >> $df # We are deleting the source directory becaues later (at 'docker run' # time), the 'source' will be mounted directly from the host operating @@ -432,12 +435,9 @@ else printf " cd /home/maneager; \x5C\n" >> $df printf " rm -rf source\n" >> $df - # Build the Maneage container and delete the temporary directory. The - # '--progress plain' option is for Docker to print all the outputs - # (otherwise, it will only print a very small part!). + # Build the Maneage container and delete the temporary directory. cd $tmp_dir docker build ./ -t $project_name \ - --progress=plain \ --shm-size=$shm_size \ --no-cache \ 2>&1 | tee build.log @@ -453,14 +453,15 @@ if ! [ x"$image_file" = x ] && ! [ -f "$image_file" ]; then # Save the image into a tarball tarname=$(echo $image_file | sed -e's|.gz$||') if [ $quiet = 0 ]; then - printf "$scriptname: info: saving docker image to '$tarname'" + printf "$scriptname: info: saving docker image to '$tarname'\n" fi docker save -o $tarname $project_name # Compress the saved image if [ $quiet = 0 ]; then printf "$scriptname: info: compressing to '$image_file' (can " - printf "take +10 minutes, but volume decreases by more than half!)" + printf "take +10 minutes, but volume decreases by more than " + printf "half!)\n" fi gzip --best $tarname fi @@ -470,7 +471,7 @@ fi if ! [ x"$build_only" = x ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: Maneaged project has been configured " - printf "successfully in the '$project_name' image" + printf "successfully in the '$project_name' image\n" fi exit 0 fi diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout index 7b521a3..7bf747a 100755 --- a/reproduce/software/shell/git-post-checkout +++ b/reproduce/software/shell/git-post-checkout @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com> -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is taken from the 'examples/hooks/pre-commit' file of the # 'metastore' package (installed within the project, with an MIT license diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit index 7b98ad0..e570346 100755 --- a/reproduce/software/shell/git-pre-commit +++ b/reproduce/software/shell/git-pre-commit @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com> -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # WARNING: # diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index 172bdb6..8236247 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -2,7 +2,7 @@ # # Very basic tools necessary to start Maneage's default building. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh index dcdc472..2959255 100755 --- a/reproduce/software/shell/prep-source.sh +++ b/reproduce/software/shell/prep-source.sh @@ -7,7 +7,7 @@ # directory that it is run in ): # ./prep-source.sh /FULL/ADDRESS/TO/DESIRED/BIN # -# Copyright (C) 2024-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2024-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -47,17 +47,18 @@ fi -# Find all the files that contain the '/bin/sh' string and correct them to -# Maneage's own Bash. We are using 'while read' to read the file names line -# by line. This is necessary to account file names that include the 'SPACE' -# character (happens in CMake for example!). +# Find all the files that contain the '/bin/sh' or '/bin/bash' strings and +# correct them to Maneage's own shell (Dash or Bash). We are using 'while +# read' to read the file names line by line. This is necessary to account +# file names that include the 'SPACE' character (happens in CMake for +# example!). # # Note that dates are important in the source directory (files depend on # each other), so we should read the original date and after making. We are # also not using GNU SED's '-i' ('--in-place') option because the host OS # may not have GNU SED. # -# Actual situation which prompted the addition of this step: a Maneage'd +# The situation which prompted the addition of this step: a Maneage'd # project (with GNU Bash 5.1.8 and Readline 8.1.1) was being built on a # system where '/bin/sh' was GNU Bash 5.2.26 and had Readline 8.2.010. The # newer version of Bash needed the newer Readline library function(s) that @@ -74,18 +75,35 @@ fi # hard-coded in the source code of almost all programs (their build # scripts); and in special programs like GNU Make, GNU M4 or CMake it is # actually hardcoded in the source code (not just build scripts). -if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash +bashpath="$bindir"/bash +if [ -f "$bindir/bash" ]; then shpath="$bashpath" else shpath="$bindir"/dash fi -grep -I -r -e'/bin/sh' $(pwd)/* \ + +# On MacOS the syntax for 'stat' is a bit different, so if we are using the +# system one on mac we need a specific syntax. The one installed by maneage +# instead uses the ordinary Linux syntax. +if [ -f "$bindir/stat" ] || [ x"$on_mac_os" = xno ]; then + format="--format %a" +else + format="-f %OLp" +fi + +# On MacOS 'touch' wants the time expressed according to ISO8601 with a +# precision up to the seconds. We then use 'sed' to remove the information +# regarding the timezone, as the format is not accepted by 'touch'. +# LCTYPE and LANG are also required on macos systems by sed. +grep -I -r -e'/bin/sh' -e'/bin/bash' $(pwd)/* \ | sed -e's|:|\t|' \ | awk 'BEGIN{FS="\t"}{print $1}' \ | sort \ | uniq \ | while read filename; do \ tmp="$filename".tmp; \ - origtime="$(date -R -r "$filename")"; \ - origperm=$(stat -c '%a' "$filename"); \ + origtimex="$(date -Iseconds -r "$filename")"; \ + origtime=$(echo $origtimex | sed 's/.\{6\}$//'); \ + origperm=$(stat $format "$filename"); \ + LC_CTYPE=C; LANG=C; \ sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \ mv "$tmp" "$filename"; \ chmod $origperm "$filename"; \ diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in index 053f5f3..21c347f 100755 --- a/reproduce/software/shell/run-parts.in +++ b/reproduce/software/shell/run-parts.in @@ -10,8 +10,8 @@ # However, it didn't have a copyright statement. So one is being added # here. # -# Copyright (C) 2025 Authors mentioned above. -# Copyright (C) 2025-2024 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2026 Authors mentioned above. +# Copyright (C) 2026-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh index 8e30931..ed1cfd0 100755 --- a/reproduce/software/shell/tarball-prepare.sh +++ b/reproduce/software/shell/tarball-prepare.sh @@ -15,9 +15,9 @@ # # Discussion: https://savannah.nongnu.org/task/?15699 # -# Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> -# Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es> +# Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -51,6 +51,9 @@ basedir=$PWD scriptname=$0 + + + # The --help output print_help() { cat <<EOF diff --git a/tex/README.md b/tex/README.md index f100c76..e94325b 100644 --- a/tex/README.md +++ b/tex/README.md @@ -1,7 +1,7 @@ Directory containing LaTeX-related files ---------------------------------------- -Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This directory contains directories to various components the LaTeX part of diff --git a/tex/src/delete-me-image-histogram.tex b/tex/src/delete-me-image-histogram.tex index 6201c31..dcb46e0 100644 --- a/tex/src/delete-me-image-histogram.tex +++ b/tex/src/delete-me-image-histogram.tex @@ -1,6 +1,6 @@ %% Plot the demonstration image and its histogram. % -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/delete-me-squared.tex b/tex/src/delete-me-squared.tex index 51e5f5b..05191df 100644 --- a/tex/src/delete-me-squared.tex +++ b/tex/src/delete-me-squared.tex @@ -1,6 +1,6 @@ %% PGFPlots code to plot a random set of numbers as demo %% -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex index e80d7d8..2b7b049 100644 --- a/tex/src/preamble-biblatex.tex +++ b/tex/src/preamble-biblatex.tex @@ -12,7 +12,7 @@ %% helps in clearly identifying the files and avoiding places that %% complain about '.bib' files. % -%% Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-maneage-default-style.tex b/tex/src/preamble-maneage-default-style.tex index b7aa811..adb3eb9 100644 --- a/tex/src/preamble-maneage-default-style.tex +++ b/tex/src/preamble-maneage-default-style.tex @@ -6,7 +6,7 @@ %% style defined here as a preamble. To ignore it, uncomment or delete the %% respective line in 'paper.tex'. % -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-maneage.tex b/tex/src/preamble-maneage.tex index 9e6cc5a..a2a3a74 100644 --- a/tex/src/preamble-maneage.tex +++ b/tex/src/preamble-maneage.tex @@ -1,6 +1,6 @@ %% Preamble for Maneage-related features. % -%% Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This LaTeX file is part of Maneage. Maneage is free software: you can %% redistribute it and/or modify it under the terms of the GNU General diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex index 74f5290..8a2a98f 100644 --- a/tex/src/preamble-pgfplots.tex +++ b/tex/src/preamble-pgfplots.tex @@ -40,7 +40,7 @@ %% hasn't changed since the last build. TiKZ/PGFPlots won't rebuild the %% plot. % -%% Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is part of Maneage (https://maneage.org). % diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex index adb99b7..bcc10e5 100644 --- a/tex/src/preamble-project.tex +++ b/tex/src/preamble-project.tex @@ -4,8 +4,8 @@ %% LaTeX usages. However, if any are not needed in your work, please feel %% free to remove them. % -%% Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -%% Copyright (C) YYYY Your Name <your@email.address> +%% Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) YYYY-YYYY Your Name <your@email.address> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/references.tex b/tex/src/references.tex index ae3e5d1..fefb636 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -1,7 +1,7 @@ %% Non-software BibTeX entries. The software-specific BibTeX entries are %% stored in a '*.tex' file under the 'tex/dependencies' directory. % -%% Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright |