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diff --git a/README-hacking.md b/README-hacking.md index ad44d3c..a86581c 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 +174,157 @@ 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/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). + - 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 @@ -580,7 +655,47 @@ 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 +715,7 @@ 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 +733,7 @@ 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 +761,7 @@ 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 +774,7 @@ 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 +827,7 @@ 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 +859,7 @@ 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 +877,11 @@ 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 +895,7 @@ 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 +914,7 @@ 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 +924,7 @@ 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 +1108,7 @@ $ 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 @@ -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 $$dir/tex/tikz fi # When submitting to places like arXiv, they will just run LaTeX once -# and won't run 'biber'. So we need to also keep the '.bbl' file into -# the distributing tarball. However, BibLaTeX is particularly -# sensitive to versioning (a '.bbl' file has to be read by the same -# BibLaTeX version that created it). This is hard to do with -# non-up-to-date places like arXiv. Therefore, we thus just copy the +# and won't run 'biber' or 'biblatex'. So we need to also keep the +# '.bbl' file into the distributing tarball. However, BibLaTeX is +# particularly sensitive to versioning (a '.bbl' file has to be read +# by the same BibLaTeX version that created it). This is hard to do +# with non-up-to-date places like arXiv. Therefore, we just copy the # whole of BibLaTeX's source (the version we are using) into the top # tarball directory. In this way, arXiv's LaTeX engine will use the # same BibLaTeX version to interpret the '.bbl' file. TIP: you can diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index b1b794c..d2db4d3 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -1,6 +1,6 @@ # Build the final PDF paper/report. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -164,9 +164,9 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ # for details. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$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 +198,9 @@ 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..4fedefd 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 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/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..4e76b13 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 diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 89738ce..81f325f 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 +15,43 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = 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ghostscript-fonts-gnu-checksum = d8de17e5d920bd3803ecdc07aca224fa5b9a26db847ddae0ecc79488dc3e867ab3155a8565f20df7855e5228bc7f36a549b082ba0b8b56c9b948d6cfb655fdc0 ghostscript-fonts-std-checksum = 40e01f88dd113c3120686c11da1c4cf4ee77c8db315b21cc936c3ccfb42cad4949e207298ec6d78d03327ff05122fcd75ac82d5e7cdc9698d4bbf1f72b19756a -gnuastro-checksum = d27399993ab65d1864c915fe107efb298c758e1f24e3f300830f8f120768dd3a54daea1d2af5537e9dd3b50a13a51edd237f434bfbb442ab992828b2dab1386a +gnuastro-checksum = f777f84d03cc106a12373416ec3617e4c598f7642f6ebf881fd59a3068c8b4cd5ba98195c1e154a4a37d3b22828b618e5ac70157c2775d11032b7e061880aa2d gperf-checksum = 854cdb24337f14b0d4199cc97c4a1d2ec7f953ad8125a47a932d93f79bdc067e2de231859ac0e842f14b1a8d80c5606fdc2c295a370df5e85ea15023b478805b gsl-checksum = 9a46b431eed536182f31e1ecad781ade214ac8bd885ac88bbfd02b6e08482c294775a529e561d358c1f0211d8d20db4ec99b448b9006c3bf7599c076d3fbbcc3 hdf5-checksum = 58d6d9a1c201efa0863d9c31d189b4d40b1a9b1fb1ab9cb3fdeb4463f508c043e467aa4d44484c2af111d4e2fb775223286da69568774e6edef285208290c67b @@ -138,9 +138,9 @@ sextractor-checksum = 4035710f9b8a20a0bb1a3913dab2dadd8444c179bf6dee425e0e8bb66a swarp-checksum = 810af6ea0a2dfc7b78b0f6aaa486b80c29f517b90c29f5037d05f31f761e96a55c8b5dcc259e1b435b25f45f01dac45ddba61da84000a69676cce119880bb05d swig-checksum = ecb1d940f584c23df036a8f77288916003f861851dfdf836ddc5bc45b95312f9259150084191c1d9f086c006e64e12a4db22f7ea382fbb71667b811b8f99995d tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108 -util-linux-checksum = 9d421976a344f982f2bd910f0c888a7df4370a1e367c7d2582d03a58cb8500f1fe65cf6a7164c492a9ebd76bff04560c344b3a0f63ecdb372bfea2379b383030 +util-linux-checksum = 3053377ca3e399a12ea86ba96ac38749ff15a42e76742ab4346eb2f96c8b24564077db44c5b173e8474c8770846dc355b1281a697ef5a168e239b1b6d693469c vim-checksum = 85d083fcf3638f2c3a049b88da46d569d6a250ae132f3821d440c07c4792befffc09e4235241ca96d7b0307a1bb96cd2222ac8a63fb41c6add8c2bdc6c17aabb -wcslib-checksum = cc72804611df1b0087faed2ec19edbc17352cc631559edc8ceb03792162837cdaa6bbf144897c69a58c9fab7e569a1958149be7eaea6552d72190406e4755d12 +wcslib-checksum = 68f40f268d4a4d6d052e444859070138f90f17fb1723cba2da88293b5f7a372885461a09da1ca0ba1686d08e7d731cae52e305b65a6f5edf13586f48a61dca55 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02 diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg index c3cea11..40f672c 100644 --- a/reproduce/software/config/numpy-scipy.cfg +++ b/reproduce/software/config/numpy-scipy.cfg @@ -7,8 +7,8 @@ # appropriate sections. 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..3566d3c 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 @@ -146,7 +146,7 @@ #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 diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 166e8ff..7d4a3b5 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 +17,39 @@ # -------------------------------------------------------------- # # 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 +coreutils-version = 9.9 +curl-version = 8.17.0 +diffutils-version = 3.12 file-version = 5.46 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 +gawk-version = 5.3.2 +gcc-version = 15.2.0 +gettext-version = 0.26 +git-version = 2.52.0 gmp-version = 6.3.0 -grep-version = 3.11 -gzip-version = 1.13 +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 = 1.4.1 +libxml2-version = 2.15.1 lzip-version = 1.25 +m4-version = 1.4.20 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 +mpfr-version = 4.2.2 +nano-version = 8.7 +openssl-version = 3.6.0 +perl-version = 5.42.0 podlators-version = 6.0.2 -readline-version = 8.2.13 +readline-version = 8.3.3 sed-version = 4.9 tar-version = 1.35 texinfo-version = 7.2 @@ -86,6 +87,15 @@ 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 # -------------------- # @@ -96,8 +106,6 @@ patchelf-version = 0.13 # '-std=c17' and then try the build. If it works, move the software back up # to the main list before the commit. ncurses-version = 6.5 -bash-version = 5.2.37 -m4-version = 1.4.19 pkgconfig-version = 0.29.2 @@ -123,7 +131,7 @@ 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 @@ -134,8 +142,8 @@ 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 icu-version = 70.1 @@ -169,10 +177,9 @@ sextractor-version = 2.25.0 swarp-version = 2.41.5 swig-version = 4.0.2 tides-version = 2.0 -util-linux-version = 2.40.4 +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 @@ -192,8 +199,12 @@ 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 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..4e85807 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 @@ -344,24 +344,22 @@ $(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)" > $@ @@ -540,6 +538,7 @@ $(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 @@ -565,7 +564,7 @@ $(ibidir)/bash-$(bash-version): \ if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link" else stopt="" fi; - export CFLAGS="$$CFLAGS -std=gnu17 \ + export CFLAGS="$$CFLAGS \ -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \ -DSTANDARD_UTILS_PATH='\"$(ibdir)\"' \ -DSYS_BASHRC='\"$(BASH_ENV)\"' " @@ -1065,10 +1064,6 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) -j$(numthreads) V=1) echo "GNU Grep $(grep-version)" > $@ -# M4 doesn't depend on PatchELF, but just to be consistent with the -# levels/phases introduced here (where the compressors are level 1, -# PatchELF is level 2, and ...), we'll set it as a dependency. -# # The '--with-syscmd-shell' is used as the default shell and if not given, # 'm4' will use '/bin/sh' (which is not under Maneage control and can cause # problems in 'high-level.mk' because it closes off the system's @@ -1076,10 +1071,9 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) # library, the high-level programs will not be built). We are setting this # default shell to Dash because M4 is built before our own Bash. Recall # that Dash is built before we enter this Makefile. -$(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/m4-$(m4-version): $(ibidir)/libiconv-$(libiconv-version) tarball=m4-$(m4-version).tar.lz $(call import-source, $(m4-url), $(m4-checksum)) - export CFLAGS="-std=gnu17 $$CFLAGS" $(call gbuild, m4-$(m4-version), static, \ --with-syscmd-shell=$(ibdir)/dash, \ -j$(numthreads) V=1) 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..83486dc 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 @@ -731,7 +731,8 @@ $(ibidir)/libtiff-$(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): @@ -1186,6 +1187,14 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ tarball=ghostscript-$(ghostscript-version).tar.lz $(call import-source, $(ghostscript-url), $(ghostscript-checksum)) +# On macOS we use the system compiler and linker. The system linker +# there doesn't support '--copy-dt-needed-entries', while the one on +# Linux crashes if we remove it. So we only activate it on macOS. + ldflags="" + if [ x$(on_mac_os) = xno ]; then + 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 +1202,13 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions cd ghostscript-$(ghostscript-version) $(shsrcdir)/prep-source.sh $(ibdir) - ./configure --prefix=$(idir) \ + ./configure $$ldflags \ --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 +1233,61 @@ $(ibidir)/ghostscript-$(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) @@ -1718,8 +1770,15 @@ $(ibidir)/util-linux-$(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 + # 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 +1788,6 @@ $(ibidir)/util-linux-$(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 +1866,7 @@ $(ibidir)/vim-$(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 \ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index c994e3f..c499996 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 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..db42d70 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 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..1785977 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;; @@ -206,8 +208,8 @@ 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 +280,9 @@ 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 +291,13 @@ 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 +311,7 @@ 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 $base_def fi @@ -329,7 +332,7 @@ EOF maneage_def=$build_dir/maneage.def cat <<EOF > $maneage_def Bootstrap: localimage -From: $base_name +From: $base_sif %setup mkdir -p \${APPTAINER_ROOTFS}/home/maneager/input @@ -384,7 +387,7 @@ EOF $software_dir_mnt \ --ignore-fakeroot-command \ \ - $project_name \ + $sif \ $maneage_def # Clean up. @@ -396,7 +399,7 @@ fi if ! [ x"$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" fi exit 0 fi @@ -418,7 +421,7 @@ 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 +456,4 @@ 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..ca3bf6e 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 @@ -1146,6 +1146,20 @@ 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 +1410,55 @@ 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 +1478,7 @@ 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 @@ -1666,53 +1730,6 @@ 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 # ---------------------------------------- @@ -1874,9 +1891,10 @@ ______________________________________________________ !!!!!!!!!!!!!!! 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..9e09282 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 diff --git a/reproduce/software/shell/docker.sh b/reproduce/software/shell/docker.sh index 714c75f..ab454aa 100755 --- a/reproduce/software/shell/docker.sh +++ b/reproduce/software/shell/docker.sh @@ -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 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..861f3bf 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 @@ -77,6 +77,20 @@ fi if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash else shpath="$bindir"/dash fi + +# 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' $(pwd)/* \ | sed -e's|:|\t|' \ | awk 'BEGIN{FS="\t"}{print $1}' \ @@ -84,8 +98,10 @@ grep -I -r -e'/bin/sh' $(pwd)/* \ | uniq \ | while read filename; do \ tmp="$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 |