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2019-07-28Single wrapper instead of old ./configure, Makefile and ./for-groupMohammad Akhlaghi-6/+6
Until now, to work on a project, it was necessary to `./configure' it and build the software. Then we had to run `.local/bin/make' to run the project and do the analysis every time. If the project was a shared project between many users on a large server, it was necessary to call the `./for-group' script. This way of managing the project had a major problem: since the user directly called the lower-level `./configure' or `.local/bin/make' it was not possible to provide high-level control (for example limiting the environment variables). This was especially noticed recently with a bug that was related to environment variables (bug #56682). With this commit, this problem is solved using a single script called `project' in the top directory. To configure and build the project, users can now run these commands: $ ./project configure $ ./project make To work on the project with other users in a group these commands can be used: $ ./project configure --group=GROUPNAME $ ./project make --group=GROUPNAME The old options to both configure and make the project are still valid. Run `./project --help' to see a list. For example: $ ./project configure -e --host-cc $ ./project make -j8 The old `configure' script has been moved to `reproduce/software/bash/configure.sh' and is called by the new `./project' script. The `./project' script now just manages the options, then passes control to the `configure.sh' script. For the "make" step, it also reads the options, then calls Make. So in the lower-level nothing has changed. Only the `./project' script is now the single/direct user interface of the project. On a parallel note: as part of bug #56682, we also found out that on some macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set to blank. This is no problem because RPATH is automatically set in macOS and the executables and libraries contain the absolute address of the libraries they should link with. But having `DYLD_LIBRARY_PATH' can conflict with some low-level system libraries and cause very hard to debug linking errors (like that reported in the bug report). This fixes bug #56682.
2019-04-14Replaced all occurances of pipeline in textMohammad Akhlaghi-11/+11
All occurances of "pipeline" have been chanaged to "project" or "template" withint the text (comments, READMEs, and comments) of the template. The main template branch is now also named `template'. This was all because `pipeline' is too generic and couldn't be distinguished from the base, and customized project.
2019-04-14Corrected copyright information for .file-metadataMohammad Akhlaghi-1/+2
Since `.file-metadata' is a binary file, we can't include a copyright inside of it so we have to use `README.md' to mention its copyright and license notice. However, this was not done clearly and is now corrected.
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-4/+2
Until now, the files where the people were meant to change didn't have a proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was wrong because the license does not convey copyright ownership. So the name of the file's original author must always be included and when people modify it (and add their own copyright-able modifications). With this commit, the file's original author (and email) are added to the copyright notice and when more than one person modified a file, both names have their individual copyright notice. Based on this, the description for adding a copyright notice in `README-hacking.md' has also been modified.
2019-04-11.file-metadata also given a copyright in top READMEMohammad Akhlaghi-3/+5
Since `.file-metadata' is a binary file and we couldn't put a copyright notice within it, it has been mentioned in `README.md' to have the same copyright. Also, the copyright modification step in `README-hacking.md' was brought to a later step to be more clear that it should always be done (on new files or files that are changed).
2019-04-07Copyright notice added to all files missing oneMohammad Akhlaghi-3/+6
Until now, for short files, we only had a license notice, not an actual copyright notice. With this commit, a copyright notice has also been added. We use this new command to find these files, suggested by `ineiev@gnu.org'.
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-0/+25
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-01-23README-pipeline.md is now called README-hacking.mdMohammad Akhlaghi-1/+1
To be more generic and recognizable, the `README-pipeline.md' script was renamed to `README-hacking.md'. In essence, it is just that: to hack the existing pipeline for your own project. We follow a similar naming convention in many GNU software.
2019-01-17README-pipeline.md referenced in README.mdMohammad Akhlaghi-1/+3
Until now, there was no reference to `README-pipeline.md' within the `README.md' file. Since `README.md' is the first file that someone reads and the basic perpose and structure of the pipeline is described in `README-pipeline.md', it was necessary to bring it up there.
2018-12-06Edited README.md to show example dependency repositoryMohammad Akhlaghi-3/+3
To help and be more clear a link to this pipeline's dependency repository has been added to `README.md'.
2018-12-05Updated README.mdMohammad Akhlaghi-15/+15
The README.md file was updated to reflect recent changes in the pipeline (especially regarding the downloader).
2018-11-22Spell check in two READMEsMohammad Akhlaghi-2/+2
A spellcheck was run on the two README files.
2018-11-22Minor edit/correction in README.mdMohammad Akhlaghi-9/+8
The note to the pipeline designers was corrected to display properly on Gitlab.
2018-11-22Placeholder in README.md for pipeline dependenciesMohammad Akhlaghi-2/+8
A placeholder link is now used in `README.md' to encourage the pipeline designers to keep a backup of all the dependencies they use.
2018-11-22Top level READMEs renamed to be similar to actual projectMohammad Akhlaghi-944/+49
Until now, were were advising the users to rename the two README files after cloning the project. This was because online Git browsers usually display the `README.md' file, so we wanted the description of the pipeline to be visible in the pipeline, and later when a project adopts it, they can have their own `README.md'. But the problem is that any change in `REAME.md' will later cause conflicts with a project's `README.md'. So we are now using the same naming convention as the papers that use the pipeline.
2018-11-22Checklist defining remote moved to topMohammad Akhlaghi-19/+26
In the checklist, we are now defining the remote host of the repository at an early stage. This is because we will need it in the `README.md' file (which now has a placeholder `XXXXXXX' instead of a valid URL).
2018-11-22Using .local instead of ./.local in READMEsMohammad Akhlaghi-6/+6
Until now, in the instructions, we were suggesting to run `./.local/bin/make', but the `./' part is extra: this is already a directory and so the shell will be able to find it. So to make things more clear and easy to read/write, we removed the `./' part from the calls to our custom Make installation.
2018-11-21Changing of README files in checklistMohammad Akhlaghi-19/+25
When you point to this project, the `README.md' file is the default file that opens on GitLab and other online git repositories. Since a reproduction pipeline project is different from the actual pipeline, its best for the default text that opens to describe the paper, not the pipeline. The old `README.md' is also kept, but its now called `REAME-pipeline.md'.
2018-11-21Pulling into pipeline branch instead of fetching in README.mdMohammad Akhlaghi-13/+15
In the previous commit, we were recommending to fetch the work from this pipeline. But since we have a separate `pipeline' branch, we can simply checkout to that branch and pull all the recent changes. So with this commit, the steps to get recent updates to the pipeline are updated.
2018-11-21Fetching pipeline updates explained in README.md checklistMohammad Akhlaghi-7/+26
Since working on the pipeline will evolve along with the projects that use it, it can be useful for projects to fetch updates in the pipeline. So the checklist in `README.md' updated to explain how to do this cleanly.
2018-11-21Updated description of Make in README.mdMohammad Akhlaghi-7/+13
Until now, because we didn't build the dependencies internally, it was important for the pipeline to be usable with any version of Make. But because of the new installation of dependencies (including GNU Make), that is no longer the case. So we can safely use GNU Make and this needs to be mentioned in `README.md'.
2018-11-20GNU Coreutils now built in basic dependenciesMohammad Akhlaghi-4/+6
GNU Coreutils are basic programs that can help in the configuration of higher-level programs. Because of that, it was a dependency of almost all software built in `dependencies.mk'. To make things more clear, easier to read and faster (when building in parallel), the building of Coreutils is now moved to the `dependencies-basic.mk' rules. There, it is built along-side Bash. Since `dependenceis-basic.mk' is run and completed before `dependencies.mk', with this, we can be sure that Coreutils is present by the time we want to build the higher-level programs. Also, Zlib is now added as a dependency of Git also (it is necessary for its build).
2018-11-19Minor corrections for easy applying of checklistMohammad Akhlaghi-26/+30
After going through the checklist for starting a new project based on the pipeline, I noticed some parts that could be modified to be more clear. They are now applied.
2018-11-19Gzip's tarball in tar.gz instead of tar.lzMohammad Akhlaghi-25/+38
Until now, we were using a customized `tar.lz' tarball for Gzip. But on systems that don't have GNU Tar, this will cause a problem (non-GNU Tar doesn't recognize `.tar.lz'). So to keep things simple, we are using the customized gzip in `tar.gz' format. After the internal build of GNU Tar and Lzip, the default method of unpacking (`tar xf XXXXX.tar.XX') will work nicely on all the standard compression algorithms and we don't have to modify our commands based on the algorithm (nice feature of GNU Tar).
2018-11-18Updated README and README.md for new dependency building featuresMohammad Akhlaghi-3/+12
The two README files have been updated to explain the new feature of downloading and building dependencies.
2018-11-14All used software with versions, acknowledgedMohammad Akhlaghi-3/+4
All the used software are now acknowledged in the template paper along with their versions. This section is also mentioned in the check list, so users don't delete it by mistake.
2018-11-13Version of programs checked on each run of pipelineMohammad Akhlaghi-9/+3
The version of all programs is now checked in `reproduce/make/src/initialize.mk' and the pipeline won't complete if any of the program versions change from those listed in `reproduce/config/pipeline/dependency-versions.mk'. Since the pipeline is systematically checking all program versions, we don't need Gnuastro's `--onlyversion' option any more. So it (and all references to it) have been removed.
2018-11-12Dependencies built at the start of the pipelineMohammad Akhlaghi-157/+161
To enable easy/proper reproduction of results, all the high-level dependencies are now built within the pipeline and installed in a fixed directory that is added to the PATH of the Makefile. This includes GNU Bash and GNU Make, which are then used to run the pipeline. The `./configure' script will first build Bash and Make within itself, then it will build All the dependencies are also built to be static. So after they are built, changing of the system's low-level libraries (like C library) won't change the tarballs. Currently the C library and C compiler aren't built within the pipeline, but we'll hopefully add them to the build process also. With this change, we now have full control of the shell and Make that will be used in the pipeline, so we can safely remove some of the generalities we had before.
2018-08-24Minor editsMohammad Akhlaghi-10/+13
After a full trial of the checklist, some further minor edits were made to make it more clear.
2018-08-24Minor corrections in README.mdMohammad Akhlaghi-7/+7
Some minor changes were made to be more clear.
2018-08-24Minor edits in README.mdMohammad Akhlaghi-11/+18
A few minor points were corrected in README.md.
2018-08-24Step to check pipeline added in README.md checklistMohammad Akhlaghi-4/+21
A step was added close to the top of the checklist to remind people to check the pipeline before making any changes. Also, the `--origin' option was removed from the `git clone' command into a separate command to rename the origin branch. This helps in readability.
2018-08-24Checklist modified to keep pipeline historyMohammad Akhlaghi-34/+55
Until now, in the check list of `README.md', we were recommending to delete the history of the pipeline and start your own history from that. But this disables users of the pipeline to keep it up to date with new features that are added to it. With this commit, the main branch is now called `pipeline' (to allow users to use `master' for their own research) and in the clone command, the pipeline's remote is now called `pipeline-origin' (to allow the user to use `origin' for their own remote).
2018-08-11Emphasized correcting name in copyright notice in checklistMohammad Akhlaghi-1/+2
While trying the checklist, I noticed that I had forgot to add my name after the copyright year and that `reproduce/src/make/paper.mk' still had my own name on it, the copyright notice also said `script' instead of `Makefile' which is now corrected.
2018-08-11Minor edits in README.md after some testsMohammad Akhlaghi-21/+7
While testing the reproduction pipeline on a small project, I noticed some parts of the checklist that were either repetative or needed to be corrected. This is done with this commit.
2018-08-11Single quote corrected in README.mdMohammad Akhlaghi-1/+1
In the previous commit, ` was mistakenly written as '. This was only noticed after pushing and rendering the Markup on the webpage.
2018-08-11Minor edit in README.mdMohammad Akhlaghi-3/+4
A minor edit was made in the copyright correction part of the checklist.
2018-08-11Corrected copyright notice correction description in checklistMohammad Akhlaghi-5/+11
To be more generic (and avoid listing file names in `README.md'), a command is now used to find the files where the name has to be added to the copyright notice. Also, I noticed that `reproduce/src/make/paper.mk' lacked a placeholder name/email, so one was added.
2018-08-11Problem with tabs in .mk file corrected in dir-locals.elMohammad Akhlaghi-3/+2
Previously we had tried to corrected the problem that `.mk' files use space instead of TAB by setting them to be read into makefile-mode at the start. However, for some reason, this caused a problem in reading the maximum line length (the value of 75 wasn't read by Emacs). So after some playing around, I found out that the problem is that the `nil' setting (for all other files) must be defined in the end, not the start of the basic settings and this solved this problem.
2018-03-14Some further minor edits to new parts of README.mdMohammad Akhlaghi-14/+16
Going through the text, some further minor edits were made.
2018-03-14Minor edits in README.mdMohammad Akhlaghi-6/+9
Some minor edits to the newly added parts of `README.md'.
2018-03-14Added future plans (and Nix/Guix usage) in README.mdMohammad Akhlaghi-4/+51
A section was added to `README.md' for describing possible future steps that we can take to make this pipeline even more robust. In it, I added a first interesting thing that I think would be really exciting to add, but I don't have time to do now.
2018-03-13Updated link to slidesMohammad Akhlaghi-1/+1
The link to the slides describing the context was the old address (which still works, but is just a symbolic link to the new address). It was thus corrected to point to the proper filename.
2018-03-09Corrected name to new repository addressMohammad Akhlaghi-3/+3
The main online repository name has been changed to `reproducible-paper' from `reproduction-pipeline-template'. So the cloning command in `README.md' had to be corrected.
2018-03-09Minor edits in README.mdMohammad Akhlaghi-5/+6
Some minor corrections were made regarding the output repository.
2018-03-09Minor typo corrected in link in README.mdMohammad Akhlaghi-2/+2
The markup for the link to the final PDF in the `README.md' file was mistakenly written and is now corrected.
2018-03-09Added description of output templateMohammad Akhlaghi-10/+15
A template was made to keep the output of this pipeline as a demonstration and it is now added to the description in `README.md'.
2018-03-09Added tip for pipeline outputsMohammad Akhlaghi-3/+22
While doing my own project (which has grown to a processing time of about half an hour), I felt that it would be very convenient to a record of the outputs at major points also. But we don't want to bloat the pipeline by commiting PDF files or large datasets that get fully changed and are just by-products. So it occurred to me to have a separate pipeline only for outputs and after trying it out, it indeed seemds to be a good solution.
2018-03-04Edits in README.mdMohammad Akhlaghi-10/+9
Some futher edits were made to the paragraph describing the contents of `README.md' for a smoother reading.
2018-03-04Minor correction in README.mdMohammad Akhlaghi-7/+8
After the last commit, another minor correction is implemeneted to further simplify the reading.