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Possible semantic conflicts (that may not show up as Git conflicts but may
cause a crash in your project after the merge):
1) The project title (and other basic metadata) should be set in
'reproduce/analysis/conf/metadata.conf'. Please include this file in
your merge (if it is ignored because of '.gitattributes'!).
2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if
you have added all analysis Makefiles to the '.gitattributes' file
(thus not merging any change in them with your branch). For example
with this command:
git diff master...maneage -- reproduce/analysis/make/initialize.mk
3) The old 'verify-txt-no-comments-leading-space' function has been
replaced by 'verify-txt-no-comments-no-space'. The new function will
also remove all white-space characters between the columns (not just
white space characters at the start of the line). Thus the resulting
check won't involve spacing between columns.
A common set of steps are always necessary to prepare a project for
publication. Until now, we would simply look at previous submissions and
try to follow them, but that was prone to errors and could cause
confusion. The internal infrastructure also didn't have some useful
features to make good publication possible. Now that the submission of a
paper fully devoted to the founding criteria of Maneage is complete
(arXiv:2006.03018), it was time to formalize the necessary steps for easier
submission of a project using Maneage and implement some low-level features
that can make things easier.
With this commit a first draft of the publication checklist has been added
to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018
and zenodo.3872248. To help guide users on implementing the good practices
for output datasets, the outputs of the default project shown in the paper
now use the new features). After reading the checklist, please inspect
these.
Some other relevant changes in this commit:
- The publication involves a copy of the necessary software
tarballs. Hence a new target ('dist-software') was also added to
package all the project's software tarballs in one tarball for easy
distribution.
- A new 'dist-lzip' target has been defined for those who want to
distribute an Lzip-compressed tarball.
- The '\includetikz' LaTeX macro now has a second argument to allow
configuring the '\includegraphics' call when the plot should not be
built, but just imported.
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The recently added description for this step in the last commit needed some
edits to be more clear and encourage re-building the project from scratch
anytime authors merge with Maneage.
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When some files should not be merged, until now we were suggesting to also
add deleted files to the '.gitattributes' file. However, this feature of
Git doesn't work for deleted files and they would still show up in the
'master' branch after a merge.
So with this commit, we have added a simple AWK command to run after a
merge that will automatically detect and delete such files (using the
output of 'git status --porcelain').
Also, two minor typos were corrected in the newly added
'servers-backup.conf' file: the copyright year was wrong and there was no
new-line at the end of the file (a good convention!).
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One of the main reasons to building Maneage is to properly
acknowledge/attribute the authors of software in research. So we have
adopted a standard of never referring to the GNU-based operating systems
running the Linux kernel simply as "Linux", we avoid terms like "Open
Sourse" and use Free Software instead (in the same spirit).
With this commit, a few instances of the cases above have been corrected,
they had slipped through our fingers when we initially imported them into
the project. In the special case of the "Journal for Open Source Software",
we simply replaced it with its abbreviation (JOSS). This was done because
in effect we were generally using journal name abbreviations in almost all
the citations already. To avoid any inconsistancies, the names of the three
other journals that weren't abbreviated are also abbreviated.
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In time, some of the copyright license description had been mistakenly
shortened to two paragraphs instead of the original three that is
recommended in the GPL. With this commit, they are corrected to be exactly
in the same three paragraph format suggested by GPL.
The following files also didn't have a copyright notice, so one was added
for them:
reproduce/software/make/README.md
reproduce/software/bibtex/healpix.tex
reproduce/analysis/config/delete-me-num.conf
reproduce/analysis/config/verify-outputs.conf
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Until now Gnuastro and Astropy where installed by default in any clean
build of Maneage. Gnuastro is used to do the demonstration analysis that is
reported in the paper and Astropy was just there to help in testing the
building of the MANY tools it depends on! It (and its dependencies) also
had several papers that helped show software citation.
However, as Boud suggested in task #15619, the burden of installing them
for a new user may be too much and any future changes will cause merge
conflicts. It may also give the impression that Maneage is only/mainly
written for astronomers.
So with this commit, I am removing Astropy as a default target. But we can
only remove Gnuastro after we include an alternative analysis in the
demonstration `delete-me' files. Following Boud's suggestion in that task,
`TARGETS.conf' was also added to the files to be ignored in any future
merge (in the checklist of `README-hacking.mk'). The solution was already
described there, but mainly focused on the deleted `delete-me' files. So
with this commit, I brought out this item as a more prominent item in the
list. Maybe we can later add the analysis done in the Maneage paper (not
yet published).
In terms of testing the software builds, we already have task #15272
(Single target to build all high-level software, for testing) that aims to
have a single configure option to install ALL high-level software and we
can ask people to try if they like and report errors.
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Recently (since Commit 7d0c5ef77), the preparation is not run automatically
every time. It is only run automatically the first time and needs to be
manually called with the `--prepare-redo' option. But this wasn't explained
in `README-hacking.md' (currently the main documentation of Maneage).
With this commit, a description about invoking the preparation process
after the first attempt of the running project has been added to
`README-hacking.md'.
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Until now, the primary Maneage URLs were under GitLab, but since we now
have a dedicated URL and Git repository, its better to transfer to this as
soon as possible. Therefore with this commit, throughout Maneage, any place
that Maneage was referenced through GitLab has been corrected.
Please correct your project's remote to point to the new repository at
`git.maneage.org/project.git', and please make sure it follows the
`maneage' branch. There is no more `master' branch on Maneage.
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Tags are not a fixed piece of history (they can easily be moved and not
imported in a different repository), so they are only confusing in the
context of Maneage (where people should branch-off the main project). the
raw commit hashes are a much more robust way to store a precise moment in
history.
Before this commit, I removed all Tags from the main Git repositories of
Maneage and thus removed any mention of Tags with
`README-hacking.md'. Ofcourse, if a project decides to use tags is upto
them, but we won't implement it in the main branch.
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Roberto Baena recently tried building a new project with Maneage and
provided the following suggestions to make it more clear for a new user:
1) In the part where we talk about creating a Git repository, we should
highlight that it must be empty. This is because some (for example Gitlab)
propose to include a `README' file. But if the project is not empty, Git
will not allow pushing to it.
2) The `(can be done later)' comment was removed from the "Delete dummy
parts") to avoid confusion about applying some of them, but not others: if
only some are done, it may cause problems in the build.
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We recently fixed the problem of TeXLive that hard-codes the year of its
build in its installation directory. But the note on this problem was still
kept in `README-hacking.md'. That part is now removed.
Also, to help in following the checklist, it is now an ordered list.
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Until now, throughout Maneage we were using the old name of "Reproducible
Paper Template". But we have finally decided to use Maneage, so to avoid
confusion, the name has been corrected in `README-hacking.md' and also in
the copyright notices.
Note also that in `README-hacking.md', the main Maneage branch is now
called `maneage', and the main Git remote has been changed to
`https://gitlab.com/maneage/project' (this is a new GitLab Group that I
have setup for all Maneage-related projects). In this repository there is
only one `maneage' branch to avoid complications with the `master' branch
of the projects using Maneage later.
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Until now the software configuration parameters were defined under the
`reproduce/software/config/installation/' directory. This was because the
configuration parameters of analysis software (for example Gnuastro's
configurations) were placed under there too. But this was terribly
confusing, because the run-time options of programs falls under the
"analysis" phase of the project.
With this commit, the Gnuastro configuration files have been moved under
the new `reproduce/analysis/config/gnuastro' directory and the software
configuration files are directly under `reproduce/software/config'. A clean
build was done with this change and it didn't crash, but it may cause
crashes in derived projects, so after merging with Maneage, please
re-configure your project to see if anything has been missed. Please let us
know if there is a problem.
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Until this commit, the year of this paper was 2019 and the linking url
was the temporal one. However, the final official publication year is
2020. With this commit, the year and the url have been changed to the
final ones.
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I had forgot to add a `./' before the call to `project' for the
`--check-config'.
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There were no conflicts in this merge.
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Until now the shell scripts in the software building phase were in the
`reproduce/software/bash' directory. But given our recent change to a
POSIX-only start, the `configure.sh' shell script (which is the main
component of this directory) is no longer written with Bash.
With this commit, to fix that problem, that directory's name has been
changed to `reproduce/software/shell'.
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Until this commit, the small section of `README-hacking.md' in which it
is explained how to do the first configuration of Git was at the
beginning of the section `First custom commit'. However, it is better to
have it just before the item `Your first commit' in that section. With
this commit, this change has been done. Now the reader has the necessary
steps for configuring Git just before it is needed for making the first
commit.
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Until now, the main commands to run the project were these: `./project
configure' (to build the software), `./project prepare' (to possibly
arrange input datasets and build special configuration Makefiles) and
finally `./project make' to run the project.
The main logic behind the "prepare" phase `top-prepare.mk' is to build
configuration files that can be fed into the "make" step and optimize its
operation. For example when the total number of necessary inputs for the
majority of the analysis is not as large as the total number of
inputs. With "prepare" (when necessary), you go through the raw inputs,
select the ones that are necessary for the rest of the project. The output
of `top-prepare.mk' is a configuration file (a Make variable) that keeps
the IDs (numbers, names, etc). That configuration file would then be used
in the `top-make.mk' to identify the lower level targets and allow optimal
project organization and management.
But the last two are both part of the analysis, and while they indeed need
different calls to Make to be executed, many projects don't actually need a
preparation phase: ultimately, its an implementation choice by the project
developers and doesn't concern the project users (or the developers when
they are running it).
To avoid confusing the users, or simply annoying them when a projet doesn't
need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk'
Makefiles are called with the single `./project make' command and
`./project prepare' has been dropped. I noticed this while writing the
paper on this system.
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Since I (Raul) did some changes (and I hope to do more :-)) in the
`README-hacking.md', I am adding my information at the beginning of this
file.
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Until this commit, we were asuming that Git was already properly
configured. However, in order to be as complete as possible, it would
be good if the basic commands to configure Git were in the
`README-hacking.md'. With this commit, a small paragraph has been added
in order to have the basic Git configuration commands (i.e. to configure
the name, email, and favorite text editor).
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Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).
To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.
The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.
THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
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Until now, it was necessry to run a long `while true' loop to see what is
currently being built at configure time. So with this commit, a new
`--checkconfig' option has been added to `./project' that can be called to
run that loop and make it easier to check.
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The checklist descriptions were slightly edited to be more clear. Also,
while following them, I noticed that while removing the "delete-me" parts
on `verify.mk', would cause an error: the `if [ $$m == delete-me ];'
statement we were saying to delete cause an error because `elif' was the
first statement Bash would see. So with this commit, the `download'
conditional (which isn't instructed to be deleted) was set to be the top
(with an `if') and the `delete-me' conditional now has an `elif'.
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Until now, the small one-line script that lists programs was introduced in
the checklist after running `./project configure'. But people would mostly
miss it because they would wait until the configuration is complete.
With this commit, that point has been put above the `./project configure'
step. Readers are instructed to open a new terminal and run that script,
then go to the next step so they see the directories get filled
actively. It will also help them understand what is going on.
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Until now the actual journal webpage was used for Raul's paper. However,
the journal webpage needs authorized access for people to read it,
therefore its will be inaccessible for many people. A better and more well
known place for the paper (atleast in astronomy) is the ADS link. In the
ADS link, if someone has access to the journal, they will get the journal's
version and if not, they will get the arXiv version. It also has a common
BibTeX export tool for all journals. We had also done this for the other
papers in that list.
With this commit, I thus changed the URL for the paper, and also removed
the "issue" number (4 in this case), since that is mostly irrelevant, only
the volume and page numbers are usually used for the other papers too.
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The "SDSS extended PSFs" paper was already included as an example of
papers wich uses this template. However, the reference was the arXiv
one. With this commit, since the paper has been finally published, it
has been added the final reference to the journal.
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Until now, if the file to be verified didn't exist, a different checksum
would be generated, and it would stop, but it wasn't immediately clear if
the differing checksum is because the file doesn't exist at all!
With this commit, before calculating the checksum, we first make sure if
the file exists. If it doesn't exist an explicit error is printed and thus
will help the project editor to find the cause of the problem.
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In the previous commit, I had forgot to update a small part in the
checklist (when modifying `top-make.mk') which is now corrected.
I also added a few sentences in the description of how to customize the
verification to make it easier to understand.
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Until now, the only verification that the template provided was the
published PDF. Users had to manually compare the published and generated
PDFs (numbers, plots, tables) and see if they obtained the same
result. However, this type of manual verification is not good and is prone
to frustration and missing important differences.
With this commit, a new Makefile has been added in the analysis steps:
`verify.mk'. It provides facilities to easily verify the results that go
into the paper. For example tables that go into making the paper's plots,
or the LaTeX macros that blend into the text. See the updated parts in
`README-hacking.md` for a more complete explanation.
This completes task #15497.
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In the previous commit, we added the files to ignore from the template
branch, but only the files that had been deleted. With this commit,
`paper.tex' is also added to the files that must be ignored from the
template branch (the file remains in the project, but in the template
branch, its contents are just dummy place-holders).
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During the checklist we guide the user to delete the dummy `delete-me*'
files from their custom branch. Later, if the dummy files are updated in
the template's master branch, if the user merges with the template branch,
these files will be written back into their project! This is very annoying!
With this commit, a step was added in the `README-hacking.md' checklist,
just after deleting the dummy files to avoid this problem using the
`.gitattributes' file, telling Git to keep the changes as implemented in
the merging branch (`ours').
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Raul's paper (that uses this template) was just published on arXiv today
(congratulations Raul!). So it has been added to the list of papers using
this template.
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Since adding this new step, I had forgot to mention it in the checklist of
`README-hacking.md'. It is added with this commit.
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The part on using shared memory was edited for a few things that weren't
clear.
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Some typos were fixed.
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The edits help it be more clear, and remind the reader to delete any
remaining file in the RAM in the end.
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When you are working with large files and there is some good RAM in the
system (large/powerful computers), it is beneficial to work in the shared
memory directory and not the actual persistent storage (like HDD or
SSD).
With this commit, a fully working demo has been added to
`README-hacking.md' (under the tips of "Make programming") to show how to
effectively work in situations like this.
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In many real-world scenarios, `./project make' can really benefit from
having some basic information about the data before being run. For example
when quering a server. If we know how many datasets were downloaded and
their general properties, it can greatly optmize the process when we are
designing the solution to be run in `./project make'.
Therefore with this commit, a new phase has been added to the template's
design: `./project prepare'. In the raw template this is empty, because the
simple analysis done in the template doesn't warrant it. But everything is
ready for projects using the template to add preparation phases prior to
the analysis.
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The description of arXiv:1909.11230 was slightly modified to be in the same
format as the other papers.
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This paper was published on arXiv today and is a good example for people to
see the application of this system in practice.
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After a re-read on Gitlab, it has been slightly edited to be more clear.
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When you want to publish your project, it is very convenient to have a
single file that contains the whole history. So a tip is added to
`README-hacking.md' that describes how to do this with `git bundle'.
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Until now, the paper's title and author information were set it
`tex/src/preamble-header.tex'. But they are actually shown in the final PDF
paper and a much better place to keep them is the top-level `paper.tex'.
With this commit, the setting of the title and author names has been moved
to `paper.tex', just after importing all the preambles. However, the basic
package importation and low-level settings are still set in
`tex/src/preamble-header.tex', because they are relatively low-level.
This task was suggested by Deepak (Indian Institute of Astrophysics).
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Until now, when describing the sections to remove for customizing a
project, I had mistakenly repeated the `%% Start of main body.'
statement.
With this commit, the second one is changed to `%% End of main body.'
This issue was reported by Deepak.
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After the checklist was applied in the 5th Indo-French Astronomy School, we
found some cases in the checklist that were extra (and thus had to be
removed), or were needed (and thus were added).
Also the non-necessary steps for a first commit were moved to a
separate/new section in the checklist for the people to add after doing
their first commit.
Also, the software part of the paper was moved to an appendix.
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Until now the only way to define the environment of the Make recipes was
through the exported Make variables (mostly in `initialize.mk' for the
analysis steps for example). However, there is only so much you can do with
environment variables! In some situations you want slightly more
complicated environment control, like setting an alias or running of
scripts (things that are commonly done in the `~/.bashrc' file of users to
configure their interactive, non-login shells).
With this commit, a `reproduce/software/bash/bashrc.sh' has been defined
for this job (which is currently empty!). Every major Make step of the
project adds this file as the `BASH_ENV' environment variable, so the shell
that is created to execute a recipe first executes this file, then the
recipe. Each top-level Makefile also defines a `PROJECT_STATUS' environment
variable that enables users to limit their envirnoment setup based on the
condition it is being setup (in particular in the early phase of
`basic.mk', where the user can't make any assumption about the programs and
has to write a portable shell script).
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Until now there was no clear explanation on `.file-metadata' within the
project. But since it sometimes appears in the Git changed files and its
binary, it was necessary to add a short explanation to inform users.
With this commit a section has been added to the "Project architecture"
section of `README-hacking.md' to give some context on what it is and how
to deal with it.
This was suggested by Hamed Altafi.
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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.
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