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In the abstract the repeated benefits of Maneage (which are also mentioned
in the criteria) were removed to fit into CiSE's online submission
guidelines. In Section II (Longevity of existing tools), the paragraph that
itemized the following paragrahs as a numbered list has been removed with
the sentence that repeatedly states the importance of reproducibility in
the sciences and some branches of the industry.
With these changes our approximate automatic count has 6277 words. This is
still very slightly larger than the 6250 word limit of the
journal. However, this count is a definite over-estimation (including many
things like page titles and page numberings from the raw PDF to text
conversion). So the actual count for the journal publication should be less
than this.
A few other tiny corrections were made:
- The year of the paper and copyright in 'README.md' was set to 2021. The
copyright of the rest of the files will be set to 2021 after the next
merge with Maneage soon (the years of core infrastructure copyrights has
already been corrected there).
- Mohammadreza's name was added in 'README.md'.
- The line to import the "necessity" appendix has been commented in the
version to have the full paper in one PDF (to be upladed to arXiv or
Zenodo).
- The supplement PDF now starts with '\appendices' so the sections have
the same labels as the single-PDF version.
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Some minor conflicts that came up during the merge were fixed.
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Until now we had described the basic commands on how to create and use
Docker images, but we hadn't mentioned how you can delete them.
With this commit the commands necessary for deleting Docker images have
also been added at the bottom of the section on Docker.
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Only two small conflicts came up:
* The addition of the hardware architecture macro in 'paper.tex' (which
was removed for now, but will be added as the referee has requested
within the text).
* The usage of "" around directory variables in 'paper.mk'.
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With the previous commit, we now build Nano by default within Maneage, and
project authors can ask to install Emacs and Vim within 'TARGETS.conf'. So
in the instructions to build within a Docker image have been removed.
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When building Maneage inside a Docker container, in the end the users want
to extract the final outputs from the container into their host operating
system to inspect more comfortably. So with this commit, a short
examplanation has been added on how to do this.
We also noticed that it is much better if the 'Dockerfile' is stored and
run in an empty directory, otherwise, it will start parsing the full
directory and its subdirectories as the docker image's environment.
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Some very minor conflicts came up and were easily corrected. They were
mostly in parts that are also shared with the demonstration in the core
Maneage branch.
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Docker is a "container" technology that allows an almost independent
operating system run on the host. It is useful when the host OS doesn't
support some features or has internal problems (for example its C library
or C compiler have problems). Fortunately a Maneaged project can easily be
built within a Docker image and a minimal image operating system.
With this commit, a section has been added to 'README.md' to describe this
process. Each step of the Dockerfile is explined, to help users that may
not be too familiar with Docker, or help Docker user who are not familiar
with Maneage.
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In 'README.md' I tried to explain a little better that TeXLive will only
install its necessary packages, not the full TeXLive library! Also in
paper.mk, I slightly improved the comments with very minor edits.
Both these parts are slated to go into the core Maneage branch, so its
important to maintain them here for now.
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The explanation was made more clear.
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The explanations are now more clear for someone that is less familiar with
Docker.
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With the new features in Maneage to install the necessry Xorg libraries,
the explanations of the Docker image creation also needed to be updated.
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Docker is a very commonly used program these days for building projects in
an almost independent operating system. So the instructions to build a
Dockerfile for the project were added in README.md.
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The git history of the project is now archived on SoftwareHeritage and a
link to it as was added in the "Reproducible supplement" tag just under the
abstract.
Also, some corrections were also made in the text. In particular, the part
explaining the separation of software and data reproducibility was slightly
clarified to be more clear
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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 previous explanation was not too clear and simply following it was
confusing. The issue was that with the tarball you have three scenarios: 1)
only build the PDF using existing figures. 2) only build the PDF, but build
the figures yourself, 3) build the full Maneaged project.
Hopefully this distinction is now more clear from the README.md file.
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Some extra explanation can help the user understand the difference between
a Git-based project and a distributed tarball.
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All the steps following the to-be-added (in 'README-hacking.md')
publication checklist prior to the final check from new clone have been
added:
- 'README.md' file has been set.
- "Reproducible supplement" was added just above the keywords, pointing to
Zenodo.
- A link to the to-be-uploaded data underlying the plot was added in the
caption of the tools-per-year plot.
- A new meta-data configuration file was added to store basic project
metadata to be used throughout the project. This will later be taken
into Maneage. For examle the project title is now stored here and
written into the paper's LaTeX source and output datasets automatically.
- Verification was activated and plot's data and LaTeX macro files are now
automatically verified.
- A complete metadata was added for the data underlying the plot.
- A generic function was added in 'initialize.mk' that will automatically
write project info and copyright in all plain-text outputs.
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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, 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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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 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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Now that its 2020, its necessary to include this year in the copyright
statements.
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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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Until now, when the project's source was downloaded from something like
arXiv, in `README.md', we were instructing them to set the executable flags
of all the files that need it. But except for `./project', the reader
shouldn't have to worry about the project internals! Once its executable,
`./project' can easily fix the executable flags of all the files that need
it automatically.
With this commit, in `README.md', we just instruct the reader to set the
executable flag of `./project' and any other file that needs an executable
flag is given one at the start of the set of commands for `./project
configure'. In customized projects, if an author needs executable flags on
any other files, they can easily add it there without involving the user.
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Konrad Hinsen pointed out that this part was missing from the instructions
in `README.md' after cloning. So it is added.
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The two modifications to the LaTeX source of an arXiv-downloaded source
weren't rendered properly on Gitlab, so they are corrected to be in the
same line and not have a separate code-block.
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Until now, we were assuming that the users would just clone the project in
Git. But after submitting arXiv:1909.11230, and trying to build directly
from the arXiv source, I noticed several problems that wouldn't allow users
to build it automatically. So I tried the build step by step and was able
to find a fix for the several issues that came up.
The scripting parts of the fix were primarily related to the fact that the
unpacked arXiv tarball isn't under version control, so some checks had to
be put there. Also, we wanted to make it easy to remove the extra files, so
an extra `--clean-texdit' option was added to `./project'.
Finally, some manual corrections were necessary (prior to running
`./project', which are now described in `README.md'. Most of the later
steps can be automated and we should do it later, I just don't have enough
time now.
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Until now customizing it was a little more detailed, for example the
copyright statement wasn't generic and was about "this template". So the
user would have to correct it.
With this commit, the copyright statment just says "this project", so it
can apply to the raw template and also any customization of it. Also, some
minor edits were made in the various parts of the text to make it more
clear.
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The Copyright year is now on a separate line (by adding a backslash), and
the `file-metadata' is now enclosed in two "`" characters to show
differently after rendering.
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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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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.
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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.
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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.
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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).
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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'.
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In order to be more clear, a copyright statement was added to all the LaTeX
and README files.
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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.
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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.
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To help and be more clear a link to this pipeline's dependency repository
has been added to `README.md'.
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The README.md file was updated to reflect recent changes in the pipeline
(especially regarding the downloader).
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A spellcheck was run on the two README files.
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The note to the pipeline designers was corrected to display properly on
Gitlab.
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A placeholder link is now used in `README.md' to encourage the pipeline
designers to keep a backup of all the dependencies they use.
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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.
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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).
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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.
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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'.
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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.
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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.
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