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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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Until now, if a project needed the healpy software package, Maneage would
crash with the following error message (abridged for full name in build
directory). This was caused by a typo in the version of 'healpix' (the
dependency of 'healpy').
make: *** No rule to make target '.../version-info/proglib/healpix-'
With this commit, the typo in line 334 of 'python.mk' is fixed, so that
when '$(ipydir)/healpy-$(healpy-version)' gets called it correctly searches
for a rule to make '$(ibidir)/healpix-$(healpix-version)'.
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Until now the './project make dist' command implicitly assumed that the
'tex/tikz' directory always contains PDF files (because of the 'cp
tex/tikz/*.pdf $$dir/tex/tikz' line). This was annoying for projects that
don't use TiKZ or PGFPlots to generate their plots, and they had to
manually comment this line.
With this commit a check has been placed to see if any PDF files exist in
there at all. If there aren't PDF files, the 'cp' command above is ignored.
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In the previous commit (Commit 1bc00c9: Only using clang in macOS systems
that also have GCC) we set the used C compiler for high-level programs to
be 'clang' on macOS systems. But I forgot to do the same kind of change in
the configure script (to prefer 'clang' when we are testing for a C
compiler on the host).
With this commit, the compiler checking phases of the configure script have
been improved, so on macOS systems, we now first search for 'clang', then
search for 'gcc'.
While doing this, I also noticed that the 'rpath' checking command was done
before we actually define 'instdir'!!! So in effect, the 'rpath' directory
was being set to '/lib'! So with this commit, this test has been taken to
after defining 'instdir'.
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Until now, when the bibliography file ('paper.bbl') had a LaTeX-related
error (for example the journal name was a LaTeX macro that isn't defined),
the first 'pdflatex' command that is run before 'biber' would crash, not
allowing the project to reach 'biber'. So the user would have to manually
remove 'paper.bbl' before running './project make'.
With this commit, we remove any possibly existing 'paper.bbl' file before
rebuilding it. Generally, this also helps in keeping things clean during
the generation of the new bibliography.
This bug was found by Mahdieh Nabavi.
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Until now, when Maneage was built on a macOS that had both a clang and GCC,
we would make links to both. But this cause many conflicts in some
high-level programs (for example Numpy and etc, all the programs where we
have explicity set 'export CC=clang' before the build recipe). This happens
because the GCC that is built on a macOS isn't complete for some
operations.
To fix this problem, when we are on a macOS, we explicity set 'gcc' to
point to 'clang' and 'g++' to point to 'clang++'. We also don't link to the
host's C-preprocessor ('cpp') on macOS systems because this is only a GNU
feature and using the GNU CPP is also known to have some basic
problems. For example this was reported by Mahdieh Nabavi (which was the
main trigger for this work):
ld: Symbol not found: ___keymgr_global
Referenced from: /Users/Mahdieh/build/software/installed/bin/cpp
Expected in: /usr/lib/libSystem.B.dylib
Also, to avoid linking to another link on the host tools (in the 'makelink'
function of 'basic.mk'), we are now using 'realpath'.
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To help in the documentation, the Git hash of the Maneage branch commit
that the project has most recently merged with (or branched from) is now
also provided as a LaTeX macro ('\maneageversion').
It is calculated in 'reproduce/analysis/make/initialize.mk' (in the recipe
to 'initialize.tex').
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Until now, the dataset's configuration names had a 'WFPC2' prefix. But this
very alien to anyone that is not familiar with the history of the Hubble
Space Telescope (the camera is no longer used! Its just used here since its
one of the standard FITS files from the FITS standard webpage).
With this commit the variable names have been modified to be more readable
and clear (having a 'DEMO-' prefix). Also the comments of 'INPUTS.conf'
(describing the purpose of each variable) were edited and made more clear.
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Until now, the 'shell' mode of the './project' script was missing in the
top output of './project --help' and in the error message printed when no
operation was given, or when more than one operation was given.
This is now corrected.
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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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In the previous commit, the modified abstract of the acknowledgments only
included the URL of Maneage, but its more formal to cite the Maneage paper,
the URL is already present in the paper.
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Until now, the acknowledgment section didn't contain the new name of
Maneage and it also included an acknowledgment of Gnuastro (which is not
appropriate for a general project which may not use Gnuastro).
With this commit this is fixed.
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The explanation was made more clear.
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Until now, when reading the host's PATH environment variable we weren't
accounting for directory names with a space character. This was most
prominently visible in the 'low-level-links' step where we put links to
some core system components into the project's build directory (mainly for
prorietary systems like macOS).
To address the problem, double quotations have been placed around the part
that we extract 'ccache' from the PATH, and the part where we make the
symbolic link. In the process the comments above 'makelink' were made more
clear and 'low-level-links' now depends on 'grep' (which is the
highest-level program it uses).
This bug was reported by Mahdieh Navabi.
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This was pointed out by Mervyn O'Luing.
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Until this commit, once Libidn was installed, insted of its own name and
version, the name and version of Libjpeg were saved (in the target if
Libidn). This robably come from a copy/paste of the rule.
With this commit, this minor bug has been corrected. I also added my name
as an author of `reproduce/software/make/xorg.mk' Makefile since I added
some code there.
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The explanations are now more clear for someone that is less familiar with
Docker.
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There weren't any conflicts in this merge.
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After recently adding util-linux to Maneage build-tree, we had forgot to
delete the unpacked and built source directory after it was installed! This
has been corrected with this commit.
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Until now, when the user specified an input and software directory, the raw
string they entered was used. But when this string was a relative location,
this could be problematic in general scenarios.
With this commit, the same function that finds the absolute location of the
build directory is used to find the absolute address of the data and
software directories.
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Until now, when the user wanted to complete remove all built files
(including software), the './project make distclean' command would fail if
the git hooks weren't installed. They are present when the project's
configuration has been successfully finished, but this bug can happen when
trying to re-do an incomplete build.
With this commit, this is fixed by adding an '-f' has been added before the
'rm' command for the Git hooks.
This commit was also done in the core Maneage branch.
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Until now, when the user wanted to complete remove all built files
(including software), the './project make distclean' command would fail if
the git hooks weren't installed. They are present when the project's
configuration has been successfully finished, but this bug can happen when
trying to re-do an incomplete build.
With this commit, this is fixed by adding an '-f' has been added before the
'rm' command for the Git hooks.
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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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There weren't any conflicts in this merge.
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Mervyn had read the paper and provided some interesting thoughts that I
tried to implement. Mervyn's comments are shown below. I just haven't
addressed the last point yet, because I am affraid it may make the text too
long (we are already on the boundary of the word-limit). We have already
discussed that it is a good research topic, and have hopefully triggered
the curiosity of the readers to test it ;-).
-------------------
Page 2: Regarding Criterion 1: Completeness. A project must be self
contained? So this includes not requiring root or administrator
privileges. This suggests that the project is only made open after the
development has been completed?
Regarding Criterion 5: 'a clerk can do it' -- in the pc world that we live
in could this be taken as a disparaging comment?
Page 5: 'The C library is linked with all programs, and this dependence can
hypothetically hinder exact reproducibility of results, but we have not
encountered this so far.' - what do you think might happen if this does
affect reproducibility? Do you have a plan to deal with this? Or are you
going to wait until you hear of such cases as the number will probably be
small? Have you done probability analysis to show that the rates are likely
to be very small? Or should you have a disclaimer with maneage?
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Until now, in order to build Ghostscript, the project used the host's Xorg
libraries. This was because we hadn't yet added the necessary build rules
for them.
With this commit, the instructions to build the necessary Xorg libraries
for Ghostscript have also been added. Also, the shared Ghostscript library
has been built with this commit and two sets of standard fonts are also
included, setting us on the path to build TeXLive from source later.
This task was done with the help and support of Raul Infante-Sainz.
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Until this commit, there was a problem when building Bison in parallel in
macOS systems. With this commit, this problem has been fixed by updating
Bison to its most recent version (3.6).
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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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Until now, the Zenodo identifier was manually written in the paper. But now
we have the Zenodo DOI in 'metadata.conf', so its much more robust to get
it from there (in case updated versions of the paper is published).
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Only two conflicts came up in the newly added comments of 'paper.mk' in the
Maneage branch. It happened because in this project we don't use
'pdflatex', but 'latex' alone.
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POSSIBLE EFFECT ON YOUR PROJECT: The changes in this commit may only cause
conflicts to your project if you have changed the software building
Makefiles in your project's branch (e.g., 'basic.mk', 'high-level.mk' and
'python.mk'). If your project has only added analysis, it shouldn't be
affected.
This is a large commit, involving a long series of corrections in a
differnt branch which is now finally being merged into the core Maneage
branch. All changes were related and came up naturally as the low-level
infrastructure was improved. So separating them in the end for the final
merge would have been very time consuming and we are merging them as one
commit.
In general, the software building Makefiles are now much more easier to
read, modify and use, along with several new features that have been
added. See below for the full list.
- Until now, Maneage needed the host to have a 'make' implementation
because Make was necessary to build Lzip. Lzip is then used to
uncompress the source of our own GNU Make. However, in the
minimalist/slim versions of operating systems (for example used to build
Docker images) Make isn't included by default. Since Lzip was the only
program before our own GNU Make was installed, we consulting Antonio
Diaz Diaz (creator of Lzip) and he kindly added the necessary
functionality to a new version of Lzip, which we are using now. Hence we
don't need to assume a Make implementation on the host any more. With
this commit, Lzip and GNU Make are built without Make, allowing
everything else to be safely built with our own custom version of GNU
Make and not using the host's 'make' at all.
- Until recently (Commit 3d8aa5953c4) GNU Make was built in
'basic.mk'. Therefore 'basic.mk' was written in a way that it can be
used with other 'make' implementations also (i.e., important shell
commands starting with '&&' and ending in '\' without any comments
between them!). Furthermore, to help in style uniformity, the rules in
'high-level.mk' and 'python.mk' also followed a similar structure. But
due to the point above, we can now guarantee that GNU Make is used from
the very first Makefile, so this hard-to-read structure has been removed
in the software build recipes and they are much more readable and
edit-friendly now.
- Until now, the default backup servers where at some fixed URLs, on our
own pages or on Gitlab. But recently we uploaded all the necessary
software to Zenodo (https://doi.org/10.5281/zenodo.3883409) which is
more suitable for this task (it promises longevity, has a fixed DOI,
while allowing us to add new content, or new software tarball
versions). With this commit, a small script has been written to extract
the most recent Zenodo upload link from the Zenodo DOI and use it for
downloading the software source codes.
- Until now, we primarily used the webpage of each software for
downloading its tarball. But this caused many problems: 1) Some of them
needed Javascript before the download, 2) Some URLs had a complex
dependency on the version number, 3) some servers would be randomly down
for maintenance and etc. So thanks to the point above, we now use the
Zenodo server as the primary download location. However, if a user wants
to use a custom software that is not (yet!) in Zenodo, the download
script gives priority to a custom URL that the users can give as Make
variables. If that variable is defined, then the script will use that
URL before going onto Zenodo. We now have a special place for such URLs:
'reproduce/software/config/urls.conf'. The old URLs (which are a good
documentation themselves) are preserved here, but are commented by
default.
- The software source code downloading and checksum verification step has
been moved into a Make function called 'import-source' (defined in the
'build-rules.mk' and loaded in all software Makefiles). Having taken all
the low-level steps there, I noticed that there is no more need for
having the tarball as a separate target! So with this commit, a single
rule is the only place that needs to be edited/added (greatly
simplifying the software building Makefiles).
- Following task #15272, A new option has been added to the './project'
script called '--all-highlevel'. When this option is given, the contents
of 'TARGETS.conf' are ignored and all the software in Maneage are built
(selected by parsing the 'versions.conf' file). This new option was
added to confirm the extensive changes made in all the software building
recipes and is great for development/testing purposes.
- Many of the software hadn't been tested for a long time! So after using
the newly added '--all-highlevel', we noticed that some need to be
updated. In general, with this commit, 'libpaper' and 'pcre' were added
as new software, and the versions of the following software was updated:
'boost', 'flex', 'libtirpc', 'openblas' and 'lzip'. A 'run-parts.in'
shell script was added in 'reproduce/software/shell/' which is installed
with 'libpaper'.
- Even though we intentionally add the necessary flags to add RPATH inside
the built executable at compilation time, some software don't do it
(different software on different operating systems!). Until now, for
historical reasons this check was done in different ways for different
software on GNU/Linux sytems. But now it is unified: if 'patchelf' is
present we apply it. Because of this, 'patchelf' has been put as a
top-level prerequisite, right after Tar and is installed before anything
else.
- In 'versions.conf', GNU Libtool is recognized as 'libtool', but in
'basic.mk', it was 'glibtool'! This caused many confusions and is
corrected with this commit (in 'basic.mk', it is also 'libtool').
- A new argument is added to the './project' script to allow easy loading
of the project's shell and environment for fast/temporary testing of
things in the same environment as the project. Before activating the
project's shell, we completely remove all host environment variables to
simulate the project's environment. It can be called with this command:
'./project shell'. A simple prompt has also been added to highlight that
the user is using the Maneage shell!
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Until now, Maneage would accept the given build directory, regardless of
the free memory available there. This could cause confusing situations for
new users who don't know about the minimum storage requirement.
With this commit, after all other checks on the given build directory are
completed, the configure script will check the available space and warns
the user if there is less than almost 5GB free space available in the build
directory (with a 5 second delay).
It won't cause a crash because some projects may require roughly smaller
than this space (the default only needs roughly 2GB). But we also don't
want the host's partition to get too close to being full, causing them
problems elsewhere. We can change the behavior as desired in future
commits.
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I visited the AMIGA group in January this year and we had some very useful
discussion on Maneage.
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After going through Terry's corrections, some things were clarified
more. Technically, I realized that many new-lines were introduced and
corrected them. Also, in Roberto's biography, I noticed that compared to
the others it has too much non-reproducibility details, so I removed the
redundant parts for this paper.
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Terry is an astronomer at IAC's Scientific Editorial Service and kindly
agreed to review this paper for us and actually pushed this commit. I am
just adding a commit message here.
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Until this commit, the file `BDIR/software/preparation-done.mk' were not
removed when cleaning the project with `./project make clean'. This file
is generated in the preparation of the data during the analysis step.
However, the cleaning is expected to remove anything generated in the
analysis process! Step by step, with the commands:
./project make ---> Will make the preparation and analysis
./project make clean ---> Will remove all analysis outputs (but
not `preparation-done.mk')
./project make ---> Won't do the preparation, only analysis!
However, in the last step it should do the preparation again, because
the input data could have change for any reason. With this commit, the
file `BDIR/software/preparation-done.mk' is removed when cleaning the
project, and consequently, in the analysis step the input data is
prepared.
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In Commit 105467fe6402 (Software tarballs are downloaded even if not
built), we introduced tests to download the tarballs of software even if
they don't need to be built on the respective host. However some small
typos in the checks existed that could cause a crash on macOS. In
particular in the building of PatchELF and libbsd we had forgot to add the
necessary 'x' before the 'yes' in the conditional to check if a we are on
macOS or not.
With this commit these two checks have been corrected. Also, in the
building of 'isl' and 'mpc', we now check for 'host_cc' (signifying that
the user wants to use their host C compiler for the high-level step)
instead of 'on_mac_os'. The reason is that even on non-macOS systems, a
user may not want to build the C compiler from scratch and use the
'--host-cc' option. In such cases, they don't need to compile 'isl' and
'mpc'.
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Until now, the data-lineage figure's step-by-step feature (using the macros
defined at the top) didn't correspond to the new format! It was still based
on the purely-hypothetical format, while the boxes and their contents had
changed.
With this commit, they macros and corresponding parts that they create have
been updated to represent the step-by-step data lineage of this paper.
Also, in the "tools-per-year" plot, the green line was brought ontop of the
histogram to be more clear (especially when transparency isn't implemented
properly in the conversion).
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Until now the color for the branching figure'e "project" branch was too
close to the Derved project branch. With this commit, I am using a slightly
darker shade of brown that is sufficiently differnet from the core Maneage
branch and the derived project branch.
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Until now, the English texts that embeds the list of software to
acknowledge in the paper was hard-wired into the low-level coding
('reproduce/software/shell/configure.sh' to be more specific). But this
file is very low-level, thus discouraging users to modify this surrounding
text.
While the list of software packages can be considered to be 'data' and is
fixed, the surrounding text to describe the lists is something the authors
should decide on. Authors of a scientific research paper take
responsibility for the full paper, including for the style of the
acknowledgments, even if these may well evolve into some standard text.
With this commit, authors who do *not* modify
'reproduce/software/config/acknowledge_software.sh' will have a default
text, with only a minor English correction from earlier versions of
Maneage. However, Authors choosing to use their own wording should be able
to modify the text parameters in
`reproduce/software/config/acknowledge_software.sh` in the obvious
way. This is much more modular than asking project authors to go looking
into the long and technical 'configure.sh' script.
Systematic issues: the file
`reproduce/software/config/acknowledge_software.sh` is an executable shell
script, because it has to be called by
`reproduce/software/shell/configure.sh`, which, in principle, does not yet
have access to `GNU make` (if I understand the bootstrap sequence
correctly). It is placed in `config/` rather than `shell/`, because the
user will expect to find configuration files in `config/`, not in `shell/`.
A possible alternative to avoid having a shell script as a configure file
would be to let `reproduce/software/config/acknowledge_software.sh` appear
to be a `make` file, but analyse it in `configure.sh` using `sed` to remove
whitespace around `=`, and adding other hacks to switch from `make` syntax
to `shell` syntax. However, this risks misleading the user, who will not
know whether s/he should follow `make` conventions or `shell` conventions.
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The 'pdflatex' program is used to build the default Maneage-branch paper.
But since the default paper uses PGFPlots to build the figures within LaTeX
as an external PDF, PGFPlots requires 'pdflatex' to be called with the
'-shell-escape' option. Generally, this option can be considered as a
security risk (in particular when 'pdflatex' is being run by an external
LaTeX file: a malicious LaTeX writer may embed commands in the LaTeX source
that will be executed on the host if this option is present).
This is not too serious of an issue in Maneage, because when someone runs
Maneage, they intentionally let it run many on their system. Hence if
someone wants to exploit a host system, they can add the necessary commands
long before 'pdflatex' is run. After all, all commands in Maneage are run
with the calling user's permissions, hence they have access to many parts
of the user's accounts. If someone is worried about security on a
non-trusted Maneage project they should act the same as they do with any
software: define a new user for it, and call it with that user (as a
weak-level security), or run it in a virtual machine or container.
However, since this option has been explicity mentioned as a security risk
before, it helps if we have a comment explaining its usage in 'paper.mk'.
With this commit, the concerned user will read a brief explanation and can
read the brief discussion at [1] and possibly re-open the discussion or
propose ways of mitigating the security risk(s).
[1] https://savannah.nongnu.org/task/?15694
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Some low-level software aren't necessary on some operating systems, for
example GCC can't be built on macOS, hence we don't build it and the
GCC-only dependencies. Also, on GNU/Linux systems users could configure
with '--host-cc' to avoid all the time it takes to build GCC when doing a
fast test.
Until now, in such cases not only was the software not installed, but the
tarballs of the software were also not downloaded. Hence making the output
of '--dist-software' incomplete (as in bug #58561).
With this commit, we now import all the necessary tarballs, when the
software isn't necessary for the particular system, it won't be built or
cited, but its tarball will be present anyway, thus allowing the output of
'--dist-software' to be complete.
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When publishing a project, it is necessary to also publish the source code
of all necessary software of the project. We had recently added a new
'./project make' target called 'dist-software' for this job, but had
forgotten to add it in the output of './project --help'! There was also a
small bug inside of it that didn't allow the successful copying of the
created tarball to the top project directory.
With this commit, an explanation for this target has been added in the
output of './project --help' and that bug has been fixed.
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Until now, when making the link to Gnuastro's configuration files, the
'configure.sh' script would incorrectly link to the old configuration
directory under the 'reproduce/software' directory. With this commit, it is
moved to the proper directory under 'reproduce/analysis'.
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Some minor conflicts came up in 'download.mk' and 'verify.mk' (as expected
in the "IMPORTANT" commits) and were easily fixed by choosing this branch's
values.
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Until now we were using 'which' for this job, but throughout Maneage, we
have used 'type', so to help in consistancy, we also use 'type' for this
final command for this project also.
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Until now, when adding the necessary library flags to the build of XLSX
I/O, we were effectively over-writing the 'LDFLAGS' variables. So the
compiler was effectively not being told where to look for the necessary
libraries.
With this commit, to fix the problem, we now append the new linking flags
to LDFLAGS in XLSX I/O's build, not over-write it.
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Marios had read the first draft of the paper (Commit f990bba) and provided
valuable feedback (shown below) that ultimately helped in the current
version. But because of all the work that was necessary in those days, I
forgot to actually thank him in the acknowledgment, while I had implemented
most of his thoughts.
Following Marios' thoughts on the Git branching figure, with this commit, I
am also adding a few sentences at the end of the caption with a very rough
summary of Git.
I also changed the branch commit-colors to shades of brown (incrementally
becoming lighter as higher-level branches are shown) to avoid the confusion
with the blue and green signs within the schematic papers shown in the
figure.
Marios' comments (April 28th, 2020, on Commit f990bba)
------------------------------------------------------
I think the structure of the paper is more or less fine. There are two
places that I thought could be improved:
1) Section 3 (Principles) was somewhat confusing to me in the way that it
was structured. I think the main source of confusion is the mixing of what
Maeage is about and what other programs have done. I would suggest to
separate the two. I would have short intro for the section, similar to what
you have now. However, I would suggest to highlight the underlying goals
motivating the principles that follow: reproducibility, open science,
something else? Then I would go into the details of the seven principles.
Some of the principles are less clear to me than others. For example, why
is simplicity a guiding principle? Then some other principles appear to be
related, for example modularity, minimal complexity and scalability to my
eyes are not necessarily separate.
Finally, I would separate the comparison with other software and either
dedicate a section to that somewhere toward the end of the paper (perhaps a
subsection for section 5) or at least condense it and put it as a closing
paragraph for Section 3. As it is now I think it draws focus from Maneage
and also includes some repetitions.
2) Section 4 (Maneage) was at times confusing because it is written, I
think in part as a demonstration of Maneage (i.e., including examples that
showed how Maneage was used to write this or other papers) and a
manual/description of the software. I wonder whether these two aspects can
be more cleanly separated. Perhaps it would be possible to first have a
section 4 where each of the modules/units of Maneage are listed and
explained and then have the following section discuss a working example of
Maneage using this or another paper.
3) I found Figure 7 [the git branching figure] and its explanation not very
intuitive. This probably has to do with my zero knowledge of github and how
versioning there works, but perhaps the description can be a bit more "user
friendly" even for those who are not familiar with the tool.
4) I find Section 6 to be rather inconsequential. It does not add anything
and it more or less is just a summary of what was discussed. I would
personally remove it and include a very short summary of the
ideals/principles/goals of Maneage at the beginning of Section 5, before
the discussion.
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After trying a clean build of Maneage in a Docker image (with a minimal
debian:stable-20200607-slim OS), I noticed that the building of OpenSSL is
failing because it doesn't find the proper Perl functionality. To fix it,
with this commit, Perl is set as a prerequisite of OpenSSL and this fixed
the problem.
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The project configuration requires a build-directory at configuration time,
two other directories can optionally be given to avoid downloading the
project's necessary data and software. It is possible to give these three
directories as command-line options, or by interactively giving them after
running the configure script.
Until now, when these directories weren't given as command-line options,
and the running shell was non-interactive, the configure script would crash
on the line trying to interactively read the user's given directories (the
'read' command).
With this commit, all the 'read' commands for these three directories are
now put within an 'if' statement. Therefore, when 'read' fails (the shell
is non-interactive), instead of a quiet crash, a descriptive message is
printed, telling the user that cause of the problem, and suggesting a fix.
This bug was found by Michael R. Crusoe.
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