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-rw-r--r--README-hacking.md34
-rwxr-xr-xproject17
-rw-r--r--reproduce/analysis/config/metadata.conf21
-rw-r--r--reproduce/analysis/make/initialize.mk35
-rw-r--r--reproduce/analysis/make/top-make.mk4
-rw-r--r--reproduce/analysis/make/top-prepare.mk2
-rw-r--r--reproduce/software/make/basic.mk8
-rw-r--r--reproduce/software/make/high-level.mk8
-rwxr-xr-xreproduce/software/shell/configure.sh69
-rw-r--r--tex/src/preamble-project.tex8
10 files changed, 144 insertions, 62 deletions
diff --git a/README-hacking.md b/README-hacking.md
index 92c878e..e42bf42 100644
--- a/README-hacking.md
+++ b/README-hacking.md
@@ -1050,11 +1050,13 @@ future.
information for plain-text data and will put it in the
`$(print-general-metadata)` variable. It is thus recommended to print
this variable into your plain-text file before printing the actual
- data (so it shows on top of the file). If you are publishing your data
- in binary formats, please add all the metadata you see in
- `$(print-general-metadata)` into each dataset file (for example
- keywords in the FITS format). If there are many files, its easy to
- define a tiny shell-script to do the job on each dataset.
+ data (so it shows on top of the file). For a real-world example, see
+ its usage in `reproduce/analysis/make/delete-me.mk` (in the `maneage`
+ branch). If you are publishing your data in binary formats, please add
+ all the metadata you see in `$(print-general-metadata)` into each
+ dataset file (for example keywords in the FITS format). If there are
+ many files, its easy to define a tiny shell-script to do the job on
+ each dataset.
- **Link to figure datasets in caption**: all the datasets that go into
the plots should be uploaded directly to Zenodo so they can be
@@ -1209,15 +1211,31 @@ future.
- **After acceptance (before publication)**: Congratulations on the
acceptance! The main science content of your paper can't be changed any
- more, but the paper will not go to the publication editor (for language
+ more, but the paper will now go to the publication editor (for language
and style). Your approval of the final proof is necessary before the
- paper is finally published. Some journals associate your paper's DOI
- during this process. So before approving the final proof do these steps:
+ paper is finally published. Use this period to finalize the final
+ metadata of your project: the journal's DOI. Some journals associate
+ your paper's DOI during this process. So before approving the final
+ proof do these steps:
* Add the Journal DOI in `reproduce/analysis/config/metadata.conf`,
and re-build your final data products, so this important metadata is
added.
+ * Once you get the final proof, and if everything is OK for you,
+ implement all the good language corrections/edits they have made
+ inside your own copy here and commit it into your project. This will
+ be the final commit of your project before publication.
+
+ * Submit your final project as a new version to Zenodo (and
+ arXiv). The Zenodo one is most important because your plots will
+ link to it and you want the commit hash in the data files that
+ readers will get from Zenodo to be the same hash as the paper.
+
+ * Tell the journal's publication editor to correct the hash and Zenodo
+ ID in your final proof confirmation (so the links point to the
+ correct place). Recall that on every new version upload in Zenodo,
+ you get a new DOI (or Zenodo ID).
diff --git a/project b/project
index a6bbf93..a99e0a6 100755
--- a/project
+++ b/project
@@ -4,6 +4,7 @@
# Run `./project --help' for a description of how to use it.
#
# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021 Raul Infante-Sainz <infantesainz@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -47,7 +48,6 @@ existing_conf=0
highlightnotes=0
separatesupplement=0
scriptname="./project"
-minmapsize=10000000000
@@ -109,7 +109,6 @@ Configure options:
-e, --existing-conf Use (possibly existing) local configuration.
--host-cc Use host system's C compiler, don't build GCC.
-i, --input-dir=STR Directory containing input datasets (optional).
- -m, --minmapsize=INT [Gnuastro] Minimum number of bytes to use RAM.
-s, --software-dir=STR Directory containing necessary software tarballs.
--check-config During configuration, show what is being built.
--clean-texdir Remove possibly existing build-time subdirectories
@@ -118,12 +117,13 @@ Configure options:
--all-highlevel Build all high-level software (for development).
Configure and Make options:
+ -d, --debug[=FLAGS] In configure: use -j1, no -k, and no Zenodo check.
+ In make: 'FLAGS' will be directly passed to 'make'.
-g, --group=STR Build and run with write permissions for a group.
-j, --jobs=INT Number of threads to build/run the software.
-?, --help Print this help list.
Make (analysis) options:
- -d, --debug=FLAGS Print various types of debugging information.
-p, --prepare-redo Re-do preparation (only done automatically once).
Make (final PDF) options:
@@ -186,9 +186,6 @@ do
-i|--input-dir) input_dir="$2"; check_v "$1" "$input_dir"; shift;shift;;
-i=*|--input-dir=*) input_dir="${1#*=}"; check_v "$1" "$input_dir"; shift;;
-i*) input_dir=$(echo "$1" | sed -e's/-i//'); check_v "$1" "$input_dir"; shift;;
- -m|--minmapsize) minmapsize="$2"; check_v "$1" "$minmapsize"; shift;shift;;
- -m=*|--minmapsize=*) minmapsize="${1#*=}"; check_v "$1" "$minmapsize"; shift;;
- -m*) minmapsize=$(echo "$1" | sed -e's/-m//'); check_v "$1" "$minmapsize"; shift;;
-s|--software-dir) software_dir="$2"; check_v "$1" "$software_dir"; shift;shift;;
-s=*|--software-dir=*) software_dir="${1#*=}"; check_v "$1" "$software_dir"; shift;;
-s*) software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
@@ -333,14 +330,14 @@ fi
if ! [ x$group = x ]; then
# Check if group is usable.
- if ! sg "$group" "echo test &> /dev/null" &> /dev/null; then
+ if ! sg "$group" "echo Group \'$group\' exists"; then
echo "$scriptname: '$group' is not a usable group name on this system.";
echo "(TIP: you can use the 'groups' command to see your groups)"
exit 1
fi
# Set the group option for running Make.
- gopt="reproducible_paper_group_name=$group"
+ gopt="maneage_group_name=$group"
fi
@@ -444,15 +441,15 @@ case $operation in
# Variables to pass to the configuration script.
export jobs=$jobs
+ export debug=$debug
export host_cc=$host_cc
export build_dir=$build_dir
export input_dir=$input_dir
export scriptname=$scriptname
- export minmapsize=$minmapsize
+ export maneage_group_name=$group
export software_dir=$software_dir
export existing_conf=$existing_conf
export all_highlevel=$all_highlevel
- export reproducible_paper_group_name=$group
# Run the configuration script
if [ x"$group" = x ]; then
diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf
index 470e429..b1f657b 100644
--- a/reproduce/analysis/config/metadata.conf
+++ b/reproduce/analysis/config/metadata.conf
@@ -1,6 +1,19 @@
-# Project meta-data that can be used in a project's output datasets and
+# Project meta-data that will be used in a project's output datasets and
# final paper. Please set the values here and use them in your analysis or
-# paper, don't repeat them
+# paper, don't repeat them.
+#
+# These variables are used in 'reproduce/analysis/make/initialize.mk': 1)
+# to create a Make variable called 'print-general-metadata'. You can simply
+# print this variable's value in any plain-text output.
+#
+# Why add a Copyright for the data? people need to know if they can "use"
+# the dataset (i.e., modify it), or possibly re-distribute it and their
+# derived products. They also need to know how they can contact the creator
+# of the datset (who is usually also the copyright owner). So take this
+# seriously and add your name and email-address (or the name of the person
+# and email of the person who was in charge of that part of the project),
+# and the copyright license name and standard link to the fully copyright
+# license.
#
# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
@@ -12,7 +25,9 @@
# Project information
metadata-title = Towards Long-term and Archivable Reproducibility
-# DOIs and identifiers.
+# DOIs and identifiers (don't include fixed URL prefixes like
+# 'https://doi.org/' or 'https://arxiv.org/abs'), they will be added
+# automatically where necessary.
metadata-arxiv = 2006.03018
metadata-doi-zenodo = 10.5281/zenodo.4291207
metadata-doi-journal = 10.1109/MCSE.2021.3072860
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 8af3199..bc73df8 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -224,7 +224,7 @@ project-package-contents = $(texdir)/$(project-package-name)
$(project-package-contents) $(mtexdir)/initialize.tex
texclean:
- rm *.pdf
+ rm -f *.pdf
rm -rf $(texdir)/build/*
mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
@@ -253,8 +253,7 @@ distclean: clean
# `rm' program. So for this recipe, we'll use the host system's
# `rm', not our own.
$$sys_rm -rf $(BDIR)
- $$sys_rm -f $(pconfdir)/LOCAL.conf
- $$sys_rm -f Makefile .gnuastro .local .build
+ $$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
@@ -367,18 +366,18 @@ $(project-package-contents): paper.pdf | $(texdir)
sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
mv $$pgfsettings.new $$pgfsettings
- # Clean temporary (currently those ending in `~') files.
- cd $(texdir)
- find $(project-package-name) -name \*~ -delete
- find $(project-package-name) -name \*.swp -delete
-
# PROJECT SPECIFIC
# ----------------
- # Put any project specific distribution steps here.
+ # Put any project-specific distribution steps here.
cd $$curdir
cp tex/build/build/appendix.bbl $$dir/
# ----------------
+ # Clean temporary files that may have been created by text editors.
+ cd $(texdir)
+ find $(project-package-name) -name \*~ -delete
+ find $(project-package-name) -name \*.swp -delete
+
# Package into `.tar.gz' or '.tar.lz'.
dist dist-lzip: $(project-package-contents)
curdir=$$(pwd)
@@ -460,15 +459,21 @@ $(data-publish-dir):; mkdir $@
# Print Copyright statement
# -------------------------
#
-# This statement can be used in published datasets that are in plain-text
-# format. It assumes you have already put the data-specific statements in
-# its first argument, it will supplement them with general project links.
-doi-prefix-url = https://doi.org
+# The 'print-general-metadata' can be used to print the general metadata in
+# published datasets that are in plain-text format. It should be called
+# with make's 'call' function like this (where 'FILENAME' is the name of
+# the file it will append this content to):
+#
+# $(call print-general-metadata, FILENAME)
+#
+# See 'reproduce/analysis/make/delete-me.mk' (in the Maneage branch) for a
+# real-world usage of this variable.
+doi-prefix-url = https://doi.org
arxiv-prefix-url = https://arxiv.org/abs
print-general-metadata = \
echo "\# Project title: $(metadata-title)" >> $(1); \
echo "\# Git commit (that produced this dataset): $(project-commit-hash)" >> $(1); \
- echo "\# Project's Git repository: $(metadata-git-repository)" >> $(1); \
+ echo "\# Git repository: $(metadata-git-repository)" >> $(1); \
if [ x$(metadata-arxiv) != x ]; then \
echo "\# Pre-print: $(arxiv-prefix-url)/abs/$(metadata-arxiv)" >> $(1); fi; \
if [ x$(metadata-doi-journal) != x ]; then \
@@ -501,6 +506,8 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
echo "\newcommand{\projectdate}{$$d}" > $@
echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
echo "\newcommand{\projectversion}{$(project-commit-hash)}" >> $@
+ echo "\newcommand{\projectgitrepo}{$(metadata-git-repository)}" >> $@
+ echo "\newcommand{\projectcopyrightowner}{$(metadata-copyright-owner)}" >> $@
# arXiv/Zenodo identifier (necessary for download link):
echo "\newcommand{\projectarxivid}{$(metadata-arxiv)}" >> $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 6b055f7..27c1b5b 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -51,7 +51,7 @@ include reproduce/software/config/LOCAL.conf
# Controlling this requires two variables that are available at this stage:
#
# - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
-# - `reproducible_paper_group_name': value to the `--group' option.
+# - `maneage_group_name': value to the `--group' option.
#
# The analysis is only done when both have the same group name. Note that
# when the project isn't being built for a group, both variables will be an
@@ -69,7 +69,7 @@ top-pdfs = paper.pdf
else
top-pdfs = paper.pdf supplement.pdf
endif
-ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
+ifeq (x$(maneage_group_name),x$(GROUP-NAME))
all: $(top-pdfs)
else
all:
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index f81ac07..fb5700e 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -35,7 +35,7 @@ include reproduce/software/config/LOCAL.conf
# -------------------------------
#
# See `top-make.mk' for complete explanation.
-ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
+ifeq (x$(maneage_group_name),x$(GROUP-NAME))
all: $(BDIR)/software/preparation-done.mk
@echo "Project preparation is complete.";
else
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 9217ee9..fb378b8 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -86,7 +86,8 @@ export SHELL := $(ibdir)/dash
export PATH := $(ibdir):$(PATH)
export PKG_CONFIG_PATH := $(ildir)/pkgconfig
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export CPPFLAGS := -I$(idir)/include $(CPPFLAGS)
+export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
+ -Wno-nullability-completeness
export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
# This is the "basic" tools where we are relying on the host operating
@@ -210,7 +211,10 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
# POSIX Threads library for multi-threaded programs.
for l in dl pthread; do
if [ -f /usr/lib/lib$$l.a ]; then
- ln -sf /usr/lib/lib$$l.* $(ildir)/
+ for f in /usr/lib/lib$$l.*; do
+ ln -sf $$(realpath $$f) \
+ $$(echo $$f | sed -e's|/usr/lib|$(ildir)|')
+ done
fi
done
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index d69722e..6ea782c 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -125,10 +125,10 @@ all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
export PATH := $(ibdir)
export CCACHE_DISABLE := 1
export SHELL := $(ibdir)/bash
-export CPPFLAGS := -I$(idir)/include
.SHELLFLAGS := --noprofile --norc -ec
export LDFLAGS := $(rpath_command) -L$(ildir)
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export CPPFLAGS := -I$(idir)/include -Wno-nullability-completeness
export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig
# Settings specific to this Makefile.
@@ -428,7 +428,8 @@ $(ibidir)/cfitsio-$(cfitsio-version):
export gbuild_tar=$(ddir)/$$customtar
$(call gbuild, cfitsio-$(cfitsio-version), , \
--enable-sse2 --enable-reentrant \
- --with-bzip2=$(idir), , make shared fpack funpack)
+ --with-bzip2=$(idir), , \
+ make shared fpack funpack)
rm $$customtar
echo "CFITSIO $(cfitsio-version)" > $@
@@ -1316,7 +1317,8 @@ $(ibidir)/swig-$(swig-version):
# pcr is a dependency of swig
tarball=swig-$(swig-version).tar.gz
$(call import-source, $(swig-url), $(swig-checksum))
- $(call gbuild, swig-$(swig-version), static, --without-pcre)
+ $(call gbuild, swig-$(swig-version), static, \
+ --without-pcre --without-tcl)
echo "Swig $(swig-version)" > $@
# The disables:
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 812f3d3..e15a8e9 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -3,6 +3,7 @@
# Necessary preparations/configurations for the reproducible project.
#
# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021 Raul Infante-Sainz <infantesainz@gmail.com>
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -423,8 +424,17 @@ if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
# Check C compiler
# ----------------
+#
+# Here we check if the C compiler works properly. About the "no warning"
+# variable ('nowarnings'):
+#
+# -Wno-nullability-completeness: on macOS Big Sur 11.2.3 and Xcode 12.4,
+# hundreds of 'nullability-completeness' warnings are printed which can
+# be very annoying and even hide important errors or warnings. It is
+# also harmless for our test here, so it is generally added.
testprog=$compilertestdir/test
testsource=$compilertestdir/test.c
+noccwarnings="-Wno-nullability-completeness"
echo; echo; echo "Checking host C compiler ('$CC')...";
cat > $testsource <<EOF
#include <stdio.h>
@@ -432,7 +442,7 @@ cat > $testsource <<EOF
int main(void){printf("...C compiler works.\n");
return EXIT_SUCCESS;}
EOF
-if $CC $testsource -o$testprog && $testprog; then
+if $CC $noccwarnings $testsource -o$testprog && $testprog; then
rm $testsource $testprog
else
rm $testsource
@@ -761,7 +771,7 @@ fi
# exists and we don't want to re-write it).
if [ $rewritepconfig = no ]; then
oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf)
- if [ "x$oldgroupname" = "x$reproducible_paper_group_name" ]; then
+ if [ "x$oldgroupname" = "x$maneage_group_name" ]; then
just_a_place_holder_to_avoid_not_equal_test=1;
else
echo "-----------------------------"
@@ -1079,7 +1089,7 @@ if [ $rewritepconfig = yes ]; then
-e's|@ddir[@]|'"$ddir"'|' \
-e's|@sys_cpath[@]|'"$sys_cpath"'|' \
-e's|@downloader[@]|'"$downloader"'|' \
- -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
+ -e's|@groupname[@]|'"$maneage_group_name"'|' \
$pconf.in >> $pconf
else
# Read the values from existing configuration file. Note that the build
@@ -1238,7 +1248,7 @@ if ! [ -d "$mtexdir" ]; then mkdir "$mtexdir"; fi
# TeX build directory. If built in a group scenario, the TeX build
# directory must be separate for each member (so they can work on their
# relevant parts of the paper without conflicting with each other).
-if [ "x$reproducible_paper_group_name" = x ]; then
+if [ "x$maneage_group_name" = x ]; then
texbdir="$texdir"/build
else
user=$(whoami)
@@ -1458,18 +1468,19 @@ fi
# which will download the DOI-resolved webpage, and extract the Zenodo-URL
# of the most recent version from there (using the 'coreutils' tarball as
# an example, the directory part of the URL for all the other software are
-# the same).
+# the same). This is not done if the option `--debug' is used.
+zenodourl=""
user_backup_urls=""
zenodocheck=.build/software/zenodo-check.html
-if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then
- zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \
- | sed -n -e'/http/p' \
- | tr ' ' '\n' \
- | grep http \
- | sed -e 's/href="//' -e 's|/coreutils| |' \
- | awk 'NR==1{print $1}')
-else
- zenodourl=""
+if [ x$debug = x ]; then
+ if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then
+ zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \
+ | sed -n -e'/http/p' \
+ | tr ' ' '\n' \
+ | grep http \
+ | sed -e 's/href="//' -e 's|/coreutils| |' \
+ | awk 'NR==1{print $1}')
+ fi
fi
rm -f $zenodocheck
@@ -1497,6 +1508,28 @@ user_backup_urls="$user_backup_urls $zenodourl"
+# Corrections for debugging mode
+# ------------------------------
+#
+# If the user wants to debug the software configuration, they are usually
+# focused on the building of the single problematic software. Therefore,
+# the default multi-threaded execution of Make with the '--keep-going'
+# option are very annoying and can even hide important warnings. Recall
+# that with '--keep-going', Make will continue building other targets, even
+# if one target fails. When the user runs './project configure --debug',
+# the 'debug' variable will not be empty and this mode will be activated.
+if [ x$debug = x ]; then
+ keepgoing="--keep-going"
+else
+ jobs=1
+ numthreads=1
+ keepgoing=""
+fi
+
+
+
+
+
# Build other basic tools our own GNU Make
# ----------------------------------------
#
@@ -1504,7 +1537,7 @@ user_backup_urls="$user_backup_urls $zenodourl"
# Bash, Make, or AWK. In this step, we'll install such low-level basic
# tools, but we have to be very portable (and use minimal features in all).
echo; echo "Building necessary software (if necessary)..."
-.local/bin/make -k -f reproduce/software/make/basic.mk \
+.local/bin/make $keepgoing -f reproduce/software/make/basic.mk \
user_backup_urls="$user_backup_urls" \
sys_library_path=$sys_library_path \
rpath_command=$rpath_command \
@@ -1532,7 +1565,7 @@ else
numthreads=$jobs
fi
.local/bin/env -i HOME=$bdir \
- .local/bin/make -k -f reproduce/software/make/high-level.mk \
+ .local/bin/make $keepgoing -f reproduce/software/make/high-level.mk \
user_backup_urls="$user_backup_urls" \
sys_library_path=$sys_library_path \
rpath_command=$rpath_command \
@@ -1725,10 +1758,10 @@ echo `.local/bin/date` > $finaltarget
#
# The configuration is now complete, we can inform the user on the next
# step(s) to take.
-if [ x$reproducible_paper_group_name = x ]; then
+if [ x$maneage_group_name = x ]; then
buildcommand="./project make -j8"
else
- buildcommand="./project make --group=$reproducible_paper_group_name -j8"
+ buildcommand="./project make --group=$maneage_group_name -j8"
fi
cat <<EOF
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index 7351d83..7fabca1 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -24,7 +24,13 @@
-%% Import graphics
+%% Packages you may need in your project
+%% -------------------------------------
+%
+%% Here you can add/remove any custom LaTeX package that you need for this
+%% project that aren't provided by the journal's style.
+
+%% For loading images into the output (with '\includegraphics').
\usepackage{graphicx}
%% IEEEtran V1.6 and later pre-defines the format of the cite.sty package
generated by cgit v1.2.1 (git 2.18.0) at 2024-05-17 04:29:06 +0000