IMPORTANT: better names for to-publish dirs and portability fixesHEADmaneage

Summary: this commit only affects the analysis of your project in case you
used the 'tex-publish-dir' or 'data-publish-dir' directories. They need to
be renamed to 'figdir' and 'drdir' respectively.

Until now, the directories containing the to-be-published data were
described deep in the middle of 'initialize.mk' (away from the other shared
directories), they also had hard-to-use (long) names. Furthermore,
'README-hacking.md' that is the main documentation of Maneage had grown
organically, such that the checklists were scattered across the file and
some things were repeated or not classified clearly. Finally, some
portability issues were reported by Stergios Amarantidis and Diana Korotun.

With this commit, the to-be-published directories have been renamed to the
more simple names of 'figdir' and 'drdir' respectively and their definition
in 'initialize.mk' has come right under the rest of the top-level
directories (to be easily found). Furthermore, the 'README-hacking.md' has
been fully restructured to be easier to navigate and follow for a new
reader. Finally, the portability issues mentioned above have been
addressed:

 - Within the '--help' output of './project', the '--keep-going' option was
   listed under "Configure and Make options", while it is only relevant as
   a Make option. It was therefore moved under Make options.

 - We had not explicitly set the locale of Maneage; causing a crash on one
   of the newly tested computers (a macOS with a non-C locale) during the
   execution of 'prep-source.sh'. With this commit, all the top-level
   Makefiles and scripts of Maneage set 'LC_ALL' to 'C' to ensure the same
   locale on any system.

 - The 'download-multi-try.sh' script would crash when building basic
   software in the following scenario: the downloader was still from the
   host, but one of its linked libraries had already been installed in
   Maneage and conflicted with the host. A step has been added to catch
   such cases and remove the Maneage'd library when this was the problem.

 - On macOS, we discovered that 'pkg-config' and 'wget' need a Python
   installation, so the necessary conditions have been added.

 - The 'apptainer.sh' script did not allow passing the '--debug' or
   '--host-cc' options to the execution of './project' within the
   container.

 - Within 'configure.sh', we wrote the absolute path of the downloader to
   use in 'LOCAL.conf'. However, we install both downloaders and it is
   safer to use Maneage's own downloader when it has been installed. So the
   downloader name in 'LOCAL.conf' now only has the name (without its
   absolute path).

1 files changed, 40 insertions, 35 deletions

diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 2752f47..250cb25 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -53,6 +53,45 @@ pconfdir    = reproduce/analysis/config
 
 
 
+# Directories for to-be-published data
+# ------------------------------------
+#
+# Its good practice (so you don't forget in the last moment!) to have all
+# the plot/figure/table data that you ultimately want to publish in a
+# single directory.
+#
+# There are two types of to-publish data in the project.
+#
+#  1. Those data that also go into your figures/plots (for example to give
+#     to LateX's PGFPlots package to create the plot internally) should be
+#     under the '$(texdir)' directory (because other LaTeX producers may
+#     also need it for example when using './project make dist', or you may
+#     want to publish the raw data behind the plots, for example see
+#     Appendix E of [1]). The contents of this directory are also directly
+#     taken into the tarball. As you see in [1], it is best to keep these
+#     files in plain-text format.
+#
+#  2. The data that are not included directly in the paper's figures and
+#     can be seen as supplements, or a "data release" associated to the
+#     report. A good place to keep them is under your build-directory
+#     (since the data may be large). These files can be custom formats like
+#     FITS files.
+#
+# RECOMMENDATION: don't put the figure/plot/table number in the names of
+# your to-be-published datasets! Given them a descriptive/short name that
+# would be clear to anyone who has read the paper. Later, in the caption
+# (or paper's tex/appendix), you will put links to the dataset on servers
+# like Zenodo (see the "Publication checklist" in 'README-hacking.md').
+#
+# [1] https://scixplorer.org/abs/2026A&A...709A.210E
+drdir = $(badir)/data-release
+figdir = $(texdir)/figures-data
+$(figdir) $(drdir):; mkdir $@
+
+
+
+
+
 # Preparation phase
 # -----------------
 #
@@ -145,6 +184,7 @@ curdir   := $(shell echo $$(pwd))
 # avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'),
 # we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'.
 .ONESHELL:
+export LC_ALL := C
 export TEXINPUTS :=
 export CCACHE_DISABLE := 1
 export PATH := $(installdir)/bin
@@ -594,41 +634,6 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 
 
 
-# Directory containing to-be-published datasets
-# ---------------------------------------------
-#
-# Its good practice (so you don't forget in the last moment!) to have all
-# the plot/figure/table data that you ultimately want to publish in a
-# single directory.
-#
-# There are two types of to-publish data in the project.
-#
-#  1. Those data that also go into LaTeX (for example to give to LateX's
-#     PGFPlots package to create the plot internally) should be under the
-#     '$(texdir)' directory (because other LaTeX producers may also need it
-#     for example when using './project make dist', or you may want to
-#     publish the raw data behind the plots, like:
-#     https://zenodo.org/record/4291207/files/tools-per-year.txt). The
-#     contents of this directory are also directly taken into the tarball.
-#
-#  2. The data that aren't included directly in the LaTeX run of the paper,
-#     can be seen as supplements. A good place to keep them is under your
-#     build-directory.
-#
-# RECOMMENDATION: don't put the figure/plot/table number in the names of
-# your to-be-published datasets! Given them a descriptive/short name that
-# would be clear to anyone who has read the paper. Later, in the caption
-# (or paper's tex/appendix), you will put links to the dataset on servers
-# like Zenodo (see the "Publication checklist" in 'README-hacking.md').
-tex-publish-dir = $(texdir)/to-publish
-data-publish-dir = $(badir)/data-to-publish
-$(tex-publish-dir):; mkdir $@
-$(data-publish-dir):; mkdir $@
-
-
-
-
-
 # Print Copyright statement
 # -------------------------
 #