aboutsummaryrefslogtreecommitdiff
path: root/reproduce
diff options
context:
space:
mode:
Diffstat (limited to 'reproduce')
-rw-r--r--reproduce/analysis/make/format.mk2
-rw-r--r--reproduce/analysis/make/initialize.mk53
-rw-r--r--reproduce/analysis/make/prepare.mk2
-rw-r--r--reproduce/software/make/basic.mk4
-rw-r--r--reproduce/software/make/high-level.mk2
-rwxr-xr-xreproduce/software/shell/configure.sh86
6 files changed, 80 insertions, 69 deletions
diff --git a/reproduce/analysis/make/format.mk b/reproduce/analysis/make/format.mk
index efd9918..fd4060a 100644
--- a/reproduce/analysis/make/format.mk
+++ b/reproduce/analysis/make/format.mk
@@ -23,7 +23,7 @@
# Save the "Table 3" spreadsheet from the downloaded `.xlsx' file into a
# simple plain-text file that is easy to use.
-a1dir = $(BDIR)/analysis1
+a1dir = $(badir)/analysis1
mk20tab3 = $(a1dir)/table-3.txt
$(a1dir):; mkdir $@
$(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 8f1769e..168010f 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -30,14 +30,24 @@
# parallel. Also, some programs may not be thread-safe, therefore it will
# be necessary to put a lock on them. This project uses the `flock' program
# to achieve this.
-texdir = $(BDIR)/tex
-lockdir = $(BDIR)/locks
-indir = $(BDIR)/inputs
-prepdir = $(BDIR)/prepare
+#
+# To help with modularity and clarity of the build directory (not mixing
+# software-environment built-products with products built by the analysis),
+# it is recommended to put all your analysis outputs in the 'analysis'
+# subdirectory of the top-level build directory.
+badir=$(BDIR)/analysis
+bsdir=$(BDIR)/software
+
+# Derived directories (the locks directory can be shared with software
+# which already has this directory.).
+texdir = $(badir)/tex
+lockdir = $(bsdir)/locks
+indir = $(badir)/inputs
+prepdir = $(padir)/prepare
mtexdir = $(texdir)/macros
+installdir = $(bsdir)/installed
bashdir = reproduce/analysis/bash
pconfdir = reproduce/analysis/config
-installdir = $(BDIR)/software/installed
@@ -56,7 +66,7 @@ installdir = $(BDIR)/software/installed
ifeq (x$(project-phase),xprepare)
$(prepdir):; mkdir $@
else
-include $(BDIR)/software/preparation-done.mk
+include $(bsdir)/preparation-done.mk
ifeq (x$(include-prepare-results),xyes)
include $(prepdir)/*.mk
endif
@@ -184,7 +194,7 @@ export MPI_PYTHON3_SITEARCH :=
# option: they add too many extra checks that make it hard to find what you
# are looking for in the outputs.
.SUFFIXES:
-$(lockdir): | $(BDIR); mkdir $@
+$(lockdir): | $(bsdir); mkdir $@
@@ -215,8 +225,8 @@ project-package-contents = $(texdir)/$(project-package-name)
texclean:
rm *.pdf
- rm -rf $(BDIR)/tex/build/*
- mkdir $(BDIR)/tex/build/tikz # 'tikz' is assumed to already exist.
+ rm -rf $(texdir)/build/*
+ mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
clean:
# Delete the top-level PDF file.
@@ -228,10 +238,10 @@ clean:
# features like ignoring the listing of a file with `!()' that we
# are using afterwards.
shopt -s extglob
- rm -rf $(BDIR)/tex/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
- rm -rf $(BDIR)/!(software|tex) $(BDIR)/tex/!(macros|$(texbtopdir))
- rm -rf $(BDIR)/tex/build/!(tikz) $(BDIR)/tex/build/tikz/*
- rm -rf $(BDIR)/software/preparation-done.mk
+ rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
+ rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir))
+ rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/*
+ rm -rf $(bsdir)/preparation-done.mk
distclean: clean
# Without cleaning the Git hooks, we won't be able to easily
@@ -398,14 +408,15 @@ dist-zip: $(project-package-contents)
dist-software:
curdir=$$(pwd)
dirname=software-$(project-commit-hash)
- cd $(BDIR)
+ cd $(bsdir)
+ if [ -d $$dirname ]; then rm -rf $$dirname; fi
mkdir $$dirname
- cp -L software/tarballs/* $$dirname/
+ cp -L tarballs/* $$dirname/
tar -cf $$dirname.tar $$dirname
gzip -f --best $$dirname.tar
rm -rf $$dirname
cd $$curdir
- mv $(BDIR)/$$dirname.tar.gz ./
+ mv $(bsdir)/$$dirname.tar.gz ./
@@ -422,9 +433,11 @@ dist-software:
#
# 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
-# '$(BDIR)/tex' directory (because other LaTeX producers may also need
-# it for example when using './project make dist'). The contents of
-# this directory are directly taken into the tarball.
+# '$(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
@@ -436,7 +449,7 @@ dist-software:
# (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 = $(BDIR)/data-to-publish
+data-publish-dir = $(badir)/data-to-publish
$(tex-publish-dir):; mkdir $@
$(data-publish-dir):; mkdir $@
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index 995132c..d0b61d9 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -23,7 +23,7 @@
#
# Without this file, `./project make' won't work.
prepare-dep = $(subst prepare, ,$(makesrc))
-$(BDIR)/software/preparation-done.mk: \
+$(bsdir)/preparation-done.mk: \
$(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
# If you need to add preparations define targets above to do the
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 2a28e76..9217ee9 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -48,7 +48,7 @@ include reproduce/software/config/checksums.conf
include reproduce/software/config/urls.conf
# Basic directories
-lockdir = $(BDIR)/locks
+lockdir = $(BDIR)/software/locks
tdir = $(BDIR)/software/tarballs
ddir = $(BDIR)/software/build-tmp
idir = $(BDIR)/software/installed
@@ -1274,7 +1274,7 @@ $(ibidir)/binutils-$(binutils-version): \
if ! [ x"$(sys_library_path)" = x ]; then
for f in $(sys_library_path)/*crt*.o; do
b=$$($(ibdir)/basename $$f)
- ln -s $$f $(ildir)/$$b
+ ln -sf $$f $(ildir)/$$b
done
fi
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 948b23a..d69722e 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -43,7 +43,7 @@ include reproduce/software/config/TARGETS.conf
include reproduce/software/config/texlive-packages.conf
# Basic directories (similar to 'basic.mk').
-lockdir = $(BDIR)/locks
+lockdir = $(BDIR)/software/locks
tdir = $(BDIR)/software/tarballs
ddir = $(BDIR)/software/build-tmp
idir = $(BDIR)/software/installed
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 219b335..812f3d3 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -44,8 +44,8 @@ need_gfortran=0
-# Internal directories
-# --------------------
+# Internal source directories
+# ---------------------------
#
# These are defined to help make this script more readable.
topdir="$(pwd)"
@@ -679,14 +679,14 @@ EOF
fi
# Then, see if the Fortran compiler works
- testsource=$compilertestdir/test.f
+ testsourcef=$compilertestdir/test.f
echo; echo; echo "Checking host Fortran compiler...";
- echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource
- echo " END" >> $testsource
- if gfortran $testsource -o$testprog && $testprog; then
- rm $testsource $testprog
+ echo " PRINT *, \"... Fortran Compiler works.\"" > $testsourcef
+ echo " END" >> $testsourcef
+ if gfortran $testsourcef -o$testprog && $testprog; then
+ rm $testsourcef $testprog
else
- rm $testsource
+ rm $testsourcef
cat <<EOF
______________________________________________________
@@ -1165,8 +1165,8 @@ rm -f "$finaltarget"
-# Project's top-level directories
-# -------------------------------
+# Project's top-level built software directories
+# ----------------------------------------------
#
# These directories are possibly needed by many steps of process, so to
# avoid too many directory dependencies throughout the software and
@@ -1200,15 +1200,41 @@ if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
itidir="$verdir"/tex
if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
+# Temporary software un-packing/build directory: if the host has the
+# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
+# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
+# today (>8GB) is large enough for the parallel building of the software.
+#
+# For the name of the directory under `/dev/shm' (for this project), we'll
+# use the names of the two parent directories to the current/running
+# directory, separated by a `-' instead of `/'. We'll then appended that
+# with the user's name (in case multiple users may be working on similar
+# project names). Maybe later, we can use something like `mktemp' to add
+# random characters to this name and make it unique to every run (even for
+# a single user).
+tmpblddir="$sdir"/build-tmp
+rm -rf "$tmpblddir"/* "$tmpblddir" # If its a link, we need to empty its
+ # contents first, then itself.
+
+
+
+
+
+# Project's top-level built analysis directories
+# ----------------------------------------------
+
+# Top-level built analysis directories.
+badir="$bdir"/analysis
+if ! [ -d "$badir" ]; then mkdir "$badir"; fi
+
# Top-level LaTeX.
-texdir="$bdir"/tex
+texdir="$badir"/tex
if ! [ -d "$texdir" ]; then mkdir "$texdir"; fi
# LaTeX macros.
mtexdir="$texdir"/macros
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).
@@ -1224,20 +1250,6 @@ if ! [ -d "$texbdir" ]; then mkdir "$texbdir"; fi
tikzdir="$texbdir"/tikz
if ! [ -d "$tikzdir" ]; then mkdir "$tikzdir"; fi
-# If 'tex/build' and 'tex/tikz' aren't symbolic links, then we are in the
-# tarball (not the Git repository), so we'll give them another name and let
-# the script continue normally.
-if rm -f tex/build; then
- rm -f tex/tikz
-else
- mv tex/tikz tex/tikz-from-tarball
- mv tex/build tex/build-from-tarball
-fi
-
-
-
-
-
# If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f' will delete
# them and we can continue. However, when the project is being built from
# the tarball, these two are not symbolic links but actual directories with
@@ -1252,7 +1264,6 @@ else
mv tex/build tex/build-from-tarball
fi
-
# Set the symbolic links for easy access to the top project build
# directories. Note that these are put in each user's source/cloned
# directory, not in the build directory (which can be shared between many
@@ -1260,7 +1271,9 @@ fi
#
# Note: if we don't delete them first, it can happen that an extra link
# will be created in each directory that points to its parent. So to be
-# safe, we are deleting all the links on each re-configure of the project.
+# safe, we are deleting all the links on each re-configure of the
+# project. Note that at this stage, we are using the host's 'ln', not our
+# own, so its best not to assume anything (like 'ln -sf').
rm -f .build .local
ln -s "$bdir" .build
@@ -1273,21 +1286,6 @@ rm -f .gnuastro
# ------------------------------------------
-# Temporary software un-packing/build directory: if the host has the
-# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
-# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
-# today (>8GB) is large enough for the parallel building of the software.
-#
-# For the name of the directory under `/dev/shm' (for this project), we'll
-# use the names of the two parent directories to the current/running
-# directory, separated by a `-' instead of `/'. We'll then appended that
-# with the user's name (in case multiple users may be working on similar
-# project names). Maybe later, we can use something like `mktemp' to add
-# random characters to this name and make it unique to every run (even for
-# a single user).
-tmpblddir="$sdir"/build-tmp
-rm -rf "$tmpblddir"/* "$tmpblddir" # If its a link, we need to empty its
- # contents first, then itself.
# Set the top-level shared memory location.
if [ -d /dev/shm ]; then shmdir=/dev/shm
@@ -1313,7 +1311,7 @@ fi
# symbolic link to it. Otherwise, just build the temporary build
# directory under the project build directory.
if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir";
-else ln -s "$tbshmdir" "$tmpblddir";
+else ln -s "$tbshmdir" "$tmpblddir";
fi