diff options
Diffstat (limited to 'reproduce')
| -rw-r--r-- | reproduce/analysis/make/format.mk | 2 | ||||
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 53 | ||||
| -rw-r--r-- | reproduce/analysis/make/prepare.mk | 2 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 4 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 2 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 86 |
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 |