diff options
| -rw-r--r-- | .file-metadata | bin | 6250 -> 6250 bytes | |||
| -rw-r--r-- | README.md | 78 | ||||
| -rwxr-xr-x | project | 13 | ||||
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 6 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 31 |
5 files changed, 113 insertions, 15 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex 9c57cfd..dbc185c 100644 --- a/.file-metadata +++ b/.file-metadata @@ -14,7 +14,8 @@ on your system if you have ever built and installed a software from source) and a downloader (Wget or cURL). Note that **Git is not mandatory**: if you don't have Git to run the first command below, go to the URL given in the command on your browser, and download the project's source (there is a -button to download a compressed tarball of the project). +button to download a compressed tarball of the project). If you have +received this source from arXiv, please see the respective section below. ```shell $ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX @@ -88,6 +89,81 @@ requiring root/administrator permissions. +Source from arXiv +----------------- +If the paper is also published on arXiv, it is highly likely that the +authors also uploaded/published the full reproducible paper template there +along with the LaTeX sources. If you have downloaded (or plan to download) +this source from arXiv, some minor extra steps are necessary: + +1. If the arXiv code for the paper is 1234.56789, then the downloaded + source will be called `1234.56789` (no special identification + suffix). However, it is actually a `.tar.gz` file. So take these steps + to unpack it to see its contents. + + ```shell + $ arxiv=1234.56789 + $ mv $arxiv $arxiv.tar.gz + $ mkdir $arxiv + $ cd $arxiv + $ tar xf ../$arxiv.tar.gz + ``` + +2. arXiv removes the executable flag from the files (for its own + security). So before following the standard procedure of projects + described in the sections above, its necessary to make the necessary + script files executable with the command below: + + ```shell + $ chmod +x project reproduce/software/bash/* reproduce/analysis/bash/* + ``` + +3. Remove extra files. In order to make sure arXiv can build the paper + (resolve conflicts due to different versions of LaTeX packages), it is + sometimes necessary to copy raw LaTeX package files in the tarball + uploaded to arXiv. Later, we will implement a feature to automatically + delete these extra files, but for now, the project's top directory + should only have the following contents (where `reproduce` and `tex` are + directories). You can safely remove any other file/directory. + + ```shell + $ ls + COPYING paper.tex project README-hacking.md README.md reproduce tex + ``` + +4. To build the figures from scratch, please you need to make the following + corrections to the respective source files. + + 4.1: `paper.tex`: uncomment the following line, so it looks like + below. See the comments above it for more information. + + ```shell + \newcommand{\makepdf}{} + ``` + + 4.2: `tex/src/preamble-pgfplots.tex`: set the `tikzsetexternalprefix` + variable to `tikz/`, so it looks like this: + + ```shell + \tikzsetexternalprefix{tikz/} + ``` + +5. In order to let arXiv build the LaTeX paper without bothering to run the + analysis pipeline it was necessary to create and fill the two + `tex/build` and `tex/tikz` subdirectories. But to do a clean build of + the project, it is necessary for these to be symbolic links to the build + directory. So when you are first configuring the project, run it with + `--clean-texdir` (only once is enough, they will be deleted permanently + after that), for example: + + ```shell + $ ./project configure --clean-texdir + ``` + + + + + Copyright information --------------------- @@ -31,6 +31,7 @@ build_dir= input_dir= make_targets= software_dir= +clean_texdir=0 existing_conf=0 scriptname="./project" minmapsize=10000000000 @@ -90,6 +91,9 @@ Configure options: -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. + --clean-texdir Remove possibly existing build-time subdirectories + under the project's 'tex/' directory (can happen + when source is from arXiv for example). Configure and Make options: -g, --group=STR Build and run with write permissions for a group. @@ -159,6 +163,8 @@ do -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;; + --clean-texdir) clean_texdir=1; shift;; + --clean-texdir=*) on_off_option_error --clean-texdir;; # Configure and Make options: -g|--group) group="$2"; check_v group "$group"; shift;shift;; @@ -217,6 +223,13 @@ case $operation in # Build the project's software. configure) + # If the user requested, clean the TeX directory from the extra + # (to-be-built) directories that may already be there (and will not + # allow the configuration to complete). + if [ x"$clean_texdir" = x1 ]; then + rm -rf tex/build tex/tikz + fi + # Variables to pass to the configuration script. export jobs=$jobs export host_cc=$host_cc diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index ee9c8c1..918ae06 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -181,7 +181,8 @@ $(lockdir): | $(BDIR); mkdir $@ # we want to ensure that the file is always built in every run: it contains # the project version which may change between two separate runs, even when # no file actually differs. -packagebasename := $(shell echo paper-$$(git describe --dirty --always --long)) +packagebasename := $(shell if [ -d .git ]; then \ + echo paper-$$(git describe --dirty --always --long); else echo NOGIT; fi) packagecontents = $(texdir)/$(packagebasename) .PHONY: all clean dist dist-zip distclean clean-mmap $(packagecontents) \ $(mtexdir)/initialize.tex @@ -342,5 +343,6 @@ dist-zip: $(packagecontents) $(mtexdir)/initialize.tex: | $(mtexdir) # Version of the project. - @v=$$(git describe --dirty --always --long); + @if [ -d .git ]; then v=$$(git describe --dirty --always --long); + else v=NO-GIT; fi echo "\newcommand{\projectversion}{$$v}" > $@ diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 17ff561..b0b757f 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -968,6 +968,11 @@ $(ibidir)/metastore: $(tdir)/metastore-$(metastore-version).tar.gz \ # # We want to inform the user if Metastore isn't built, so we don't # continue the call to `gbuild' with an `&&'. + # + # Checking for presence of `.git'. When the project source is + # downloaded from a non-Git source (for example from arXiv), there + # is no `.git' directory to work with. So until we find a better + # solution, avoid the step to to add the Git hooks. current_dir=$$(pwd); \ $(call gbuild, $<, metastore-$(metastore-version), static,, \ NO_XATTR=1 V=1,,pwd,PREFIX=$(idir)); \ @@ -975,18 +980,20 @@ $(ibidir)/metastore: $(tdir)/metastore-$(metastore-version).tar.gz \ if [ "x$(needpatchelf)" != x ]; then \ $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/metastore; \ fi; \ - user=$$(whoami); \ - group=$$(groups | awk '{print $$1}'); \ - cd $$current_dir; \ - for f in pre-commit post-checkout; do \ - sed -e's|@USER[@]|'$$user'|g' \ - -e's|@GROUP[@]|'$$group'|g' \ - -e's|@BINDIR[@]|$(ibdir)|g' \ - -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \ - reproduce/software/bash/git-$$f > .git/hooks/$$f \ - && chmod +x .git/hooks/$$f \ - && echo "Metastore (forked) $(metastore-version)" > $@; \ - done; \ + if [ -d .git ]; then \ + user=$$(whoami); \ + group=$$(groups | awk '{print $$1}'); \ + cd $$current_dir; \ + for f in pre-commit post-checkout; do \ + sed -e's|@USER[@]|'$$user'|g' \ + -e's|@GROUP[@]|'$$group'|g' \ + -e's|@BINDIR[@]|$(ibdir)|g' \ + -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \ + reproduce/software/bash/git-$$f > .git/hooks/$$f \ + && chmod +x .git/hooks/$$f; \ + done; \ + fi \ + && echo "Metastore (forked) $(metastore-version)" > $@; \ else \ echo; echo; echo; \ echo "*****************"; \ |