diff options
| -rw-r--r-- | .file-metadata | bin | 6829 -> 6092 bytes | |||
| -rw-r--r-- | README-hacking.md | 2 | ||||
| -rwxr-xr-x | configure | 60 | ||||
| -rw-r--r-- | paper.tex | 4 | ||||
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 2 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 5 |
6 files changed, 54 insertions, 19 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex 6230664..e448006 100644 --- a/.file-metadata +++ b/.file-metadata diff --git a/README-hacking.md b/README-hacking.md index ed3cc5f..37429b3 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -687,7 +687,7 @@ get more advanced in later stages of your work. $ git merge template # Import all the work into master. ``` - - **Adding this project to a fork of your project**: As you and your + - **Adding this template to a fork of your project**: As you and your colleagues continue your project, it will be necessary to have separate forks/clones of it. But when you clone your own project on a different system, or a colleague clones it to collaborate with you, @@ -176,8 +176,6 @@ done # # These are defined to help make this script more readable. topdir=$(pwd) -lbdir=.build -installedlink=.local optionaldir="/optional/path" adir=reproduce/analysis/config cdir=reproduce/software/config @@ -383,7 +381,7 @@ the source directory. The build directory also needs a relatively large amount of free space (atleast serveral Giga-bytes), while the source directory (all plain text) will usually be a mega-byte or less. -'$lbdir' (a symbolic link to the build directory) will also be created +'.build' (a symbolic link to the build directory) will also be created during this configuration. It can help encourage you to set the actual build directory in a very different address from this one (one that can be deleted and has large volume), while having easy access to it from here. @@ -623,48 +621,88 @@ fi -# Setup the top-level directories +# Project's top-level directories # ------------------------------- -rm -f $lbdir -ln -s $bdir $lbdir - +# +# These directories are possibly needed by many steps of process, so to +# avoid too many directory dependencies throughout the software and +# analysis Makefiles (thus making them hard to read), we are just building +# them here +# Top-level software sdir=$bdir/software if ! [ -d $sdir ]; then mkdir $sdir; fi +# Software tarballs tardir=$sdir/tarballs if ! [ -d $tardir ]; then mkdir $tardir; fi +# Installed software instdir=$sdir/installed if ! [ -d $instdir ]; then mkdir $instdir; fi +# Temporary software un-packing. tmpblddir=$sdir/build-tmp if ! [ -d $tmpblddir ]; then mkdir $tmpblddir; fi +# To record software versions and citation. verdir=$instdir/version-info if ! [ -d $verdir ]; then mkdir $verdir; fi +# Program and library versions and citation. ibidir=$verdir/proglib if ! [ -d $ibidir ]; then mkdir $ibidir; fi +# Python module versions and citation. ipydir=$verdir/python if ! [ -d $ipydir ]; then mkdir $ipydir; fi +# Used software BibTeX entries. ictdir=$verdir/cite if ! [ -d $ictdir ]; then mkdir $ictdir; fi +# TeXLive versions. itidir=$verdir/tex if ! [ -d $itidir ]; then mkdir $itidir; fi +# Top-level LaTeX. texdir=$bdir/tex -if ! [ -d $texdir ]; then mkdir $texdir; ln -s $texdir tex/build; fi +if ! [ -d $texdir ]; then mkdir $texdir; fi +# LaTeX macros. mtexdir=$texdir/macros if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi -rm -f $installedlink -ln -s $instdir $installedlink + +# TeX build directory. If built in a group scenario, the TeX build +# directory must be separate for each member (so they can work on their +# relevant parts of the paper without conflicting with each other). +if [ "x$reproducible_paper_group_name" = x ]; then + texbdir=$texdir/build +else + user = $(whoami) + texbdir = $texdir/build-$user +fi +if ! [ -d $texbdir ]; then mkdir $texbdir; fi + +# TiKZ (for building figures within LaTeX). +tikzdir=$texbdir/tikz +if ! [ -d $tikzdir ]; then mkdir $tikzdir; 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 +# users and thus may already exist). +# +# 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. +rm -f .build .local tex/build tex/tikz .gnuastro +ln -s $bdir .build +ln -s $instdir .local +ln -s $texdir tex/build +ln -s $tikzdir tex/tikz # --------- Delete for no Gnuastro --------- -rm -f .gnuastro ln -s $topdir/reproduce/software/config/gnuastro .gnuastro # ------------------------------------------ @@ -95,8 +95,8 @@ are actually macros that were calculated from the same dataset (they will change if the dataset, or function that produced it, changes). The individual {\small PDF} file of Figure \ref{delete-me} is available -under the \texttt{tex/build/tikz/} directory of your build directory. You -can use this PDF file in other contexts (for example in slides showing your +under the \texttt{tex/tikz/} directory of your build directory. You can use +this PDF file in other contexts (for example in slides showing your progress or after publishing the work). If you want to directly use the {\small PDF} file in the figure without having to let {\small T}i{\small KZ} decide if it should be remade or not, you can also comment the diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 5f8a062..fe7b5ea 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -151,8 +151,6 @@ export MPI_PYTHON3_SITEARCH := # are looking for in the outputs. .SUFFIXES: $(lockdir): | $(BDIR); mkdir $@ -$(texbdir): | $(texdir); mkdir $@ -$(tikzdir): | $(texbdir); mkdir $@ && ln -fs $@ tex/tikz diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index c1d5b33..34d88a4 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -91,7 +91,7 @@ $(mtexdir)/project.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s) # been modified, we don't want to re-build the bibliography, only the final # PDF. $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ - | $(tikzdir) $(texbdir) $(mtexdir)/project.tex + | $(mtexdir)/project.tex # If `$(mtexdir)/project.tex' is empty, don't build PDF. @macros=$$(cat $(mtexdir)/project.tex) if [ x"$$macros" != x ]; then @@ -118,8 +118,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ # to run everything cleanly from there, it is necessary to add the current # directory (top project directory) to the `TEXINPUTS' environment # variable. -paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl \ - | $(tikzdir) $(texbdir) +paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # If `$(mtexdir)/project.tex' is empty, don't build the PDF. @macros=$$(cat $(mtexdir)/project.tex) |