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Diffstat (limited to 'reproduce/src/make/initialize.mk')
| -rw-r--r-- | reproduce/src/make/initialize.mk | 341 |
1 files changed, 0 insertions, 341 deletions
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk deleted file mode 100644 index cd533f2..0000000 --- a/reproduce/src/make/initialize.mk +++ /dev/null @@ -1,341 +0,0 @@ -# Project initialization. -# -# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# -# This Makefile is free software: you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This Makefile is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -# Public License for more details. -# -# A copy of the GNU General Public License is available at -# <http://www.gnu.org/licenses/>. - - - - - -# High-level directory definitions -# -------------------------------- -# -# Basic directories that are used throughout the project. -# -# Locks are used to make sure that an operation is done in series not in -# parallel (even if Make is run in parallel with the `-j' option). The most -# common case is downloads which are better done in series and not in -# 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 -srcdir = reproduce/src -lockdir = $(BDIR)/locks -indir = $(BDIR)/inputs -mtexdir = $(texdir)/macros -pconfdir = reproduce/config/pipeline -installdir = $(BDIR)/dependencies/installed -# --------- Delete for no Gnuastro --------- -gconfdir = reproduce/config/gnuastro -# ------------------------------------------ - - - - - -# TeX build directory -# ------------------ -# -# In scenarios where multiple users are working on the project -# simultaneously, they can't all build the final paper together, there will -# be conflicts! It is possible to manage the working on the analysis, so no -# conflict is caused in that phase, but it would be very slow to only let -# one of the project members to build the paper at every instance -# (independent parts of the paper can be added to it independently). To fix -# this problem, when we are in a group setting, we'll use the user's ID to -# create a separate LaTeX build directory for each user. -# -# The same logic applies to the final paper PDF: each user will create a -# separte final PDF (for example `paper-user1.pdf' and `paper-user2.pdf') -# and no `paper.pdf' will be built. This isn't a problem because -# `initialize.tex' is a .PHONY prerequisite, so the rule to build the final -# paper is always executed (even if it is present and nothing has -# changed). So in terms of over-all efficiency and processing steps, this -# doesn't change anything. -ifeq (x$(GROUP-NAME),x) -texbdir = $(texdir)/build -final-paper = paper.pdf -else -user = $(shell whoami) -texbdir = $(texdir)/build-$(user) -final-paper = paper-$(user).pdf -endif -tikzdir = $(texbdir)/tikz - - - - - -# Original system environment -# --------------------------- -# -# Before defining the local sub-environment here, we'll need to save the -# system's environment for some scenarios (for example after `clean'ing the -# built programs). -sys-path := $(PATH) -sys-rm := $(shell which rm) -curdir := $(shell echo $$(pwd)) - - - - - -# High level environment -# ---------------------- -# -# We want the full recipe to be executed in one call to the shell. Also we -# want Make to run the specific version of Bash that we have installed -# during `./configure' time. -# -# Regarding the directories, this project builds its major dependencies -# itself and doesn't use the local system's default tools. With these -# environment variables, we are setting it to prefer the software we have -# build here. -.ONESHELL: -.SHELLFLAGS = -ec -export CCACHE_DISABLE := 1 -export PATH := $(installdir)/bin -export LD_LIBRARY_PATH := $(installdir)/lib -export LDFLAGS := -L$(installdir)/lib -export SHELL := $(installdir)/bin/bash -export CPPFLAGS := -I$(installdir)/include - - - - - -# Python enviroment -# ----------------- -# -# The main Python environment variable is `PYTHONPATH'. However, so far we -# have found several other Python-related environment variables on some -# systems which might interfere. To be safe, we are removing all their -# values. -export PYTHONPATH := $(installdir)/lib/python/site-packages -export PYTHONPATH3 := $(PYTHONPATH) -export _LMFILES_ := -export PYTHONPATH2 := -export LOADEDMODULES := -export MPI_PYTHON_SITEARCH := -export MPI_PYTHON2_SITEARCH := -export MPI_PYTHON3_SITEARCH := - - - - - -# High-level level directories -# ---------------------------- -# -# These are just the top-level directories for all the separate steps. The -# directories (or possible sub-directories) for individual steps will be -# defined and added within their own Makefiles. -# -# The `.SUFFIXES' rule with no prerequisite is defined to eliminate all the -# default implicit rules. The default implicit rules are to do with -# programming (for example converting `.c' files to `.o' files). The -# problem they cause is when you want to debug the make command with `-d' -# 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 $@ -$(texbdir): | $(texdir); mkdir $@ -$(tikzdir): | $(texbdir); mkdir $@ && ln -fs $@ tex/tikz - - - - - -# High-level Makefile management -# ------------------------------ -# -# About `.PHONY': these are targets that must be built even if a file with -# their name exists. -# -# Only `$(mtexdir)/initialize.tex' corresponds to a file. This is because -# 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)) -packagecontents = $(texdir)/$(packagebasename) -.PHONY: all clean dist dist-zip distclean clean-mmap $(packagecontents) \ - $(mtexdir)/initialize.tex - -# --------- Delete for no Gnuastro --------- -clean-mmap:; rm -f reproduce/config/gnuastro/mmap* -# ------------------------------------------ - -clean: clean-mmap - # Delete the top-level PDF file. - rm -f *.pdf - - # Delete all the built outputs except the dependency - # programs. We'll use Bash's extended options builtin (`shopt') to - # enable "extended glob" (for listing of files). It allows extended - # features like ignoring the listing of a file with `!()' that we - # are using afterwards. - shopt -s extglob - rm -rf $(BDIR)/!(dependencies) - -distclean: clean - # We'll be deleting the built environent programs and just need the - # `rm' program. So for this recipe, we'll use the host system's - # `rm', not our own. - $(sys-rm) -rf $(BDIR) reproduce/build - $(sys-rm) -f Makefile .gnuastro .local - $(sys-rm) -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf - - - - - -# Packaging rules -# --------------- -# -# With the rules in this section, you can package the project in a state -# that is ready for building the final PDF with LaTeX. This is useful for -# collaborators who only want to contribute to the text of your project, -# without having to worry about the technicalities of the analysis. -$(packagecontents): | $(texdir) - - # Set up the output directory, delete it if it exists and remake it - # to fill with new contents. - dir=$(texdir)/$(packagebasename) - rm -rf $$dir - mkdir $$dir - - # Build a small Makefile to help in automatizing the paper building - # (including the bibliography). - m=$$dir/Makefile - echo "paper.pdf: paper.tex paper.bbl" > $$m - printf "\tpdflatex -shell-escape -halt-on-error paper\n" >> $$m - echo "paper.bbl: tex/src/references.tex" >> $$m - printf "\tpdflatex -shell-escape -halt-on-error paper\n" >> $$m - printf "\tbiber paper\n" >> $$m - echo ".PHONY: clean" >> $$m - echo "clean:" >> $$m - printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n" >> $$m - printf "\trm -f *.blg *.log *.out *.run.xml\n" >> $$m - - # Copy the top-level contents into it. - cp configure COPYING for-group README.md README-hacking.md $$dir/ - - # Build the top-level directories. - mkdir $$dir/reproduce $$dir/tex $$dir/tex/tikz $$dir/tex/pipeline - - # Copy all the `reproduce' contents except for the `build' symbolic - # link. - shopt -s extglob - cp -r tex/src $$dir/tex/src - cp tex/tikz/*.pdf $$dir/tex/tikz - cp -r reproduce/!(build) $$dir/reproduce - cp -r tex/pipeline/!($(packagebasename)) $$dir/tex/pipeline - cp -r tex/dependencies $$dir/tex/dependencies - - # Clean up un-necessary/local files: 1) the $(texdir)/build* - # directories (when building in a group structure, there will be - # `build-user1', `build-user2' and etc), are just temporary LaTeX - # build files and don't have any relevant/hand-written files in - # them. 2) The `LOCAL.mk' and `gnuastro-local.conf' files just have - # this machine's local settings and are irrelevant for anyone else. - rm -rf $$dir/tex/pipeline/build* - rm $$dir/reproduce/config/pipeline/LOCAL.mk - rm $$dir/reproduce/config/gnuastro/gnuastro-local.conf - - # PROJECT SPECIFIC: under this comment, copy any other file for - # packaging, or remove any of the copied files above to suite your - # project. - - # Since the packaging is mainly intended for high-level building of - # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in - # the paper. - sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \ - paper.tex > $$dir/paper.tex - - # Just in case the package users want to rebuild some of the - # figures (manually un-comments the `makepdf' command we commented - # above), correct the TikZ external directory, so the figures can - # be rebuilt. - pgfsettings="$$dir/tex/src/preamble-pgfplots.tex" - sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new - mv $$pgfsettings.new $$pgfsettings - - # Clean temporary (currently those ending in `~') files. - cd $(texdir) - find $(packagebasename) -name \*~ -delete - -# Package into `.tar.gz'. -dist: $(packagecontents) - curdir=$$(pwd) - cd $(texdir) - tar -cf $(packagebasename).tar $(packagebasename) - gzip -f --best $(packagebasename).tar - cd $$curdir - mv $(texdir)/$(packagebasename).tar.gz ./ - -# Package into `.zip'. -dist-zip: $(packagecontents) - curdir=$$(pwd) - cd $(texdir) - zip -q -r $(packagebasename).zip $(packagebasename) - cd $$curdir - mv $(texdir)/$(packagebasename).zip ./ - - - - - -# Check the version of programs which write their version -# ------------------------------------------------------- -pvcheck = prog="$(strip $(1))"; \ - ver="$(strip $(2))"; \ - name="$(strip $(3))"; \ - macro="$(strip $(4))"; \ - verop="$(strip $(5))"; \ - if [ "x$$verop" = x ]; then V="--version"; else V=$$verop; fi; \ - v=$$($$prog $$V | awk '/'$$ver'/{print "y"; exit 0}'); \ - if [ x$$v != xy ]; then \ - echo; echo "PROJECT ERROR: Not running $$name $$ver"; echo; \ - exit 1; \ - fi; \ - echo "\newcommand{\\$$macro}{$$ver}" >> $@ - -lvcheck = idir=$(BDIR)/dependencies/installed/include; \ - f="$$idir/$(strip $(1))"; \ - ver="$(strip $(2))"; \ - name="$(strip $(3))"; \ - macro="$(strip $(4))"; \ - v=$$(awk '/^\#/&&/define/&&/'$$ver'/{print "y";exit 0}' $$f); \ - if [ x$$v != xy ]; then \ - echo; echo "PROJECT ERROR: Not linking with $$name $$ver"; \ - echo; exit 1; \ - fi; \ - echo "\newcommand{\\$$macro}{$$ver}" >> $@ - - - - -# Project initialization results -# ------------------------------ -# -# This file will store some basic info about the project that is necessary -# for the final PDF. Since these are not version controlled, it must be -# calculated everytime the project is run. So even though this file -# actually exists, it is also aded as a `.PHONY' target above. -$(mtexdir)/initialize.tex: | $(mtexdir) - - # Version of the project. - @v=$$(git describe --dirty --always); - echo "\newcommand{\pipelineversion}{$$v}" > $@ |