aboutsummaryrefslogtreecommitdiff
path: root/reproduce/analysis/make/initialize.mk
blob: 79f92665eb0620e7684f5947a6d5e1c644b27065 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
# Project initialization.
#
# Copyright (C) 2018-2020 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
lockdir     = $(BDIR)/locks
indir       = $(BDIR)/inputs
prepdir     = $(BDIR)/prepare
mtexdir     = $(texdir)/macros
bashdir     = reproduce/analysis/bash
pconfdir    = reproduce/analysis/config
installdir  = $(BDIR)/software/installed
# --------- Delete for no Gnuastro ---------
gconfdir    = reproduce/software/config/gnuastro
# ------------------------------------------





# Preparation phase
# -----------------
#
# This Makefile is loaded both for the `prepare' phase and the `make'
# phase. But the preparation files should be dealt with differently
# (depending on the phase). In the `prepare' phase, the main directory
# should be created, and in the `make' phase, its contents should be
# loaded.
#
# If you don't need any preparation, please simply comment these lines.
ifeq (x$(project-phase),xprepare)
$(prepdir):; mkdir $@
else
include $(BDIR)/software/preparation-done.mk
ifeq (x$(include-prepare-results),xyes)
include $(prepdir)/*.mk
endif
endif





# 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)
texbtopdir  = build
final-paper = paper.pdf
else
user        = $(shell whoami)
texbtopdir  = build-$(user)
final-paper = paper-$(user).pdf
endif
texbdir     = $(texdir)/$(texbtopdir)
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).
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 `./project 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.
#
# `TEXINPUTS': we have to remove all possible user-specified directories to
# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'),
# we are also going to overwrite `TEXINPUTS' just before `pdflatex'.
.ONESHELL:
.SHELLFLAGS = -ec
export TEXINPUTS :=
export CCACHE_DISABLE := 1
export PATH := $(installdir)/bin
export LDFLAGS := -L$(installdir)/lib
export SHELL := $(installdir)/bin/bash
export CPPFLAGS := -I$(installdir)/include
export LD_LIBRARY_PATH := $(installdir)/lib

# Until we build our own C library, without this, the project's GCC won't
# be able to compile anything if the host C library isn't in a standard
# place: in particular Debian-based operatings sytems. On other systems, it
# will be empty.
export CPATH := $(SYS_CPATH)

# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
# ultimately redundant. But on some systems, even having a single value
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=

# OpenMPI can depend on an existing `ssh' or `rsh' binary. However, because
# of security reasons, its best to not install them, disable any
# remote-shell accesss through this environment variable.
export OMPI_MCA_plm_rsh_agent=/bin/false

# Recipe startup script.
export PROJECT_STATUS := make
export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh



# 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 $@





# 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 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

# --------- 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)/tex/macros/!(dependencies.tex|dependencies-bib.tex)
	rm -rf $(BDIR)/!(software|tex) $(BDIR)/tex/!(macros|$(texbtopdir))
	rm -rf $(BDIR)/tex/build/!(tikz) $(BDIR)/tex/build/tikz/*

distclean: clean
        #  Without cleaning the Git hooks, we won't be able to easily
        #  commit or checkout after this task is done. So we'll remove them
        #  first.
	rm .git/hooks/post-checkout .git/hooks/pre-commit

        # 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.
	$$sys_rm -rf $(BDIR)
	$$sys_rm -f Makefile .gnuastro .local .build
	$$sys_rm -f $(pconfdir)/LOCAL.conf $(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): paper.pdf | $(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 (see next step for `paper.tex').
	cp COPYING project README.md README-hacking.md $$dir/

        # 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. This will disable usage of TiKZ.
	sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
	    paper.tex > $$dir/paper.tex

        # Build the top-level directories.
	mkdir $$dir/reproduce $$dir/tex $$dir/tex/tikz $$dir/tex/build

        # Copy all the necessary `reproduce' and `tex' contents.
	shopt -s extglob
	cp -r tex/src                            $$dir/tex/src
	cp tex/tikz/*.pdf                        $$dir/tex/tikz
	cp -r reproduce/*                        $$dir/reproduce
	cp -r tex/build/!(paper-v*)              $$dir/tex/build

        # 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.conf' and `gnuastro-local.conf' files just
        # have this machine's local settings and are irrelevant for anyone
        # else.
	rm -rf $$dir/tex/build/build*
	rm $$dir/reproduce/software/config/installation/LOCAL.conf
	rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf

        # When submitting to places like arXiv, they will just run LaTeX
        # once and won't run `biber'. So we need to also keep the `.bbl'
        # file into the distributing tarball. However, BibLaTeX is
        # particularly sensitive to versioning (a `.bbl' file has to be
        # read by the same BibLaTeX version that created it). This is hard
        # to do with non-up-to-date places like arXiv. Therefore, we thus
        # just copy the whole of BibLaTeX's source (the version we are
        # using) into the top tarball directory. In this way, arXiv's LaTeX
        # engine will use the same BibLaTeX version to interpret the `.bbl'
        # file. TIP: you can use the same strategy for other LaTeX packages
        # that may cause problems on the arXiv server.
	cp tex/build/build/paper.bbl $$dir/
	tltopdir=.local/texlive/2019/texmf-dist/tex/latex
	find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \
	     | xargs -0 cp -t $$dir

        # Just in case the package users want to rebuild some of the
        # figures (manually un-comment 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
	find $(packagebasename) -name \*.swp -delete

        # PROJECT SPECIFIC
        # ----------------
        # Put any project specific distribution steps here.
        # ----------------

# Package into `.tar.gz'.
dist: $(packagecontents)
	curdir=$$(pwd)
	cd $(texdir)
	tar -cf $(packagebasename).tar $(packagebasename)
	gzip -f --best $(packagebasename).tar
	rm -rf $(packagebasename)
	cd $$curdir
	mv $(texdir)/$(packagebasename).tar.gz ./

# Package into `.zip'.
dist-zip: $(packagecontents)
	curdir=$$(pwd)
	cd $(texdir)
	zip -q -r $(packagebasename).zip $(packagebasename)
	rm -rf $(packagebasename)
	cd $$curdir
	mv $(texdir)/$(packagebasename).zip ./





# 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.
	@if [ -d .git ]; then v=$$(git describe --dirty --always --long);
	else                  v=NO-GIT; fi
	echo "\newcommand{\projectversion}{$$v}" > $@