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-rw-r--r--reproduce/analysis/make/delete-me.mk2
-rw-r--r--reproduce/analysis/make/initialize.mk150
-rw-r--r--reproduce/analysis/make/paper.mk49
-rw-r--r--reproduce/analysis/make/prepare.mk4
-rw-r--r--reproduce/analysis/make/top-make.mk8
-rw-r--r--reproduce/analysis/make/top-prepare.mk10
-rw-r--r--reproduce/analysis/make/verify.mk2
7 files changed, 164 insertions, 61 deletions
diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk
index f4c8600..a20abc6 100644
--- a/reproduce/analysis/make/delete-me.mk
+++ b/reproduce/analysis/make/delete-me.mk
@@ -1,6 +1,6 @@
# Dummy Makefile to create a random dataset for plotting.
#
-# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index eb5f2ff..1f2158a 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
# Project initialization.
#
-# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -41,7 +41,7 @@ bsdir=$(BDIR)/software
# Derived directories (the locks directory can be shared with software
# which already has this directory.).
texdir = $(badir)/tex
-lockdir = $(bsdir)/locks
+lockdir = $(badir)/.locks
indir = $(badir)/inputs
prepdir = $(badir)/prepare
mtexdir = $(texdir)/macros
@@ -63,15 +63,18 @@ pconfdir = reproduce/analysis/config
# loaded.
#
# If your project doesn't need any preparation, you can ignore this.
+#
+# The '-' behind the include commands is used for adding the files only if
+# it is possible (they exist). This is necessary because sometimes the user
+# will have only '*.conf' or '*.mk' files, or with 'make clean' (where the
+# preparation Makefile may call initialize.mk before the main
+# 'top-make.mk'). If the '-' is not used, Make will complain about not
+# finding these files.
ifeq (x$(project-phase),xprepare)
$(prepdir):; mkdir $@
else
-include $(bsdir)/preparation-done.mk
+-include $(badir)/preparation-done.mk
ifeq (x$(include-prepare-results),xyes)
-# The '-' behind the include is The '-' is used for adding the files only
-# if it is possible (they exist). This is necessary because sometimes the
-# user will have only '*.conf' or '*.mk' files. So, if the '-' is not used,
-# Make will complain about not finding these files.
-include $(prepdir)/*.mk $(prepdir)/*.conf
endif
endif
@@ -227,7 +230,7 @@ project-commit-hash := $(shell \
export LD_LIBRARY_PATH="$(installdir)/lib"; \
echo $$($(installdir)/bin/git describe --dirty --always --long); \
else echo NOGIT; fi)
-project-package-name := maneaged-$(project-commit-hash)
+project-package-name = maneaged-$(project-commit-hash)
project-package-contents = $(texdir)/$(project-package-name)
@@ -262,16 +265,8 @@ clean:
# executing 'build'.
rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf
-# Delete all the built outputs except the dependency programs. We'll
-# use Bash's extended options builtin ('shopt') to enable "extended
-# glob" (for listing of files). It allows extended features like
-# ignoring the listing of a file with '!()' that we are using
-# afterwards.
- shopt -s extglob
- rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
- rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir))
- rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/*
- rm -rf $(bsdir)/preparation-done.mk
+# Delete the full 'badir' (containing all analysis outputs).
+ rm -rf $(badir)
distclean: clean
# Without cleaning the Git hooks, we won't be able to easily commit
@@ -282,7 +277,7 @@ distclean: clean
# 'rm' program. So for this recipe, we'll use the host system's 'rm',
# not our own.
$$sys_rm -rf $(BDIR)
- $$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
+ $$sys_rm -f .local .build
@@ -438,13 +433,15 @@ dist-software:
-# Download input data
-# --------------------
+# Import input data
+# -----------------
#
-# 'reproduce/analysis/config/INPUTS.conf' contains the input dataset
-# properties. In most cases, you will not need to edit this rule. Simply
-# follow the instructions of 'INPUTS.conf' and set the variables names
-# according to the described standards and everything should be fine.
+# The list files to be imported (downloaded from a server, or linked from a
+# local location), are listed in 'reproduce/analysis/config/INPUTS.conf'
+# along with their URLs and verification checksums. In most cases, you will
+# not need to edit this rule. Simply follow the instructions at the top of
+# 'INPUTS.conf' and set the variables names according to the described
+# standards and everything should be fine.
#
# TECHNICAL NOTE on the '$(foreach, n ...)' loop of 'inputdatasets': we are
# using several (relatively complex!) features particular to Make: In GNU
@@ -464,17 +461,64 @@ dist-software:
# process with a file and make sure that only one downloading event is in
# progress at every moment.
$(indir):; mkdir $@
-downloadwrapper = $(bashdir)/download-multi-try
-inputdatasets = $(foreach i, \
- $(patsubst INPUT-%-sha256,%, \
- $(filter INPUT-%-sha256,$(.VARIABLES))), \
- $(indir)/$(i))
+downloadwrapper = $(bashdir)/download-multi-try.sh
+inputdatasets := $(foreach i, \
+ $(patsubst INPUT-%-sha256,%, \
+ $(filter INPUT-%-sha256,$(.VARIABLES))) \
+ $(patsubst INPUT-%-fitsdatasum,%, \
+ $(filter INPUT-%-fitsdatasum,$(.VARIABLES))), \
+ $(indir)/$(i))
$(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
-# Set the necessary parameters for this input file as shell variables
-# (to help in readability).
- url=$(INPUT-$*-url)
- sha=$(INPUT-$*-sha256)
+# Starting rule with '@': In case there is a username or password
+# given for the database, we don't want the values to be printed in
+# the terminal as the pipeline is running. We are therefore starting
+# this recipe with an '@' (so Make doesn't print the used
+# commands). To help the user know what is happening (in case they
+# can't tell from the Wget outputs), we'll just start the recipe with
+# a notice on what is being imported.
+ @echo "Importing $@"
+
+# If a username or password has been provided, add them to the WGET
+# command. The two variables are defined in the local configuation
+# file 'reproduce/software/config/LOCAL.conf' that is not under
+# version control. Different servers may use different authentication
+# formats. If the default one doesn't work for your server, comment
+# it and uncomment the one that works. If your serve needs a
+# different kind of authentication format, please add it yourself. In
+# case you need a new format, we encourage you to send the format to
+# us using the link below:
+# https://savannah.nongnu.org/support/?group=reproduce&func=additem
+ authopt=""
+ if [ x"$(DATABASEAUTHTYPE)" != x ]; then
+ case "$(DATABASEAUTHTYPE)" in
+
+# Format: '--user=XXXX --password=YYYY'
+ userpass)
+ if [ x'$(DATABASEUSER)' != x ]; then
+ authopt="--user='$(DATABASEUSER)'"; fi
+ if [ x'$(DATABASEPASS)' != x ]; then
+ authopt="$$authopt --password='$(DATABASEPASS)'"; fi
+ ;;
+
+# Format: --post-data 'username=XXXX&password=YYYY'
+ postdata)
+ if [ x'$(DATABASEUSER)' != x ]; then
+ authopt="--post-data 'username=$(DATABASEUSER)"; fi
+ if [ x'$(DATABASEPASS)' != x ]; then
+ authopt="$$authopt""&password=$(DATABASEPASS)'";
+ else authopt="$$authopt'" # To close the single quote
+ fi
+ ;;
+
+# Unrecognized format.
+ *)
+ printf "Maneage: 'DATABASEAUTHTYPE' format not recognized! "
+ printf "Please see the description of this variable in "
+ printf "'$(bsdir)/config/LOCAL.conf' for the acceptable "
+ printf "values."; exit 1;;
+ esac
+ fi
# Download (or make the link to) the input dataset. If the file
# exists in 'INDIR', it may be a symbolic link to some other place in
@@ -488,13 +532,29 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
ln -fs $$(readlink -f $(INDIR)/$*) $$unchecked
else
touch $(lockdir)/download
- $(downloadwrapper) "wget --no-use-server-timestamps -O" \
- $(lockdir)/download $$url $$unchecked
+ $(downloadwrapper) "wget $$authopt --no-use-server-timestamps -O" \
+ $(lockdir)/download "$(INPUT-$*-url)" $$unchecked
+ fi
+
+# Set the checksum related variables.
+ if [ x"$(INPUT-$*-sha256)" != x ]; then
+ suffix=sha256
+ sumin=$(INPUT-$*-sha256)
+ verifname="SHA256 checksum"
+ sum=$$(sha256sum $$unchecked | awk '{print $$1}')
+ elif [ x"$(INPUT-$*-fitsdatasum)" != x ]; then
+ suffix=fitsdatasum
+ sumin=$(INPUT-$*-fitsdatasum)
+ verifname="FITS standard DATASUM"
+ if [ x"$(INPUT-$*-fitshdu)" = x ]; then hdu=1;
+ else hdu="$(INPUT-$*-fitshdu)"; fi
+ sum=$$(astfits $$unchecked -h$$hdu --datasum | awk '{print $$1}')
+ else
+ echo "$@: checksum for verifyication not recognized!"; exit 1
fi
-# Check the checksum to see if this is the proper dataset.
- sum=$$(sha256sum $$unchecked | awk '{print $$1}')
- if [ $$sum = $$sha ]; then
+# Verify the input.
+ if [ $$sum = $$sumin ]; then
mv $$unchecked $@
echo "Integrity confirmed, using $@ in this project."
@@ -502,11 +562,11 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
else
# The user has asked to update the checksum in 'INPUTS.conf'.
- if [ $$sha = "--auto-replace--" ]; then
+ if [ $$sumin = "--auto-replace--" ]; then
# Put the updated 'INPUTS.conf' in a temporary file.
inputstmp=$@.inputs
- awk '{if($$1 == "INPUT-$*-sha256") \
+ awk '{if($$1 == "INPUT-$*-'$$suffix'") \
$$3="'$$sum'"; print}' \
$(pconfdir)/INPUTS.conf > $$inputstmp
@@ -520,10 +580,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
# Error on non-matching checksums.
else
echo; echo;
- echo "Wrong SHA256 checksum for input file '$*':"
+ echo "Wrong $$verifname for input file '$*':"
echo " File location: $$unchecked"; \
- echo " Expected SHA256 checksum: $$sha"; \
- echo " Calculated SHA256 checksum: $$sum"; \
+ echo " Expected $$verifname: $$sumin"; \
+ echo " Calculated $$verifname: $$sum"; \
echo; exit 1
fi
fi
@@ -607,7 +667,7 @@ print-general-metadata = \
# 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: | $(mtexdir)
+$(mtexdir)/initialize.tex:
# Version and title of project. About the starting '@': since these
# commands are run every time with './project make', it is annoying
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 740dc7d..b1b794c 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -1,6 +1,6 @@
# Build the final PDF paper/report.
#
-# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -18,6 +18,7 @@
+
# LaTeX macros for paper
# ----------------------
#
@@ -92,6 +93,38 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
+# TeX build directory
+# -------------------
+#
+# If built in a group scenario, the TeX build directory must be separate
+# for each member (so they can work on their relevant parts of the paper
+# without conflicting with each other).
+ifeq ($(strip $(maneage_group_name)),)
+texbdir:=$(texdir)/build
+else
+texbdir:=$(texdir)/build-$(shell whoami)
+endif
+tikzdir:=$(texbdir)/tikz
+
+
+
+
+
+# Software info in TeX
+# --------------------
+#
+# The information of the installed software is placed in the
+# '.build/software' directory (which the TeX build should not depend
+# on). Therefore, we should copy those macros here in the LaTeX build
+# directory, so the TeX directory is completely independent from each
+# other.
+$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex
+ cp $(bsdir)/config/*.tex $(mtexdir)/
+
+
+
+
+
# The bibliography
# ----------------
#
@@ -104,8 +137,9 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
# recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
# been modified, we don't want to re-build the bibliography, only the final
# PDF.
-$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
+$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \
| $(mtexdir)/project.tex
+
# If '$(mtexdir)/project.tex' is empty, don't build PDF.
@macros=$$(cat $(mtexdir)/project.tex)
if [ x"$$macros" != x ]; then
@@ -128,9 +162,13 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# use PGFPlots, then you should remove the '-shell-escape' option
# for better security. See https://savannah.nongnu.org/task/?15694
# for details.
+#
+# We need the modification to 'LD_LIBRARY_PATH' because we do not
+# build LaTeX from source and it uses '/bin/sh' (among other
+# possible system-wide things).
+ export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
biber paper
-
fi
@@ -158,6 +196,11 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
# See above for a warning and brief discussion on the the pdflatex
# option '-shell-escape'.
+#
+# We need the modification to 'LD_LIBRARY_PATH' because we do not
+# build LaTeX from source and it uses '/bin/sh' (among other
+# possible system-wide things).
+ export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
# Come back to the top project directory and copy the built PDF
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index ebc2b4d..ffb2a3c 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -1,6 +1,6 @@
# Basic preparations, called by './project make'.
#
-# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
@@ -25,7 +25,7 @@
#
# We need to remove the 'prepare' word from the list of 'makesrc'.
prepare-dep = $(filter-out prepare, $(makesrc))
-$(bsdir)/preparation-done.mk: \
+$(badir)/preparation-done.mk: \
$(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
# If you need to add preparations (mainly automatically generated
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index d6e3822..e87aed8 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -1,6 +1,6 @@
# Top-level Makefile (first to be loaded).
#
-# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -19,9 +19,9 @@
-# Load the local configuration (created after running
-# './project configure').
-include reproduce/software/config/LOCAL.conf
+# Load the local configuration (created after running './project
+# configure').
+include .build/software/config/LOCAL.conf
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index 28dfc4a..d2d1c14 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -4,7 +4,7 @@
# are not included here. Please see that file for thorough comments on each
# step.
#
-# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
@@ -23,9 +23,9 @@
-# Load the local configuration (created after running
-# './project configure').
-include reproduce/software/config/LOCAL.conf
+# Load the local configuration (created after running './project
+# configure').
+include .build/software/config/LOCAL.conf
@@ -36,7 +36,7 @@ include reproduce/software/config/LOCAL.conf
#
# See 'top-make.mk' for complete explanation.
ifeq (x$(maneage_group_name),x$(GROUP-NAME))
-all: $(BDIR)/software/preparation-done.mk
+all: $(BDIR)/analysis/preparation-done.mk
@echo "Project preparation is complete.";
else
all:
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index 25b3bec..c74f8ca 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -1,6 +1,6 @@
# Verify the project outputs before building the paper.
#
-# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2025 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
generated by cgit v1.2.1 (git 2.18.0) at 2025-07-06 09:39:09 +0000