Imported recent work in Maneage, minor conflicts fixed

Some minor conflicts (all expected from the commit messages in the Maneage
branch) occurred but were easily fixed.

4 files changed, 42 insertions, 20 deletions

diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf
index 470e429..b1f657b 100644
--- a/reproduce/analysis/config/metadata.conf
+++ b/reproduce/analysis/config/metadata.conf
@@ -1,6 +1,19 @@
-# Project meta-data that can be used in a project's output datasets and
+# Project meta-data that will be used in a project's output datasets and
 # final paper. Please set the values here and use them in your analysis or
-# paper, don't repeat them
+# paper, don't repeat them.
+#
+# These variables are used in 'reproduce/analysis/make/initialize.mk': 1)
+# to create a Make variable called 'print-general-metadata'. You can simply
+# print this variable's value in any plain-text output.
+#
+# Why add a Copyright for the data? people need to know if they can "use"
+# the dataset (i.e., modify it), or possibly re-distribute it and their
+# derived products. They also need to know how they can contact the creator
+# of the datset (who is usually also the copyright owner). So take this
+# seriously and add your name and email-address (or the name of the person
+# and email of the person who was in charge of that part of the project),
+# and the copyright license name and standard link to the fully copyright
+# license.
 #
 # Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
@@ -12,7 +25,9 @@
 # Project information
 metadata-title = Towards Long-term and Archivable Reproducibility
 
-# DOIs and identifiers.
+# DOIs and identifiers (don't include fixed URL prefixes like
+# 'https://doi.org/' or 'https://arxiv.org/abs'), they will be added
+# automatically where necessary.
 metadata-arxiv          = 2006.03018
 metadata-doi-zenodo     = 10.5281/zenodo.4291207
 metadata-doi-journal    = 10.1109/MCSE.2021.3072860
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 8af3199..bc73df8 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -224,7 +224,7 @@ project-package-contents = $(texdir)/$(project-package-name)
         $(project-package-contents) $(mtexdir)/initialize.tex
 
 texclean:
-	rm *.pdf
+	rm -f *.pdf
 	rm -rf $(texdir)/build/*
 	mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
 
@@ -253,8 +253,7 @@ 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 $(pconfdir)/LOCAL.conf
-	$$sys_rm -f Makefile .gnuastro .local .build
+	$$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
 
 
 
@@ -367,18 +366,18 @@ $(project-package-contents): paper.pdf | $(texdir)
 	sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
 	mv $$pgfsettings.new $$pgfsettings
 
-        # Clean temporary (currently those ending in `~') files.
-	cd $(texdir)
-	find $(project-package-name) -name \*~ -delete
-	find $(project-package-name) -name \*.swp -delete
-
         # PROJECT SPECIFIC
         # ----------------
-        # Put any project specific distribution steps here.
+        # Put any project-specific distribution steps here.
 	cd $$curdir
 	cp tex/build/build/appendix.bbl $$dir/
         # ----------------
 
+        # Clean temporary files that may have been created by text editors.
+	cd $(texdir)
+	find $(project-package-name) -name \*~ -delete
+	find $(project-package-name) -name \*.swp -delete
+
 # Package into `.tar.gz' or '.tar.lz'.
 dist dist-lzip: $(project-package-contents)
 	curdir=$$(pwd)
@@ -460,15 +459,21 @@ $(data-publish-dir):; mkdir $@
 # Print Copyright statement
 # -------------------------
 #
-# This statement can be used in published datasets that are in plain-text
-# format. It assumes you have already put the data-specific statements in
-# its first argument, it will supplement them with general project links.
-doi-prefix-url = https://doi.org
+# The 'print-general-metadata' can be used to print the general metadata in
+# published datasets that are in plain-text format. It should be called
+# with make's 'call' function like this (where 'FILENAME' is the name of
+# the file it will append this content to):
+#
+#    $(call print-general-metadata, FILENAME)
+#
+# See 'reproduce/analysis/make/delete-me.mk' (in the Maneage branch) for a
+# real-world usage of this variable.
+doi-prefix-url   = https://doi.org
 arxiv-prefix-url = https://arxiv.org/abs
 print-general-metadata = \
 	echo "\# Project title: $(metadata-title)" >> $(1); \
 	echo "\# Git commit (that produced this dataset): $(project-commit-hash)" >> $(1); \
-	echo "\# Project's Git repository: $(metadata-git-repository)" >> $(1); \
+	echo "\# Git repository: $(metadata-git-repository)" >> $(1); \
 	if [ x$(metadata-arxiv) != x ]; then \
 	  echo "\# Pre-print: $(arxiv-prefix-url)/abs/$(metadata-arxiv)" >> $(1); fi; \
 	if [ x$(metadata-doi-journal) != x ]; then \
@@ -501,6 +506,8 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\projectdate}{$$d}" > $@
 	echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
 	echo "\newcommand{\projectversion}{$(project-commit-hash)}" >> $@
+	echo "\newcommand{\projectgitrepo}{$(metadata-git-repository)}" >> $@
+	echo "\newcommand{\projectcopyrightowner}{$(metadata-copyright-owner)}" >> $@
 
         # arXiv/Zenodo identifier (necessary for download link):
 	echo "\newcommand{\projectarxivid}{$(metadata-arxiv)}" >> $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 6b055f7..27c1b5b 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -51,7 +51,7 @@ include reproduce/software/config/LOCAL.conf
 # Controlling this requires two variables that are available at this stage:
 #
 #   - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
-#   - `reproducible_paper_group_name': value to the `--group' option.
+#   - `maneage_group_name': value to the `--group' option.
 #
 # The analysis is only done when both have the same group name. Note that
 # when the project isn't being built for a group, both variables will be an
@@ -69,7 +69,7 @@ top-pdfs = paper.pdf
 else
 top-pdfs = paper.pdf supplement.pdf
 endif
-ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
+ifeq (x$(maneage_group_name),x$(GROUP-NAME))
 all: $(top-pdfs)
 else
 all:
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index f81ac07..fb5700e 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -35,7 +35,7 @@ include reproduce/software/config/LOCAL.conf
 # -------------------------------
 #
 # See `top-make.mk' for complete explanation.
-ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
+ifeq (x$(maneage_group_name),x$(GROUP-NAME))
 all: $(BDIR)/software/preparation-done.mk
 	@echo "Project preparation is complete.";
 else