Imported recent updates in Maneage, minor conflicts fixed

Some very minor conflicts came up and were easily corrected. They were
mostly in parts that are also shared with the demonstration in the core
Maneage branch.

5 files changed, 82 insertions, 34 deletions

diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf
index ee52abb..7d8bb50 100644
--- a/reproduce/analysis/config/INPUTS.conf
+++ b/reproduce/analysis/config/INPUTS.conf
@@ -5,30 +5,34 @@
 #
 # Necessary variables for each input dataset are listed below. Its good
 # that all the variables of each file have the same base-name (in the
-# example below 'WFPC2') with descriptive suffixes, also put a short
-# comment above each group of variables for each dataset, shortly
-# explaining what it is.
+# example below 'DEMO') with descriptive suffixes, also put a short comment
+# above each group of variables for each dataset, shortly explaining what
+# it is.
 #
-#  1) Local file name ('WFPC2IMAGE' below): this is the name of the dataset
+#  1) Local file name ('DEMO-DATA' below): this is the name of the dataset
 #     on the local system (in 'INDIR', given at configuration time). It is
 #     recommended that it be the same name as the online version of the
-#     file like the case here (note how this variable is used in 'WFPC2URL'
+#     file like the case here (note how this variable is used in 'DEMO-URL'
 #     for the dataset's full URL). However, this is not always possible, so
 #     the local and server filenames may be different. Ultimately, the file
 #     name is irrelevant, we check the integrity with the checksum.
 #
-#  2) The MD5 checksum of the file ('WFPC2MD5' below): this is very
+#  2) The MD5 checksum of the file ('DEMO-MD5' below): this is very
 #     important for an automatic verification of the file. You can
-#     calculate it by running 'md5sum' on your desired file.
+#     calculate it by running 'md5sum' on your desired file. You can also
+#     use any other checksum tool that you prefer, just be sure to correct
+#     the respective command in 'reproduce/analysis/make/download.mk'.
 #
-#  3) The human-readable size of the file ('WFPC2SIZE' below): this is an
-#     optional feature which you can use for in the script that is loaded
-#     at configure time ('reproduce/software/shell/configure.sh'). When
-#     asking for the input-data directory, you can print some basic
-#     information of the files for users to get a better feeling of the
-#     volume. See that script for an example using this demo dataset.
+#  3) The human-readable size of the file ('DEMO-SIZE' below): this is an
+#     optional variable, mainly to help a reader of your project get a
+#     sense of the volume they need to download if they don't already have
+#     the dataset. So it is highly recommended to add it (future readers of
+#     your project's source will appreciate it!). You can get it from the
+#     output of 'ls -lh' command on the file. Optionally you can use it in
+#     messages during the configuration phase (when Maneage asks for the
+#     input data directory), along with other info about the file(s).
 #
-#  4) The full dataset URL ('WFPC2URL' below): this is the full URL
+#  4) The full dataset URL ('DEMO-URL' below): this is the full URL
 #     (including the file-name) that can be used to download the dataset
 #     when necessary. Also, see the description above on local filename.
 #
@@ -39,6 +43,11 @@
 # this notice are preserved.  This file is offered as-is, without any
 # warranty.
 
+
+
+
+
+# Dataset used in this analysis and its checksum for integrity checking.
 MK20DATA = menke20.xlsx
 MK20MD5  = 8e4eee64791f351fec58680126d558a0
 MK20SIZE = 1.9MB
diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index d5f8cef..fb3f21e 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -84,9 +84,11 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 	sum=$$(md5sum $$unchecked | awk '{print $$1}')
 	if [ $$sum = $$mdf ]; then
 	  mv $$unchecked $@
+	  echo "Integrity confirmed, using $@ in this project."
 	else
 	  echo; echo;
 	  echo "Wrong MD5 checksum for input file '$$localname':"
+	  echo "  File location: $$unchecked"; \
 	  echo "  Expected MD5 checksum:   $$mdf"; \
 	  echo "  Calculated MD5 checksum: $$sum"; \
 	  echo; exit 1
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 6b25f02..fbd110f 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -302,27 +302,47 @@ $(project-package-contents): paper.pdf | $(texdir)
 	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.
+        # Copy ONLY the version-controlled files in 'reproduce' and
+        # 'tex/src'. This is important because files like 'LOCAL.conf' (in
+        # 'reproduce/software/config') should not be archived, they contain
+        # information about the host computer and are irrelevant for
+        # others. Also some project authors may have temporary files here
+        # that are not under version control and thus shouldn't be archived
+        # (although this is bad practice, but that is up to the user).
+        #
+        # To keep the sub-directory structure, we are packaging the files
+        # with Tar, piping it, and unpacking it in the archive
+        # directory. So afterwards we need to come back to the current
+        # directory.
+	tar -c -f - $$(git ls-files reproduce tex/src) \
+	    | (cd $$dir ; tar -x -f -)
+	cd $(curdir)
+
+        # Build the other two subdirectories of 'tex/' that we need in the
+        # archive (in the actual project, these are symbolic links to the
+        # build directory).
+	mkdir $$dir/tex/tikz $$dir/tex/build
+
+        # Copy the 'tex/build' directory into the archive (excluding the
+        # temporary archive directory that we are now copying to). We will
+        # be using Bash's extended globbing ('extglob') for excluding this
+        # directory.
 	shopt -s extglob
-	cp -r tex/src                            $$dir/tex/src
-	cp -r tex/img                            $$dir/tex/img
-	cp tex/tikz/*.eps                        $$dir/tex/tikz
-	cp -r reproduce/*                        $$dir/reproduce
+	cp -r tex/img                              $$dir/tex/img
+	cp tex/tikz/*.eps                          $$dir/tex/tikz
 	cp -r tex/build/!($(project-package-name)) $$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.
+        # Clean up the $(texdir)/build* directories in the archive (when
+        # building in a group structure, there will be `build-user1',
+        # `build-user2' and etc). These are just temporary LaTeX build
+        # files and don't have any relevant/hand-written files in them.
 	rm -rf $$dir/tex/build/build*
-	rm $$dir/reproduce/software/config/LOCAL.conf
-	rm $$dir/reproduce/analysis/config/gnuastro/gnuastro-local.conf
+
+        # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
+        # PGFPlots was used to generate them), copy them too.
+	if ls tex/tikz/*.pdf &> /dev/null; then
+	  cp tex/tikz/*.pdf $$dir/tex/tikz
+	fi
 
         # 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'
@@ -474,3 +494,14 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
         # Zenodo identifier (necessary for download link):
 	v=$$(echo $(metadata-doi-zenodo) | sed -e's/\./ /g' | awk '{print $$NF}')
 	echo "\newcommand{\projectzenodoid}{$$v}" >> $@
+
+        # Calculate the latest Maneage commit used to build this
+        # project:
+        #  - The '--dirty' option (used in 'project-commit-hash') isn't
+        #    applicable to "commit-ishes" (direct quote from Git's error
+        #    message!).
+        #  - The project may not have the 'maneage' branch (for example
+        #    after cloning from a fork that didn't include it!). In this
+        #    case, we'll just return the string a clear string.
+	v=$$(git describe --always --long maneage) || v=maneage-ref-missing
+	echo "\newcommand{\maneageversion}{$$v}" >> $@
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 90d71c1..2c08847 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -115,7 +115,13 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir);
 
-          # Note: the option '-shell-escape' is "normally disallowed for
+          # Delete any possibly existing target (a '.bbl' file) to avoid
+          # complications with LaTeX being run before the command that
+          # generates it. Otherwise users will have to manually delete
+          # it. It will be built anyway once this rule is done.
+	  rm -f $@
+
+          # The pdflatex option '-shell-escape' is "normally disallowed for
           # security reasons" according to the `info pdflatex' manual, but
           # is enabled here in order to allow the use of PGFPlots. If you
           # do not use PGFPlots, then you should remove the `-shell-escape'
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index dd224d6..fe828dd 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -22,7 +22,7 @@
 # Verification functions
 # ----------------------
 #
-# These functions are used by the final rule in this Makefil
+# These functions are used by the final rule in this Makefile
 verify-print-error-start = \
   echo; \
   echo "VERIFICATION ERROR"; \
@@ -87,7 +87,7 @@ verify-txt-no-comments-no-space = \
 # -------------------------------------------
 #
 # This is the FINAL analysis step (before going onto the paper. Please use
-# this step to veryify the contents of the figures/tables used in the paper
+# this step to verify the contents of the figures/tables used in the paper
 # and the LaTeX macros generated from all your processing. It should depend
 # on all the LaTeX macro files that are generated (their contents will be
 # checked), and any files that go into the tables/figures of the paper