Imported Maneage, minor conflicts fixed, a bug found and fixed

Some minor conflicts came up in 'initialize.mk' and 'verify.mk'. For the
former, I chose the version on Maneage, for the latter, I kept the 'master'
version on the checksums of this project, but kept the Maneage version for
the rest of the improvements there (like printing the verified files as
LaTeX comments in 'verify.tex'.

While testing the conflicts, I noticed a bug (in the LaTeX macro for the
number of years in the Menke+20 paper) in the previous build, thanks to the
verification step :-)! Fortunately it wasn't actually printed in the PDF,
so a normal reader won't recognize.

The bug was caused by the recently added meta-data/commented lines in the
'tools-per-year.txt' file: when calculating the number of years studied in
that paper, we were simply counting all the lines and we had forgot to
correct this after adding comments. As a result, the un-used LaTeX macro
file was saying that they have studied 47 years instead of the real 31
years! This element was actually used in the very first (+40 page!) draft
of the paper that was summarized to fit into the journal limits.

1 files changed, 31 insertions, 10 deletions

diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index fb8afc0..dd224d6 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -40,22 +40,34 @@ verify-print-tips = \
   echo "the following project source file:"; \
   echo "    reproduce/analysis/make/verify.mk"
 
-verify-txt-no-comments-leading-space = \
+# Removes following components of a plain-text file, calculates checksum
+# and compares with given checksum:
+#   - All commented lines (starting with '#') are removed.
+#   - All empty lines are removed.
+#   - All space-characters in remaining lines are removed (so the width of
+#     the printed columns won't invalidate the verification).
+#
+# It takes three arguments:
+#   - First argument: Full address of file to check.
+#   - Second argument: Expected checksum of the file to check.
+#   - File name to write result.
+verify-txt-no-comments-no-space = \
   infile=$(strip $(1)); \
   inchecksum=$(strip $(2)); \
+  innobdir=$$(echo $$infile | sed -e's|$(BDIR)/||g'); \
   if ! [ -f "$$infile" ]; then \
     $(call verify-print-error-start); \
     echo "The following file (that should be verified) doesn't exist:"; \
     echo "    $$infile"; \
     echo; exit 1; \
   fi; \
-  checksum=$$(sed -e 's/^[[:space:]]*//g' \
+  checksum=$$(sed -e 's/[[:space:]][[:space:]]*//g' \
                   -e 's/\#.*$$//' \
                   -e '/^$$/d' $$infile \
-	          | md5sum \
-	          | awk '{print $$1}'); \
+                  | md5sum \
+                  | awk '{print $$1}'); \
   if [ x"$$inchecksum" = x"$$checksum" ]; then \
-    echo "Verified: $$infile"; \
+    echo "%% (VERIFIED) $$checksum $$innobdir" >> $(3); \
   else \
     $(call verify-print-error-start); \
     $(call verify-print-tips); \
@@ -105,6 +117,15 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
         # Make sure that verification is actually requested.
 	if [ x"$(verify-outputs)" = xyes ]; then
 
+          # Make sure the temporary output doesn't exist (because we want
+          # to append to it). We are making a temporary output target so if
+          # there is a crash in the middle, Make will not continue. If we
+          # write in the final target progressively, the file will exist,
+          # and its date will be more recent than all prerequisites, so
+          # next time the project is run, Make will continue and ignore the
+          # rest of the checks.
+	  rm -f $@.tmp
+
           # Verify the figure datasets.
 	  $(call verify-txt-no-comments-leading-space, \
 	         $(a2mk20f1c), 76fc5b13495c4d8e8e6f8d440304cf69)
@@ -114,14 +135,14 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
 	    file=$(mtexdir)/$$m.tex
 	    if   [ $$m == download  ]; then s=64da83ee3bfaa236849927cdc001f5d3
 	    elif [ $$m == format    ]; then s=e04d95a539b5540c940bf48994d8d45f
-	    elif [ $$m == demo-plot ]; then s=2504472bd2b3f60b5a26c5f2a3a67251
+	    elif [ $$m == demo-plot ]; then s=48bffe6cf8db790c63a33302d20db77f
 	    else echo; echo "'$$m' not recognized."; exit 1
 	    fi
-	    $(call verify-txt-no-comments-leading-space, $$file, $$s)
+	    $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp)
 	  done
 
-          # Make an empty final target.
-	  echo "%% Project outputs are verified." > $@
+          # Move temporary file to final target.
+	  mv $@.tmp $@
 	else
-	  echo "%% Project outputs NOT VERIFIED!!!" > $@
+	  echo "% Verification was DISABLED!" > $@
 	fi