Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

1 files changed, 36 insertions, 24 deletions

diff --git a/project b/project
index a99e0a6..8db213a 100755
--- a/project
+++ b/project
@@ -1,10 +1,10 @@
 #!/bin/sh
 #
 # High-level script to manage the project.
-# Run `./project --help' for a description of how to use it.
+# Run './project --help' for a description of how to use it.
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021      Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -30,7 +30,7 @@ set -e
 
 
 # Default option values
-jobs=0     # 0 is for the default for the `configure.sh' script.
+jobs=0     # 0 is for the default for the 'configure.sh' script.
 group=
 debug=
 host_cc=0
@@ -60,9 +60,9 @@ scriptname="./project"
 # into the respective variable.
 #
 # Each option has two lines because we want to process both these formats:
-# `--name=value' and `--name value'. The former (with `=') is a single
+# '--name=value' and '--name value'. The former (with '=') is a single
 # command-line argument, so we just need to shift the counter by one. The
-# latter (without `=') is two arguments, so we'll need two shifts.
+# latter (without '=') is two arguments, so we'll need two shifts.
 #
 # Note on the case strings: for every option, we need three lines: one when
 # the option name and value are separate. Another when there is an equal
@@ -127,6 +127,7 @@ Make (analysis) options:
   -p, --prepare-redo       Re-do preparation (only done automatically once).
 
 Make (final PDF) options:
+      --refresh-bib        Force refresh the bibliography.
       --highlight-new      Highlight '\new' parts of text as green.
       --highlight-notes    Show '\tonote' regions as red text in PDF.
       --supplement         Build the appendices as a separate supplement PDF.
@@ -174,7 +175,6 @@ do
   make)         func_operation_set $1; shift;;
   shell)        func_operation_set $1; shift;;
 
-
   # Configure options:
   -b|--build-dir)        build_dir="$2";                                     check_v "$1" "$build_dir";    shift;shift;;
   -b=*|--build-dir=*)    build_dir="${1#*=}";                                check_v "$1" "$build_dir";    shift;;
@@ -213,12 +213,23 @@ do
   # value, it is like giving it a value of `a'):
   --supplement)           separatesupplement=1;                                            shift;;
   --supplement=*)         on_off_option_error --supplement;;
+
+  # Note that Make's 'debug' can take values, but when called without any
+  # value, it is like giving it a value of 'a'):
+  --refresh-bib)          [ -f tex/src/references.tex ] && touch tex/src/references.tex;   shift;;
   --highlight-new)        highlightnew=1;                                                  shift;;
   --highlight-new=*)      on_off_option_error --highlight-new;;
   --highlight-notes)      highlightnotes=1;                                                shift;;
   --highlight-notes=*)    on_off_option_error --highlight-notes;;
-  -d|--debug)             if [ x"$2" = x ]; then debug=a;          shift;
-                          else debug="$2"; check_v debug "$debug"; shift;shift; fi;;
+  -d|--debug)             if [ x$operation = x ]; then
+                              echo "Please set the operation before calling '--debug'"; exit 1
+                          elif [ x$operation = xconfigure ]; then debug=a;   shift;
+                          elif [ x$operation = xmake ]; then
+                              if [ x"$2" = x ]; then echo "In make-mode, '--debug' needs a value"; exit 1
+                              else debug="$2"; check_v debug "$debug"; shift;shift; fi
+                          else
+                              echo "Operation '$operation' not recognized, please use 'configure' or 'make'"
+                          fi;;
   -d=*|--debug=*)         debug="${1#*=}";                       check_v debug "$debug";   shift;;
   -d*)                    debug=$(echo "$1" | sed -e's/-d//');   check_v debug "$debug";   shift;;
   -p|--prepare-redo)      prepare_redo=1;                                                  shift;;
@@ -239,8 +250,8 @@ done
 # Check configuration status
 # --------------------------
 if ! [ x$check_config = x ]; then
-    # Find the color option to pass to `ls'. Note that `--color' (for GNU
-    # Coreutils `ls') should be checked first because it also has `-G', but
+    # Find the color option to pass to 'ls'. Note that '--color' (for GNU
+    # Coreutils 'ls') should be checked first because it also has '-G', but
     # for something else.
     if   ls --color 2> /dev/null > /dev/null; then coloropt="--color=auto"
     elif ls -G      2> /dev/null > /dev/null; then coloropt="-G"
@@ -286,7 +297,7 @@ EOF
             check=$(ls .local/version-info/python/)
             if ! [ "x$check" = x ]; then
                 printresults=1
-                ln -s .local/version-info/python/*  $checkdir/
+                ln -s "$(pwd)"/.local/version-info/python/*  $checkdir/
             fi
             check=$(ls .local/version-info/proglib/)
             if ! [ "x$check" = x ]; then
@@ -300,7 +311,7 @@ EOF
 
                 # Then sort all the links based on the most recent dates of the
                 # files they link to (with '-L').
-                ls -Llt $checkdir \
+                ls -Llt $checkdir  \
                     | awk '/^-/ && c++<5 {printf "[at %s] %s\n", $(NF-1), $NF}'
             fi
         else
@@ -376,10 +387,11 @@ EOF
 # Run operations in controlled environment
 # ----------------------------------------
 controlled_env() {
+
     # Get the full address of the build directory:
     bdir=`.local/bin/realpath .build`
 
-    # Remove all existing environment variables (with `env -i') and only
+    # Remove all existing environment variables (with 'env -i') and only
     # use some pre-defined environment variables, then build the project.
     envmake=".local/bin/env -i HOME=$bdir sys_rm=$(which rm) $gopt"
     envmake="$envmake separatesupplement=$separatesupplement "
@@ -388,7 +400,7 @@ controlled_env() {
     envmake="$envmake --no-builtin-rules --no-builtin-variables -f $1"
     if ! [ x"$debug" = x  ]; then envmake="$envmake --debug=$debug"; fi
 
-    # Set the number of jobs. Note that for the `configure.sh' script the
+    # Set the number of jobs. Note that for the 'configure.sh' script the
     # default value has to be 0, so the default is the maximum number of
     # threads. But here, the default value is 1.
     if ! [ x"$jobs"  = x0 ]; then envmake="$envmake -j$jobs";  fi
@@ -420,7 +432,7 @@ case $operation in
         #
         # In some scenarios (for example when using a tarball from arXiv),
         # it may happen that the host server has removed the executable
-        # flags of all the files. In `README.md' we instruct the readers on
+        # flags of all the files. In 'README.md' we instruct the readers on
         # setting the executable flag of this script. But we don't want the
         # user to have to worry about any other file that needs an
         # executable flag.
@@ -461,7 +473,7 @@ case $operation in
             # Set the group writing permission for everything in the
             # installed software directory. The common build process sets
             # the writing permissions of the installed programs/libraries
-            # to `755'. So group members can't write over a file. This
+            # to '755'. So group members can't write over a file. This
             # creates problems when another group member wants to update
             # the software for example. We thus need to manually add the
             # group writing flag to all installed software files.
@@ -478,17 +490,17 @@ case $operation in
     make)
 
         # Make sure the configure script has been completed properly
-        # (`configuration-done.txt' exists).
+        # ('configuration-done.txt' exists).
         if ! [ -f .build/software/configuration-done.txt ]; then
             configuration_necessary
         fi
 
         # Run data preparation phase (optionally build Makefiles with
-        # special values for optimizing the main `top-make.mk'). But note
+        # special values for optimizing the main 'top-make.mk'). But note
         # that data preparation is only done automatically the first time
-        # the project is built (when `.build/software/preparation-done.mk'
+        # the project is built (when '.build/software/preparation-done.mk'
         # doesn't yet exist). After that, if the user wants to re-do the
-        # preparation they have to use the `--prepare-redo' option.
+        # preparation they have to use the '--prepare-redo' option.
         if ! [ -f .build/software/preparation-done.mk ] \
                 || [ x"$prepare_redo" = x1 ]; then
             controlled_env reproduce/analysis/make/top-prepare.mk
@@ -518,7 +530,7 @@ case $operation in
     shell)
 
         # Make sure the configure script has been completed properly
-        # (`configuration-done.txt' exists).
+        # ('configuration-done.txt' exists).
         if ! [ -f .build/software/configuration-done.txt ]; then
             configuration_necessary
         fi
@@ -540,7 +552,7 @@ case $operation in
                        OMPI_MCA_plm_rsh_agent=/bin/false \
                        PYTHONPATH="$instdir"/lib/python/site-packages \
                        PYTHONPATH3="$instdir"/lib/python/site-packages \
-                       PS1="[\[\033[32m\](maneage)\[\033[00m\] \u@\h \W]$ " \
+                       PS1="[\[\033[01;35m\]maneage@\h \W\[\033[32m\]\[\033[00m\]]$ " \
                        "$instdir"/bin/bash
         ;;
 
@@ -556,5 +568,5 @@ Please run with '--help' for more information.
 
 EOF
         exit 1
-    ;;
+        ;;
 esac