Imported recent work in master, minor conflict fixed in paper.mk

Only two conflicts came up in the newly added comments of 'paper.mk' in the
Maneage branch. It happened because in this project we don't use
'pdflatex', but 'latex' alone.

1 files changed, 72 insertions, 27 deletions

diff --git a/project b/project
index c117933..b6f17bb 100755
--- a/project
+++ b/project
@@ -41,6 +41,7 @@ make_targets=
 software_dir=
 clean_texdir=0
 prepare_redo=0
+all_highlevel=0
 existing_conf=0
 scriptname="./project"
 minmapsize=10000000000
@@ -77,6 +78,7 @@ operation is defined by the (mandatory) second argument:
 
   configure    - Configure project for this machine (e.g., build software).
   make         - Run the project (do analysis and build outputs).
+  shell        - Execute the project's shell for interactive testing.
 
 RECOMMENDATION: If this is the first time you are configuring this
 template, please don't use the options and let the script explain each
@@ -92,6 +94,9 @@ Project 'make' special features.
                            uploaded to servers like 'arXiv.org'.
   ./project make dist-lzip Similar to 'dist', but compress to '.tar.lz'.
   ./project make dist-zip  Similar to 'dist', but compress to '.zip'.
+  ./project make dist-software  Build a .tar.gz tarball containing all
+                                software source tarballs necessary for the
+                                project.
 
 With the options below you can modify the default behavior.
 Configure options:
@@ -105,6 +110,7 @@ Configure options:
       --clean-texdir       Remove possibly existing build-time subdirectories
                            under the project's 'tex/' directory (can happen
                            when source is from arXiv for example).
+      --all-highlevel      Build all high-level software (for development).
 
 Configure and Make options:
   -g, --group=STR          Build and run with write permissions for a group.
@@ -156,6 +162,7 @@ do
   # Main operation.
   configure)    func_operation_set $1; shift;;
   make)         func_operation_set $1; shift;;
+  shell)        func_operation_set $1; shift;;
 
 
   # Configure options:
@@ -179,6 +186,8 @@ do
   --check-config=*)      on_off_option_error --check-config;;
   --clean-texdir)        clean_texdir=1;                                                           shift;;
   --clean-texdir=*)      on_off_option_error --clean-texdir;;
+  --all-highlevel)       all_highlevel=1;                                                          shift;;
+  --all-highlevel=*)     on_off_option_error --all-highlevel;;
 
   # Configure and Make options:
   -g|--group)             group="$2";                            check_v group "$group";   shift;shift;;
@@ -271,6 +280,35 @@ fi
 
 
 
+# Error when configuration isn't run
+configuration_necessary() {
+    cat <<EOF
+
+The project is either (1) not configured on this system, or (2) the
+configuration wasn't successful.
+
+(1) If it hasn't been configured at all, use the command below to configure
+it (set a build directory and let it build its necessary software in it).
+
+      $ ./project configure
+
+(2) If it has been configured, but the configuration failed in a step, you
+can re-configure it using your previous settings with the command
+below. All successful steps will be skipped, allowing a fast completion.
+
+      $ ./project configure -e
+
+If there was a problem, please let us know by filling this online form:
+      http://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+EOF
+    exit 1
+}
+
+
+
+
+
 # Run operations in controlled environment
 # ----------------------------------------
 controlled_env() {
@@ -321,11 +359,12 @@ case $operation in
         # user to have to worry about any other file that needs an
         # executable flag.
         #
-        # Basically, all the files (shell scripts) in the two
-        # `reproduce/*/bash' should need executable flags, so we are giving
-        # them executable flags by default. If any other file in your project
-        # needs such flags, add them here.
-        chmod +x reproduce/software/shell/* reproduce/analysis/bash/*
+        # Basically, all the project shell scripts need executable flags so
+        # to make sure they have them, we are activating the executable
+        # flags by default here every time './project configure' is run. If
+        # any other file in your project needs such flags, add them here.
+        chmod +x reproduce/software/shell/* reproduce/software/config/*.sh \
+              reproduce/analysis/bash/*
 
         # If the user requested, clean the TeX directory from the extra
         # (to-be-built) directories that may already be there (and will not
@@ -343,6 +382,7 @@ case $operation in
         export minmapsize=$minmapsize
         export software_dir=$software_dir
         export existing_conf=$existing_conf
+        export all_highlevel=$all_highlevel
         export reproducible_paper_group_name=$group
 
         # Run the configuration script
@@ -368,33 +408,13 @@ case $operation in
 
 
 
-    # Run the project.
+    # Batch execution of the project.
     make)
 
         # Make sure the configure script has been completed properly
         # (`configuration-done.txt' exists).
         if ! [ -f .build/software/configuration-done.txt ]; then
-            cat <<EOF
-
-The project is either (1) not configured on this system, or (2) the
-configuration wasn't successful.
-
-(1) If it hasn't been configured at all, use the command below to configure
-it (set a build directory and let it build its necessary software in it).
-
-      $ ./project configure
-
-(2) If it has been configured, but the configuration failed in a step, you
-can re-configure it using your previous settings with the command
-below. All successful steps will be skipped, allowing a fast completion.
-
-      $ ./project configure -e
-
-If there was a problem, please let us know by filling this online form:
-      http://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-EOF
-            exit 1
+            configuration_necessary
         fi
 
         # Run data preparation phase (optionally build Makefiles with
@@ -425,7 +445,32 @@ EOF
         ;;
 
 
+    shell)
 
+        # Make sure the configure script has been completed properly
+        # (`configuration-done.txt' exists).
+        if ! [ -f .build/software/configuration-done.txt ]; then
+            configuration_necessary
+        fi
+
+        # Run the project's own shell without inheriting any environment
+        # from the host.
+        bdir=`.local/bin/realpath .build`
+        instdir=$bdir/software/installed
+        .local/bin/env -i \
+                       HOME=$bdir \
+                       CCACHE_DISABLE=1 \
+                       PATH=$instdir/bin \
+                       LDFLAGS=-L$instdir/lib \
+                       SHELL=$instdir/bin/bash \
+                       CPPFLAGS=-I$instdir/include \
+                       LD_LIBRARY_PATH=$instdir/lib \
+                       OMPI_MCA_plm_rsh_agent=/bin/false \
+                       PYTHONPATH=$instdir/lib/python/site-packages \
+                       PYTHONPATH3=$instdir/lib/python/site-packages \
+                       PS1="[\[\033[32m\](maneage)\[\033[00m\] \u@\h \W]$ " \
+                       $instdir/bin/bash
+        ;;
 
 
     # Operation not specified.