Imported recent work on Maneage, minor conflicts fixed

A few minor conflicts occurred and were fixed.

1 files changed, 92 insertions, 65 deletions

diff --git a/project b/project
index 51274eb..e2d4c66 100755
--- a/project
+++ b/project
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 #
 # High-level script to manage the project.
 # Run `./project --help' for a description of how to use it.
@@ -33,9 +33,11 @@ host_cc=0
 operation=
 build_dir=
 input_dir=
+check_config=
 make_targets=
 software_dir=
 clean_texdir=0
+prepare_redo=0
 existing_conf=0
 scriptname="./project"
 minmapsize=10000000000
@@ -65,14 +67,12 @@ print_help() {
     # Print the output.
     cat <<EOF
 Usage: $scriptname configure [OPTIONS]
-       $scriptname prepare   [OPTIONS]
        $scriptname make      [OPTIONS]
 
 Top-level script to manage the reproducible project. The high-level
 operation is defined by the (mandatory) second argument:
 
   configure    - Configure project for this machine (e.g., build software).
-  prepare      - Low-level preparations to optimize building with 'make'.
   make         - Run the project (do analysis and build outputs).
 
 RECOMMENDATION: If this is the first time you are configuring this
@@ -97,6 +97,7 @@ Configure options:
   -i, --input-dir=STR      Directory containing input datasets (optional).
   -m, --minmapsize=INT     [Gnuastro] Minimum number of bytes to use RAM.
   -s, --software-dir=STR   Directory containing necessary software tarballs.
+      --check-config       During configuration, show what is being built.
       --clean-texdir       Remove possibly existing build-time subdirectories
                            under the project's 'tex/' directory (can happen
                            when source is from arXiv for example).
@@ -108,6 +109,7 @@ Configure and Make options:
 
 Make options:
   -d, --debug=FLAGS        Print various types of debugging information.
+  -p, --prepare-redo       Re-do preparation (only done automatically once).
 
 Mandatory or optional arguments to long options are also mandatory or optional
 for any corresponding short options.
@@ -144,12 +146,11 @@ func_operation_set() {
     fi
 }
 
-while [[ $# -gt 0 ]]
+while [ $# -gt 0 ]
 do
  case $1 in
   # Main operation.
   configure)    func_operation_set $1; shift;;
-  prepare)      func_operation_set $1; shift;;
   make)         func_operation_set $1; shift;;
 
 
@@ -161,8 +162,8 @@ do
   -e*|--existing-conf=*) on_off_option_error --existing-conf -e;;
   --host-cc)             host_cc=1;                                                                shift;;
   --host-cc=*)           on_off_option_error --host-cc;;
-  -i|--inputdir)         input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
-  -i=*|--inputdir=*)     input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
+  -i|--input-dir)        input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
+  -i=*|--input-dir=*)    input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
   -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//'); check_v "$1" "$input_dir";    shift;;
   -m|--minmapsize)       minmapsize="$2";                            check_v "$1" "$minmapsize";   shift;shift;;
   -m=*|--minmapsize=*)   minmapsize="${1#*=}";                       check_v "$1" "$minmapsize";   shift;;
@@ -170,6 +171,8 @@ do
   -s|--software-dir)     software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
   -s=*|--software-dir=*) software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
   -s*)                   software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
+  --check-config)        check_config=1;                                                           shift;;
+  --check-config=*)      on_off_option_error --check-config;;
   --clean-texdir)        clean_texdir=1;                                                           shift;;
   --clean-texdir=*)      on_off_option_error --clean-texdir;;
 
@@ -183,12 +186,17 @@ do
   -'?'|--help)            print_help; exit 0;;
   -'?'*|--help=*)         on_off_option_error --help -?;;
 
-  # Make options (note that Make's `debug' can take values, but when called
-  # without any value, it is like giving it a value of `a'):
+  # Make options
+  # ------------
+  #
+  # Note that Make's `debug' can take values, but when called without any
+  # value, it is like giving it a value of `a'):
   -d|--debug)             if [ x"$2" = x ]; then debug=a;          shift;
                           else debug="$2"; check_v debug "$debug"; shift;shift; 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;;
+  -p=*|--prepare-redo=*)  on_off_option_error --prepare-redo;                              shift;;
 
   # Unrecognized option:
   -*) echo "$scriptname: unknown option '$1'"; exit 1;;
@@ -202,6 +210,44 @@ done
 
 
 
+# Check configuration status
+# --------------------------
+if ! [ x$check_config = x ]; then
+    # Find the color option to pass to `ls'. Note that `--color' (for GNU
+    # Coreutils `ls') should be checked first because it also has `-G', but
+    # for something else.
+    if   ls --color 2> /dev/null > /dev/null; then coloropt="--color=auto"
+    elif ls -G      2> /dev/null > /dev/null; then coloropt="-G"
+    else                               coloropt=""
+    fi
+
+    # Print a notice to let the user know what is happening.
+    cat <<EOF
+
+This is an infinite loop that will print what software are being built at
+every moment. It is actually a listing ('ls' command) of the temporary
+directory where software source code are unpacked while they are being
+built. If the project isn't being configured, the output (every second)
+will either be empty (only a date) or a with an error about a non-existant
+directory. This feature is thus only useful when the project's software are
+being built.
+
+EOF
+
+    # Run the infinite loop.
+    while true; do
+        echo;
+        echo "$(date)    [[press CTRL-C to stop]]";
+        ls $coloropt .build/software/build-tmp || junk=1;
+        sleep 1;
+    done
+    exit 0
+fi
+
+
+
+
+
 # Basic group settings
 # --------------------
 if ! [ x$group = x ]; then
@@ -252,48 +298,10 @@ controlled_env() {
 
 
 
-# Error messages
-# --------------
-#
-# Having the error messages here helps the over-all process be more
-# readable.
-print_error_abort() {
-    case $1 in
-        prepare)
-            cat <<EOF
-
-The project isn't configured for this system, or the configuration wasn't
-successful. To configure the project, please use this command:
-
-      $ ./project configure
-
-(TIP: if you have already ran this command once, run it with '-e' to use
-the previous configuration, run with '--help' for more info)
-
-EOF
-            exit 1;
-        ;;
-        make)
-            cat <<EOF
-
-The project preparation hasn't been completed, or it wasn't successful. To
-prepare the project prior to building it, please use this command:
-
-      $ ./project prepare
-
-EOF
-            exit 1;
-        ;;
-    esac
-}
-
-
-
-
 # Do requested operation
 # ----------------------
 perms="u+r,u+w,g+r,g+w,o-r,o-w,o-x"
-configscript=./reproduce/software/bash/configure.sh
+configscript=./reproduce/software/shell/configure.sh
 case $operation in
 
     # Build the project's software.
@@ -313,7 +321,7 @@ case $operation in
         # `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/bash/* reproduce/analysis/bash/*
+        chmod +x reproduce/software/shell/* 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
@@ -356,30 +364,44 @@ case $operation in
 
 
 
-    # Run the input management.
-    prepare)
+    # Run the project.
+    make)
 
         # Make sure the configure script has been completed properly
         # (`configuration-done.txt' exists).
         if ! [ -f .build/software/configuration-done.txt ]; then
-            print_error_abort $operation
-        fi
+            cat <<EOF
 
-        # Run input-preparations in control environment
-        controlled_env reproduce/analysis/make/top-prepare.mk
-        ;;
+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
 
-    # Run the project
-    make)
+If there was a problem, please let us know by filling this online form:
+      http://savannah.nongnu.org/support/?func=additem&group=reproduce
 
-        # Make sure the configure script has been completed properly
-        # (`configuration-done.txt' exists).
-        if ! [ -f .build/software/preparation-done.mk ]; then
-            print_error_abort $operation
+EOF
+            exit 1
+        fi
+
+        # Run data preparation phase (optionally build Makefiles with
+        # special values for optimizing the main `top-make.mk'). But note
+        # that data preparation is only done automatically the first time
+        # the project is built (when `.build/software/preparation-done.mk'
+        # doesn't yet exist). After that, if the user wants to re-do the
+        # preparation they have to use the `--prepare-redo' option.
+        if ! [ -f .build/software/preparation-done.mk ] \
+                || [ x"$prepare_redo" = x1 ]; then
+            controlled_env reproduce/analysis/make/top-prepare.mk
         fi
 
         # Run the actual project.
@@ -392,9 +414,14 @@ case $operation in
 
     # Operation not specified.
     *)
-        echo "No operation defined."
-        echo "Please run with '--help' for more information."
-        echo "Available operations are: 'configure', 'prepare', or 'make')."
+        cat <<EOF
+
+No operation defined!
+
+Please run with '--help' for more information.
+(TIP: available operations are: 'configure' or 'make').
+
+EOF
         exit 1
     ;;
 esac