IMPORTANT: Project preparation is now also done with project make

Until now, the main commands to run the project were these: `./project
configure' (to build the software), `./project prepare' (to possibly
arrange input datasets and build special configuration Makefiles) and
finally `./project make' to run the project.

The main logic behind the "prepare" phase `top-prepare.mk' is to build
configuration files that can be fed into the "make" step and optimize its
operation. For example when the total number of necessary inputs for the
majority of the analysis is not as large as the total number of
inputs. With "prepare" (when necessary), you go through the raw inputs,
select the ones that are necessary for the rest of the project. The output
of `top-prepare.mk' is a configuration file (a Make variable) that keeps
the IDs (numbers, names, etc). That configuration file would then be used
in the `top-make.mk' to identify the lower level targets and allow optimal
project organization and management.

But the last two are both part of the analysis, and while they indeed need
different calls to Make to be executed, many projects don't actually need a
preparation phase: ultimately, its an implementation choice by the project
developers and doesn't concern the project users (or the developers when
they are running it).

To avoid confusing the users, or simply annoying them when a projet doesn't
need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk'
Makefiles are called with the single `./project make' command and
`./project prepare' has been dropped. I noticed this while writing the
paper on this system.

1 files changed, 22 insertions, 60 deletions

diff --git a/project b/project
index 5d161be..d994b09 100755
--- a/project
+++ b/project
@@ -66,14 +66,12 @@ 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
@@ -151,7 +149,6 @@ do
  case $1 in
   # Main operation.
   configure)    func_operation_set $1; shift;;
-  prepare)      func_operation_set $1; shift;;
   make)         func_operation_set $1; shift;;
 
 
@@ -294,44 +291,6 @@ 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"
@@ -398,32 +357,30 @@ 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
-
-        # Run input-preparations in control environment
-        controlled_env reproduce/analysis/make/top-prepare.mk
-        ;;
-
-
+            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
 
-    # Run the project
-    make)
+[[ TIP: If you have already configured it once, run it with '-e' to use the
+previous configuration. Run with '--help' for more info ]]
 
-        # 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 input-preparations (optionally build Makefiles with special
+        # values for optimizing the main `top-make.mk').
+        controlled_env reproduce/analysis/make/top-prepare.mk
+
         # Run the actual project.
         controlled_env reproduce/analysis/make/top-make.mk
         ;;
@@ -434,9 +391,14 @@ 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