Change/extend inputs for MakePythonExecutable

- Instead of specifying a BUILDDIR, the caller must specify an OUTPUT_DIR directory where the output file will be written.
- The script now additionally accepts a list of directories that will be prepended to the system path in the generated script. This shouldn't be necessary for most commands.

cmake/MakePythonExecutable.cmake

@@ -1,7 +1,8 @@
-# Creates within the bin/ sub-directory of the project build directory
-#   a short Python executable that is used to run a Python command from the terminal
-# Receives name of the command as ${CMDNAME}; output build directory as ${BUILDDIR}
-set(BINPATH "${BUILDDIR}/temporary/python/${CMDNAME}")
+# Creates a short Python executable that is used to run a Python command from the terminal.
+# Inputs:
+#   - CMDNAME: Name of the command
+#   - OUTPUT_DIR: Directory in which to create the executable
+#   - EXTRA_PATH_DIRS: an optional list of directories to be prepended to the Python path (shouldn't be necessary for most commands).
 
 set(BINPATH_CONTENTS
     "#!/usr/bin/python3\n"
@@ -13,9 +14,18 @@ set(BINPATH_CONTENTS
     "\n"
     "mrtrix_lib_path = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, 'lib'))\n"
     "sys.path.insert(0, mrtrix_lib_path)\n"
-    "from mrtrix3.app import _execute\n"
 )
 
+if(EXTRA_PATH_DIRS)
+    foreach(PATH_DIR ${EXTRA_PATH_DIRS})
+        string(APPEND BINPATH_CONTENTS
+            "sys.path.insert(0, '${PATH_DIR}')\n"
+        )
+    endforeach()
+endif()
+
+string(APPEND BINPATH_CONTENTS "from mrtrix3.app import _execute\n")
+
 # Three possible interfaces:
 #   1. Standalone file residing in commands/
 #   2. File stored in location commands/<cmdname>/<cmdname>.py, which will contain usage() and execute() functions

python/mrtrix3/commands/CMakeLists.txt

@@ -75,12 +75,11 @@ foreach(CMDNAME ${PYTHON_COMMAND_LIST})
     add_custom_command(
         TARGET MakePythonExecutables
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-        COMMAND ${CMAKE_COMMAND} -DCMDNAME=${CMDNAME} -DBUILDDIR=${PROJECT_BINARY_DIR} -P ${PROJECT_SOURCE_DIR}/cmake/MakePythonExecutable.cmake
+        COMMAND ${CMAKE_COMMAND} -DCMDNAME=${CMDNAME} -DOUTPUT_DIR="${PROJECT_BINARY_DIR}/bin" -P ${PROJECT_SOURCE_DIR}/cmake/MakePythonExecutable.cmake
     )
     list(APPEND PYTHON_BIN_FILES ${PROJECT_BINARY_DIR}/bin/${CMDNAME})
 endforeach()
 
-
 # We need to generate a list of MRtrix3 commands:
 #   function run.command() does different things if it is executing an MRtrix3 command vs. an external command,
 #   but unlike prior software versions we cannot simply interrogate the contents of the bin/ directory at runtime