Python API: Store list of MRtrix3 commands using cmake

cmake/FindVersion.cmake

@@ -34,9 +34,8 @@ if(NOT MRTRIX_VERSION)
     message(STATUS "Failed to determine version from Git, using default base version: ${MRTRIX_BASE_VERSION}")
 endif()
 
-
 configure_file(
     ${SRC}
     ${DST}
     @ONLY
-)
+)

python/mrtrix3/CMakeLists.txt

@@ -1,4 +1,5 @@
 set(PYTHON_VERSION_FILE ${CMAKE_CURRENT_SOURCE_DIR}/_version.py)
+set(PYTHON_CMDLIST_FILE ${CMAKE_CURRENT_SOURCE_DIR}/_commands.py)
 
 find_package(Git QUIET)
 
@@ -35,6 +36,16 @@ execute_process(
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
 )
 
+# TODO 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
+execute_process(
+    COMMAND ${CMAKE_COMMAND}
+    -D DST=${PYTHON_CMDLIST_FILE}
+    -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/_commands.py.in
+    -P ${PROJECT_SOURCE_DIR}/cmake/FindCommands.cmake
+    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+)
+
 add_custom_target(LinkPythonFiles ALL)
 add_custom_command(
     TARGET LinkPythonFiles

python/mrtrix3/__init__.py

@@ -36,11 +36,6 @@ class MRtrixError(MRtrixBaseError): #pylint: disable=unused-variable
   COMMAND_HISTORY_STRING += '  (version=' + __version__ + ')'
 
 
-# Location of binaries that belong to the same MRtrix3 installation as the Python library being invoked
-BIN_PATH = os.path.abspath(os.path.join(os.path.abspath(os.path.dirname(os.path.abspath(__file__))), os.pardir, os.pardir, 'bin'))
-# Must remove the '.exe' from Windows binary executables
-EXE_LIST = [ os.path.splitext(name)[0] for name in os.listdir(BIN_PATH) ] #pylint: disable=unused-variable
-
 
 # 'CONFIG' is a dictionary containing those entries present in the MRtrix config files
 # Can add default values here that would otherwise appear in multiple locations

python/mrtrix3/_commands.py.in

@@ -0,0 +1,3 @@
+#pylint: disable=unused-variable
+COMMAND_PATH = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), os.pardir, os.pardir, 'bin'))
+COMMAND_LIST = [@MRTRIX_COMMAND_LIST@]

python/mrtrix3/_version.py.in

@@ -1,2 +1,2 @@
 __version__ = "@MRTRIX_VERSION@" #pylint: disable=unused-variable
-__tag__ = "@MRTRIX_GIT_TAG@" #pylint: disable=unused-variable
+__tag__ = "@MRTRIX_GIT_TAG@" #pylint: disable=unused-variable

python/mrtrix3/run.py

@@ -14,7 +14,8 @@
 # For more details, see http://www.mrtrix.org/.
 
 import collections, itertools, os, shlex, shutil, signal, string, subprocess, sys, tempfile, threading
-from mrtrix3 import ANSI, BIN_PATH, COMMAND_HISTORY_STRING, EXE_LIST, MRtrixBaseError, MRtrixError
+from mrtrix3 import ANSI, COMMAND_HISTORY_STRING, MRtrixBaseError, MRtrixError
+from mrtrix3._commands import COMMAND_PATH, COMMAND_LIST
 
 IOStream = collections.namedtuple('IOStream', 'handle filename')
 
@@ -338,7 +339,7 @@ def quote_nonpipe(item):
         cmdstack[-1].extend([ '-append_property', 'command_history', COMMAND_HISTORY_STRING ])
 
     for line in cmdstack:
-      is_mrtrix_exe = line[0] in EXE_LIST
+      is_mrtrix_exe = line[0] in COMMAND_LIST
       if is_mrtrix_exe:
         line[0] = version_match(line[0])
         if shared.get_num_threads() is not None:
@@ -526,9 +527,9 @@ def exe_name(item):
     path = item
   elif item.endswith('.exe'):
     path = item
-  elif os.path.isfile(os.path.join(BIN_PATH, item)):
+  elif os.path.isfile(os.path.join(COMMAND_PATH, item)):
     path = item
-  elif os.path.isfile(os.path.join(BIN_PATH, item + '.exe')):
+  elif os.path.isfile(os.path.join(COMMAND_PATH, item + '.exe')):
     path = item + '.exe'
   elif shutil.which(item) is not None:
     path = item
@@ -549,10 +550,10 @@ def exe_name(item):
 #   which checks system32\ before PATH)
 def version_match(item):
   from mrtrix3 import app #pylint: disable=import-outside-toplevel
-  if not item in EXE_LIST:
-    app.debug('Command ' + item + ' not found in MRtrix3 bin/ directory')
+  if not item in COMMAND_LIST:
+    app.debug('Command ' + item + ' not a part of MRtrix3')
     return item
-  exe_path_manual = os.path.join(BIN_PATH, exe_name(item))
+  exe_path_manual = os.path.join(COMMAND_PATH, exe_name(item))
   if os.path.isfile(exe_path_manual):
     app.debug('Version-matched executable for ' + item + ': ' + exe_path_manual)
     return exe_path_manual