Fix Python commands, documentation generation, CLI test

- Fix importlib call in cmake-generated Python executables for stand-alone Python files; this regressed in cleanup commit 291a747, which worked for the Python CLI test (as both executable and source file resided in the same directory) but broke execution of other Python commands. - Change handling of Python CLI test: executable will be placed in ${PROJECT_BINARY_DIR}/bin; source code will be placed in ${PROJECT_BUILD_DIR}/lib/mrtrix3/commands/. - Update docs/generate_user_docs.sh to reflect new handling of Python commands. - Auto-update of some Python command help pages to propagate prior changes. - Add per-test labels to unit tests.
MRtrix3 · Jun 21, 2024 · 3fce648 · 3fce648
1 parent f87bc0e
commit 3fce648
Show file tree

Hide file tree

Showing 9 changed files with 38 additions and 40 deletions.
diff --git a/cmake/MakePythonExecutable.cmake b/cmake/MakePythonExecutable.cmake
@@ -2,7 +2,6 @@
 # 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"
@@ -14,18 +13,10 @@ 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"
+    "\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
@@ -47,7 +38,7 @@ if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${CMDNAME}/__init__.py")
     endif()
 elseif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${CMDNAME}.py")
     string(APPEND BINPATH_CONTENTS
-        "module = importlib.import_module('${CMDNAME}')\n"
+        "module = importlib.import_module('.${CMDNAME}', 'mrtrix3.commands')\n"
         "_execute(module.usage, module.execute)\n"
     )
 else()

diff --git a/docs/generate_user_docs.sh b/docs/generate_user_docs.sh
@@ -42,7 +42,7 @@ function prepend {
 # Generating documentation for all commands
 
 mrtrix_root=$( cd "$(dirname "${BASH_SOURCE}")"/../ ; pwd -P )
-export PATH=$build_dir/bin:${mrtrix_root}/python/bin:"$PATH"
+export PATH=$build_dir/bin:$PATH
 dirpath=${mrtrix_root}'/docs/reference/commands'
 export LC_ALL=C
 
@@ -82,8 +82,8 @@ cmdlist=""
 for n in `find "${mrtrix_root}"/cmd/ -name "*.cpp"`; do
   cmdlist=$cmdlist$'\n'`basename $n`
 done
-for n in `find "${mrtrix_root}"/python/bin/ -type f -print0 | xargs -0 grep -l "import mrtrix3"`; do
-  cmdlist=$cmdlist$'\n'`basename $n`
+for n in `ls "${mrtrix_root}"/python/mrtrix3/commands/ --ignore=__init__.py* --ignore=CMakeLists.txt`; do
+  cmdlist=$cmdlist$'\n'`basename $n .py`
 done
 
 for n in `echo "$cmdlist" | sort`; do

diff --git a/docs/reference/commands/5ttgen.rst b/docs/reference/commands/5ttgen.rst
@@ -15,7 +15,7 @@ Usage
 
     5ttgen algorithm [ options ] ...
 
--  *algorithm*: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: freesurfer, fsl, gif, hsvs
+-  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: freesurfer, fsl, gif, hsvs
 
 Description
 -----------

diff --git a/docs/reference/commands/dwi2mask.rst b/docs/reference/commands/dwi2mask.rst
@@ -15,7 +15,7 @@ Usage
 
     dwi2mask algorithm [ options ] ...
 
--  *algorithm*: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: 3dautomask, ants, b02template, consensus, fslbet, hdbet, legacy, mean, mtnorm, synthstrip, trace
+-  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: 3dautomask, ants, b02template, consensus, fslbet, hdbet, legacy, mean, mtnorm, synthstrip, trace
 
 Description
 -----------

diff --git a/docs/reference/commands/dwi2response.rst b/docs/reference/commands/dwi2response.rst
@@ -15,7 +15,7 @@ Usage
 
     dwi2response algorithm [ options ] ...
 
--  *algorithm*: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: dhollander, fa, manual, msmt_5tt, tax, tournier
+-  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: dhollander, fa, manual, msmt_5tt, tax, tournier
 
 Description
 -----------

diff --git a/docs/reference/commands/dwibiascorrect.rst b/docs/reference/commands/dwibiascorrect.rst
@@ -15,7 +15,7 @@ Usage
 
     dwibiascorrect algorithm [ options ] ...
 
--  *algorithm*: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ants, fsl, mtnorm
+-  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: ants, fsl, mtnorm
 
 Description
 -----------

diff --git a/docs/reference/commands/dwinormalise.rst b/docs/reference/commands/dwinormalise.rst
@@ -15,7 +15,7 @@ Usage
 
     dwinormalise algorithm [ options ] ...
 
--  *algorithm*: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: group, manual, mtnorm
+-  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: group, manual, mtnorm
 
 Description
 -----------

diff --git a/testing/tools/CMakeLists.txt b/testing/tools/CMakeLists.txt
@@ -15,9 +15,12 @@ set(CPP_TOOLS_SRCS
     testing_npywrite.cpp
 )
 
-set(PYTHON_TOOLS_SRCS
+set(PYTHON_TOOLS_STANDALONE
     testing_check_npy.py
     testing_gen_npy.py
+)
+
+set(PYTHON_TOOLS_MRTRIXAPI
     testing_python_cli.py
 )
 
@@ -36,28 +39,32 @@ function(add_cpp_tool TOOL_SRC)
     add_dependencies(testing_tools ${TOOL_NAME})
 endfunction()
 
-function(add_python_tool TOOL_SRC IS_MRTRIX_CMD)
+function(add_python_tool_standalone TOOL_SRC)
     get_filename_component(TOOL_NAME ${TOOL_SRC} NAME_WE)
-    # If the tool behaves like a Python MRtrix3 command, then we need to generate its executable using
-    # the MakePythonExecutable script
-    if(IS_MRTRIX_CMD)
-        set(MRTRIX_PYTHON_LIB_PATH "${PROJECT_BINARY_DIR}/lib")
-        add_custom_command(
-            TARGET testing_tools PRE_BUILD
-            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-            COMMAND ${CMAKE_COMMAND} -DCMDNAME=${TOOL_NAME} -DOUTPUT_DIR="${CMAKE_CURRENT_BINARY_DIR}" -DEXTRA_PATH_DIRS="${MRTRIX_PYTHON_LIB_PATH}" -P ${PROJECT_SOURCE_DIR}/cmake/MakePythonExecutable.cmake
-        )
-        # Install "module" file alongside the executable
-        configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${TOOL_SRC} ${CMAKE_CURRENT_BINARY_DIR}/${TOOL_SRC} COPYONLY)
-    else()
-        configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${TOOL_SRC} ${CMAKE_CURRENT_BINARY_DIR}/${TOOL_NAME} COPYONLY)
-    endif()
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${TOOL_SRC} ${CMAKE_CURRENT_BINARY_DIR}/${TOOL_NAME} COPYONLY)
+endfunction()
+
+# If the tool behaves like a Python MRtrix3 command, then we need to generate its executable using
+# the MakePythonExecutable script
+function(add_python_tool_mrtrixapi TOOL_SRC)
+    get_filename_component(TOOL_NAME ${TOOL_SRC} NAME_WE)
+    set(MRTRIX_PYTHON_LIB_PATH "${PROJECT_BINARY_DIR}/lib")
+    add_custom_command(
+        TARGET testing_tools PRE_BUILD
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        COMMAND ${CMAKE_COMMAND} -DCMDNAME=${TOOL_NAME} -DOUTPUT_DIR="${PROJECT_BINARY_DIR}/bin" -P ${PROJECT_SOURCE_DIR}/cmake/MakePythonExecutable.cmake
+    )
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${TOOL_SRC} ${PROJECT_BINARY_DIR}/lib/mrtrix3/commands/${TOOL_SRC} COPYONLY)
 endfunction()
 
 foreach(CMD ${CPP_TOOLS_SRCS})
     add_cpp_tool(${CMD})
 endforeach(CMD)
 
-add_python_tool(testing_check_npy.py FALSE)
-add_python_tool(testing_gen_npy.py FALSE)
-add_python_tool(testing_python_cli.py TRUE)
+foreach(CMD ${PYTHON_TOOLS_STANDALONE})
+    add_python_tool_standalone(${CMD})
+endforeach(CMD)
+
+foreach(CMD ${PYTHON_TOOLS_MRTRIXAPI})
+    add_python_tool_mrtrixapi(${CMD})
+endforeach(CMD)
diff --git a/testing/unit_tests/CMakeLists.txt b/testing/unit_tests/CMakeLists.txt
@@ -73,7 +73,7 @@ function (add_bash_unit_test FILE_SRC)
         WORKING_DIRECTORY ${DATA_DIR}
         EXEC_DIRECTORIES "${EXEC_DIRS}"
         ENVIRONMENT "PYTHONPATH=${PYTHON_ENV_PATH}"
-        LABELS "unittest"
+        LABELS "unittest;${NAME}"
     )
 endfunction()