Fix Python commands & documentation generation

- Fix importlib call in cmake-generated Python executables for stand-alone Python files; this regressed in cleanup commit 291a747. - Update docs/generate_user_docs.sh to reflect new handling of Python commands. - Auto-update of some Python command help pages.
MRtrix3 · Jun 21, 2024 · 8822ce8 · 8822ce8
1 parent f87bc0e
commit 8822ce8
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/cmake/MakePythonExecutable.cmake b/cmake/MakePythonExecutable.cmake
@@ -47,7 +47,7 @@ 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
 -----------