Argparse module not able to access packages when creating the documen…

…tation. Argparse filename used instead.

docs/geos-ats.rst

@@ -13,7 +13,7 @@ run_geos_ats
 Primary entry point for running integrated tests.
 
 .. argparse::
-   :module: geos.ats.command_line_parsers
+   :filename: ..\geos-ats\src\geos\ats\command_line_parsers.py
    :func: build_command_line_parser
    :prog: run_geos_ats
 

docs/geos-mesh.rst

@@ -16,13 +16,13 @@ Modules
 To list all the modules available through ``mesh-doctor``, you can simply use the ``--help`` option, which will list all available modules as well as a quick summary.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 Then, if you are interested in a specific module, you can ask for its documentation using the ``mesh-doctor module_name --help`` pattern.
 For example
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py collocated_nodes --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``mesh-doctor`` loads its module dynamically.
 If a module can't be loaded, ``mesh-doctor`` will proceed and try to load other modules.
@@ -45,7 +45,7 @@ Displays the neighboring nodes that are closer to each other than a prescribed t
 It is not uncommon to define multiple nodes for the exact same position, which will typically be an issue for ``geos`` and should be fixed.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py collocated_nodes --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``element_volumes``
 """""""""""""""""""
@@ -54,7 +54,7 @@ Computes the volumes of all the cells and displays the ones that are below a pre
 Cells with negative volumes will typically be an issue for ``geos`` and should be fixed.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py element_volumes --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``fix_elements_orderings``
 """"""""""""""""""""""""""
@@ -64,7 +64,7 @@ The ``fix_elements_orderings`` module can rearrange the nodes of given types of
 This can be convenient if you cannot regenerate the mesh.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py fix_elements_orderings --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``generate_cube``
 """""""""""""""""
@@ -74,7 +74,7 @@ It can also generate fields with simple values.
 This tool can also be useful to generate a trial mesh that will later be refined or customized.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py generate_cube --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``generate_fractures``
 """"""""""""""""""""""
@@ -83,7 +83,7 @@ For a conformal fracture to be defined in a mesh, ``geos`` requires the mesh to
 The ``generate_fractures`` module will split the mesh and generate the multi-block ``vtk`` files.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py generate_fractures --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``generate_global_ids``
 """""""""""""""""""""""
@@ -92,7 +92,7 @@ When running ``geos`` in parallel, `global ids` can be used to refer to data acr
 The ``generate_global_ids`` can generate `global ids` for the imported ``vtk`` mesh.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py generate_global_ids --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``non_conformal``
 """""""""""""""""
@@ -103,7 +103,7 @@ The angle between two faces can also be precribed.
 This module can be a bit time consuming.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py non_conformal --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``self_intersecting_elements``
 """"""""""""""""""""""""""""""
@@ -112,7 +112,7 @@ Some meshes can have cells that auto-intersect.
 This module will display the elements that have faces intersecting.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py self_intersecting_elements --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 ``supported_elements``
 """"""""""""""""""""""
@@ -126,7 +126,7 @@ The ``supported_elements`` check will validate that no unsupported element is in
 It will also verify that the ``VTK_POLYHEDRON`` cells can effectively get converted into a supported type of element.
 
 .. command-output:: python src/geos/mesh/doctor/mesh_doctor.py supported_elements --help
-   :cwd: ../geos-mesh
+   :cwd: ..\geos-mesh
 
 
 
@@ -144,7 +144,7 @@ convert_abaqus
 Compile an xml file with advanced features into a single file that can be read by GEOS.
 
 .. argparse::
-   :module: geos.mesh.conversion.main
+   :filename: ..\geos-mesh\src\geos\mesh\conversion\main.py
    :func: build_abaqus_converter_input_parser
    :prog: convert_abaqus
 

docs/geos-xml-tools.rst

@@ -15,7 +15,7 @@ convert_abaqus
 Convert an abaqus format mesh file to gmsh or vtk format.
 
 .. argparse::
-   :module: geos.xml_tools.command_line_parsers
+   :filename: ..\geos-xml-tools\src\geos\xml_tools\command_line_parsers.py
    :func: build_preprocessor_input_parser
    :prog: preprocess_xml
 
@@ -26,7 +26,7 @@ format_xml
 Formats an xml file.
 
 .. argparse::
-   :module: geos.xml_tools.command_line_parsers
+   :filename: ..\geos-xml-tools\src\geos\xml_tools\command_line_parsers.py
    :func: build_xml_formatter_input_parser
    :prog: format_xml
 
@@ -37,7 +37,7 @@ check_xml_attribute_coverage
 Checks xml attribute coverage for files in the GEOS repository.
 
 .. argparse::
-   :module: geos.xml_tools.command_line_parsers
+   :filename: ..\geos-xml-tools\src\geos\xml_tools\command_line_parsers.py
    :func: build_attribute_coverage_input_parser
    :prog: check_xml_attribute_coverage
 
@@ -48,7 +48,7 @@ check_xml_redundancy
 Checks for redundant attribute definitions in an xml file, such as those that duplicate the default value.
 
 .. argparse::
-   :module: geos.xml_tools.command_line_parsers
+   :filename: ..\geos-xml-tools\src\geos\xml_tools\command_line_parsers.py
    :func: build_xml_redundancy_input_parser
    :prog: check_xml_redundancy
 

geos-mesh/pyproject.toml

@@ -51,6 +51,3 @@ warn_unused_configs = true
 ignore_missing_imports = true
 allow_redefinition = true
 plugins = "numpy.typing.mypy_plugin"
-
-[tool.setuptools.packages.find]
-where = ["src"]