diff --git a/docs/geos-ats.rst b/docs/geos-ats.rst index 2327707..02cae08 100644 --- a/docs/geos-ats.rst +++ b/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 diff --git a/docs/geos-mesh.rst b/docs/geos-mesh.rst index 8582f10..ea96005 100644 --- a/docs/geos-mesh.rst +++ b/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 diff --git a/docs/geos-xml-tools.rst b/docs/geos-xml-tools.rst index 72ef2a1..c6b0951 100644 --- a/docs/geos-xml-tools.rst +++ b/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 diff --git a/geos-mesh/pyproject.toml b/geos-mesh/pyproject.toml index cc9c081..a15ceba 100644 --- a/geos-mesh/pyproject.toml +++ b/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"] \ No newline at end of file