solidipes-solid-mech-plugin 0.0.10__tar.gz → 0.0.12__tar.gz

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/.gitlab-ci.yml

@@ -31,9 +31,14 @@ test:
       - PYTHON_VERSION: ["3.10", "3.11"]
   rules:
   image: python:${PYTHON_VERSION}
+  before_script:
+    - echo "CI_COMMIT_BRANCH=${CI_COMMIT_BRANCH}"
+    - echo "CI_MERGE_REQUEST_TARGET_BRANCH_NAME=${CI_MERGE_REQUEST_TARGET_BRANCH_NAME}"
+    - export BRANCH="${CI_COMMIT_BRANCH}${CI_MERGE_REQUEST_TARGET_BRANCH_NAME}"
+    - if [[ -z "${BRANCH}" ]]; then echo "force branch to main"; export BRANCH="main"; fi
   script:
-    - apt update && apt install -y --no-install-recommends firefox-esr libgl1-mesa-glx xvfb
-    - git clone -b ${SOLIDIPES_BRANCH} --single-branch https://gitlab.com/solidipes/solidipes.git
+    - apt update && apt install -y --no-install-recommends firefox-esr libgl1 xvfb
+    - git clone -b ${BRANCH} --single-branch https://gitlab.com/solidipes/solidipes.git
     - pip install ./solidipes
     - pip install .[test]
     - python3 -m pytest

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: solidipes-solid-mech-plugin
-Version: 0.0.10
+Version: 0.0.12
 Summary: Plugin for Solidipes with solid mechanics components
 Author-email: Son Pham-Ba <son.phamba@epfl.ch>, Guillaume Anciaux <guillaume.anciaux@epfl.ch>
 License: GPL-3.0-or-later
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: solidipes-core-plugin>=0.0.5
+Requires-Dist: solidipes-core-plugin>=0.0.40
 Requires-Dist: ipython~=8.18.1
 Requires-Dist: mergedeep~=1.3.4
 Requires-Dist: meshio[all]~=5.3.5

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/pyproject.toml

@@ -11,7 +11,7 @@ readme = "README.md"
 requires-python = ">=3.10,<3.13"
 
 dependencies = [
-	"solidipes-core-plugin>=0.0.5",
+	"solidipes-core-plugin>=0.0.40",
 	"ipython~=8.18.1",
 	"mergedeep~=1.3.4",
 	"meshio[all]~=5.3.5",

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin/loaders/abaqus.py

@@ -4,6 +4,7 @@ import mergedeep
 import numpy as np
 import pandas as pd
 import pyparsing as pp
+from solidipes.validators.validator import add_validation_error, validator
 from solidipes_core_plugin.loaders.code_snippet import CodeSnippet
 
 
@@ -114,13 +115,11 @@ class ParseAbaqus:
 class Abaqus(CodeSnippet):
     supported_mime_types = {"application/fem/abaqus": "inp"}
 
-    def __init__(self, **kwargs):
-        from solidipes_core_plugin.viewers.xml import XML
+    from solidipes_core_plugin.viewers.xml import XML
 
-        from ..viewers.pyvista_plotter import PyvistaPlotter
+    from ..viewers.pyvista_plotter import PyvistaPlotter
 
-        super().__init__(**kwargs)
-        self.compatible_viewers[:0] = [PyvistaPlotter, XML]
+    _compatible_viewers = [PyvistaPlotter, XML]
 
     @CodeSnippet.loadable
     def structure(self):
@@ -131,6 +130,16 @@ class Abaqus(CodeSnippet):
         except Exception as e:
             print(e)
 
+    @validator(description="Loadable meshes")
+    def _is_mesh_loadable(self) -> bool:
+        if not self.structure:
+            add_validation_error([f"Invalid structure: {self.structure}"])
+            return False
+        if not self.meshes:
+            add_validation_error([f"Invalid meshes: {self.meshes}"])
+            return False
+        return True
+
     @property
     def xml(self):
         return self.structure
@@ -170,15 +179,30 @@ class Abaqus(CodeSnippet):
         import pyvista as pv
 
         try:
-            import meshio
-
             fname = self.file_info.path
+            import sys
+
             from pyvista.core.utilities import from_meshio
 
-            return {"meshio_reader": from_meshio(meshio.read(fname))}
-        except Exception:
+            original_exit = sys.exit
+
+            def my_exit(code):
+                raise RuntimeError(f"Meshio: sys.exit({code})")
+
+            sys.exit = my_exit
+            import meshio
+
+            _mesh = meshio.read(fname)
+
+            res = {"meshio_reader": from_meshio(_mesh)}
+            sys.exit = original_exit
+            return res
+        except Exception as e:
+            print(e)
             pass
 
+        sys.exit = original_exit
+
         meshes = {}
         for p, part in enumerate(self.parts):
             mesh = meshio.Mesh(self.nodes(p), self.elements(p))

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin/loaders/meshio.py

@@ -4,11 +4,9 @@ from solidipes.loaders.file import File
 class Meshio(File):
     """File loaded with meshio"""
 
-    def __init__(self, **kwargs):
-        from ..viewers.pyvista_plotter import PyvistaPlotter
+    from ..viewers.pyvista_plotter import PyvistaPlotter
 
-        super().__init__(**kwargs)
-        self.compatible_viewers[:0] = [PyvistaPlotter]
+    _compatible_viewers = [PyvistaPlotter]
 
     @File.loadable
     def mesh(self):

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin/loaders/pyvista_mesh.py

@@ -48,6 +48,8 @@ def get_cell_data_from_id_or_array(func):
 class PyvistaMesh(File):
     """Mesh file loaded with pyvista"""
 
+    from ..viewers.pyvista_plotter import PyvistaPlotter
+
     supported_mime_types = {
         "meshing/GMSH": "msh",
         "meshing/StepFile": "stl",
@@ -55,12 +57,7 @@ class PyvistaMesh(File):
         "meshing/AVS": "avs",
     }
 
-    def __init__(self, **kwargs):
-        from ..viewers.pyvista_plotter import PyvistaPlotter
-
-        super().__init__(**kwargs)
-        #: Fully loaded pyvista mesh
-        self.compatible_viewers[:0] = [PyvistaPlotter]
+    _compatible_viewers = [PyvistaPlotter]
 
     def copy_pyvista_data_to_collection(self):
         """Add pyvista data to data collection"""
@@ -87,11 +84,11 @@ class PyvistaMesh(File):
         self.copy_pyvista_data_to_collection()
         return self.pyvista_mesh
 
-    @property
+    @File.rocrate_metadata
     def point_data_names(self):
         return self.pyvista_mesh.point_data.keys()
 
-    @property
+    @File.rocrate_metadata
     def cell_data_names(self):
         return self.pyvista_mesh.cell_data.keys()
 
@@ -100,10 +97,12 @@ class PyvistaMesh(File):
 
     def add_point_data(self, array, name):
         self.pyvista_mesh.point_data.set_array(array, name)
+        del self._data_collection["point_data_names"]
         self.add(name + POINT_DATA_SUFFIX, array)
 
     def remove_point_data(self, name):
         self.pyvista_mesh.point_data.remove(name)
+        del self._data_collection["point_data_names"]
         self.remove(name + POINT_DATA_SUFFIX)
 
     def get_cell_data(self, name):
@@ -111,10 +110,12 @@ class PyvistaMesh(File):
 
     def add_cell_data(self, array, name):
         self.pyvista_mesh.cell_data.set_array(array, name)
+        del self._data_collection["cell_data_names"]
         self.add(name + CELL_DATA_SUFFIX, array)
 
     def remove_cell_data(self, name):
         self.pyvista_mesh.cell_data.remove(name)
+        del self._data_collection["cell_data_names"]
         self.remove(name + CELL_DATA_SUFFIX)
 
     @get_point_data_from_id_or_array

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin/loaders/xdmf.py

@@ -9,11 +9,9 @@ from solidipes_core_plugin.loaders.xml import XML
 class XDMF(Sequence, XML):
     supported_mime_types = {"mesh/XDMF": "xdmf"}
 
-    def __init__(self, **kwargs):
-        from ..viewers.pyvista_plotter import PyvistaPlotter
+    from ..viewers.pyvista_plotter import PyvistaPlotter
 
-        super().__init__(**kwargs)
-        self.compatible_viewers[:0] = [PyvistaPlotter]
+    _compatible_viewers = [PyvistaPlotter]
 
     def _load_hdf5_data_item(self, item):
         if item["@Format"] == "HDF":

solidipes_solid_mech_plugin-0.0.12/solidipes_solid_mech_plugin/ontologies/solidipes_solid_mech.py

@@ -0,0 +1,47 @@
+from pydantic import Field, model_validator
+from solidipes.ontologies.solidipes import File, build_ontology_model
+from solidipes.ontologies.solidipes import entity_classes as base_entity_classes
+from solidipes.utils.utils import string_to_regex_pattern as regexify
+
+
+class Mesh(File):
+    """Mesh file entity."""
+
+    ontology_class: str | None = Field(
+        default=None, pattern=regexify("solidipes_solid_mech_plugin.loaders.pyvista_mesh.PyvistaMesh")
+    )
+    cell_data_names: list[str]
+    point_data_names: list[str]
+
+
+class InputMesh(Mesh):
+    """Mesh file entity with no fields."""
+
+    cell_data_names: list[str] = Field(default_factory=list, min_length=0, max_length=0)
+    point_data_names: list[str] = Field(default_factory=list, min_length=0, max_length=0)
+
+
+class OutputMesh(Mesh):
+    """Mesh file entity with at least one field."""
+
+    cell_data_names: list[str]
+    point_data_names: list[str]
+
+    @model_validator(mode="after")
+    def _check_at_least_one_field(self):
+        if not self.cell_data_names and not self.point_data_names:
+            raise ValueError(
+                "OutputMesh requires at least one field is required in cell_data_names or point_data_names."
+            )
+        return self
+
+
+custom_entity_classes = [
+    InputMesh,
+    OutputMesh,
+]
+
+entity_classes = custom_entity_classes + base_entity_classes
+
+
+ROCrateMetadata = build_ontology_model(entity_classes)

solidipes_solid_mech_plugin-0.0.12/solidipes_solid_mech_plugin/ontologies/solidipes_solid_mech.yaml

@@ -0,0 +1,18 @@
+id: https://gitlab.com/solidipes/solidipes-solid-mech-plugin/-/raw/main/solidipes_solid_mech_plugin/ontologies/solidipes_solid_mech.yaml
+name: solidipes_solid_mech
+prefixes:
+  solidipes: https://gitlab.com/solidipes/solidipes/-/raw/ontology-validation/solidipes/ontologies/
+imports:
+  - solidipes:solidipes
+default_range: string
+
+classes:
+  MeshFile:
+    is_a: File
+    attributes:
+      has_displacement_field:
+        range: bool
+        recommended: true
+      ontology_class:
+        pattern: "^solidipes_solid_mech_plugin.loaders.pyvista_mesh.PyvistaMesh$"
+        required: true

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin.egg-info/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: solidipes-solid-mech-plugin
-Version: 0.0.10
+Version: 0.0.12
 Summary: Plugin for Solidipes with solid mechanics components
 Author-email: Son Pham-Ba <son.phamba@epfl.ch>, Guillaume Anciaux <guillaume.anciaux@epfl.ch>
 License: GPL-3.0-or-later
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: solidipes-core-plugin>=0.0.5
+Requires-Dist: solidipes-core-plugin>=0.0.40
 Requires-Dist: ipython~=8.18.1
 Requires-Dist: mergedeep~=1.3.4
 Requires-Dist: meshio[all]~=5.3.5

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin.egg-info/SOURCES.txt

@@ -24,17 +24,21 @@ solidipes_solid_mech_plugin/loaders/meshio.py
 solidipes_solid_mech_plugin/loaders/parse_inp.py
 solidipes_solid_mech_plugin/loaders/pyvista_mesh.py
 solidipes_solid_mech_plugin/loaders/xdmf.py
+solidipes_solid_mech_plugin/ontologies/solidipes_solid_mech.py
+solidipes_solid_mech_plugin/ontologies/solidipes_solid_mech.yaml
 solidipes_solid_mech_plugin/viewers/__init__.py
 solidipes_solid_mech_plugin/viewers/pyvista_plotter.py
 solidipes_solid_mech_plugin/viewers/xdmf.py
 tests/conftest.py
 tests/test_load_modules.py
+tests/test_ontologies.py
 tests/test_pyvista_mesh.py
 tests/test_pyvista_plotter.py
 tests/test_streamlit_pyvista.py
 tests/test_xdmf_mesh.py
 tests/assets/generate_assets.py
 tests/assets/pyvista_mesh.vtu
+tests/assets/pyvista_mesh_no_fields.vtu
 tests/assets/pyvista_plot.png
 tests/assets/test_mesh_loaded.png
 tests/assets/xdmf_mesh.h5

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/solidipes_solid_mech_plugin.egg-info/requires.txt

@@ -1,4 +1,4 @@
-solidipes-core-plugin>=0.0.5
+solidipes-core-plugin>=0.0.40
 ipython~=8.18.1
 mergedeep~=1.3.4
 meshio[all]~=5.3.5

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/tests/assets/generate_assets.py

@@ -6,22 +6,25 @@ def main():
 
 
 def generate_pyvista_assets():
-    generate_vtu()
+    generate_vtu("pyvista_mesh.vtu", with_fields=True)
+    generate_vtu("pyvista_mesh_no_fields.vtu", with_fields=False)
     generate_pyvista_plot()
 
 
-def generate_vtu():
+def generate_vtu(filename: str, with_fields: bool):
     points = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]
     cells = [3, 0, 1, 2]
     cell_types = [pv.CellType.TRIANGLE]
 
     mesh = pv.UnstructuredGrid(cells, cell_types, points)
-    mesh.point_data.set_array([1, 2, 3], "point 1D")
-    mesh.point_data.set_array(pv.pyvista_ndarray([[1, 2, 3], [4, 5, 6], [7, 8, 9]]), "point 3D")
-    mesh.cell_data.set_array([1], "cell 1D")
-    mesh.cell_data.set_array(pv.pyvista_ndarray([[1, 2, 3]]), "cell 3D")
 
-    mesh.save("pyvista_mesh.vtu")
+    if with_fields:
+        mesh.point_data.set_array([1, 2, 3], "point 1D")
+        mesh.point_data.set_array(pv.pyvista_ndarray([[1, 2, 3], [4, 5, 6], [7, 8, 9]]), "point 3D")
+        mesh.cell_data.set_array([1], "cell 1D")
+        mesh.cell_data.set_array(pv.pyvista_ndarray([[1, 2, 3]]), "cell 3D")
+
+    mesh.save(filename)
 
 
 def generate_pyvista_plot():

solidipes_solid_mech_plugin-0.0.12/tests/assets/pyvista_mesh_no_fields.vtu

@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="3" NumberOfCells="1">
+      <PointData>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1">
+          AQAAAACAAABIAAAAEgAAAA==eJxjYMAHPtjjlUaSBwA9VgJf
+          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              0
+            </Value>
+            <Value index="1">
+              1
+            </Value>
+          </InformationKey>
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="2">
+          AQAAAACAAAAYAAAAEAAAAA==eJxjYIAARijNBKUBADgABA==
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="binary" RangeMin="3" RangeMax="3">
+          AQAAAACAAAAIAAAACwAAAA==eJxjZoAAAAAgAAQ=
+        </DataArray>
+        <DataArray type="UInt8" Name="types" format="binary" RangeMin="5" RangeMax="5">
+          AQAAAACAAAABAAAACQAAAA==eJxjBQAABgAG
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>

{solidipes_solid_mech_plugin-0.0.10 → solidipes_solid_mech_plugin-0.0.12}/tests/conftest.py

@@ -4,7 +4,7 @@ from pathlib import Path
 from typing import Generator
 
 import pytest
-from solidipes.loaders.cached_metadata import CachedMetadata
+import solidipes as sp
 from solidipes.scripts.init import main as init
 
 sys.path.append(os.path.join(os.path.dirname(__file__), "helpers"))
@@ -24,7 +24,7 @@ def study_dir(tmp_path: Path) -> Generator[Path, None, None]:
 
     yield tmp_path
 
-    CachedMetadata.close_cached_metadata()
+    sp.close_cached_metadata()
 
 
 @pytest.fixture

solidipes_solid_mech_plugin-0.0.12/tests/test_ontologies.py

@@ -0,0 +1,41 @@
+import os
+from pathlib import Path
+
+import pytest
+import solidipes as sp
+import utils
+from solidipes.validators.ontology import set_ontology_identifier
+
+ontology_identifier = os.path.join(
+    os.path.dirname(__file__), "..", "solidipes_solid_mech_plugin", "ontologies", "solidipes_solid_mech.py"
+)
+
+
+@pytest.fixture
+def study_dir_custom_ontology(study_dir: Path) -> Path:
+    """Get the study directory with the custom ontology applied."""
+
+    set_ontology_identifier(ontology_identifier)
+    return study_dir
+
+
+class TestPyvistaMeshOntology:
+    def test_input_mesh(self, study_dir_custom_ontology: Path) -> None:
+        """Check that a mesh without fields is detected as an InputMesh."""
+        from solidipes.validators.ontology import OntologyValidator, get_global_validator
+
+        validator = get_global_validator(OntologyValidator)
+        file_path = utils.get_asset_path("pyvista_mesh_no_fields.vtu")
+        file = sp.load_file(file_path)
+        class_name = validator.ontology.get_file_class_name(file)
+        assert class_name == "InputMesh"
+
+    def test_output_mesh(self, study_dir_custom_ontology: Path) -> None:
+        """Check that a mesh with at least one field is detected as an OutputMesh."""
+        from solidipes.validators.ontology import OntologyValidator, get_global_validator
+
+        validator = get_global_validator(OntologyValidator)
+        file_path = utils.get_asset_path("pyvista_mesh.vtu")
+        file = sp.load_file(file_path)
+        class_name = validator.ontology.get_file_class_name(file)
+        assert class_name == "OutputMesh"