updating pip

.github/workflows/black.yml

@@ -26,7 +26,7 @@ jobs:
         pip install black
     - name: Run black
       run: |
-        black .
+        black --line-length 100 .
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         commit_message: "[skip ci] Apply formatting changes"

.github/workflows/ci_with_benchmarks.yml

@@ -27,7 +27,7 @@ jobs:
 
       - name: install non pypi dependencies for cad creation
         shell: bash
-        run: |s
+        run: |
           wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
           bash Miniforge3.sh -b -p "${HOME}/conda"
           source "${HOME}/conda/etc/profile.d/conda.sh"
@@ -40,10 +40,10 @@ jobs:
           mamba install -y -c cadquery -c conda-forge moab gmsh python-gmsh cadquery=master "openmc=0.13.3=dagmc*nompi*"
           mamba install -y -c conda-forge "openmc=0.13.3=dagmc*nompi*"
  
-      - name: install package
+      - name: install nuclear data
         run: |
-          pip install .[tests]
-          pip install cad_to_dagmc openmc_data_downloader
+          python -m pip install --upgrade pip
+          python -m pip install cad_to_dagmc openmc_data_downloader
           openmc_data_downloader -l ENDFB-7.1-NNDC -i Fe56 Be9
 
       - name: run benchmarks
@@ -52,5 +52,5 @@ jobs:
         run: |
           git clone https://github.com/fusion-energy/model_benchmark_zoo.git
           cd model_benchmark_zoo
-          pip install .
+          python -m pip install .
           pytest tests/test_cad_to_dagmc

.github/workflows/ci_with_install.yml

@@ -46,7 +46,8 @@ jobs:
           
       - name: install package
         run: |
-          pip install .
+          python -m pip install --upgrade pip 
+          python -m pip install .
           python -c "import cad_to_dagmc"
           mamba install -y -c conda-forge "openmc=0.13.3=dagmc*nompi*"
 
@@ -111,5 +112,5 @@ jobs:
 
       - name: Run pytest
         run: |
-          pip install .[tests]
+          python -m pip install .[tests]
           pytest tests -v

examples/cadquery_compound.py

@@ -17,12 +17,7 @@
 cq_shape_1 = r.extrude(-1)
 
 s2 = cq.Workplane("XY")
-r2 = (
-    s2.lineTo(3.0, 0)
-    .lineTo(3.0, 1.0)
-    .spline(spline_points, includeCurrent=True)
-    .close()
-)
+r2 = s2.lineTo(3.0, 0).lineTo(3.0, 1.0).spline(spline_points, includeCurrent=True).close()
 cq_shape_2 = r2.extrude(1)
 
 

examples/cadquery_object_and_stp_file.py

@@ -5,7 +5,5 @@
 
 my_model = CadToDagmc()
 my_model.add_cadquery_object(object=result, material_tags=["mat1"])
-my_model.add_stp_file(
-    filename="single_cube.stp", material_tags=["mat2"], scale_factor=0.1
-)
+my_model.add_stp_file(filename="single_cube.stp", material_tags=["mat2"], scale_factor=0.1)
 my_model.export_dagmc_h5m_file(max_mesh_size=0.2, min_mesh_size=0.1)

examples/cadquery_text.py

@@ -16,6 +16,4 @@
     ],  # 5 volumes one for each letter
 )
 
-my_model.export_dagmc_h5m_file(
-    filename="cadquery_text.h5m", max_mesh_size=0.2, min_mesh_size=0.1
-)
+my_model.export_dagmc_h5m_file(filename="cadquery_text.h5m", max_mesh_size=0.2, min_mesh_size=0.1)

examples/create_stp_files_for_examples.py

@@ -46,12 +46,7 @@
     (0.5, 1.0),
     (0, 1.0),
 ]
-r = (
-    result.lineTo(3.0, 0)
-    .lineTo(3.0, 1.0)
-    .spline(spline_points, includeCurrent=True)
-    .close()
-)
+r = result.lineTo(3.0, 0).lineTo(3.0, 1.0).spline(spline_points, includeCurrent=True).close()
 result = r.extrude(1.5)
 assembly = Assembly()
 assembly.add(result)

examples/single_stp_file_multiple_volumes.py

@@ -2,7 +2,5 @@
 
 my_model = CadToDagmc()
 # the d and c from the word dagmc would be tagged with one material and the agm are tagged with another material
-my_model.add_stp_file(
-    "text_dagmc.stp", material_tags=["mat1", "mat2", "mat2", "mat2", "mat1"]
-)
+my_model.add_stp_file("text_dagmc.stp", material_tags=["mat1", "mat2", "mat2", "mat2", "mat1"])
 my_model.export_dagmc_h5m_file()

src/cad_to_dagmc/core.py

@@ -81,7 +81,8 @@ def define_moab_core_and_tags() -> typing.Tuple[core.Core, dict]:
 
 def vertices_to_h5m(
     vertices: typing.Union[
-        typing.Iterable[typing.Tuple[float, float, float]], typing.Iterable["cadquery.occ_impl.geom.Vector"]
+        typing.Iterable[typing.Tuple[float, float, float]],
+        typing.Iterable["cadquery.occ_impl.geom.Vector"],
     ],
     triangles_by_solid_by_face: typing.Iterable[typing.Iterable[typing.Tuple[int, int, int]]],
     material_tags: typing.Iterable[str],
@@ -102,11 +103,7 @@ def vertices_to_h5m(
         raise ValueError(msg)
 
     # limited attribute checking to see if user passed in a list of CadQuery vectors
-    if (
-        hasattr(vertices[0], "x")
-        and hasattr(vertices[0], "y")
-        and hasattr(vertices[0], "z")
-    ):
+    if hasattr(vertices[0], "x") and hasattr(vertices[0], "y") and hasattr(vertices[0], "z"):
         vertices_floats = []
         for vert in vertices:
             vertices_floats.append((vert.x, vert.y, vert.z))
@@ -156,9 +153,7 @@ def vertices_to_h5m(
                 if len(face_ids_with_solid_ids[face_id]) == 2:
                     other_solid_id = face_ids_with_solid_ids[face_id][1]
                     other_volume_set = volume_sets_by_solid_id[other_solid_id]
-                    sense_data = np.array(
-                        [other_volume_set, volume_set], dtype="uint64"
-                    )
+                    sense_data = np.array([other_volume_set, volume_set], dtype="uint64")
                 else:
                     sense_data = np.array([volume_set, 0], dtype="uint64")
 
@@ -229,7 +224,6 @@ def mesh_brep(
     gmsh.option.setNumber("General.Terminal", 1)
     gmsh.model.add("made_with_brep_to_h5m_package")
     volumes = gmsh.model.occ.importShapesNativePointer(brep_object)
-    # gmsh.model.occ.importShapes(brep_object)
     gmsh.model.occ.synchronize()
 
     gmsh.option.setNumber("Mesh.Algorithm", mesh_algorithm)
@@ -296,8 +290,7 @@ def mesh_to_h5m_in_memory_method(
             for nodeTag in nodeTags:
                 shifted_node_tags.append(nodeTag - 1)
             grouped_node_tags = [
-                shifted_node_tags[i : i + n]
-                for i in range(0, len(shifted_node_tags), n)
+                shifted_node_tags[i : i + n] for i in range(0, len(shifted_node_tags), n)
             ]
             nodes_in_each_surface[surface] = grouped_node_tags
         triangles_by_solid_by_face[vol_id] = nodes_in_each_surface
@@ -354,9 +347,7 @@ def merge_surfaces(parts):
     if len(parts) == 1:
         # merged_solid = cq.Compound(solids)
 
-        if isinstance(
-            parts[0], (cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid)
-        ):
+        if isinstance(parts[0], (cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid)):
             # stp file
             return parts[0], parts[0].wrapped
         else:
@@ -460,10 +451,7 @@ def export_dagmc_h5m_file(
         for part in self.parts:
             assembly.add(part)
 
-        (
-            imprinted_assembly,
-            imprinted_solids_with_original_id,
-        ) = cq.occ_impl.assembly.imprint(assembly)
+        imprinted_assembly, imprinted_solids_with_org_id = cq.occ_impl.assembly.imprint(assembly)
 
         gmsh, volumes = mesh_brep(
             brep_object=imprinted_assembly.wrapped._address(),
@@ -473,9 +461,7 @@ def export_dagmc_h5m_file(
         )
 
         original_ids = get_ids_from_assembly(assembly)
-        scrambled_ids = get_ids_from_imprinted_assembly(
-            imprinted_solids_with_original_id
-        )
+        scrambled_ids = get_ids_from_imprinted_assembly(imprinted_solids_with_org_id)
 
         # both id lists should be the same length as each other and the same
         # length as the self.material_tags

tests/test_file_creation.py

@@ -133,31 +133,17 @@ def test_cq_compound():
     ]
 
     s = cq.Workplane("XY")
-    r = (
-        s.lineTo(3.0, 0)
-        .lineTo(3.0, 1.0)
-        .spline(spline_points, includeCurrent=True)
-        .close()
-    )
+    r = s.lineTo(3.0, 0).lineTo(3.0, 1.0).spline(spline_points, includeCurrent=True).close()
     cq_shape_1 = r.extrude(-1)
 
     s2 = cq.Workplane("XY")
-    r2 = (
-        s2.lineTo(3.0, 0)
-        .lineTo(3.0, 1.0)
-        .spline(spline_points, includeCurrent=True)
-        .close()
-    )
+    r2 = s2.lineTo(3.0, 0).lineTo(3.0, 1.0).spline(spline_points, includeCurrent=True).close()
     cq_shape_2 = r2.extrude(1)
 
-    compound_of_workplanes = cq.Compound.makeCompound(
-        [cq_shape_1.val(), cq_shape_2.val()]
-    )
+    compound_of_workplanes = cq.Compound.makeCompound([cq_shape_1.val(), cq_shape_2.val()])
 
     my_model = CadToDagmc()
-    my_model.add_cadquery_object(
-        object=compound_of_workplanes, material_tags=["mat1", "mat2"]
-    )
+    my_model.add_cadquery_object(object=compound_of_workplanes, material_tags=["mat1", "mat2"])
     my_model.export_dagmc_h5m_file(
         filename="compound_dagmc.h5m", max_mesh_size=0.2, min_mesh_size=0.1
     )

tests/test_h5m_in_simulation.py

@@ -121,9 +121,7 @@ def test_h5m_with_multi_volume_not_touching():
         "tests/two_disconnected_cubes.h5m",
     ]
     for mat_tags, h5m_file in zip(material_tags, h5m_files):
-        transport_particles_on_h5m_geometry(
-            h5m_filename=h5m_file, material_tags=mat_tags
-        )
+        transport_particles_on_h5m_geometry(h5m_filename=h5m_file, material_tags=mat_tags)
 
 
 def test_h5m_with_multi_volume_touching():
@@ -136,6 +134,4 @@ def test_h5m_with_multi_volume_touching():
         "tests/two_connected_cubes.h5m",
     ]
     for mat_tags, h5m_file in zip(material_tags, h5m_files):
-        transport_particles_on_h5m_geometry(
-            h5m_filename=h5m_file, material_tags=mat_tags
-        )
+        transport_particles_on_h5m_geometry(h5m_filename=h5m_file, material_tags=mat_tags)

tests/test_loading_from_file_vs_shape_object.py

@@ -18,9 +18,7 @@
 
 def test_order_material_ids_by_brep_order():
     # two entries, reverse order
-    new_order = cad_to_dagmc.order_material_ids_by_brep_order(
-        ["1", "2"], ["2", "1"], ["m1", "m2"]
-    )
+    new_order = cad_to_dagmc.order_material_ids_by_brep_order(["1", "2"], ["2", "1"], ["m1", "m2"])
     assert new_order == ["m2", "m1"]
 
     # three entries, partly duplicate materials

tests/test_match.py

@@ -24,9 +24,7 @@ def get_ids_from_imprinted_assembly(solid_id_dict):
     return ids
 
 
-imprinted_assembly, imprinted_solids_with_original_id = cq.occ_impl.assembly.imprint(
-    assembly
-)
+imprinted_assembly, imprinted_solids_with_original_id = cq.occ_impl.assembly.imprint(assembly)
 
 original_ids = get_ids_from_assembly(assembly)
 scrambled_ids = get_ids_from_imprinted_assembly(imprinted_solids_with_original_id)

tests/test_package.py

@@ -49,9 +49,7 @@ def get_volumes_and_materials_from_h5m(filename: str) -> dict:
     return vol_mat
 
 
-def transport_particles_on_h5m_geometry(
-    h5m_filename, material_tags, cross_sections_xml=None
-):
+def transport_particles_on_h5m_geometry(h5m_filename, material_tags, cross_sections_xml=None):
     """A function for testing the geometry file with particle transport in DAGMC OpenMC"""
 
     materials = openmc.Materials()