solidipes-solid-mech-plugin 0.0.15__tar.gz → 0.0.16__tar.gz

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: solidipes-solid-mech-plugin
-Version: 0.0.15
+Version: 0.0.16
 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
@@ -12,9 +12,12 @@ Requires-Dist: ipython~=8.18.1
 Requires-Dist: mergedeep~=1.3.4
 Requires-Dist: meshio[all]~=5.3.5
 Requires-Dist: streamlit~=1.45.0
-Requires-Dist: trame~=3.5.2
-Requires-Dist: streamlit-pyvista==0.0.21
+Requires-Dist: trame<4,>=3.13.2
+Requires-Dist: trame-pyvista>=0.2.1
+Requires-Dist: trame-vtk>=2.11.15
+Requires-Dist: streamlit-pyvista~=0.0.24
 Requires-Dist: h5py~=3.13.0
+Requires-Dist: netCDF4~=1.7.0
 Provides-Extra: dev
 Requires-Dist: pillow~=10.4.0; extra == "dev"
 Requires-Dist: pixelmatch~=0.3.0; extra == "dev"

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/pyproject.toml

@@ -16,9 +16,12 @@ dependencies = [
 	"mergedeep~=1.3.4",
 	"meshio[all]~=5.3.5",
 	"streamlit~=1.45.0",
-	"trame~=3.5.2",
-	"streamlit-pyvista==0.0.21",
+	"trame>=3.13.2,<4",
+	"trame-pyvista>=0.2.1",
+	"trame-vtk>=2.11.15",
+	"streamlit-pyvista~=0.0.24",
 	"h5py~=3.13.0",
+	"netCDF4~=1.7.0",
 ]
 
 [project.optional-dependencies]

solidipes_solid_mech_plugin-0.0.16/solidipes_solid_mech_plugin/loaders/exodus.py

@@ -0,0 +1,184 @@
+import re
+
+import numpy as np
+from solidipes.loaders.file import File
+from solidipes.loaders.sequence import Sequence
+from solidipes_core_plugin.loaders.netcdf import NetCDF
+
+
+def _decode_exodus_string(raw) -> str:
+    """Decode a character array row from an Exodus II netCDF file."""
+    if isinstance(raw, np.ndarray):
+        raw = raw.tobytes()
+
+    if isinstance(raw, (bytes, np.bytes_)):
+        return raw.decode("utf-8", errors="ignore").strip("\x00").strip()
+
+    return str(raw)
+
+
+class Exodus(Sequence, NetCDF):
+    """Exodus II finite element database file, read with meshio and netCDF4.
+
+    Every Exodus file is treated as a sequence of time steps (a mesh-only
+    database counts as a single frame). Nodal and elemental result variables
+    are exposed as point and cell data for each available time step, and the
+    mesh can be viewed with the PyvistaPlotter.
+
+    The `netcdf` loadable and the netCDF metadata (dimensions, variables,
+    global attributes) are inherited from the NetCDF loader.
+    """
+
+    from ..viewers.pyvista_plotter import PyvistaPlotter
+
+    supported_mime_types = {"application/x-netcdf": ["e", "exo", "gen"]}
+    _compatible_viewers = [PyvistaPlotter]
+
+    @File.loadable
+    def meshio_mesh(self):
+        """Static mesh (connectivity and coordinates) read with meshio"""
+        import meshio
+
+        return meshio.read(self.file_info.path)
+
+    @File.rocrate_metadata
+    def title(self):
+        return self.netcdf.title
+
+    @File.rocrate_metadata
+    def n_time_steps(self):
+        if "time_step" not in self.netcdf.dimensions:
+            return 1
+
+        # A mesh-only database has an empty (or missing) time_step dimension:
+        # the mesh itself counts as a single frame
+        return max(1, len(self.netcdf.dimensions["time_step"]))
+
+    @File.rocrate_metadata
+    def n_nodes(self):
+        return len(self.netcdf.dimensions["num_nodes"])
+
+    @File.rocrate_metadata
+    def n_elements(self):
+        return len(self.netcdf.dimensions["num_elem"])
+
+    @File.rocrate_metadata
+    def nodal_variable_names(self):
+        if "name_nod_var" not in self.netcdf.variables:
+            return []
+
+        return [_decode_exodus_string(raw) for raw in self.netcdf.variables["name_nod_var"][:]]
+
+    @File.rocrate_metadata
+    def element_block_names(self):
+        if "eb_names" not in self.netcdf.variables:
+            return {}
+
+        return {i + 1: _decode_exodus_string(raw) for i, raw in enumerate(self.netcdf.variables["eb_names"][:])}
+
+    @File.rocrate_metadata
+    def elemental_variable_names(self):
+        """List of (element_block_number, variable_number, name) triples"""
+        names = []
+
+        for key, var in self.netcdf.variables.items():
+            if not key.startswith("name_elem_var"):
+                continue
+
+            block = int(key[len("name_elem_var") :]) if len(key) > len("name_elem_var") else 1
+
+            for i, raw in enumerate(var[:]):
+                name = _decode_exodus_string(raw)
+
+                if name:
+                    names.append((block, i + 1, name))
+
+        return names
+
+    @property
+    def _element_count(self):
+        return self.n_time_steps
+
+    def select_frame(self, frame):
+        self.select_element(frame)
+
+    @property
+    def mesh(self):
+        """Pyvista mesh of the currently selected time step"""
+        return self._current_element
+
+    def _load_element(self, n):
+        """Load the mesh with nodal and elemental data at time step n"""
+        import pyvista as pv
+        from meshio import Mesh
+
+        meshio_mesh = self.meshio_mesh
+        point_data = self._point_data_at_step(n)
+        cell_data = self._cell_data_at_step(n)
+        mesh = Mesh(meshio_mesh.points, meshio_mesh.cells, point_data=point_data, cell_data=cell_data)
+        return pv.from_meshio(mesh)
+
+    def _point_data_at_step(self, n):
+        """Nodal variable values at time step n"""
+        nc = self.netcdf
+        names = self.nodal_variable_names
+        data = {}
+
+        if "vals_nod_var" in nc.variables:
+            # Standard layout: single variable with dimensions
+            # (time_step, num_nod_var, num_nodes)
+            all_data = np.asarray(nc.variables["vals_nod_var"][n])
+
+            for i, name in enumerate(names):
+                data[name] = all_data[i]
+
+        else:
+            # Alternative layout: one variable per nodal variable
+            for i, name in enumerate(names):
+                var_name = f"vals_nod_var{i + 1}"
+
+                if var_name in nc.variables:
+                    data[name] = np.asarray(nc.variables[var_name][n])
+
+        return data
+
+    def _cell_data_at_step(self, n):
+        """Elemental variable values at time step n, per meshio cell block"""
+        nc = self.netcdf
+        names = self.elemental_variable_names
+
+        if len(names) == 0:
+            return {}
+
+        # Collect data per (variable index, element block)
+        raw: dict[int, dict[int, np.ndarray]] = {}
+
+        for key, var in nc.variables.items():
+            match = re.fullmatch(r"vals_elem_var(\d+)?(?:eb(\d+))?", key)
+
+            if match is None:
+                continue
+
+            var_index = 0 if match.group(1) is None else int(match.group(1)) - 1
+            block = 0 if match.group(2) is None else int(match.group(2)) - 1
+            raw.setdefault(var_index, {})[block] = np.asarray(var[n])
+
+        cell_sizes = [len(c.data) for c in self.meshio_mesh.cells]
+        offsets = np.cumsum([0, *cell_sizes])
+
+        cell_data = {}
+
+        for block, var_index, name in names:
+            if var_index - 1 not in raw:
+                continue
+
+            by_block = raw[var_index - 1]
+            concatenated = np.concatenate([by_block[b] for b in sorted(by_block)])
+
+            if len(concatenated) != offsets[-1]:
+                # Element blocks without data for this variable: skip
+                continue
+
+            cell_data[name] = [concatenated[start:stop] for start, stop in zip(offsets[:-1], offsets[1:])]
+
+        return cell_data

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/solidipes_solid_mech_plugin/viewers/pyvista_plotter.py

@@ -95,7 +95,7 @@ class PyvistaPlotter(Viewer):
                 method
         """
         from streamlit_pyvista.mesh_viewer_component import MeshViewerComponent  # noqa: E402
-        from streamlit_pyvista.server_managers import ServerManagerProxified  # noqa: E402
+        from streamlit_pyvista.server_managers import ServerManager  # noqa: E402
         from streamlit_pyvista.trame_viewers import get_advanced_viewer_path  # noqa: E402
 
         max_frames = 500
@@ -133,7 +133,7 @@ class PyvistaPlotter(Viewer):
             MeshViewerComponent(
                 paths,
                 trame_viewer_class=get_advanced_viewer_path(),
-                server_manager_class=ServerManagerProxified,
+                server_manager_class=ServerManager,
             ).show()
         elif viewer_backends.current_backend == "python":
             self.shown = True
@@ -143,7 +143,7 @@ class PyvistaPlotter(Viewer):
             MeshViewerComponent(
                 paths,
                 trame_viewer_class=get_advanced_viewer_path(),
-                server_manager_class=ServerManagerProxified,
+                server_manager_class=ServerManager,
             ).show()
 
     def save(self, path, **kwargs):

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/solidipes_solid_mech_plugin.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: solidipes-solid-mech-plugin
-Version: 0.0.15
+Version: 0.0.16
 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
@@ -12,9 +12,12 @@ Requires-Dist: ipython~=8.18.1
 Requires-Dist: mergedeep~=1.3.4
 Requires-Dist: meshio[all]~=5.3.5
 Requires-Dist: streamlit~=1.45.0
-Requires-Dist: trame~=3.5.2
-Requires-Dist: streamlit-pyvista==0.0.21
+Requires-Dist: trame<4,>=3.13.2
+Requires-Dist: trame-pyvista>=0.2.1
+Requires-Dist: trame-vtk>=2.11.15
+Requires-Dist: streamlit-pyvista~=0.0.24
 Requires-Dist: h5py~=3.13.0
+Requires-Dist: netCDF4~=1.7.0
 Provides-Extra: dev
 Requires-Dist: pillow~=10.4.0; extra == "dev"
 Requires-Dist: pixelmatch~=0.3.0; extra == "dev"

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/solidipes_solid_mech_plugin.egg-info/SOURCES.txt

@@ -20,6 +20,7 @@ solidipes_solid_mech_plugin.egg-info/top_level.txt
 solidipes_solid_mech_plugin/loaders/__init__.py
 solidipes_solid_mech_plugin/loaders/abaqus.py
 solidipes_solid_mech_plugin/loaders/abaqus_python_code.py
+solidipes_solid_mech_plugin/loaders/exodus.py
 solidipes_solid_mech_plugin/loaders/geo_msh.py
 solidipes_solid_mech_plugin/loaders/geof_mesh.py
 solidipes_solid_mech_plugin/loaders/meshio.py
@@ -31,6 +32,7 @@ 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_exodus_mesh.py
 tests/test_load_modules.py
 tests/test_ontologies.py
 tests/test_pyvista_mesh.py

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/solidipes_solid_mech_plugin.egg-info/requires.txt

@@ -3,9 +3,12 @@ ipython~=8.18.1
 mergedeep~=1.3.4
 meshio[all]~=5.3.5
 streamlit~=1.45.0
-trame~=3.5.2
-streamlit-pyvista==0.0.21
+trame<4,>=3.13.2
+trame-pyvista>=0.2.1
+trame-vtk>=2.11.15
+streamlit-pyvista~=0.0.24
 h5py~=3.13.0
+netCDF4~=1.7.0
 
 [dev]
 pillow~=10.4.0

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/solidipes_solid_mech_plugin.egg-info/scm_file_list.json

@@ -13,6 +13,7 @@
     "solidipes_solid_mech_plugin/loaders/__init__.py",
     "solidipes_solid_mech_plugin/loaders/abaqus.py",
     "solidipes_solid_mech_plugin/loaders/abaqus_python_code.py",
+    "solidipes_solid_mech_plugin/loaders/exodus.py",
     "solidipes_solid_mech_plugin/loaders/geo_msh.py",
     "solidipes_solid_mech_plugin/loaders/geof_mesh.py",
     "solidipes_solid_mech_plugin/loaders/meshio.py",
@@ -32,6 +33,7 @@
     "tests/assets/xdmf_mesh.xdmf",
     "tests/conftest.py",
     "tests/helpers/utils.py",
+    "tests/test_exodus_mesh.py",
     "tests/test_load_modules.py",
     "tests/test_ontologies.py",
     "tests/test_pyvista_mesh.py",

solidipes_solid_mech_plugin-0.0.16/solidipes_solid_mech_plugin.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.0.16",
+  "distance": 0,
+  "node": "gcfd62de0a703eb7a2bab88cd4f3655c523025f43",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-10-21"
+}

solidipes_solid_mech_plugin-0.0.16/tests/test_exodus_mesh.py

@@ -0,0 +1,88 @@
+import os
+
+import pytest
+from solidipes.loaders import load_file
+
+meshio = pytest.importorskip("meshio")
+netCDF4 = pytest.importorskip("netCDF4")
+
+
+@pytest.fixture
+def exodus_file_path(tmp_path, study_dir):
+    """Create a small Exodus II file with a nodal variable and return its path."""
+    import numpy as np
+
+    points = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0], [0.0, 1.0, 0.0]]
+    cells = [("quad", np.array([[0, 1, 2, 3]]))]
+    mesh = meshio.Mesh(points, cells, point_data={"v": np.array([0.1, 0.2, 0.3, 0.4])})
+
+    path = os.path.join(tmp_path, "test.e")
+    meshio.write(path, mesh, file_format="exodus")
+    return path
+
+
+@pytest.fixture
+def exodus_file(exodus_file_path):
+    file = load_file(exodus_file_path)
+    return file
+
+
+def test_file_type(exodus_file):
+    """The Exodus loader is selected for .e files"""
+    from solidipes.loaders.file import File
+
+    assert isinstance(exodus_file, File)
+    assert type(exodus_file).__name__ == "Exodus"
+
+
+def test_metadata(exodus_file):
+    assert exodus_file.n_nodes == 4
+    assert exodus_file.n_elements == 1
+    assert exodus_file.n_time_steps == 1
+    assert exodus_file.nodal_variable_names == ["v"]
+
+
+def test_mesh(exodus_file):
+    import numpy as np
+    import pyvista as pv
+
+    mesh = exodus_file.mesh
+    assert isinstance(mesh, pv.UnstructuredGrid)
+    assert mesh.n_points == 4
+    assert mesh.n_cells == 1
+    assert "v" in mesh.array_names
+    assert np.allclose(mesh.point_data["v"], [0.1, 0.2, 0.3, 0.4])
+
+
+def test_time_steps(exodus_file_path):
+    """Add a second time step and check that it can be selected"""
+    import numpy as np
+
+    with netCDF4.Dataset(exodus_file_path, "a") as nc:
+        var = nc.variables["vals_nod_var1"]
+        var[1] = np.array([0.5, 0.6, 0.7, 0.8])
+        nc.variables["time_whole"][1] = 1.0
+
+    exodus_file = load_file(exodus_file_path)
+    assert exodus_file.n_time_steps == 2
+
+    mesh_0 = exodus_file.mesh
+    assert np.allclose(mesh_0.point_data["v"], [0.1, 0.2, 0.3, 0.4])
+
+    exodus_file.select_frame(1)
+    mesh_1 = exodus_file.mesh
+    assert np.allclose(mesh_1.point_data["v"], [0.5, 0.6, 0.7, 0.8])
+
+
+def test_validation(exodus_file):
+    assert exodus_file.is_valid
+
+
+def test_inherited_netcdf(exodus_file):
+    """The netCDF loadable and metadata are inherited from the NetCDF loader"""
+    import netCDF4
+
+    assert isinstance(exodus_file.netcdf, netCDF4.Dataset)
+    assert exodus_file.dimensions["num_nodes"] == 4
+    assert exodus_file.global_attributes["title"].startswith("Created by meshio")
+    assert "coord" in exodus_file.variables

{solidipes_solid_mech_plugin-0.0.15 → solidipes_solid_mech_plugin-0.0.16}/tests/test_streamlit_pyvista.py

@@ -1,7 +1,9 @@
+import glob
 import os
 import shutil
 import signal
 import subprocess
+import tempfile
 import time
 
 import pytest
@@ -14,6 +16,59 @@ max_loading_checks = 20
 delay_page_load = 1
 test_download_dir = os.path.join(os.getcwd(), "_downloads")
 
+# Command-line substrings identifying processes of the solidipes/streamlit-pyvista
+# stack that must not survive between runs
+leftover_process_patterns = [
+    "server_manager_proxified",
+    "server_manager.py",
+    "streamlit-pyvista-cache/viewer_",
+    "streamlit-pyvista-proxy",
+    "streamlit run",
+    "solidipes report web-report",
+]
+
+
+def cleanup_leftover_processes():
+    """Kill leftover processes from previous runs.
+
+    The viewer component reuses any process already listening on its ports
+    (proxy: 5000, server manager: 9422), so a stale server left behind by a
+    crashed or timed-out earlier run breaks the current one (blank viewer,
+    websocket never connecting). Clean them up before starting.
+    """
+    victims = []
+    for proc_dir in glob.glob("/proc/[0-9]*"):
+        try:
+            with open(f"{proc_dir}/cmdline", "rb") as f:
+                cmdline = f.read().replace(b"\x00", b" ").decode(errors="ignore")
+        except OSError:
+            continue
+        pid = int(proc_dir.rsplit("/", 1)[-1])
+        if pid == os.getpid():
+            continue
+        if any(pattern in cmdline for pattern in leftover_process_patterns):
+            victims.append(pid)
+    for pid in victims:
+        try:
+            os.kill(pid, signal.SIGTERM)
+        except OSError:
+            pass
+    if not victims:
+        return
+    time.sleep(2)
+    for pid in victims:
+        try:
+            os.kill(pid, signal.SIGKILL)
+        except OSError:
+            pass
+    time.sleep(1)
+
+
+@pytest.fixture()
+def clean_environment():
+    cleanup_leftover_processes()
+    yield
+
 
 @pytest.fixture()
 def sb(request):
@@ -59,6 +114,12 @@ class WebReportLauncher:
         self.streamlit_subprocess = None
         self.out = None
         self.err = None
+        # Output goes to files, not pipes: every child (streamlit app, server
+        # manager, proxy, trame viewers) logs to the inherited descriptors, and
+        # an unread PIPE fills its 64KB buffer after a minute or two, blocking
+        # any process that logs and freezing the proxy mid-request
+        self.out_file = tempfile.TemporaryFile("w+")
+        self.err_file = tempfile.TemporaryFile("w+")
 
     def launch(self, dir_path):
         self.streamlit_subprocess = subprocess.Popen(
@@ -72,8 +133,8 @@ class WebReportLauncher:
                 "--server.headless",
                 "true",
             ],
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
+            stdout=self.out_file,
+            stderr=self.err_file,
             preexec_fn=os.setsid,
         )
         return self
@@ -83,10 +144,25 @@ class WebReportLauncher:
             return
         os.killpg(os.getpgid(self.streamlit_subprocess.pid), signal.SIGTERM)
         try:
-            self.out, self.err = self.streamlit_subprocess.communicate(timeout=5)
+            self.streamlit_subprocess.wait(timeout=5)
         except subprocess.TimeoutExpired:
-            return None, ""
+            # Force-kill the whole group so no orphan (server manager, proxy,
+            # trame viewers) survives this run and breaks the next one
+            os.killpg(os.getpgid(self.streamlit_subprocess.pid), signal.SIGKILL)
+            try:
+                self.streamlit_subprocess.wait(timeout=5)
+            except subprocess.TimeoutExpired:
+                pass
         self.streamlit_subprocess = None
+        self.out = self._read_file(self.out_file)
+        self.err = self._read_file(self.err_file)
+
+    @staticmethod
+    def _read_file(f):
+        f.seek(0)
+        content = f.read()
+        f.close()
+        return content
 
     def get_outputs(self):
         return self.out, self.err
@@ -138,7 +214,27 @@ def gracefully_stop_report(web_report):
     web_report.terminate()
     _, streamlit_errors = web_report.get_outputs()
     streamlit_errors = str(streamlit_errors).replace("\\n", "\n")
-    error_found = "Traceback" in streamlit_errors or "already in use" in streamlit_errors
+    # Terminating a healthy run always leaves benign teardown tracebacks in the
+    # subprocess tree (multiprocessing managers exiting via sys.exit, the server
+    # manager catching SIGTERM); only other tracebacks are real faults
+    benign_markers = [
+        "sys.exit(0) or quit was called",
+        "Signals.SIGTERM: 15",
+        # streamlit CLI exits normally through click when terminated
+        "click.exceptions.Exit",
+        # streamlit-pyvista bug: e.stderr is None when the server manager is
+        # SIGTERM'd mid-teardown, causing a TypeError at re-check
+        "argument of type 'NoneType' is not iterable",
+    ]
+    # Scan traceback blocks individually: the string "Address already in use"
+    # also appears quoted inside a known-benign traceback's source line, so a
+    # naive whole-output search would false-positive
+    error_found = False
+    blocks = streamlit_errors.split("Traceback (most recent call last):")
+    for block in blocks[1:]:
+        if any(marker in block for marker in benign_markers):
+            continue
+        error_found = True
     if error_found:
         raise RuntimeError("Error encountered in Streamlit: \n{}".format(streamlit_errors))
 
@@ -150,7 +246,10 @@ def click_solidipes_mesh_button(sb):
 
 
 def click_wireframe_checkbox(sb):
-    sb.click("label[for='wireframe_checkbox']")
+    # The trame viewer boots (VTK import + server start) after the iframe is
+    # rendered, which can take tens of seconds on slow machines: wait for the
+    # checkbox instead of relying on the 7s default timeout.
+    sb.click("label[for='wireframe_checkbox']", timeout=60)
     print("Clicked on the wireframe checkbox")
 
 
@@ -160,11 +259,14 @@ def download_mesh(sb):
     sb.wait(10)
 
 
-def test_streamlit_pyvista_in_web_report(sb, tmp_path, web_report):
+def test_streamlit_pyvista_in_web_report(sb, tmp_path, web_report, clean_environment):
     dir_path = init_study_dir(tmp_path, git=True)
     os.makedirs(f"{dir_path}/data", exist_ok=True)
     shutil.copy2(utils.get_asset_path("pyvista_mesh.vtu"), f"{dir_path}/data/")
     start_web_report_without_fault(sb, dir_path, web_report, target="?page=display_page&file=./data/pyvista_mesh.vtu")
+    # The viewer iframe is rendered after the streamlit script run completes,
+    # which can be slow; wait for it instead of checking once.
+    sb.wait_for_element_present('iframe[data-testid="stIFrame"]', timeout=120)
     iframes = sb.find_elements('iframe[data-testid="stIFrame"]')
     assert len(iframes) > 0
     sb.switch_to_frame(iframes[0])