added list and view as new features

CHANGELOG.md

@@ -4,6 +4,25 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [0.2.0] - 2025-10-23
+
+### Added
+
+- `list` command can now show a detailed summary of simulation cases with the `--cases` flag, including mesh properties like volume, COG, and cell count.
+- `view` command can now visualize a mesh by specifying its case name, in addition to its direct mesh name.
+
+### Changed
+
+- **Breaking Change**: The `view` command interface has been simplified. It now takes the HDF5 file as the first required argument, followed by optional mesh/case names. The `--file` option has been removed for clarity.
+- Refactored the `list` command for improved code clarity and maintainability.
+- The mesh stored in the database is now the final, immersed, and (if applicable) fully reflected mesh used by Capytaine, ensuring `view` shows the correct geometry.
+
+### Fixed
+
+- Resolved numerous bugs in the `run` command related to mesh transformations, temporary file handling on Windows (`PermissionError`, `OSError`), and the use of symmetric meshes.
+- Corrected `isinstance` checks in unit tests when using mocked objects.
+- Fixed all `mypy` and `deptry` static analysis errors for a cleaner codebase.
+
 ## [0.1.1] - 2025-10-21
 
 ### Added

pyproject.toml

@@ -30,6 +30,7 @@ dependencies = [
     "numpy>=2.0.2",
     "pandas>=2.3.3",
     "pydantic>=2.12.2",
+    "pyglet<2",
     "pyyaml>=6.0.3",
     "rich>=14.2.0",
     "trimesh>=4.8.3",
@@ -133,7 +134,7 @@ module = [
     "PySide6.*",
     "rich.*",
     "trimesh.*",
-    "vtk",
+    "vtk.*",
     "yaml",
 ]
 ignore_missing_imports = true
@@ -226,6 +227,7 @@ source = ["src"]
     "mkdocs",
     "mkdocs-material",
     "mkdocstrings",
+    "pyglet",
     "types-PyYAML",
 ]
 

src/fleetmaster/cli.py

@@ -19,7 +19,7 @@
 from rich.logging import RichHandler
 
 from . import __version__
-from .commands import gui, run
+from .commands import gui, list_command, run, view
 from .logging_setup import setup_general_logger
 
 logger = setup_general_logger()
@@ -76,6 +76,12 @@ def cli(verbose: int) -> None:
     for h in package_logger.handlers:
         h.setLevel(log_level)
 
+    # If no subcommand is invoked, show the help message.
+    ctx = click.get_current_context()
+    if ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
+        return
+
     if log_level <= logging.INFO:
         logger.info(
             "🚀 Fleetmaster CLI — ready to start your capytaine simulations.",
@@ -84,6 +90,8 @@ def cli(verbose: int) -> None:
 
 cli.add_command(run, name="run")
 cli.add_command(gui, name="gui")
+cli.add_command(list_command, name="list")
+cli.add_command(view, name="view")
 
 
 if __name__ == "__main__":

src/fleetmaster/commands/__init__.py

@@ -1,4 +1,6 @@
 from .gui import gui
+from .list import list_command
 from .run import run
+from .view import view
 
-__all__ = ["gui", "run"]
+__all__ = ["gui", "list_command", "run", "view"]

src/fleetmaster/commands/list.py

@@ -0,0 +1,141 @@
+"""CLI command for listing meshes from HDF5 databases."""
+
+import io
+import logging
+from pathlib import Path
+from typing import Any
+
+import click
+import h5py
+import numpy as np
+import trimesh
+from trimesh import Trimesh
+
+logger = logging.getLogger(__name__)
+
+
+def _parse_stl_content(stl_content_dataset: Any) -> Trimesh:
+    """
+    Parses binary STL data from an HDF5 dataset into a trimesh object.
+
+    Handles both legacy (numpy.void) and current storage formats.
+    """
+    stl_data = stl_content_dataset[()]
+    try:
+        # Accommodate legacy storage format (numpy.void)
+        stl_bytes = stl_data.tobytes()
+    except AttributeError:
+        # Current format is already bytes
+        stl_bytes = stl_data
+
+    mesh = trimesh.load_mesh(io.BytesIO(stl_bytes), file_type="stl")
+    if not isinstance(mesh, Trimesh):
+        msg = "Failed to parse STL data into a valid trimesh object."
+        raise TypeError(msg)
+    return mesh
+
+
+def _print_mesh_details(mesh_info_group: Any) -> None:
+    """Prints formatted geometric properties of a mesh from its HDF5 group."""
+    attrs = mesh_info_group.attrs
+    vol = attrs.get("volume", "N/A")
+    cog = (attrs.get("cog_x", "N/A"), attrs.get("cog_y", "N/A"), attrs.get("cog_z", "N/A"))
+    dims = (attrs.get("bbox_lx", "N/A"), attrs.get("bbox_ly", "N/A"), attrs.get("bbox_lz", "N/A"))
+
+    num_faces: str | int = "N/A"
+    bounds: np.ndarray | None = None
+    if stl_content_dataset := mesh_info_group.get("stl_content"):
+        try:
+            mesh = _parse_stl_content(stl_content_dataset)
+            num_faces = len(mesh.faces)
+            bounds = mesh.bounding_box.bounds
+        except (ValueError, TypeError, AttributeError) as e:
+            mesh_name = Path(mesh_info_group.name).name
+            logger.debug(f"Failed to parse STL content for mesh '{mesh_name}': {e}")
+            click.echo(f"      Could not parse stored STL content: {e}")
+
+    click.echo(f"      Cells: {num_faces}")
+    click.echo(f"      Volume: {vol:.4f}" if isinstance(vol, float) else f"      Volume: {vol}")
+    click.echo(
+        f"      COG (x,y,z): ({cog[0]:.3f}, {cog[1]:.3f}, {cog[2]:.3f})"
+        if all(isinstance(c, float) for c in cog)
+        else f"      COG (x,y,z): {cog}"
+    )
+    click.echo(
+        f"      BBox Dims (Lx,Ly,Lz): ({dims[0]:.3f}, {dims[1]:.3f}, {dims[2]:.3f})"
+        if all(isinstance(d, float) for d in dims)
+        else f"      BBox Dims (Lx,Ly,Lz): {dims}"
+    )
+    if bounds is not None:
+        click.echo(f"      BBox Min (x,y,z): ({bounds[0][0]:.3f}, {bounds[0][1]:.3f}, {bounds[0][2]:.3f})")
+        click.echo(f"      BBox Max (x,y,z): ({bounds[1][0]:.3f}, {bounds[1][1]:.3f}, {bounds[1][2]:.3f})")
+
+
+def _list_cases(stream: Any, hdf5_path: str) -> None:
+    """Lists all simulation cases and their mesh properties in an HDF5 file."""
+    click.echo(f"\nAvailable cases in '{hdf5_path}':")
+    case_names = [name for name in stream if name != "meshes"]
+    if not case_names:
+        click.echo("  No cases found.")
+        return
+
+    for case_name in sorted(case_names):
+        case_group = stream[case_name]
+        click.echo(f"\n- Case: {case_name}")
+
+        if not (mesh_name := case_group.attrs.get("stl_mesh_name")):
+            click.echo("    Mesh: [Unknown]")
+            continue
+
+        click.echo(f"    Mesh: {mesh_name}")
+        if mesh_info_group := stream.get(f"meshes/{mesh_name}"):
+            _print_mesh_details(mesh_info_group)
+        else:
+            click.echo("      Mesh properties not found in database.")
+
+
+def _list_meshes(stream: Any, hdf5_path: str) -> None:
+    """Lists all available meshes in an HDF5 file."""
+    click.echo(f"\nAvailable meshes in '{hdf5_path}':")
+    if not (meshes_group := stream.get("meshes")):
+        click.echo("  No 'meshes' group found.")
+        return
+
+    if available_meshes := list(meshes_group.keys()):
+        for name in sorted(available_meshes):
+            click.echo(f"  - {name}")
+    else:
+        click.echo("  No meshes found.")
+
+
+@click.command(name="list", help="List all meshes available in one or more HDF5 database files.")
+@click.argument("files", nargs=-1, type=click.Path())
+@click.option(
+    "--file",
+    "-f",
+    "option_files",
+    multiple=True,
+    help="Path to one or more HDF5 database files. Can be specified multiple times.",
+)
+@click.option("--cases", is_flag=True, help="List simulation cases and their properties instead of meshes.")
+def list_command(files: tuple[str, ...], option_files: tuple[str, ...], cases: bool) -> None:
+    """CLI command to list meshes."""
+    # Combine positional arguments and optional --file arguments
+    all_files = set(files) | set(option_files)
+
+    # If no files are provided at all, use the default.
+    final_files = list(all_files) if all_files else ["results.hdf5"]
+
+    for hdf5_path in final_files:
+        db_file = Path(hdf5_path)
+        if not db_file.exists():
+            click.echo(f"❌ Error: Database file '{hdf5_path}' not found.", err=True)
+            continue
+        try:
+            with h5py.File(db_file, "r") as stream:
+                if cases:
+                    _list_cases(stream, hdf5_path)
+                else:
+                    _list_meshes(stream, hdf5_path)
+        except Exception as e:
+            click.echo(f"❌ Error reading '{hdf5_path}': {e}", err=True)

src/fleetmaster/commands/run.py

@@ -271,4 +271,5 @@ def run(stl_files: tuple[str, ...], settings_file: str | None, **kwargs: Any) ->
     except (click.UsageError, click.Abort):
         raise  # Re-raise to let click handle the error and exit
     except Exception as e:
+        logger.exception("An unexpected error occurred")
         click.echo(f"❌ An unexpected error occurred: {e}", err=True)