cleaned before tag

Author: MbBrainz

.github/workflows/github-actions.yml

@@ -8,12 +8,29 @@ on:
       - main
       - 'releases/**'
 jobs:
-  build:
+  ruff-lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Lint with Ruff
+      run: |
+        pip install ruff
+        ruff --format=github --target-version=py37 .
+    continue-on-error: true
+
+  pytest:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.9", "3.10"]
-
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -25,15 +42,30 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r requirements-dev.txt
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      - name: Lint with flake8
+
+      - name: Test coverage pytest
         run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+          pytest --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
+        continue-on-error: true
+
       - name: Test with pytest
         run: |
           pytest 
-      - name: Test coverage pytest
+
+  build-package:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
         run: |
-          pytest --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build

docs/source/conf.py

@@ -31,6 +31,10 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
+import sphinx_rtd_theme
+
+import irregular_object_packing
+
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
@@ -75,7 +79,6 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-import irregular_object_packing
 
 # The short X.Y version.
 version = irregular_object_packing.__version__
@@ -107,7 +110,6 @@
 # a list of builtin themes.
 #
 html_theme = "sphinx_rtd_theme"
-import sphinx_rtd_theme
 
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 

irregular_object_packing/packing/chordal_axis_transform.py

@@ -495,6 +495,10 @@ def main():
     plotter.add_arrows(np.array(centerpoints), np.array(normal), mag=0.5, color="y")
 
     plotter.add_mesh(cat_boxes[box_idx], show_edges=True, color="r", opacity=0.7)
+    for i in range(len(boxes)):
+        if i != box_idx:
+            plotter.add_mesh(cat_boxes[i], show_edges=True, color="yellow", opacity=0.3)
+
     # plotter.add_mesh(cat_boxes[1], show_edges=True, color="orange", opacity=0.5)
     plot_boxes = [box1, box2, box3, box4]
     for box in plot_boxes:

irregular_object_packing/packing/growth_based_optimisation.py

@@ -1,19 +1,15 @@
 # %%
 from dataclasses import dataclass
-from importlib import reload
-from time import sleep, time
+from time import sleep
 
-import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import pyvista as pv
 import trimesh
-from IPython.display import HTML, display
 from pyvista import PolyData
 from scipy.optimize import minimize
 from tqdm.auto import tqdm
 
-import irregular_object_packing.packing.plots as plots
 from irregular_object_packing.mesh.collision import (
     compute_all_collisions,
     compute_container_violations,
@@ -37,7 +33,6 @@
     IterationData,
     OptimizerData,
 )
-from irregular_object_packing.tools.profile import pprofile
 
 # pv.set_jupyter_backend("panel")
 LOG_LVL_ERROR = 0
@@ -453,105 +448,105 @@ def simple_shapes_setup() -> "Optimizer":
 #     optimizer.setup()s
 # %%
 
+# # # %%
+# # optimizer = Optimizer.simple_shapes_setup()
+# optimizer = Optimizer.default_setup()
+# optimizer.setup()
 # # %%
-# optimizer = Optimizer.simple_shapes_setup()
-optimizer = Optimizer.default_setup()
-optimizer.setup()
-# %%
-optimizer.run()
+# optimizer.run()
 
-# %%
+# # %%
 
-reload(plots)
-save_path = f"../dump/collisions_{time()}"
-plots.generate_gif(optimizer , save_path + ".gif")
-# %%
+# reload(plots)
+# save_path = f"../dump/scale_fix_{time()}"
+# plots.generate_gif(optimizer , save_path + ".gif")
+# # %%
 
-display(HTML(f'<img src="{save_path}.gif"/>'))
+# display(HTML(f'<img src="{save_path}.gif"/>'))
 
-# %%
+# # %%
 
-reload(plots)
+# reload(plots)
 
 
-def plot_step(optimizer, step):
-    plotter = pv.Plotter()
-    meshes, cat_meshes, container = optimizer.recreate_scene(step)
-    plots.plot_simulation_scene(plotter, meshes, cat_meshes, container, c_kwargs={"show_edges": True, "edge_color": "purple"})
-    plotter.add_text(optimizer.status(step).table_str, position="upper_left")
+# def plot_step(optimizer, step):
+#     plotter = pv.Plotter()
+#     meshes, cat_meshes, container = optimizer.recreate_scene(step)
+#     plots.plot_simulation_scene(plotter, meshes, cat_meshes, container, c_kwargs={"show_edges": True, "edge_color": "purple"})
+#     plotter.add_text(optimizer.status(step).table_str, position="upper_left")
 
-    plotter.show()
-    return plotter
+#     plotter.show()
+#     return plotter
 
 
-plot_step(optimizer, 33)
+# plot_step(optimizer, 33)
 
 
-# %%
-obj_i, step = 6, 31
-meshes_before, meshes_after, cat_meshes, container = optimizer.recreate_scene(step)
-# plots.plot_step_comparison(
-#     optimizer.mesh_before,
-#     optimizer.mesh_after(step, obj_i),
-#     optimizer.cat_mesh(step, obj_i),
-#     # other_meshes=optimizer.violating_meshes(step),
+# # %%
+# obj_i, step = 6, 31
+# meshes_before, meshes_after, cat_meshes, container = optimizer.recreate_scene(step)
+# # plots.plot_step_comparison(
+# #     optimizer.mesh_before,
+# #     optimizer.mesh_after(step, obj_i),
+# #     optimizer.cat_mesh(step, obj_i),
+# #     # other_meshes=optimizer.violating_meshes(step),
+# # )
+# # %%
+# reload(plots)
+# obj_i = 6
+# plotter = plots.plot_step_single(
+#     meshes_before[obj_i], cat_meshes[obj_i], container=container, cat_opacity=0.7, mesh_opacity=1 , clipped=True, title="cat overlap",
+#     c_kwargs={"show_edges": True, "edge_color": "purple", "show_vertices": True, "point_size": 10},
+#     m_kwargs={"show_edges": True, "show_vertices": True, "point_size": 10, },
+#     cat_kwargs={"show_edges": True, "show_vertices": True, "point_size": 5, },
 # )
-# %%
-reload(plots)
-obj_i = 6
-plotter = plots.plot_step_single(
-    meshes_before[obj_i], cat_meshes[obj_i], container=container, cat_opacity=0.7, mesh_opacity=1 , clipped=True, title="cat overlap",
-    c_kwargs={"show_edges": True, "edge_color": "purple", "show_vertices": True, "point_size": 10},
-    m_kwargs={"show_edges": True, "show_vertices": True, "point_size": 10, },
-    cat_kwargs={"show_edges": True, "show_vertices": True, "point_size": 5, },
-)
 
-# %%
-# store cat mesh in file
-obj_i, step = 10, 5
-issue_name = f"cat_penetrate_{int(time())}"
-cat_mesh = optimizer.cat_mesh(step, obj_i)
-cat_filename = f"cat[o{obj_i}i{step}].stl"
-obj_filename = f"obj[o{obj_i}i{step}].stl"
-mkdir(f"../dump/issue_reports/{issue_name}")
-folder_dir = f"../dump/issue_reports/{issue_name}/"
-cat_mesh.save(folder_dir + cat_filename)
-meshes[obj_i].save(folder_dir + obj_filename)
-# %%
+# # %%
+# # store cat mesh in file
+# obj_i, step = 10, 5
+# issue_name = f"cat_penetrate_{int(time())}"
+# cat_mesh = optimizer.cat_mesh(step, obj_i)
+# cat_filename = f"cat[o{obj_i}i{step}].stl"
+# obj_filename = f"obj[o{obj_i}i{step}].stl"
+# mkdir(f"../dump/issue_reports/{issue_name}")
+# folder_dir = f"../dump/issue_reports/{issue_name}/"
+# cat_mesh.save(folder_dir + cat_filename)
+# meshes[obj_i].save(folder_dir + obj_filename)
+# # %%
 
-# %%
+# # %%
 
-tetmesh, filtered_tetmesh, _ = optimizer.reconstruct_delaunay(step)
-tetmesh.save(folder_dir + f"tetmesh[i{step}].vtk")
-filtered_tetmesh.save(folder_dir + f"filtered_tetmesh[i{step}].vtk")
+# tetmesh, filtered_tetmesh, _ = optimizer.reconstruct_delaunay(step)
+# tetmesh.save(folder_dir + f"tetmesh[i{step}].vtk")
+# filtered_tetmesh.save(folder_dir + f"filtered_tetmesh[i{step}].vtk")
 
 
-# %%
+# # %%
 
 
-@pprofile
-def profile_optimizer():
-    optimizer.run()
+# @pprofile
+# def profile_optimizer():
+#     optimizer.run()
 
 
-profile_optimizer()
-# # %%
+# profile_optimizer()
+# # # %%
 
 
-# %%
+# # %%
 
 
-fig, ax = plt.subplots()
+# fig, ax = plt.subplots()
 
-a = [0.05, 0.15, 0.25]
-b = [0.1, 0.2, 0.3, 0.5]
+# a = [0.05, 0.15, 0.25]
+# b = [0.1, 0.2, 0.3, 0.5]
 
-x = np.linspace(0, 1, 100)
+# x = np.linspace(0, 1, 100)
 
-for ai in a:
-    for bi in b:
-        print(f"{ai} {bi}`")
-        ax.plot(mesh_simplification_condition(x, ai, bi), label=f"a:{ai:.2f},  b:{bi:.2f}")
-ax.legend()
+# for ai in a:
+#     for bi in b:
+#         print(f"{ai} {bi}`")
+#         ax.plot(mesh_simplification_condition(x, ai, bi), label=f"a:{ai:.2f},  b:{bi:.2f}")
+# ax.legend()
 
-# %%
+# # %%

irregular_object_packing/packing/plots.py

@@ -28,7 +28,7 @@ def create_plot(
         # object_mesh = pv.PolyData(object_meshes[i])
         object_mesh = pv.wrap(object_meshes[i])
         # object_mesh.transform(np.eye(4), object_locations[i])
-        plotter.add_mesh(object_mesh.decimate(0.1), color="r", opacity=0.7)
+        plotter.add_mesh(object_mesh.decimate(0.1), color="r", opacity=0.7) # noqa E501
 
         plotter.add_mesh(object_cells[i], color="y", opacity=0.3)
 
@@ -118,6 +118,13 @@ def plot_step_comparison(
     return plotter
 
 
+def none_to_dict(obj):
+    if obj is None:
+        return {}
+    else:
+        return obj
+
+
 def plot_step_single(
     mesh,
     cat_cell_mesh_1,
@@ -127,8 +134,10 @@ def plot_step_single(
     plotter=None,
     clipped=False,
     title="Title",
-    c_kwargs={}, m_kwargs={}, cat_kwargs={},
+    c_kwargs=None, m_kwargs=None, cat_kwargs=None,
 ):
+    c_kwargs, m_kwargs, cat_kwargs = [none_to_dict(d) for d in [c_kwargs, m_kwargs, cat_kwargs]]
+
     if plotter is None:
         plotter = pv.Plotter()
 
@@ -219,7 +228,7 @@ def create_packed_scene(
         new_mesh = new_mesh.scale(mesh_scale)
         new_mesh = new_mesh.translate(coord)
 
-        colors.append(trimesh.visual.random_color())
+        colors.append(trimesh.visual.random_color()) # noqa E501
         objects.append(new_mesh)
 
     plotter = pv.Plotter()
@@ -230,8 +239,10 @@ def create_packed_scene(
     return plotter
 
 
-def plot_simulation_scene(plotter, meshes, cat_meshes, container, c_kwargs={}, m_kwargs={}, cat_kwargs={},
+def plot_simulation_scene(plotter, meshes, cat_meshes, container, c_kwargs=None, m_kwargs=None, cat_kwargs=None,
                           ):
+    c_kwargs, m_kwargs, cat_kwargs = [none_to_dict(d) for d in [c_kwargs, m_kwargs, cat_kwargs]]
+
     for i in range(len(meshes)):
         try:
             plotter.add_mesh(meshes[i], opacity=0.95, color="red", cmap='bwr', scalars="collisions", **m_kwargs)
@@ -247,10 +258,10 @@ def generate_gif(optimizer, save_path, title="Optimization"):
     plotter.open_gif(save_path)
     plotter.add_title(title)
 
-    meshes, cat_meshes, container = optimizer.recreate_scene(0)
+    _, after_meshes, cat_meshes, container = optimizer.recreate_scene(0)
     for i in range(0, optimizer.idx):
-        prev_meshes = meshes
-        meshes, cat_meshes, container = optimizer.recreate_scene(i)
+        prev_meshes = after_meshes
+        _, after_meshes, cat_meshes, container = optimizer.recreate_scene(i)
         plotter.clear()
         plot_simulation_scene(plotter, prev_meshes, cat_meshes, container)
 
@@ -260,7 +271,7 @@ def generate_gif(optimizer, save_path, title="Optimization"):
         plotter.write_frame()
         plotter.clear()
 
-        plot_simulation_scene(plotter, meshes, cat_meshes, container)
+        plot_simulation_scene(plotter, after_meshes, cat_meshes, container)
         plotter.add_text(f"step {i}", position="upper_right")
         plotter.add_text(optimizer.status(i).table_str, position="upper_left")
         plotter.write_frame()