Merge pull request #15 from zincware/SamTov_summed_mesh

Project Updates

.github/workflows/lint.yaml

@@ -0,0 +1,39 @@
+name: Linting
+
+on:
+  push:
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Black Check
+        uses: psf/black@stable
+
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+      - name: Install isort
+        run: |
+          pip install isort
+      - name: run isort
+        run: |
+          isort --check-only --quiet .
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+      - name: Install flake8
+        run: |
+          pip install flake8
+      - name: run flake8
+        run: |
+          flake8 . --count --show-source --statistics

.github/workflows/publish-to-pypi.yaml

@@ -0,0 +1,36 @@
+name: Publish Python distributions to PyPI
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python distributions to PyPI and TestPyPI
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pytest.yaml

@@ -5,11 +5,6 @@ name: pytest
 
 on:
   push:
-    branches:
-      - main
-  pull_request:
-    branches:
-      - main
 
 jobs:
   build:
@@ -19,13 +14,13 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-        - 3.7
         - 3.8
         - 3.9
+        - "3.10"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -35,8 +30,5 @@ jobs:
         run: |
           pip install .
       - name: Pytest
-        env:
-          CUDA_VISIBLE_DEVICES: -1
-          TF_CPP_MIN_LOG_LEVEL: 3
         run: |
           pytest .

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+exclude: '.git|.tox'
+default_stages: [commit]
+fail_fast: true
+
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-isort]

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "CI"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

CI/unit_tests/particle/test_particle.py

@@ -69,28 +69,4 @@ def test_construct_mesh_dict(self):
         self.particle.construct_mesh_dict()
 
         # Check that all particle are in the dict.
-        self.assertEqual(len(self.particle.mesh_dict), self.particle.position.shape[1])
-
-        # Check that they are named correctly.
-        # Check that they are centered correctly.
-        for i, item in enumerate(self.particle.mesh_dict):
-            self.assertEqual(item, f"my_particle_{i}")
-            np.testing.assert_array_almost_equal(
-                self.particle.mesh_dict[item].get_center(), self.particle.position[0][i]
-            )
-
-    def test_update_positions(self):
-        """
-        Test the update position method in the Particle module.
-
-        Returns
-        -------
-        Test whether the positions are updated.
-        """
-        self.particle.construct_mesh_dict()
-        self.particle.update_position_data(1)
-
-        for i, item in enumerate(self.particle.mesh_dict):
-            np.testing.assert_array_almost_equal(
-                self.particle.mesh_dict[item].get_center(), self.particle.position[1][i]
-            )
+        self.assertEqual(len(self.particle.mesh_dict), self.particle.position.shape[0])

README.rst

@@ -9,6 +9,7 @@ simulation.
 Simply define the particles in the simulation with details including their positions,
 colour, direction, and shape, and the visualization engine will display the system
 using the Open3D engine.
+ZnVis works both from a Python script and in Jupyter!
 
 Installation
 ^^^^^^^^^^^^
@@ -33,13 +34,6 @@ Once complete, you will be able to start using the visualizer by importing it as
 
    import znvis
 
-Known limitations
-^^^^^^^^^^^^^^^^^
-Currently it seems that for medium sized systems (400 particles) running the visualizer
-can result in a memory access failure after a while.
-This appears to be a fault in the back-end libraries used and has been brought up.
-We are working on how to extend ZnVis to arbitrary sized systems.
-
 
 .. badges
 

dev-requirements.txt

@@ -12,5 +12,4 @@ nbsphinx-link
 isort
 coverage
 coveralls
-mdanalysis
 black

docs/source/_developer_docs/_modules/modules.rst

@@ -0,0 +1,8 @@
+ZnVis
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   setup
+   znvis

docs/source/_developer_docs/_modules/setup.rst

@@ -0,0 +1,7 @@
+setup module
+============
+
+.. automodule:: setup
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/_developer_docs/_modules/znvis.mesh.rst

@@ -0,0 +1,45 @@
+znvis.mesh package
+==================
+
+Submodules
+----------
+
+znvis.mesh.custom module
+------------------------
+
+.. automodule:: znvis.mesh.custom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+znvis.mesh.cylinder module
+--------------------------
+
+.. automodule:: znvis.mesh.cylinder
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+znvis.mesh.mesh module
+----------------------
+
+.. automodule:: znvis.mesh.mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+znvis.mesh.sphere module
+------------------------
+
+.. automodule:: znvis.mesh.sphere
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: znvis.mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/_developer_docs/_modules/znvis.particle.rst

@@ -0,0 +1,21 @@
+znvis.particle package
+======================
+
+Submodules
+----------
+
+znvis.particle.particle module
+------------------------------
+
+.. automodule:: znvis.particle.particle
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: znvis.particle
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/_developer_docs/_modules/znvis.rst

@@ -0,0 +1,22 @@
+znvis package
+=============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   znvis.mesh
+   znvis.particle
+   znvis.testing
+   znvis.transformations
+   znvis.visualizer
+
+Module contents
+---------------
+
+.. automodule:: znvis
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/_developer_docs/_modules/znvis.testing.rst

@@ -0,0 +1,21 @@
+znvis.testing package
+=====================
+
+Submodules
+----------
+
+znvis.testing.znvis\_process module
+-----------------------------------
+
+.. automodule:: znvis.testing.znvis_process
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: znvis.testing
+   :members:
+   :undoc-members:
+   :show-inheritance: