cellier 0.0.2__tar.gz

cellier-0.0.2/.copier-answers.yml

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+# Do not edit - changes here will be overwritten by Copier
+_commit: v1
+_src_path: gh:pydev-guide/pyrepo-copier
+author_email: kevin.yamauchi@gmail.com
+author_name: Kevin Yamauchi
+git_versioning: true
+github_username: kevinyamauchi
+mode: customize
+module_name: cellier
+project_license: BSD-3-Clause
+project_name: cellier
+project_short_description: A workshop for rendering cellular models.
+test_pre_release: false
+use_mypy: false
+use_pre_commit: true
+use_ruff: true
+

cellier-0.0.2/.github/ISSUE_TEMPLATE.md

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+* cellier version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

cellier-0.0.2/.github/TEST_FAIL_TEMPLATE.md

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+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

cellier-0.0.2/.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

cellier-0.0.2/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  
+
+# cancel in-progress runs that use the same workflow and branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[test]
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+  deploy:
+    name: Deploy
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

cellier-0.0.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+.DS_Store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDE settings
+.vscode/
+.idea/

cellier-0.0.2/.pre-commit-config.yaml

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+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.16
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.19.0
+    hooks:
+      - id: typos
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: ruff
+        args: [--fix]  # may also add '--unsafe-fixes'
+      - id: ruff-format

cellier-0.0.2/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, Kevin Yamauchi
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cellier-0.0.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: cellier
+Version: 0.0.2
+Summary: A workshop for rendering cellular models.
+Project-URL: homepage, https://github.com/kevinyamauchi/cellier
+Project-URL: repository, https://github.com/kevinyamauchi/cellier
+Author-email: Kevin Yamauchi <kevin.yamauchi@gmail.com>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Requires-Dist: psygnal
+Requires-Dist: pydantic
+Requires-Dist: pygfx
+Requires-Dist: qtpy
+Requires-Dist: superqt
+Requires-Dist: zarr
+Provides-Extra: dev
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: pyside
+Requires-Dist: pyside6; extra == 'pyside'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Description-Content-Type: text/markdown
+
+# cellier
+
+[![License](https://img.shields.io/pypi/l/cellier.svg?color=green)](https://github.com/kevinyamauchi/cellier/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/cellier.svg?color=green)](https://pypi.org/project/cellier)
+[![Python Version](https://img.shields.io/pypi/pyversions/cellier.svg?color=green)](https://python.org)
+[![CI](https://github.com/kevinyamauchi/cellier/actions/workflows/ci.yml/badge.svg)](https://github.com/kevinyamauchi/cellier/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/kevinyamauchi/cellier/branch/main/graph/badge.svg)](https://codecov.io/gh/kevinyamauchi/cellier)
+
+A workshop for rendering cellular models.

cellier-0.0.2/README.md

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+# cellier
+
+[![License](https://img.shields.io/pypi/l/cellier.svg?color=green)](https://github.com/kevinyamauchi/cellier/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/cellier.svg?color=green)](https://pypi.org/project/cellier)
+[![Python Version](https://img.shields.io/pypi/pyversions/cellier.svg?color=green)](https://python.org)
+[![CI](https://github.com/kevinyamauchi/cellier/actions/workflows/ci.yml/badge.svg)](https://github.com/kevinyamauchi/cellier/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/kevinyamauchi/cellier/branch/main/graph/badge.svg)](https://codecov.io/gh/kevinyamauchi/cellier)
+
+A workshop for rendering cellular models.

cellier-0.0.2/docs/events.md

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+# Events in cellier
+
+## Overview
+Cellier uses events to make sure that the model and view are kept in sync. Cellier has two main types of views. The controls, which are the GUI elements used to modify the state of the viewer model (e.g., selecting a colormap, or the dims sliders) and the renderer, which is a view of the data specified by the viewer model. All events are routed through the `EventBus` class.
+
+## EventBus
+
+The event bus serves as the interface between the model and the views. The models and the views connect their events to the `EventBus`. There are no direct connections between the models and the views. This allows for a clean separation of concerns and makes it easy to add new views or models without modifying existing code.
+
+## Types of events
+- visual model updates: these are emitted by the visual model when its state changes. 
+- visual control updates: these are emitted by GUI elements that modify the state of the visual model.

cellier-0.0.2/docs/making_new_visual.md

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+# Making a new visual
+
+This page describes the steps for creating a new visual type.
+
+1. Make a new DataStore type. This must be a subclass of the `BaseDataStore` class and implement the `get_slice()` method.
+2. Make a new DataStream type. This must be a subclass of the `BaseDataStream` class and implement the `get_data_store_slice()` class.
+3. Make a new visual model (`cellier/models/visuals`)
+4. Make a new constructor function that creates the pygfx WorldObject instance from the visual model. These go in `cellier/render`. See `cellier/render/mesh.py` for an example.
+5. Add the constructor function to the `construct_pygfx_object()` function in `cellier/render/utils.py`. This function takes the visual model and dispatches the correct constructor function.

cellier-0.0.2/examples/make_points_example_config.py

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+"""Script to to create a points viewer configuration."""
+
+import numpy as np
+
+from cellier.models.data_manager import DataManager
+from cellier.models.data_stores.points import PointsMemoryStore
+from cellier.models.data_streams.points import PointsSynchronousDataStream
+from cellier.models.nodes.points_node import PointsNode, PointsUniformMaterial
+from cellier.models.scene.cameras import PerspectiveCamera
+from cellier.models.scene.canvas import Canvas
+from cellier.models.scene.dims_manager import CoordinateSystem, DimsManager
+from cellier.models.scene.scene import Scene
+from cellier.models.viewer import SceneManager, ViewerModel
+
+# make a 4D point cloud
+n_points = 500
+rng = np.random.default_rng(0)
+spatial_coordinates = 50 * rng.uniform(0, 1, (n_points, 3))
+temporal_coordinates = rng.choice(np.arange(10), (n_points, 1))
+coordinates = np.column_stack((temporal_coordinates, spatial_coordinates))
+print(coordinates.shape)
+
+
+# make the points store
+points_store = PointsMemoryStore(coordinates=coordinates)
+
+# make the points stream
+points_stream = PointsSynchronousDataStream(data_store_id=points_store.id, selectors=[])
+
+# make the data_stores manager
+data = DataManager(
+    stores={points_store.id: points_store}, streams={points_stream.id: points_stream}
+)
+
+# make the scene coordinate system
+coordinate_system_3d = CoordinateSystem(
+    name="scene_3d", axis_labels=["t", "z", "y", "x"]
+)
+dims_3d = DimsManager(
+    point=(0, 0, 0, 0),
+    margin_negative=(0, 0, 0, 0),
+    margin_positive=(0, 0, 0, 0),
+    coordinate_system=coordinate_system_3d,
+    displayed_dimensions=(1, 2, 3),
+)
+
+coordinate_system_2d = CoordinateSystem(
+    name="scene_2d", axis_labels=["t", "z", "y", "x"]
+)
+dims_2d = DimsManager(
+    point=(0, 0, 0, 0),
+    margin_negative=(0, 0.5, 0, 0),
+    margin_positive=(0, 0.5, 0, 0),
+    coordinate_system=coordinate_system_2d,
+    displayed_dimensions=(2, 3),
+)
+
+# make the points visual
+points_material_3d = PointsUniformMaterial(
+    size=1, color=(1, 1, 1, 1), size_coordinate_space="data"
+)
+points_visual_3d = PointsNode(
+    name="points_node_3d", data_stream_id=points_stream.id, material=points_material_3d
+)
+
+points_material_2d = PointsUniformMaterial(
+    size=5, color=(1, 1, 1, 1), size_coordinate_space="data"
+)
+points_visual_2d = PointsNode(
+    name="points_node_2d", data_stream_id=points_stream.id, material=points_material_2d
+)
+
+# make the canvas
+camera_3d = PerspectiveCamera()
+canvas_3d = Canvas(camera=camera_3d)
+
+camera_2d = PerspectiveCamera()
+canvas_2d = Canvas(camera=camera_2d)
+
+# make the scene
+scene_3d = Scene(
+    dims=dims_3d, visuals=[points_visual_3d], canvases={canvas_3d.id: canvas_3d}
+)
+scene_2d = Scene(
+    dims=dims_2d, visuals=[points_visual_2d], canvases={canvas_2d.id: canvas_2d}
+)
+
+scene_manager = SceneManager(scenes={scene_3d.id: scene_3d, scene_2d.id: scene_2d})
+
+# make the viewer model
+viewer_model = ViewerModel(data=data, scenes=scene_manager)
+
+print(viewer_model)
+
+viewer_model.to_json_file("points_example_config.json")

cellier-0.0.2/examples/make_single_canvas_config.py

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+"""Script to show how to assemble a viewer model."""
+
+import numpy as np
+
+from cellier.models.data_manager import DataManager
+from cellier.models.data_stores.mesh import MeshMemoryStore
+from cellier.models.data_streams.mesh import MeshSynchronousDataStream
+from cellier.models.nodes.mesh_node import MeshNode, MeshPhongMaterial
+from cellier.models.scene.cameras import PerspectiveCamera
+from cellier.models.scene.canvas import Canvas
+from cellier.models.scene.dims_manager import CoordinateSystem, DimsManager
+from cellier.models.scene.scene import Scene
+from cellier.models.viewer import SceneManager, ViewerModel
+
+# the mesh data_stores
+vertices = np.array([[10, 10, 10], [10, 10, 20], [10, 20, 20]], dtype=np.float32)
+faces = np.array([[0, 1, 2]], dtype=np.float32)
+
+colors = np.array(
+    [
+        [1, 0, 1, 1],
+        [0, 1, 0, 1],
+        [0, 0, 1, 1],
+    ],
+    dtype=np.float32,
+)
+
+# make the mesh store
+mesh_store = MeshMemoryStore(vertices=vertices, faces=faces)
+
+# make the mesh stream
+mesh_stream = MeshSynchronousDataStream(data_store_id=mesh_store.id, selectors=[])
+
+# make the data_stores manager
+data = DataManager(
+    stores={mesh_store.id: mesh_store}, streams={mesh_stream.id: mesh_stream}
+)
+
+# make the scene coordinate system
+coordinate_system = CoordinateSystem(name="scene_0", axis_labels=["z", "y", "x"])
+dims = DimsManager(coordinate_system=coordinate_system, displayed_dimensions=(0, 1, 2))
+
+# make the mesh visual
+mesh_material = MeshPhongMaterial()
+mesh_visual = MeshNode(
+    name="mesh_visual", data_stream_id=mesh_stream.id, material=mesh_material
+)
+
+# make the canvas
+camera = PerspectiveCamera()
+canvas = Canvas(camera=camera)
+
+# make the scene
+scene = Scene(dims=dims, visuals=[mesh_visual], canvases=[canvas])
+scene_manager = SceneManager(scenes={scene.id: scene})
+
+# make the viewer model
+viewer_model = ViewerModel(data=data, scenes=scene_manager)
+
+print(viewer_model)
+
+viewer_model.to_json_file("single_canvas_config.json")