pyphenix 0.1.0__tar.gz

pyphenix-0.1.0/.copier-answers.yml

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+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: v2.0.1
+_src_path: https://github.com/napari/napari-plugin-template
+display_name: PyPhenix
+email: ferrin@calicolabs.com
+full_name: Max Ferrin
+github_repository_url: https://github.com/ferrinm/pyphenix
+github_username_or_organization: ferrinm
+include_reader_plugin: true
+include_sample_data_plugin: false
+include_widget_plugin: true
+include_writer_plugin: true
+install_dependabot: true
+install_precommit: true
+license: GNU GPL v3.0
+module_name: pyphenix
+plugin_name: pyphenix
+short_description: A data loader and widget to visualize high-dimensional data collected
+    on the Opera Phenix

pyphenix-0.1.0/.dir-locals.el

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+;; Set the Jupyter kernel for all jupyter-python blocks in this project
+((jupyter-python-mode . ((org-babel-default-header-args :kernel . "s1_pyphenix"))))
+
+;; tangle source code upon saving
+(org-mode . ((eval . (add-hook 'after-save-hook
+                               (lambda ()
+                                 (when (derived-mode-p 'org-mode)
+                                   (org-babel-tangle)))
+                               nil t)))))

pyphenix-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: "\U0001F41B Bug Report"
+description: Report a bug encountered while using pyphenix
+labels:
+  - "bug"
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to report this issue! 🙏🏼
+
+        Please fill out the sections below to help us reproduce the problem.
+
+  - type: textarea
+    id: bug-report
+    attributes:
+      label: "\U0001F41B Bug Report"
+      description: "Please provide a clear and concise description of the bug."
+      placeholder: "What went wrong? What did you expect to happen?"
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: "\U0001F4A1 Steps to Reproduce"
+      description: "Please provide a minimal code snippet or list of steps to reproduce the bug."
+      placeholder: |
+        1. Go to '...'
+        2. Click on '....'
+        3. Scroll down to '....'
+        4. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: "\U0001F4A1 Expected Behavior"
+      description: "Please provide a clear and concise description of what you expected to happen."
+      placeholder: "What did you expect to happen?"
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: "\U0001F30E Environment"
+      description: |
+        Please provide detailed information regarding your environment. Please paste the output of `napari --info` here or copy  the information from the "napari info" dialog in the napari Help menu.
+
+        Otherwise, please provide information regarding your operating system (OS), Python version, napari version, Qt backend and version, Qt platform, method of installation, and any other relevant information related to your environment.
+
+
+      placeholder: |
+        napari: 0.5.0
+        Platform: macOS-13.2.1-arm64-arm-64bit
+        System: MacOS 13.2.1
+        Python: 3.11.4 (main, Aug 7 2023, 20:34:01) [Clang 14.0.3 (clang-1403.0.22.14.1)]
+        Qt: 5.15.10
+        PyQt5: 5.15.10
+        NumPy: 1.25.1
+        SciPy: 1.11.1
+        Dask: 2023.7.1
+        VisPy: 0.13.0
+        magicgui: 0.7.2
+        superqt: 0.5.4
+        in-n-out: 0.1.8
+        app-model: 0.2.0
+        npe2: 0.7.2
+
+        OpenGL:
+        - GL version: 2.1 Metal - 83
+        - MAX_TEXTURE_SIZE: 16384
+
+        Screens:
+        - screen 1: resolution 1512x982, scale 2.0
+
+        Settings path:
+        - /Users/.../napari/napari_5c6993c40c104085444cfc0c77fa392cb5cb8f56/settings.yaml
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+        label: "\U0001F4A1 Additional Context"
+        description: "Please provide any additional information or context regarding the problem here."
+        placeholder: "Add any other context about the problem here."

pyphenix-0.1.0/.github/ISSUE_TEMPLATE/documentation.md

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+---
+name: "\U0001F4DA Documentation"
+about: Report an issue with pyphenix documentation
+title: ''
+labels: documentation
+assignees: ''
+
+---
+
+## 📚 Documentation
+<!-- A clear and concise description of the documentation that needs to be created/updated -->

pyphenix-0.1.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "\U0001F680 Feature Request"
+about: Submit a proposal/request for a new pyphenix feature
+title: ''
+labels: feature
+assignees: ''
+
+---
+
+## 🚀 Feature
+<!-- A clear and concise description of the feature proposal -->
+
+## Motivation
+
+<!-- Please outline the motivation for the proposal. Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too -->
+
+## Pitch
+
+<!-- A clear and concise description of what you want to happen. -->
+
+## Alternatives
+
+<!-- A clear and concise description of any alternative solutions or features you've considered, if any. -->
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

pyphenix-0.1.0/.github/ISSUE_TEMPLATE/task.md

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+---
+name: "\U0001F9F0 Task"
+about: Maintenance, follow-ups, and other defined to-do items
+title: ''
+labels: task
+assignees: ''
+
+---
+
+## 🧰 Task
+<!-- A clear and concise description of the task -->

pyphenix-0.1.0/.github/PULL_REQUEST_TEMPLATE.md

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+# References and relevant issues
+<!-- What relevant resources were used in the creation of this PR?
+If this PR addresses an existing issue on the repo,
+please link to that issue here as "Closes #(issue-number)"
+If this PR depends on another PR/issue (even in another repo),
+please link to it with "Depends on #PR-number" or "Depends on org/repo#PR-number"
+-->
+
+# Description
+<!-- What does this pull request (PR) do? Is it a new feature, a bug fix,
+an improvement, or something else? Why is it necessary? If relevant, please add
+a screenshot or a screen capture: "An image is worth a thousand words!" -->

pyphenix-0.1.0/.github/dependabot.yml

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+# Dependabot configuration
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuring-dependabot-version-updates#enabling-github-dependabot-version-updates
+# https://til.simonwillison.net/github/dependabot-python-setup
+
+version: 2
+updates:
+  # Monitor pip dependencies
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: monthly
+    groups:
+      python-packages:
+        patterns:
+          - "*"
+
+  # Monitor GitHub Actions and propose updates for security and maintenance
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+    groups:
+      github-actions:
+        patterns:
+          - "*"

pyphenix-0.1.0/.github/workflows/test_and_deploy.yml

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+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup python
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: "true"
+      - name: Install Windows OpenGL
+        uses: pyvista/setup-headless-display-action@v4.2
+        with:
+          qt: true
+          wm: herbstluftwm
+
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        run: uvx --with tox-gh-actions tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+  build-and-inspect-package:
+    name: Build & inspect package.
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  deploy:
+    # this will run when you have tagged a commit, starting with "v*"
+    # and requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    needs: [test, build-and-inspect-package]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Download built artifact to dist/
+        uses: actions/download-artifact@v7
+        with:
+          name: Packages
+          path: dist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

pyphenix-0.1.0/.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/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py
+
+# emacs files
+*.el
+
+# personal testing emacs org-mode file
+README.org

pyphenix-0.1.0/.napari-hub/DESCRIPTION.md

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+<!-- This file is a placeholder for customizing description of your plugin 
+on the napari hub if you wish. The readme file will be used by default if
+you wish not to do any customization for the napari hub listing.
+
+If you need some help writing a good description, check out our 
+[guide](https://github.com/chanzuckerberg/napari-hub/wiki/Writing-the-Perfect-Description-for-your-Plugin)
+-->
+
+The developer has not yet provided a napari-hub specific description.

pyphenix-0.1.0/.napari-hub/config.yml

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+# You may use this file to customize how your plugin page appears
+# on the napari hub: https://www.napari-hub.org/
+# See their wiki for details https://github.com/chanzuckerberg/napari-hub/wiki
+
+# Please note that this file should only be used IN ADDITION to entering
+# metadata fields (such as summary, description, authors, and various URLS)
+# in your standard python package metadata (e.g. setup.cfg, setup.py, or
+# pyproject.toml), when you would like those fields to be displayed
+# differently on the hub than in the napari application.

pyphenix-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: ^\.napari-hub/.*
+      - id: check-yaml # checks for correct yaml syntax for github actions ex.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.3.0
+    hooks:
+      - id: napari-plugin-checks
+  # https://mypy.readthedocs.io/en/stable/
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.9.0
+  #   hooks:
+  #     - id: mypy

pyphenix-0.1.0/.python-version

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+3.13