napari-afmslicer 0.0.1__tar.gz

napari_afmslicer-0.0.1/.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: AFMSlicer
+email: n.shephard@sheffield.ac.uk
+full_name: Neil Shephard
+github_repository_url: https://github.com/ns-rse/napari-afmslicer
+github_username_or_organization: ns-rse
+include_reader_plugin: true
+include_sample_data_plugin: true
+include_widget_plugin: true
+include_writer_plugin: true
+install_dependabot: true
+install_precommit: true
+license: GNU GPL v3.0
+module_name: napari_afmslicer
+plugin_name: napari-afmslicer
+short_description: A simple plugin to use AFMSlicer with napari

napari_afmslicer-0.0.1/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: "\U0001F41B Bug Report"
+description: Report a bug encountered while using napari-afmslicer
+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."

napari_afmslicer-0.0.1/.github/ISSUE_TEMPLATE/documentation.md

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

napari_afmslicer-0.0.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "\U0001F680 Feature Request"
+about: Submit a proposal/request for a new napari-afmslicer 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. -->

napari_afmslicer-0.0.1/.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 -->

napari_afmslicer-0.0.1/.github/PULL_REQUEST_TEMPLATE.md

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+# <!-- Informative Title -->
+
+## 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!" -->
+
+---
+
+## Check list
+
+- [ ] Existing tests pass.
+- [ ] Pre-commit checks pass.
+- [ ] New functions/methods have typehints and docstrings.
+- [ ] New functions/methods have tests which check the intended behaviour is correct.

napari_afmslicer-0.0.1/.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:
+          - "*"

napari_afmslicer-0.0.1/.github/workflows/cd.yml

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+name: CD
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+permissions: {}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+
+      - uses: hynek/build-and-inspect-python-package@v3.0.1
+
+  publish:
+    needs: [dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: Packages
+          path: dist
+
+      - name: Generate artifact attestation for sdist and wheel
+        uses: actions/attest@v4
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # with:
+        #   # Remember to tell (test-)pypi about this repo before publishing
+        #   # Remove this line to publish to PyPI
+        #   repository-url: https://test.pypi.org/legacy/

napari_afmslicer-0.0.1/.github/workflows/test.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: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - 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@v5.1
+        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@v7

napari_afmslicer-0.0.1/.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/
+.vscode/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Environments
+.env
+.venv
+env
+venv/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# ruff
+.ruff_cache/
+
+# OS
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# pytest-testmon
+.testmondata*
+
+# written by setuptools_scm
+**/_version.py
+
+# Emacs
+\#*
+*~
+
+# Other directories
+tmp/

napari_afmslicer-0.0.1/.justfile

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+@default:
+    @just --list
+
+# Profile a test file.
+test_profile:
+    mkdir prof
+    python -m cProfile -o prof/$(git rev-parse HEAD)_$(date +%Y%m%d).prof $(which pytest) tests/test_<file>.py
+
+# uv pip install package with dev group dependencies
+pip_install:
+    uv pip install --editable . --group dev
+
+# Serve mkdocs
+mkdocs:
+    mkdocs serve --watch docs
+
+# Pre-commit ruff-check all files
+pc_ruff:
+    pre-commit run ruff-check --all-files
+
+# Pre-commit numpydoc all files
+pc_npd:
+    pre-commit run numpydoc-validation --all-files
+
+# Pre-commit blacken all files
+pc_black:
+    pre-commit run blacken-docs --all-files
+
+# Pre-commit prettier all files
+pc_prettier:
+    pre-commit run prettier --all-files
+
+# Pre-commit markdownlint-cli2 all files
+pc_markdown:
+    pre-commit run markdownlint-cli2 --all-files
+
+# Pre-commit pylint all files
+pc_pylint:
+    pre-commit run pylint --all-files
+
+# Pytest everything
+pytest:
+    pytest --cov=src --cov-branch --numprocesses=logical
+
+# Pytest with Matplotlib html report
+pytest_mpl_html_report:
+    mkdir -p tmp/mpl
+    pytest tests/test_plotting.py --mpl-generate-summary html --mpl-results-path tmp/mpl
+
+# Pytest update Matplotlib snapshots
+pytest_mpl_update:
+    mkdir -p tests/__mpl_snapshots__/
+    pytest tests/test_plotting.py --mpl-generate-path=tests/__mpl_snapshots__
+    pytest tests/test_classes.py --mpl-generate-path=tests/__mpl_snapshots__
+
+# Pytest update Syrupy snapshots
+pytest_snapshot_update:
+    pytest --snapshot-update
+
+# Pytest update Maplotlib and Syrupy snapshots
+pytest_update:
+    just pytest_mpl_update
+    just pytest_snapshot_update
+
+# uv sync and lock
+uv_upgrade:
+    uv sync
+    uv lock --upgrade

napari_afmslicer-0.0.1/.markdownlint-cli2.yaml

@@ -0,0 +1,22 @@
+# Configuration
+config:
+  line-length:
+    line_length: 120
+    code_blocks: false
+    tables: false
+  html:
+    allowed_elements:
+      - div
+      - br
+
+globs:
+  - "**/*.md"
+
+ignores:
+  - "tmp/"
+  - "paper.md"
+  - ".venv/"
+  - ".github/CONTRIBUTING.md"
+  - ".napari-hub/DESCRIPTION.md"
+
+fix: true

napari_afmslicer-0.0.1/.napari-hub/DESCRIPTION.md

@@ -0,0 +1,9 @@
+<!-- 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.

napari_afmslicer-0.0.1/.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.

napari_afmslicer-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,73 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=18384"]
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+        types: [python, yaml, markdown]
+        exclude: ^(tests/resources|tests/__snapshots__|\.napari-hub)/.*$
+      - id: mixed-line-ending
+        types: [python, yaml, markdown]
+        exclude: ^(tests/resources|tests/__snapshots__|\.napari-hub)/.*$
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: no-commit-to-branch
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+        types: [python, yaml, markdown]
+        exclude: ^(tests/resources|tests/__snapshots__|\.napari-hub)/.*$
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.10
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.10.0
+    hooks:
+      - id: black
+  - repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.3.0
+    hooks:
+      - id: napari-plugin-checks
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.4.3"
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli; python_version<'3.11'
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.11.0
+    hooks:
+      - id: numpydoc-validation
+        # exclude: ""
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.23.3
+    hooks:
+      - id: markdownlint-cli2
+        args: []
+  # 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
+  - repo: local
+    hooks:
+      - id: pylint
+        args: ["--rcfile=.pylintrc.toml"]
+        name: Pylint
+        entry: python -m pylint
+        language: system
+        files: \.py$
+ci:
+  autofix_prs: true
+  autofix_commit_msg: "[pre-commit.ci] Fixing issues with pre-commit"
+  autoupdate_schedule: monthly
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit-autoupdate"
+  skip: [pylint] # Optionally list ids of hooks to skip on CI