playNano 0.1.0__tar.gz

playnano-0.1.0/.flake8

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+# .flake8
+[flake8]
+extend-ignore = D202, D203, D211, D213, E203, E213, E266, E501, W503
+max-line-length = 88
+exclude = .git,__pycache__,build,dist,.venv,docs, docs/**, notebooks, *.ipynb, *.oft, *ttf,
+max-complexity = 22

playnano-0.1.0/.gitattributes

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+# Enforce Unix-style line endings for source code and docs
+*.py     text eol=lf
+*.md     text eol=lf
+*.txt    text eol=lf
+*.yml    text eol=lf
+*.toml   text eol=lf
+
+# Fonts are binary – no conversion
+*.otf    binary
+*.ttf    binary

playnano-0.1.0/.github/workflows/docs.yaml

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+name: docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install -e .[docs]
+
+      - name: Build HTML docs
+        run: sphinx-build docs docs/_build/html
+
+      - name: Configure Git
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Deploy to GitHub Pages
+        if: github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html

playnano-0.1.0/.github/workflows/pre-commit.yaml

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+name: Run pre-commit hooks
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Install markdownlint-cli
+        run: npm install -g markdownlint-cli
+
+      - name: Clear pre-commit cache
+        run: pre-commit clean
+
+      - name: Cache pre-commit
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: ${{ runner.os }}-pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+          restore-keys: |
+            ${{ runner.os }}-pre-commit-
+
+      - name: Run pre-commit hooks
+        run: pre-commit run --all-files --show-diff-on-failure

playnano-0.1.0/.github/workflows/test.yaml

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+name: Run Tests and Upload Coverage
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.10', '3.11', '3.12']
+      fail-fast: false
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies on Linux
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libegl1 libxrender1 libxext6 libx11-6
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+          pip install numpy h5py Pillow matplotlib afmreader
+          pip install pytest>=7.0 pytest-cov pytest-qt flake8 pre-commit
+
+      - name: Run tests with coverage
+        run: |
+          pytest --cov=playNano --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          flags: unittests
+          name: playNano-tests-${{ matrix.os }}-py${{ matrix.python-version }}
+          fail_ci_if_error: true

playnano-0.1.0/.gitignore

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+# Logs
+*.log
+
+# Python cache/compiled files
+__pycache__/
+*.py[cod]
+
+# Ruff / linting cache
+.ruff_cache/
+
+# OS-specific
+.DS_Store
+Thumbs.db
+
+# Editor / IDE settings
+.vscode/
+.idea/
+
+# Virtual environments
+.venv/
+env/
+*.env
+
+# Test / coverage / CI artifacts
+htmlcov/
+.tox/
+.nox/
+.coverage*
+.cache/
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Documentation builds
+docs/_build/
+
+# Jupyter notebook checkpoints
+**/.ipynb_checkpoints/
+
+# Build & distribution artifacts
+build/
+dist/
+*.egg-info/

playnano-0.1.0/.markdownlint.yaml

@@ -0,0 +1,8 @@
+default: true
+
+MD013:
+  line_length: 120
+
+MD033:
+  allowed_elements:
+    - div

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

@@ -0,0 +1,50 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: ^(docs/|tests/resources/spm_folder_0|src/playNano/fonts/|LICENSE)
+      - id: end-of-file-fixer
+        exclude: ^(docs/|tests/resources/spm_folder_0|src/playNano/fonts/|LICENSE)
+      - id: check-yaml
+        exclude: ^(docs/|src/playNano/fonts/|LICENSE)
+      - id: check-added-large-files
+        exclude: ^(docs/|src/playNano/fonts/|LICENSE)
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+        name: isort (python import sorting)
+        language_version: python3.11
+        exclude: ^(docs/|src/playNano/fonts/|LICENSE)$
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.7
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+        additional_dependencies: [ "ruff>=0.0.285" ]
+        exclude: ^(docs/|notebooks/|src/playNano/fonts/|LICENSE)$
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3.11
+        exclude: ^(docs/|src/playNano/fonts/|LICENSE)$
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-docstrings]
+        exclude: ^(docs/|src/playNano/fonts/|LICENSE)$
+
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.18.1
+    hooks:
+      - id: markdownlint-cli2
+        args: [--fix]
+        exclude: ^(docs/|src/playNano/fonts/|LICENSE)$

playnano-0.1.0/CHANGELOG.md

@@ -0,0 +1,74 @@
+<!-- markdownlint-disable MD033 MD024-->
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+- Next change in the project
+
+## [0.1.0] - 2025-09-17
+
+### Added
+
+- First public release 🎉
+
+- **AFM data loading & playback**
+  - Load HS‑AFM videos from .h5-jpk and .asd files and folders of .spm and .jpk files.
+  - Time‑aware frame navigation and consistent pixel/scale metadata.
+
+- **Processing pipeline with masks & full provenance**
+  - Sequential filters and masks (e.g., plane removal, row/median alignment, polynomial flatten, Gaussian filtering).
+  - Each step is recorded with index, name, parameters, timestamps, and environment details under `stack.provenance`.
+  - Processed snapshots and masks are stored with ordered keys like `step_<n>_<name>` for reliable inspection and re‑use.
+
+- **Reproducible export & re‑import (analysis‑ready)**
+  - Save the current stack state (with stages, masks, and provenance) to **HDF5 (`.h5`)** or **NumPy bundles (`.npz`)**.
+  - Re‑load bundles later to continue processing and run analyses with the full history intact.
+  - Export to **OME‑TIFF** for interoperability and to **GIF** (with optional scale bars)
+    for quick sharing and presentation.
+
+- **Interactive GUI (PySide6) for exploration**
+  - Real‑time playback, frame seeking, and snapshot previews.
+  - **Z‑range control** (auto or manual) to maintain consistent height scaling across frames.
+  - **Annotations/overlays** (i.e. timestamps, raw data label, scale bar) rendered on top of frames.
+  - Built‑in dark theme stylesheet for high‑contrast analysis.
+
+- **Analysis framework**
+  - Build analysis pipelines from built-in and pluggable analysis modules.
+  - Built-in analysis modules (e.g., LoG blob detection, DBSCAN/K‑Means/X‑Means clustering, particle tracking).
+  - Produces labeled masks, per‑feature properties (area, min/max/mean, bbox, centroid), and summary statistics.
+  - Analysis outputs are keyed and traced in provenance for reproducibility.
+
+- **Command Line Interface (CLI)**
+  - `playnano` entrypoint to run processing pipelines, export bundles (TIFF/NPZ/HDF5), and create GIFs from the shell.
+
+- **Notebooks**
+  - Jupyter notebooks included to demonstrate programmatic workflow.
+  - Overview notebook covers the whole loading, processing, analysis and export workflow.
+  - Processing notebook focuses on processing and export of loaded data.
+
+- **Documentation**:
+  - Created a Sphinx documentation site on GitHub Pages.
+  - **User Guide** covering installation, quick start, GUI and CLI usage, processing, analysis and exports.
+  - **API Reference** generated with `sphinx-autoapi` for all packages.
+  - **CLI reference** with examples and typical workflows.
+  - Furo theme and MyST Markdown configuration for a clean, consistent look.
+
+### Changed
+
+- N/A (initial public release).
+
+### Fixed
+
+- N/A (initial public release).
+
+---
+
+[Unreleased]: https://github.com/derollins/playNano/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/derollins/playNano/releases/tag/v0.1.0