Migrate to poetry and pyproject.toml, adopt ruff and pre-commit, reorganize tests and CI, and update docs

.github/workflows/lint.yml

@@ -0,0 +1,33 @@
+name: lint
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.8.3
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Install dependencies
+        run: poetry install --no-root --no-interaction --only dev
+
+      - name: Run linting
+        run: poetry run make lint

.github/workflows/test.yml

@@ -0,0 +1,45 @@
+name: test
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - 'v*'
+  pull_request:
+    branches:
+      - master
+
+  workflow_dispatch:
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        # TODO: Consider testing on macOS and Windows.
+        os: [ubuntu-latest] #, macos-latest, windows-latest]
+        # TODO: Consider testing on Python 3.9 - 3.12.
+        python-version: ["3.12"]
+        poetry-version: ["1.8.3"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Setup a local virtual environment
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry config virtualenvs.in-project true --local
+      - uses: actions/cache@v3
+        name: Cache dependencies
+        with:
+          path: ./.venv
+          key: venv-${{ hashFiles('poetry.lock') }}
+      - name: Install project dependencies
+        run: poetry install --no-interaction
+      - name: Run tests
+        run: poetry run pytest

.gitignore

@@ -19,8 +19,6 @@ readlif.egg-info
 #Ignore all compiled python files (e.g. from running the unit tests):
 *.pyc
 *.pyo
-*.py{}
-*.py-e
 
 #Ignore testing files
 ignore.py
@@ -29,4 +27,4 @@ ignore.py
 htmlcov
 
 #Ignore testing files that I don't have permission to share
-tests/private/*
+tests/private/*

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+exclude: (/ignore/|/dist/)
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: debug-statements
+      - id: trailing-whitespace
+      - id: mixed-line-ending
+      - id: end-of-file-fixer
+
+  - repo: local
+    hooks:
+      - id: format
+        name: Format
+        entry: make format
+        language: system
+        pass_filenames: false
+
+      - id: lint
+        name: Lint
+        entry: make lint
+        language: system
+        pass_filenames: false

.readthedocs.yml

@@ -20,4 +20,4 @@ formats: all
 python:
   version: 3.7
   install:
-    - requirements: docs/requirements.txt
+    - requirements: docs/requirements.txt

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "editor.formatOnSave": false
+}

CHANGELOG.md

@@ -0,0 +1,71 @@
+
+## Changelog
+
+#### 0.6.5
+- Added a new attribute `settings` to `LifImage` which contains useful capture settings (Thanks to PR from @tmtenbrink).
+
+#### 0.6.4
+- Fixed bug and incompatibility in 0.6.3.
+- Added preliminary fix for images captured with stage navigator.
+
+#### 0.6.3
+- Added support for updated LasX with additional data in the LIF file.
+- Changed the way file names are assigned, now includes folder path. This fix is intended to clarify imaging sets with many duplicate names.
+
+#### 0.6.2
+- Fixed bug where the time and image scale were calculated incorrectly.
+- Clarified scaling documentation.
+
+#### 0.6.1
+- Update readme.
+
+#### 0.6.0
+- Added support for non-XY images with `get_plane()`. See docs for usage. Note: Reading arbitrary planes (i.e. an XZ plane of an XY image) is not yet supported.
+
+#### 0.5.2
+- Bugfix: Fix error in mosaic parsing. `PosX` metadata was incorrectly read from `PosY`.
+
+#### 0.5.1
+- Bugfix: switch from `io.BufferedIOBase` to `io.IOBase`.
+
+#### 0.5.0
+- Added support for loading files from buffers (thanks to PR from @JacksonMaxfield).
+
+#### 0.4.1
+- Fixed critical documentaiton error: `LifImage.scale` is in px/µm, not px/nm for X and Y dimensions.
+
+#### 0.4.0
+- Added support for tiled images:
+    - `m` was added as a new dimension (for tiled images).
+    - `LifImage` changes:
+        - New `get_iter_m()` function.
+        - New `mosaic_position` attribute with `(FieldX, FieldY, PosX, PosY)`.
+- Under the hood changes:
+    - `LifImage.dims` is now a named tuple for clearer code.
+- Other changes:
+    - Prettier outputs for `repr()`.
+    - Switch to github CI.
+
+#### 0.3.1
+- Added error message for tiled images, pending feature addition.
+
+#### 0.3.0
+- Added support for 16-bit images, increased minimum Pillow version to 7.2.0.
+    - New `LifImage` attribute `bit_depth` is a tuple of intigers descibing the bit depth for each channel in the image.
+    - Thanks to @DirkRemmers for providing the example file.
+- Changed type from `str` to `int` for `dims` and `channels` in the `info` dictionary.
+- Added python 3.9 to build testing.
+
+#### 0.2.1
+- Fixed `ZeroDivisionError` when the Z-dimension is defined, but has a length of 0.
+- Clarified an error message.
+- Added fix for truncated files.
+
+#### 0.2.0
+- `LifImage.scale` now returns px/nm conversions.
+
+#### 0.1.1
+- Style changes.
+
+#### 0.1.0
+- Initial release.