Debug 3D to 2D phase reconstruction

.git-blame-ignore-revs

@@ -1,4 +1,8 @@
 # .git-blame-ignore-revs
 # created as described in: https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
-# black-format all `.py` files except recorder_ui.py
-82f6df5ed34460374ce7c0fdca089d8caa570b9f
+
+# black-format files
+07517c3353c392106cabae003d589946ea25918a
+82f6df5ed34460374ce7c0fdca089d8caa570b9f
+aa7050f973f36dc204ea495e105b5432223dc68d
+a3dd7e5e9bc0bed404792e9b241f1639ade76f33

.github/workflows/pr.yml

@@ -0,0 +1,99 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: lint, style, and tests
+
+on:
+  pull_request:
+
+jobs:
+  style:
+    name: Style Check
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black==25.1.0
+      - name: Check code styling with Black
+        run: |
+          black --diff -S -t py310 waveorder
+          black --check -S -t py310 waveorder
+
+  # lint:
+  #   name: Lint Check
+  #   runs-on: ubuntu-latest
+
+  #   strategy:
+  #     matrix:
+  #       python-version: ["3.10"]
+
+  #   steps:
+  #     - uses: actions/checkout@v3
+  #     - name: Set up Python
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install flake8
+  #     - name: Check code with Flake8
+  #       # E203 conflicts with black
+  #       run: |
+  #         flake8 waveorder --extend-ignore=E203
+
+  isort:
+    name: isort Check
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install isort
+      - name: Check code with isort
+        run: |
+          isort --check waveorder
+
+  #   needs: [style, isort] # lint
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       python-version: ["3.10", "3.11", "3.12"]
+
+  #   steps:
+  #     - uses: actions/checkout@v3
+
+  #     - uses: actions/setup-python@v4
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install ".[all,dev]"
+
+  #     - name: Test with pytest
+  #       run: |
+  #         pytest -v
+  #         pytest -v --cov=./ --cov-report=xml

.github/workflows/test.yml

@@ -0,0 +1,45 @@
+name: test
+
+on: [push]
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # https://github.com/napari/cookiecutter-napari-plugin/commit/cb9a8c152b68473e8beabf44e7ab11fc46483b5d
+      - name: Test
+        uses: aganders3/headless-gui@v1
+        with:
+          run: python -m tox
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3

.gitignore

@@ -143,9 +143,15 @@ dmypy.json
 
 # written by setuptools_scm
 */_version.py
-recOrder/_version.py
+waveorder/_version.py
 *.autosave
 
+# images
+*.npz
+*.png
+*.tif[f]
+*.pdf
+
 # example data
 /examples/data_temp/*
 /logs/*

.pre-commit-config.yaml

@@ -1,8 +1,33 @@
 repos:
--   repo: https://github.com/python/black
-    rev: 21.6b0
+# basic pre-commit
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
     hooks:
-    - id: black
-      language_version: python3
-      pass_filenames: false
-      args: [.]
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: check-toml
+      - id: detect-private-key
+# sorting imports
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+# syntax linting and formatting
+  - repo: https://github.com/myint/autoflake
+    rev: v2.1.1
+    hooks:
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports,
+               --ignore-init-module-imports]
+  # - repo: https://github.com/PyCQA/flake8
+  #   rev: 6.0.0
+  #   hooks:
+  #     - id: flake8
+  #       args: [--ignore, "E203,W503", --min-python-version, '3.10']
+  #       additional_dependencies: [flake8-typing-imports==1.12.0]
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black