Merge pull request #183 from mehta-lab/recorder-merge

Merge `recOrder` into `waveorder`

Author: talonchandler

.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 files
 07517c3353c392106cabae003d589946ea25918a
+82f6df5ed34460374ce7c0fdca089d8caa570b9f
+aa7050f973f36dc204ea495e105b5432223dc68d
+a3dd7e5e9bc0bed404792e9b241f1639ade76f33

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: ''
+assignees: ''
+
+---
+
+**Summary and expected behavior**
+
+**Code for reproduction (using python script or command line interface)**
+```
+# paste your code here
+
+```
+
+**Screenshots or steps for reproduction (using napari GUI)**
+
+**Include relevant logs which are created next to the output dir, name of the dataset, yaml file(s) if encountering reconstruction errors.**
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Environment:**
+
+Operating system:
+Python version:
+Python environment (command line, IDE, Jupyter notebook, etc):
+Micro-Manager/pycromanager version:

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,12 @@
+---
+name: Documentation
+about: Help us improve documentation
+title: "[DOC]"
+labels: ''
+assignees: ''
+
+---
+
+**Suggested improvement**
+
+**Optional: Pull request with better documentation**

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FEATURE]"
+labels: ''
+assignees: ''
+
+---
+
+**Problem**
+
+**Proposed solution**
+
+
+**Alternatives you have considered, if any**
+
+**Additional context**
+Note relevant experimental conditions or datasets

.github/workflows/pr.yml

@@ -5,8 +5,6 @@ name: lint, style, and tests
 
 on:
   pull_request:
-    branches:
-      - main
 
 jobs:
   style:
@@ -77,25 +75,25 @@ jobs:
         run: |
           isort --check waveorder
 
-  tests:
-    needs: [style, isort] # lint
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+  #   needs: [style, isort] # lint
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       python-version: ["3.10", "3.11", "3.12"]
 
-    steps:
-      - uses: actions/checkout@v3
+  #   steps:
+  #     - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
+  #     - uses: actions/setup-python@v4
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ".[dev]"
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install ".[all,dev]"
 
-      - name: Test with pytest
-        run: |
-          pytest -v --cov=./ --cov-report=xml
+  #     - name: Test with pytest
+  #       run: |
+  #         pytest -v
+  #         pytest -v --cov=./ --cov-report=xml

.github/workflows/pytests.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

.github/workflows/test.yml

@@ -143,11 +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/*

.gitignore

@@ -1,4 +1,3 @@
-
 repos:
 # basic pre-commit
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -31,4 +30,4 @@ repos:
   - repo: https://github.com/psf/black
     rev: 25.1.0
     hooks:
-      - id: black
+      - id: black

.pre-commit-config.yaml

@@ -43,8 +43,7 @@ identifiers:
   - type: url
     value: 'https://www.napari-hub.org/plugins/recOrder-napari'
     description: >-
-      recOrder-napari plugin for label-free imaging that
-      depends on waveOrder library
+      waveorder plugin for label-free imaging (TODO: update URL)
   - type: doi
     value: 10.1364/BOE.455770
     description: >-