Substantial refactoring, linting, CI/CD updates (#107)

* Switching to poetry + ruff

* fixed main.yml

* this will do

* maybe this?

* update lock

* fix: ruff errors

* fix: python version error

* all lint checks pass

* tests should work...

* update pytest version

* new poetry install

* windows ghaction poetry install... work pls

* yml fix

* poetry version=1.8.2

* still fixing main.yml

* maybe it's poetry?

* oh boy!

* kill old unit test ci/cd

* update ci/cd badge

---------

Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com>

.github/workflows/main-ci.yml → .github/workflows/deprecated_ci.yml

@@ -1,7 +1,6 @@
 name: main-ci
 
 on: 
-  pull_request:
   workflow_dispatch:
 
 jobs:

.github/workflows/main.yml

@@ -0,0 +1,129 @@
+name: bob-the-builder
+
+# only run on pushes to main or pull requests
+on:
+  push:
+    # push to any branch *
+    branches: '*'
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+
+  tests:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15 # Consider increasing timeout
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: 
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+        python-version:
+          - '3.10'
+          - '3.11'
+          - '3.12'
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Pip install
+        run: pip install .
+      - name: Run tests
+        run: pip install pytest && pytest tests -v
+
+  cd:
+    permissions:
+        contents: write
+        packages: write
+        issues: write
+        pull-requests: write
+
+    needs: [tests]
+
+    # if pulling to main, deploy to PyPI
+    if: github.ref == 'refs/heads/main'
+
+    # Set up operating system
+    runs-on: ubuntu-latest
+
+    outputs:
+      released: ${{ steps.release.outputs.released }}
+      version: ${{ steps.release.outputs.version }}
+      tag: ${{ steps.release.outputs.tag }}
+
+    # Define job steps
+    steps:
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.12
+
+    - name: Check-out repository
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+  pip-squeak:
+    needs: cd
+    if: needs.cd.outputs.released == 'true'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the code with tag ${{ needs.cd.outputs.tag }}
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ needs.cd.outputs.tag }}
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+
+      - name: Install Package Builder
+        run:
+          python3 -m pip install build
+
+      - name: Build package
+        run:
+          python3 -m build --sdist --wheel --outdir dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          user: ${{ secrets.pypi_token }}
+          password: ${{ secrets.pypi_api }}
+
+
+  does-the-pip-squeak:
+    needs: pip-squeak
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.12", "3.11", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install using PyPi
+        run: |
+          pip install med-imagetools==${{ needs.cd.outputs.version }}
+          autopipeline

.gitignore

@@ -2,6 +2,9 @@
 examples/autotest.py
 .idea
 temp_outputs
+.ruff_cache
+data*
+*built_with*
 
 #vscode files
 /.idea
@@ -10,7 +13,7 @@ temp_outputs
 data
 examples/data/tcia_n*
 scratch.ipynb
-tests/temp
+tests/temp*
 
 # macOS
 .DS_Store

README.md

@@ -1,5 +1,5 @@
 # Med-Imagetools: Transparent and Reproducible Medical Image Processing Pipelines in Python
-[![main-ci](https://github.com/bhklab/med-imagetools/actions/workflows/main-ci.yml/badge.svg)](https://github.com/bhklab/med-imagetools/actions/workflows/main-ci.yml)
+[![CI/CD Status](https://github.com/bhklab/med-imagetools/actions/workflows/main.yml/badge.svg)](https://github.com/bhklab/med-imagetools/actions/workflows/main.yml)
 ![GitHub repo size](https://img.shields.io/github/repo-size/bhklab/med-imagetools)
 ![GitHub contributors](https://img.shields.io/github/contributors/bhklab/med-imagetools)
 ![GitHub stars](https://img.shields.io/github/stars/bhklab/med-imagetools?style=social)