Refactor: Add dockerfile, fix some type errors, update type annotations, add some error-handling, formatting

.github/workflows/ci-cd.yml

@@ -1,9 +1,14 @@
 name: ci-cd
 
-on: [push, pull_request]
+# only run on pushes to main or pull requests
+on:
+  push:
+    branches: [ "*" ]
+  pull_request:
+    branches: [ main ]
 
 jobs:
-  ci:
+  Unit-Testing:
     # Set up operating system
     runs-on: ubuntu-latest
 
@@ -24,22 +29,23 @@ jobs:
         run: poetry install
 
       - name: Test with pytest
-        run: poetry run pytest tests/ --cov=readii --cov-report=xml
+        # Github action runners now have 4 cores
+        run: poetry run pytest -s -v -n 4 tests/
 
-      - name: Use Codecov to track coverage
-        uses: codecov/codecov-action@v3
-        with:
-          files: ./coverage.xml   # coverage report
+      # Commented out until we have a repo for coverage
+      # - name: Test with pytest
+      #   run: poetry run pytest tests/ --cov=readii --cov-report=xml
 
-      - name: Build documentation
-        run: poetry run make html --directory docs/
+      # - name: Use Codecov to track coverage
+      #   uses: codecov/codecov-action@v3
+      #   with:
+      #     files: ./coverage.xml   # coverage report
 
-  cd:
-    # Only run this job if the "ci" job passes
-    needs: ci
+  Continuous-Deployment:
+    needs: Unit-Testing
 
     # # Only run this job if new work is pushed to "main"
-    # if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    if: github.ref == 'refs/heads/main'
 
     # Set up operating system
     runs-on: ubuntu-latest
@@ -75,32 +81,36 @@ jobs:
           echo "${{ steps.release.outputs.version }}"
           echo "${{ steps.release.outputs.tag }}"
 
-
       - name: Install packaging-related tool
+        if: steps.release.outputs.released == 'true'
         run:
           python3 -m pip install build twine
 
       - name: Build package
+        if: steps.release.outputs.released == 'true'
         run: |
-          poetry version $(git describe --tags --abbrev=0 | sed 's/^v//')
+          poetry version ${{ steps.release.outputs.version }}
           python -m build --sdist --wheel --outdir dist/ .
           ls dist/
 
       - name: Publish to TestPyPI
+        if: steps.release.outputs.released == 'true'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
 
       - name: Test install from TestPyPI
+        if: steps.release.outputs.released == 'true'
         run: |
             pip install \
             --index-url https://test.pypi.org/simple/ \
             --extra-index-url https://pypi.org/simple \
             readii
 
       - name: Publish to PyPI
+        if: steps.release.outputs.released == 'true'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
@@ -130,11 +140,12 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
+        if: steps.release.outputs.released == 'true'
         id: meta
         uses: docker/metadata-action@v3
         with:
           images: |
-            ${{ secrets.BHKLAB_DOCKERHUB_USERNAME }}/readii:${{ steps.release.outputs.tag }}
+            bhklab/readii:${{ steps.release.outputs.tag }}
             ghcr.io/${{ github.repository }}/readii:${{ steps.release.outputs.tag }}
 
       - name: Build
@@ -146,8 +157,8 @@ jobs:
           file: ./Dockerfile
           push: true
           tags: |
-            ${{ secrets.BHKLAB_DOCKERHUB_USERNAME }}/readii:${{ steps.release.outputs.tag }}
-            ${{ secrets.BHKLAB_DOCKERHUB_USERNAME }}/readii:latest
+            bhklab/readii:${{ steps.release.outputs.tag }}
+            bhklab/readii:latest
             ghcr.io/${{ github.repository }}/readii:${{ steps.release.outputs.tag }}
             ghcr.io/${{ github.repository }}/readii:latest
           labels: ${{ steps.meta.outputs.labels }}

CHANGELOG.md

@@ -2,6 +2,21 @@
 
 
 
+## v1.2.0 (2024-03-15)
+
+### Feature
+
+* feat: adding dockerfile and gha to build and deploy ([`b7d6b73`](https://github.com/bhklab/readii/commit/b7d6b734ef6b955e5b61ff2d980a08893dc2dddb))
+
+### Fix
+
+* fix: wrong group in toml ([`b55baab`](https://github.com/bhklab/readii/commit/b55baabb4800e074f0f08684874947052ecb9195))
+
+* fix: test builds and update toml to include this branch ([`af61beb`](https://github.com/bhklab/readii/commit/af61beba9a677a86695268a55bd2887138fb2c59))
+
+* fix: test deployment ([`aa1dcb4`](https://github.com/bhklab/readii/commit/aa1dcb479720f8eec295071ad0b45aedaaf275d2))
+
+
 ## v1.1.3 (2024-03-06)
 
 ### Build

README.md

@@ -1,4 +1,7 @@
 # READII
+![Docker Pulls](https://img.shields.io/docker/pulls/bhklab/readii)
+![GitHub Release](https://img.shields.io/github/v/release/bhklab/readii)
+
 
 **R**adiomic **E**xtraction and **A**nalysis for **DI**COM **I**mages
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "readii"
-version = "1.1.3"
+version = "1.2.0"
 description = "A package to extract radiomic features!"
 authors = ["Katy Scott"]
 license = "MIT"
@@ -21,21 +21,29 @@ pyarrow = "^15.0.0"
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"
 pytest-cov = "^4.1.0"
+pytest-xdist = "^3.5.0"
 jupyter = "^1.0.0"
 myst-nb = {version = "^1.0.0", python = "^3.9"}
 sphinx-autoapi = "^3.0.0"
 sphinx-rtd-theme = "^1.3.0"
 python-semantic-release = "^8.5.2"
 
 [tool.semantic_release]
-version_toml = ["pyproject.toml:tool.poetry.version"] # version location
-branch = "main"                             # branch to make releases of
+version_variables = [
+    "src/readii/__init__.py:__version__",
+]
+version_toml = [
+    "pyproject.toml:tool.poetry.version"
+] # version location
 changelog_file = "CHANGELOG.md"             # changelog file
 dist_path = "dist/"                         # where to put dists
 upload_to_release = true                    # auto-create GitHub release
 remove_dist = false                         # don't remove dists
 patch_without_tag = true                    # patch release by default
 
+[tool.semantic_release.branches.main]
+match = "(main|master)"
+
 [tool.poetry.scripts]
 readii = "readii.pipeline:main"
 

src/readii/__init__.py

@@ -1,3 +1,4 @@
 # read version from installed package
 from importlib.metadata import version
-__version__ = version("readii")
+__version__ = "1.2.0"
+