Merge pull request #177 from fabricebrito/calrissian-172

Addresses issue #172 introducing hatch and pyproject.toml

.github/workflows/build-and-test.yaml

@@ -0,0 +1,35 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Build & Tests
+on: [push, pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: "pip"
+    - name: Install dependencies
+      run: |
+        # python -m pip install --upgrade pip
+        pip install hatch
+    - name: Cache Hatch
+      id: cache-hatch
+      uses: actions/cache@v3
+      with:
+        path: /home/runner/.local/share/hatch/env/virtual/
+        key: ${{ runner.os }}-hatch
+    - name: Build
+      run: hatch build
+    - name: Test
+      run: |
+        hatch -e test run nose2 --verbose

.github/workflows/package.yaml

@@ -1,65 +1,45 @@
-name: package
+name: Publish to PyPI
+
 on:
   release:
     types: [created]
 
+permissions:
+  contents: read
+
 jobs:
+  deploy:
 
-  version:
     runs-on: ubuntu-latest
-    outputs:
-      app-version: ${{ steps.set-version.outputs.version }}
-    steps:
-    - uses: actions/checkout@v4
-    - run: echo "APP_VERSION=$(python setup.py --version)" >> $GITHUB_ENV
-    - run: echo app version is $APP_VERSION
-    - id: set-version
-      run: echo "::set-output name=version::$APP_VERSION"
 
-  deploy:
-    runs-on: ubuntu-latest
-
+    environment: release
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: '3.10'
+        cache: 'pip'
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python3 -m venv venv
-        . venv/bin/activate
-        pip install setuptools wheel twine
-        pip install -r requirements.txt
-    - name: verify git tag vs. version
-      run: |
-        python3 -m venv venv
-        . venv/bin/activate
-        python setup.py verify        
-    - name: Build
-      run: |
-        . venv/bin/activate
-        python setup.py bdist_wheel --universal
-    - name: Publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_APIKEY }}
-      run: |
-        . venv/bin/activate
-        twine upload dist/*
-
-  container-build:
-    needs: version
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4   
-    - run: echo version ${{needs.version.outputs.app-version}}
-    - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
-    - name: build & push image
-      run: |
-        IMAGE_ID=ghcr.io/duke-gcb/calrissian/calrissian
-        docker build . --file Dockerfile --tag calrissian
-        docker tag calrissian $IMAGE_ID:${{needs.version.outputs.app-version}}
-        docker push $IMAGE_ID:${{needs.version.outputs.app-version}}
-
+        # python -m pip install --upgrade pip 
+        pip install hatch
+    - name: Build package
+      run: hatch build
+    - name: Test package
+      run: hatch -e test run nose2 --verbose
+    - name: Publish package distributions to Test PyPI
+      if: github.ref != 'refs/heads/main'
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        skip-existing: true
+        repository-url: https://test.pypi.org/legacy/
+    - name: Publish package distributions to PyPI
+      if: github.ref == 'refs/heads/main'
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        skip-existing: true
+        repository-url: https://upload.pypi.org/legacy/

.gitignore

@@ -11,3 +11,4 @@ build
 *.whl
 *.zip
 env-calrissian*
+*.tar.gz

CHANGELOG.md

@@ -5,6 +5,33 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [v0.18.0] - 2024-12-13
+
+### Changes
+
+- Drop setup.py and requirements.txt in favour of PEP 517 and 518 by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/177
+
+## [v0.17.2] - 2024-05-02
+
+### Changes
+
+- calls `setup_kubernetes` before `_setup` to set `cudaDeviceCount` by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/170
+
+## [v0.17.1] - 2024-05-02
+
+### Changes
+
+## [v0.17.0] - 2024-05-02
+
+- broken release
+
+### Changes
+
+- Create codemeta.json by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/163
+- Conformance 1.2.1 by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/164
+- Update README.md by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/165
+- adds `cudaVersionMin`, `cudaComputeCapability` in `CUDARequirement` by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/168
+
 ## [v0.16.0] - 2023-11-23
 
 ### Changes

Dockerfile

@@ -1,22 +1,56 @@
-FROM python:3.10.0-slim-buster
-LABEL maintainer="dan.leehr@duke.edu"
+# Stage 1: Build stage
+FROM rockylinux:9.3-minimal AS build
 
-# cwltool requires nodejs
-RUN apt-get update && apt-get install -y nodejs
+# Install necessary build tools
+RUN microdnf install -y curl tar
 
-RUN mkdir -p /app
-COPY . /app
-RUN pip install /app
-WORKDIR /app
+# Download the hatch tar.gz file from GitHub
+RUN curl -L https://github.com/pypa/hatch/releases/latest/download/hatch-x86_64-unknown-linux-gnu.tar.gz -o /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz
+
+# Extract the hatch binary
+RUN tar -xzf /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz -C /tmp/
+
+# Stage 2: Final stage
+FROM rockylinux:9.3-minimal
+
+# Install runtime dependencies
+RUN microdnf install -y --nodocs nodejs && \
+    microdnf clean all
 
-# Create a default user and home directory
+# Set up a default user and home directory
 ENV HOME=/home/calrissian
-# home dir is created by useradd with group (g=0) to comply with
-# https://docs.openshift.com/container-platform/3.11/creating_images/guidelines.html#openshift-specific-guidelines
+
+# Create a user with UID 1001, group root, and a home directory
 RUN useradd -u 1001 -r -g 0 -m -d ${HOME} -s /sbin/nologin \
-      -c "Default Calrissian User" calrissian && \
-  chown -R 1001:0 /app && \
-  chmod g+rwx ${HOME}
+        -c "Default Calrissian User" calrissian && \
+    mkdir -p /app && \
+    mkdir -p /prod && \
+    chown -R 1001:0 /app && \
+    chmod g+rwx ${HOME} /app
+
+# Copy the hatch binary from the build stage
+COPY --from=build /tmp/hatch /usr/bin/hatch
+
+# Ensure the hatch binary is executable
+RUN chmod +x /usr/bin/hatch
 
+# Switch to the non-root user
 USER calrissian
+
+# Copy the application files into the /app directory
+COPY --chown=1001:0 . /tmp
+WORKDIR /tmp
+
+# Set up virtual environment paths
+ENV VIRTUAL_ENV=/app/envs/calrissian
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+# Prune any existing environments and create a new production environment
+RUN cd /tmp && hatch env prune && \
+    hatch env create prod && \
+    rm -fr /tmp/* /tmp/.git /tmp/.pytest_cache
+
+WORKDIR /app
+
+# Set the default command to run when the container starts
 CMD ["calrissian"]

README.md

@@ -63,3 +63,45 @@ When encountering a Kubernetes API exception, Calrissian uses a library to retry
 - `RETRY_MIN`: Default `5`. Minimum interval between retries.
 - `RETRY_MAX`: Default `1200`. Maximum interval between retries.
 - `RETRY_ATTEMPTS`: Default `10`. Max number of retries before giving up.
+
+## For developers
+
+### Installing for Development
+
+Note that for development you can just use [Hatch] directly as described below. 
+
+### Installing Hatch
+
+The main tool that is used for development is [Hatch]. It manages dependencies (in a virtualenv that is created on the fly) and is also the command runner.
+
+So first, [install it][install Hatch]. Ideally in an isolated way with **`pipx install hatch`** (after [installing `pipx`]), or just `pip install hatch` as a more well-known way.
+
+### Running tests
+
+```
+hatch run test:test
+```
+
+Verbose: 
+
+```
+hatch run test:testv
+```
+
+### Running test coverage
+
+```
+hatch run test:cov
+```
+
+### Running calrissian
+
+```
+hatch run calrissian
+```
+
+### Serve the documentation
+
+```
+hatch run docs:serve
+```

calrissian/__about__.py

@@ -0,0 +1 @@
+version="0.18.0"