Adds pyproject.toml using hatch and refactors dockerfile

.github/workflows/package.yaml

@@ -0,0 +1,41 @@
+name: Publish to PyPI
+
+on:
+  push:
+    branches: [ "hatch" ] #main can be added 
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+  id-token: write  # Ensure this permission is available for trusted publishing
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment: release
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - name: Install dependencies
+        run: 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
 *.pyc
 .DS_Store
 src/test.cwl
+__pycache__

Dockerfile

@@ -1,21 +1,52 @@
-FROM ubuntu:20.04
-
-SHELL ["/bin/bash", "-c"]
-ENV BASH_ENV=~/.bashrc                                          \
-    MAMBA_ROOT_PREFIX=/opt/conda                                \
-    PATH=$PATH:/opt/conda/envs/env_cwl_wrapper/bin
-
-# Install basic commands and mamba
-RUN apt-get update                                                                                                          && \
-    apt-get install -y ca-certificates wget bash bzip2 gcc linux-libc-dev libc6-dev curl                                    && \
-    wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba --strip-components=1 && \
-    ./micromamba shell init -s bash -p ~/micromamba                                                                         && \
-    apt-get clean autoremove --yes                                                                                          && \
-    rm -rf /var/lib/{apt,dpkg,cache,log}                                                                                    && \
-    cp ./micromamba /usr/bin
-
-COPY . /tmp
-
-RUN micromamba create -f /tmp/environment.yml                                                                               && \
-    cd /tmp                                                                                                                 && \
-    /opt/conda/envs/env_cwl_wrapper/bin/python setup.py install
+# Stage 1: Build stage
+FROM rockylinux:9.3-minimal AS build
+
+# Install necessary build tools & hatch 
+RUN microdnf install -y curl tar && \
+ 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 && \
+ tar -xzf /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz -C /tmp/ && chmod +x /tmp/hatch
+
+# Stage 2: Final stage
+FROM rockylinux:9.3-minimal
+
+# Install runtime dependencies
+RUN microdnf install -y --nodocs nodejs wget && \
+    microdnf clean all
+
+# install yq
+RUN wget https://github.com/mikefarah/yq/releases/download/v4.44.5/yq_linux_amd64 -O /usr/bin/yq && \
+    chmod +x /usr/bin/yq 
+
+
+# Set up a default user and home directory
+ENV HOME=/home/wrapper
+
+# 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 CWL Wrapper User" wrapper && \
+    mkdir -p /app && \
+    mkdir -p /prod && \
+    chown -R 1001:0 /app && \
+    chmod g+rwx ${HOME} /app
+
+# Copy the hatch binary from the build stage
+COPY --from=build /tmp/hatch /usr/bin/hatch
+
+# Switch to the non-root user
+USER wrapper
+
+# Copy the application files into the /app directory
+COPY --chown=1001:0 . /app
+WORKDIR /app
+
+# Set up virtual environment paths
+ENV VIRTUAL_ENV=/app/envs/wrapper
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+# Prune any existing environments and create a new production environment
+RUN hatch env prune && \
+    hatch env create prod && \
+    rm -fr /tmp/* /app/.git /app/.pytest_cache
+
+# Set the default command to run when the container starts
+CMD ["bash", "-c", "source /app/envs/wrapper/bin/activate && cwl-wrapper"]