Merge pull request #67 from EnzymeML/v2-migration

PyEnzyme v2.0.0

Author: JR-1991

.github/workflows/build.yml

@@ -0,0 +1,13 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "./pyenzyme"
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "./tests"

.github/workflows/lint.yml

@@ -0,0 +1,29 @@
+name: Unit Tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install pytest-cov openpyxl pytest-httpx  pysces lmfit seaborn numexpr python-libcombine deepdiff
+          pip3 install -e .
+
+      - name: Test with pytest
+        run: |
+          python3 -m pytest -v

.github/workflows/python-publish.yml

@@ -131,15 +131,24 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# pyrightconfig
+pyrightconfig.json
+
 # pytype static type analyzer
 .pytype/
 
 # Cython debug symbols
 cython_debug/
 pyenzyme/Examples/getJSONValid.py
 
-# test dirs 
+# test dirs
 tests/tmp
 
 # PyCharm IDE
-.idea/
+.idea/
+
+# Mac OS
+.DS_Store
+
+# Poetry
+poetry.lock

.github/workflows/stale.yml

@@ -1,18 +1,12 @@
-FROM python:3.9
-WORKDIR /app
-
-COPY . /app
+ARG PYTHON_VERSION=3.11.9
+FROM python:${PYTHON_VERSION}-slim-bullseye
 
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends git \
-    && apt-get install -y --no-install-recommends gcc \
-    && apt-get install -y --no-install-recommends cmake \
-    && apt-get purge -y --auto-remove
+RUN apt-get update
+RUN pip install poetry
 
+WORKDIR /app
+COPY . /app
 
-RUN pip3 install git+https://github.com/EnzymeML/PyEnzyme.git
-RUN pip3 install fastapi uvicorn jinja2
-
-COPY pyenzyme_server.py /app
+RUN poetry install --with tests
 
-CMD ["uvicorn", "pyenzyme_server:app", "--host", "0.0.0.0", "--port", "80"]
+ENTRYPOINT ["poetry", "run", "pytest", "-vv"]