Merge branch 'master' of github.com:Clinical-Genomics/cg into remove-…

…concatenation-balsamic

.bumpversion.cfg

@@ -1,10 +1,10 @@
 [bumpversion]
-current_version = 51.9.6
+current_version = 51.9.7
 commit = True
 tag = True
 tag_name = v{new_version}
 message = Bump version: {current_version} → {new_version} [skip ci]
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
 [bumpversion:file:cg/__init__.py]

.github/workflows/build_and_publish.yml

@@ -18,23 +18,16 @@ jobs:
         with:
           python-version: "3.11"
 
-      - name: Install build tools
-        run: >-
-          python -m
-          pip install
-          wheel
-          twine
-          --user
-
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python
-          setup.py
-          sdist
-          bdist_wheel
-
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
         with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
+          virtualenvs-create: false
+
+      - name: Build and Publish Distribution to PyPI 📦
+        env:
+          PYPI_USERNAME: __token__
+          PYPI_PASSWORD: ${{ secrets.pypi_password }}
+        run: |
+          poetry publish --no-interaction --build \
+            --username $PYPI_USERNAME \
+            --password $PYPI_PASSWORD

.github/workflows/installations.yml

@@ -19,21 +19,20 @@ jobs:
         with:
           python-version: ${{ matrix.python-version}}
 
-      - name: Install and Upgrade Pip
-        run: |
-          python -m pip install --upgrade pip
-          echo ${{ matrix.python-version}}
-          pip --version
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: false
 
       - name: Cache Dependencies
         uses: actions/cache@v3
         id: cache
         with:
           path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('**/requirements*.txt') }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }}
 
       - name: Install Dependencies
         if: steps.cache.outputs.cache-hit != 'true'
         run: |
-          pip install -r requirements.txt -r requirements-dev.txt
-          pip check
+          poetry install --no-interaction
+          poetry check

.github/workflows/tests_and_coverage.yml

@@ -19,18 +19,21 @@ jobs:
         with:
           python-version: "3.11"
 
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: false
+
       - name: Cache dependencies
         uses: actions/cache@v3
         id: cache
         with:
           path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('**/requirements*.txt') }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }}
 
       - name: Install Dependencies
         if: steps.cache.outputs.cache-hit != 'true'
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt -r requirements-dev.txt
+        run: poetry install --no-interaction
 
       - name: Test with pytest & Coveralls
         run: |

CONTRIBUTING.md

@@ -97,6 +97,10 @@ Enhancement suggestions are tracked as [GitHub issues](https://guides.github.com
 
 First of all, make sure that you are managing your python versions that are used on your machine, [never use the OS native python](https://docs.python-guide.org/starting/installation/). Suggested ways to handle python version are either through [homebrew](https://brew.sh/#install)(OSX), [pyenv](https://github.com/pyenv/pyenv) or [conda](https://docs.anaconda.com/anaconda/install/).
 
+For local development, it is recommended to use Poetry. Ensure that you have Poetry installed and run
+```bash
+poetry install
+```
 
 On our servers where the production and stage versions of CG are run the packages are maintained by using conda environments. For local development it is suggested to follow the [python packaging guidelines](https://packaging.python.org/tutorials/managing-dependencies/) where it is suggested to manage your local python environment with [pipenv](https://pipenv.pypa.io/en/latest/). CG has a Pipfile.lock file which will ensure that the installation will work if the environment is set up in the correct way. To use a **combination of conda and pipenv** make sure that you point to the conda installation of python when creating your pipenv virtual environment (`pipenv --python=$(conda run which python) --site-packages`) more about that [here](https://pipenv.pypa.io/en/latest/advanced/#pipenv-and-other-python-distributions) and in [this](https://stackoverflow.com/questions/50546339/pipenv-with-conda) stack overflow thread. (It is not necessary to use conda on for local development)
 

Dockerfile

@@ -28,13 +28,14 @@ ENV GOOGLE_OAUTH_CLIENT_SECRET="1"
 
 
 WORKDIR /home/src/app
-COPY cg ./cg
-COPY templates ./templates
-COPY MANIFEST.in pyproject.toml requirements* setup.py ./
+COPY pyproject.toml poetry.lock ./ 
 
+RUN pip install --no-cache-dir poetry \
+    && poetry config virtualenvs.create false \
+    && poetry install --no-interaction --no-ansi
 
-RUN pip install -r requirements.txt
-RUN pip install -e .
+COPY cg ./cg
+COPY templates ./templates
 
 CMD gunicorn \
     --workers=$GUNICORN_WORKERS \

Dockerfile-cli

@@ -4,8 +4,14 @@ RUN addgroup --system nonroot \
     && adduser --system --ingroup nonroot nonroot
 
 WORKDIR /app
-COPY . /app/
 
-RUN pip install .
+RUN pip install --no-cache-dir poetry
+
+COPY pyproject.toml poetry.lock /app/
+
+RUN poetry config virtualenvs.create false \
+    && poetry install --no-dev --no-interaction --no-ansi
+
+COPY . /app/
 
-USER nonroot
+USER nonroot

README.md

@@ -21,27 +21,18 @@ Please check out our [guide for contributing to cg](CONTRIBUTING.md)
 
 ## Installation
 
-Cg written in Python 3.6+ and is available on the [Python Package Index][pypi] (PyPI).
+Cg written in Python 3.9+ and is available on the [Python Package Index][pypi] (PyPI).
 
 ```bash
 pip install cg
 ```
 
-If you would like to install the latest development version:
+If you would like to install the latest development version, use [poetry](https://python-poetry.org/docs/).
 
 ```bash
 git clone https://github.com/Clinical-Genomics/cg
 cd cg
-```
-To install CG either use pipenv (as described in contributing) and run
-```bash
-pipenv install -e .
-```
-
-or (without pipenv)
-
-```bash
-pip install -r requirements-dev.txt --editable .
+poetry install
 ```
 
 

cg/__init__.py

@@ -1,4 +1,2 @@
-import pkg_resources
-
 __title__ = "cg"
-__version__ = "51.9.6"
+__version__ = "51.9.7"