Merge pull request #139 from Clinical-Genomics/deprecate_python3.8

Updated actions using the latest base images and to run using Python 3.9

.github/workflows/black.yml

@@ -9,9 +9,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: install black
         run: |
           pip install black==22.3.0

.github/workflows/dockerhub_stage_push.yml

@@ -15,7 +15,7 @@ jobs:
 
      - name: Get branch name
        id: branch-name
-       uses: tj-actions/branch-names@v7
+       uses: tj-actions/branch-names@v8
 
      - name: Login to Docker Hub
        uses: docker/login-action@v3
@@ -29,7 +29,7 @@ jobs:
 
      - name: Build and push
        if: steps.branch-name.outputs.is_default == 'false'
-       uses: docker/build-push-action@v5
+       uses: docker/build-push-action@v6
        with:
          context: ./
          file: ./Dockerfile

.github/workflows/keep_changelog.yml

@@ -8,7 +8,7 @@ jobs:
   changelog:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - uses: dangoslen/changelog-enforcer@v3
       with:
         changeLogPath: 'CHANGELOG.md'

.github/workflows/lint.yml

@@ -9,9 +9,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@master
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: install flake8
         run: |
           pip install flake8

.github/workflows/test_n_coverage.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8' ]
+        python-version: [ '3.9' ]
     steps:
       - uses: actions/checkout@v4
       - name: Install poetry
@@ -18,7 +18,7 @@ jobs:
           rm install-poetry.py
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'poetry'
@@ -37,7 +37,7 @@ jobs:
         run: poetry run pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           flags: unittests
           files: ./coverage.xml

.github/workflows/vulture.yml

@@ -13,7 +13,7 @@ jobs:
 
       - name: Find changed Python files
         id: files
-        uses: Ana06/get-changed-files@v2.0.0
+        uses: Ana06/get-changed-files@v2.3.0
         with:
           filter: "*.py"
 

CHANGELOG.md

@@ -6,9 +6,12 @@
 - Updated API submission schema to the latest available on `ncbi/clinvar` GitHub pages
 - Modified the json submission example to use one from the ClinVar GitHib repo (`sample_clinical_significance_hgvs_submission.json`)
 - Removed the example of an old json submission (before 2022-11-21) 
+- Updated actions using the latest base images and to run using Python 3.9
+- Docker image uses Python 3.11 instead of 3.8
 ### Fixed
 - Updated issue templates
 - Updated a number of libraries to address all current security advisories
+- Warnings in the Dockerfile
 
 ## [2.6]
 ### Added

Dockerfile

@@ -1,7 +1,7 @@
 ###########
 # BUILDER #
 ###########
-FROM clinicalgenomics/python3.8-venv:1.0 AS BUILDER
+FROM clinicalgenomics/python3.11-venv:1.0 AS builder
 
 # Install and run commands from virtual environment
 RUN python3 -m venv /home/worker/venv
@@ -16,10 +16,10 @@ RUN poetry install --no-interaction
 #########
 # FINAL #
 #########
-FROM clinicalgenomics/python3.8-venv:1.0 AS DEPLOYER
+FROM clinicalgenomics/python3.11-venv:1.0
 
 RUN groupadd --gid 1000 worker && useradd -g worker --uid 1000 --create-home worker
-COPY --chown=worker:worker --from=BUILDER /home/worker/venv /home/worker/venv
+COPY --chown=worker:worker --from=builder /home/worker/venv /home/worker/venv
 
 RUN mkdir /home/worker/app
 WORKDIR /home/worker/app
@@ -37,16 +37,18 @@ ENV GUNICORN_THREADS=1
 ENV GUNICORN_BIND="0.0.0.0:8000"
 ENV GUNICORN_TIMEOUT=400
 
-CMD gunicorn \
-    --workers=$GUNICORN_WORKERS \
-    --worker-class=uvicorn.workers.UvicornWorker \
-    --bind=$GUNICORN_BIND  \
-    --threads=$GUNICORN_THREADS \
-    --timeout=$GUNICORN_TIMEOUT \
-    --proxy-protocol \
-    --forwarded-allow-ips="10.0.2.100,127.0.0.1" \
-    --log-syslog \
-    --access-logfile - \
-    --error-logfile - \
-    --log-level="debug" \
-    preClinVar.main:app
+CMD [ \
+    "gunicorn", \
+    "--workers=${GUNICORN_WORKERS}", \
+    "--worker-class=uvicorn.workers.UvicornWorker", \
+    "--bind=${GUNICORN_BIND}", \
+    "--threads=${GUNICORN_THREADS}", \
+    "--timeout=${GUNICORN_TIMEOUT}", \
+    "--proxy-protocol", \
+    "--forwarded-allow-ips=10.0.2.100,127.0.0.1", \
+    "--log-syslog", \
+    "--access-logfile", "-", \
+    "--error-logfile", "-", \
+    "--log-level=debug", \
+    "preClinVar.main:app" \
+]

README.md

@@ -37,7 +37,7 @@ The server will be running and accepting requests sent from outside the containe
 
 ## Installing the application on a local conda environment
 
-Given a conda environment sontaining python 3.8 and [poetry](https://github.com/python-poetry/poetry), clone the repository from Github with the following command:
+Given a conda environment containing Python 3.9 and [poetry](https://github.com/python-poetry/poetry), clone the repository from Github with the following command:
 
 ```
 git clone https://github.com/Clinical-Genomics/preClinVar.git