Feature/python 3 10

.github/workflows/dependabot-auto-merge.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - name: Dependabot metadata
         id: metadata
-        uses: dependabot/fetch-metadata@v1.3.5
+        uses: dependabot/fetch-metadata@v1.5.1
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Wait other jobs are passed or failed

.github/workflows/docs.yml

@@ -13,15 +13,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - uses: rojopolis/spellcheck-github-actions@0.29.0
+    - uses: rojopolis/spellcheck-github-actions@0.33.0
       name: Spellcheck
 
   code_docs:
     strategy:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.10"]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/int.yml

@@ -9,7 +9,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.10"]
 
     runs-on: ${{ matrix.os }}
 
@@ -39,7 +39,7 @@ jobs:
         driver-opts: network=host
 
     - name: Build
-      uses: docker/build-push-action@v3
+      uses: docker/build-push-action@v4
       with:
         context: .
         push: true

.github/workflows/publish.yml

@@ -37,7 +37,7 @@ jobs:
             type=ref,event=tag
 
       - name: Build and push
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v4
         with:
           context: .
           file: ./Dockerfile
@@ -51,7 +51,7 @@ jobs:
             org.opencontainers.image.revision=${{ github.sha }}
 
       - name: Build and push dataloader
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v4
         with:
           run: |
             pushd deploy/dataloader

.github/workflows/style.yml

@@ -8,7 +8,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.10"]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/unit.yml

@@ -11,7 +11,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.10"]
 
     runs-on: ${{ matrix.os }}
 
@@ -29,7 +29,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install tox tox-gh-actions coverage
-    - name: Run unit tests for python 3.8
+    - name: Run unit tests for python 3.10
       run: |
         tox -e unit_tests
         coverage lcov -o lcov.info

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-alpine3.15 as BUILD
+FROM python:3.10.12-alpine3.18 as BUILD
 
 RUN apk add --update \
     && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev\
@@ -18,7 +18,7 @@ COPY setup.py /root/beacon/setup.py
 COPY beacon_api /root/beacon/beacon_api
 RUN pip install /root/beacon
 
-FROM python:3.8-alpine3.15
+FROM python:3.10.12-alpine3.18
 
 RUN apk add --no-cache --update bash
 
@@ -29,7 +29,7 @@ LABEL org.label-schema.vcs-url="https://github.com/CSCFI/beacon-python"
 RUN apk add --update \
     && apk add --no-cache curl bzip2 xz
 
-COPY --from=BUILD usr/local/lib/python3.8/ usr/local/lib/python3.8/
+COPY --from=BUILD usr/local/lib/python3.10/ usr/local/lib/python3.10/
 
 COPY --from=BUILD /usr/local/bin/gunicorn /usr/local/bin/
 

README.md

@@ -10,7 +10,7 @@ Documentation: https://beacon-python.readthedocs.io
 ### Quick start
 
 `beacon-python` Web Server requires:
-* Python 3.8+;
+* Python 3.10+;
 * running DB [PostgreSQL Server](https://www.postgresql.org/) 9.6+ (recommended 13).
 
 ```shell

beacon_api/app.py

@@ -135,7 +135,7 @@ def main():
 
 
 if __name__ == "__main__":
-    if sys.version_info < (3, 8):
-        LOG.error("beacon-python requires python 3.8")
+    if sys.version_info < (3, 10):
+        LOG.error("beacon-python requires python 3.10")
         sys.exit(1)
     main()

beacon_api/extensions/mate_name.py

@@ -45,7 +45,6 @@ async def fetch_fusion_dataset(db_pool, assembly_id, position, chromosome, refer
                     db_response = await statement.fetch(datasets_query, access_query, assembly_id, chromosome)
 
                 else:
-
                     # UBER QUERY - TBD if it is what we need
                     # referenceBases, alternateBases and variantType fields are NOT part of beacon's specification response
                     query = """SELECT a.datasetId as "datasetId", b.accessType as "accessType", a.chromosome as "referenceName",

docs/instructions.rst

@@ -3,7 +3,7 @@ Instructions
 
 .. note:: In order to run ``beacon-python`` Web Server requirements are as specified below:
 
-  * Python 3.8+;
+  * Python 3.10+;
   * running DB `PostgreSQL Server <https://www.postgresql.org/>`_  9.6+ (recommended 13).
 
 .. _env-setup:

docs/optionals.rst

@@ -10,7 +10,7 @@ Handover Protocol
 
 The handover protocol is a feature comparable to `HATEOAS and HAL <https://restfulapi.net/hateoas/>`_. It can be used to convey
 extra information regarding the Beacon service, or the dataset response.
-More information about the handover protocol can be read from the `Beacon Project page <https://beacon-project.io/roadmap/handover.html>`_ and
+More information about the handover protocol can be read from the `Beacon Project page <http://docs.genomebeacons.org/handovers/>`_ and
 Beacon Specification's `handover issue <https://github.com/ga4gh-beacon/specification/issues/114>`_ at Github.
 
 The handover protocol can be configured in ``config.ini`` as follows:

readthedocs.yml

@@ -4,7 +4,7 @@ build:
     image: latest
 requirements_file: docs/docs.txt
 python:
-   version: 3.8
+   version: 3.10
    use_system_site_packages: true
    setup_py_install: true
    extra_requirements:

requirements.txt

@@ -1,11 +1,11 @@
-aiohttp==3.8.3
+aiohttp==3.8.4
 aiohttp-cors==0.7.0
 asyncpg==0.27.0
 jsonschema==4.17.3
-Cython==0.29.33
+Cython==0.29.35
 cyvcf2==0.30.18
 uvloop==0.17.0
 aiocache==0.11.1
-ujson==5.7.0
+ujson==5.8.0
 Authlib==1.2.0
 gunicorn==20.1.0

setup.py

@@ -33,38 +33,37 @@
         "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "License :: OSI Approved :: Apache Software License",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.10",
     ],
     install_requires=[
         "asyncpg==0.27.0",
-        "aiohttp==3.8.3",
+        "aiohttp==3.8.4",
         "Authlib==1.2.0",
         "aiohttp-cors==0.7.0",
         "jsonschema==4.17.3",
         "gunicorn==20.1.0",
         "uvloop==0.17.0",
         "cyvcf2==0.30.18",
         "aiocache==0.11.1",
-        "ujson==5.7.0",
+        "ujson==5.8.0",
     ],
     extras_require={
         "vcf": [
-            "numpy==1.24.1",
+            "numpy==1.25.0",
             "cyvcf2==0.30.18",
-            "Cython==0.29.33",
+            "Cython==0.29.35",
         ],
         "test": [
-            "coverage==7.0.4",
-            "pytest<7.3",
-            "pytest-cov==4.0.0",
-            "testfixtures==7.0.4",
-            "tox==4.2.6",
+            "coverage==7.2.7",
+            "pytest<7.4",
+            "pytest-cov==4.1.0",
+            "testfixtures==7.1.0",
+            "tox==4.6.2",
             "flake8==6.0.0",
-            "flake8-docstrings==1.6.0",
+            "flake8-docstrings==1.7.0",
             "aioresponses==0.7.4",
-            "black==22.12.0",
+            "black==23.3.0",
         ],
-        "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.1.1"],
+        "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.2"],
     },
 )

tests/test_app.py

@@ -5,7 +5,7 @@
 import json
 from authlib.jose import jwt
 import os
-from test.support import EnvironmentVarGuard
+from test.support.os_helper import EnvironmentVarGuard
 from aiocache import caches
 
 

tests/test_basic.py

@@ -8,7 +8,7 @@
 from beacon_api.permissions.ga4gh import check_ga4gh_token, decode_passport, get_ga4gh_permissions
 from .test_app import PARAMS, generate_token
 from testfixtures import TempDirectory
-from test.support import EnvironmentVarGuard
+from test.support.os_helper import EnvironmentVarGuard
 
 
 def mock_token(bona_fide, permissions, auth):

tox.ini

@@ -56,4 +56,4 @@ commands = py.test  -x --cov=beacon_api tests/ --cov-fail-under=80
 
 [gh-actions]
 python =
-    3.8: flake8, unit_tests, docs, bandit, mypy
+    3.10: flake8, unit_tests, docs, bandit, mypy