Update GHA.

Author: guzman-raphael

.github/workflows/development.yaml

@@ -28,7 +28,7 @@ jobs:
       DOCKER_CLIENT_TIMEOUT: "120"
       COMPOSE_HTTP_TIMEOUT: "120"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Validate version and release notes
         run: |
           DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
@@ -46,7 +46,7 @@ jobs:
           echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
       - if: matrix.py_ver == '3.8' && matrix.distro == 'alpine'
         name: Add pip artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: pip-datajoint-${{env.DJ_VERSION}}
           path: dist
@@ -55,18 +55,19 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # py_ver: ["3.10"]
-        py_ver: ["3.9"]
+        py_ver: ["3.11"]
         mysql_ver: ["8.0", "5.7"]
         include:
-          # - py_ver: "3.9"
-          #   mysql_ver: "5.7"
+          - py_ver: "3.10"
+            mysql_ver: "5.7"
+          - py_ver: "3.9"
+            mysql_ver: "5.7"
           - py_ver: "3.8"
             mysql_ver: "5.7"
           - py_ver: "3.7"
             mysql_ver: "5.7"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{matrix.py_ver}}
         uses: actions/setup-python@v4
         with:
@@ -83,6 +84,7 @@ jobs:
           MYSQL_VER: ${{matrix.mysql_ver}}
           DISTRO: alpine
           MINIO_VER: RELEASE.2021-09-03T03-56-13Z
+          DOCKER_CLIENT_TIMEOUT: "120"
           COMPOSE_HTTP_TIMEOUT: "120"
         run: |
           export HOST_UID=$(id -u)
@@ -103,7 +105,7 @@ jobs:
       DOCKER_CLIENT_TIMEOUT: "120"
       COMPOSE_HTTP_TIMEOUT: "120"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Deploy docs
         run: |
           export MODE=BUILD
@@ -135,7 +137,7 @@ jobs:
     outputs:
       release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{matrix.py_ver}}
         uses: actions/setup-python@v4
         with:
@@ -162,7 +164,7 @@ jobs:
           prerelease: false
           draft: false
       - name: Fetch pip artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: pip-datajoint-${{env.DJ_VERSION}}
           path: dist

.gitignore

@@ -24,7 +24,6 @@ notebook
 .vscode
 __main__.py
 jupyter_custom.js
-apk_requirements.txt
 .eggs
 *.code-workspace
 docs/site

Dockerfile

@@ -1,5 +1,9 @@
-FROM datajoint/djbase
-
-COPY --chown=anaconda:anaconda . /tmp/src
-RUN pip install --no-cache-dir /tmp/src && \
-    rm -rf /tmp/src
+ARG IMAGE
+ARG PY_VER
+ARG DISTRO
+FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO}
+COPY --chown=anaconda:anaconda ./setup.py ./datajoint.pub ./requirements.txt /main/
+COPY --chown=anaconda:anaconda ./datajoint /main/datajoint
+RUN \
+    pip install --no-cache-dir /main && \
+    rm -r /main/*

LNX-docker-compose.yml

@@ -1,12 +1,12 @@
 # docker compose -f LNX-docker-compose.yml --env-file LNX.env up --exit-code-from app --build
-version: '2.2'
+version: '2.4'
 x-net: &net
   networks:
       - main
 services:
   db:
     <<: *net
-    image: datajoint/mysql:$MYSQL_VER
+    image: datajoint/mysql:${MYSQL_VER}
     environment:
       - MYSQL_ROOT_PASSWORD=simple
     # ports:
@@ -15,7 +15,7 @@ services:
     #   - ./mysql/data:/var/lib/mysql
   minio:
     <<: *net
-    image: minio/minio:$MINIO_VER
+    image: minio/minio:${MINIO_VER}
     environment:
       - MINIO_ACCESS_KEY=datajoint
       - MINIO_SECRET_KEY=datajoint
@@ -77,9 +77,8 @@ services:
         set -e
         pip install --user nose nose-cov
         pip install -e .
-        pip freeze | grep datajoint
+        pip list --format=freeze | grep datajoint
         nosetests -vsw tests --with-coverage --cover-package=datajoint
-        # jupyter notebook
     # ports:
     #   - "8888:8888"
     user: ${HOST_UID}:anaconda

apk_requirements.txt

@@ -1,4 +1,4 @@
-# PY_VER=3.8 IMAGE=djbase DISTRO=alpine DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py) HOST_UID=$(id -u) docker compose -f docker-compose-build.yaml up --exit-code-from app --build
+# PY_VER=3.10 IMAGE=djbase DISTRO=debian DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py) HOST_UID=$(id -u) docker compose -f docker-compose-build.yaml up --exit-code-from app --build
 #
 # Intended for updating dependencies and docker image.
 # Used to build release artifacts.
@@ -17,7 +17,7 @@ services:
       - .:/main
     command:
       - sh
-      - -lc
+      - -c
       - |
         set -e
         rm -R build dist *.egg-info || echo "No prev build"

docker-compose-build.yaml

@@ -1,12 +1,12 @@
 # docker compose -f local-docker-compose.yml --env-file LNX.env up --build
-version: '2.2'
+version: '2.4'
 x-net: &net
   networks:
       - main
 services:
   db:
     <<: *net
-    image: datajoint/mysql:$MYSQL_VER
+    image: datajoint/mysql:${MYSQL_VER}
     environment:
       - MYSQL_ROOT_PASSWORD=simple
     # ports:
@@ -16,7 +16,7 @@ services:
     #   - ./mysql/data:/var/lib/mysql
   minio:
     <<: *net
-    image: minio/minio:$MINIO_VER
+    image: minio/minio:${MINIO_VER}
     environment:
       - MINIO_ACCESS_KEY=datajoint
       - MINIO_SECRET_KEY=datajoint
@@ -84,16 +84,14 @@ services:
         set -e
         pip install --user nose nose-cov
         pip install -e .
-        pip freeze | grep datajoint
+        pip list --format=freeze | grep datajoint
         ## You may run the below tests once sh'ed into container i.e. docker exec -it datajoint-python_app_1 sh
         # nosetests -vsw tests; #run all tests
         # nosetests -vs --tests=tests.test_external_class:test_insert_and_fetch; #run specific basic test
         # nosetests -vs --tests=tests.test_fetch:TestFetch.test_getattribute_for_fetch1; #run specific Class test
         # flake8 datajoint --count --select=E9,F63,F7,F82 --show-source --statistics
         # flake8 --ignore=E203,E722,W503 datajoint --count --max-complexity=62 --max-line-length=127 --statistics
         # black datajoint --check -v
-        ## Interactive Jupyter Notebook environment
-        jupyter notebook &
         ## Remote debugger
         set +e
         while true