Merge pull request #1012 from A-Baji/switch-to-djtest

Update testing image from pydev to djtest

Author: guzman-raphael

.github/workflows/development.yaml

@@ -18,8 +18,8 @@ jobs:
     strategy:
       matrix:
         include:
-          - py_ver: 3.8
-            distro: alpine
+          - py_ver: '3.9'
+            distro: debian
             image: djbase
     env:
       PY_VER: ${{matrix.py_ver}}
@@ -28,7 +28,7 @@ jobs:
       DOCKER_CLIENT_TIMEOUT: "120"
       COMPOSE_HTTP_TIMEOUT: "120"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Validate version and release notes
         run: |
           DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
@@ -44,9 +44,9 @@ jobs:
           export HOST_UID=$(id -u)
           docker-compose -f docker-compose-build.yaml up --exit-code-from app --build
           echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
-      - if: matrix.py_ver == '3.8' && matrix.distro == 'alpine'
+      - if: matrix.py_ver == '3.9' && matrix.distro == 'debian'
         name: Add pip artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: pip-datajoint-${{env.DJ_VERSION}}
           path: dist
@@ -55,13 +55,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        py_ver: ["3.8"]
+        py_ver: ["3.9"]
         mysql_ver: ["8.0", "5.7"]
         include:
+          - 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:
@@ -76,14 +78,12 @@ jobs:
         env:
           PY_VER: ${{matrix.py_ver}}
           MYSQL_VER: ${{matrix.mysql_ver}}
-          ALPINE_VER: "3.10"
+          DISTRO: alpine
           MINIO_VER: RELEASE.2021-09-03T03-56-13Z
+          DOCKER_CLIENT_TIMEOUT: "120"
           COMPOSE_HTTP_TIMEOUT: "120"
-          COVERALLS_SERVICE_NAME: travis-ci
-          COVERALLS_REPO_TOKEN: fd0BoXG46TPReEem0uMy7BJO5j0w1MQiY
         run: |
           export HOST_UID=$(id -u)
-          export HOST_GID=$(id -g)
           docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app
       - name: Run style tests
         run: |
@@ -101,7 +101,7 @@ 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
@@ -119,8 +119,8 @@ jobs:
     strategy:
       matrix:
         include:
-          - py_ver: 3.8
-            distro: alpine
+          - py_ver: '3.9'
+            distro: debian
             image: djbase
     env:
       PY_VER: ${{matrix.py_ver}}
@@ -133,7 +133,7 @@ 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 ${{matrix.py_ver}}
         uses: actions/setup-python@v4
         with:
@@ -160,7 +160,7 @@ jobs:
           prerelease: false
           draft: false
       - name: Fetch pip artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: pip-datajoint-${{env.DJ_VERSION}}
           path: dist
@@ -192,3 +192,19 @@ jobs:
           docker-compose -f docker-compose-build.yaml run \
             -e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} app \
             sh -lc "pip install twine && python -m twine upload dist/*"
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{secrets.docker_username}}
+          password: ${{secrets.docker_password}}
+      - name: Publish image
+        run: |
+          IMAGE=$(docker images --filter "reference=datajoint/datajoint*" --format "{{.Repository}}")
+          TAG=$(docker images --filter "reference=datajoint/datajoint*" --format "{{.Tag}}")
+          docker push "${IMAGE}:${TAG}"
+          docker tag "${IMAGE}:${TAG}" "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
+          docker push "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
+          [ "$PY_VER" == "3.9" ] && [ "$DISTRO" == "debian" ] \
+                  && docker tag "${IMAGE}:${TAG}" "${IMAGE}:latest" \
+                  && docker push "${IMAGE}:latest" \
+              || echo "skipping 'latest' tag..."

.gitignore

@@ -26,4 +26,4 @@ __main__.py
 jupyter_custom.js
 .eggs
 *.code-workspace
-docs/site
+docs/site

CHANGELOG.md

@@ -4,6 +4,7 @@
 * Bugfix - Activating a schema requires all tables to exist even if `create_tables=False` PR [#1058](https://github.com/datajoint/datajoint-python/pull/1058)
 * Update - Populate call with `reserve_jobs=True` to exclude `error` and `ignore` keys - PR [#1062](https://github.com/datajoint/datajoint-python/pull/1062)
 * Add - Support for inserting data with CSV files - PR [#1067](https://github.com/datajoint/datajoint-python/pull/1067)
+* Update - Switch testing image from `pydev` to `djtest` PR [#1012](https://github.com/datajoint/datajoint-python/pull/1012)
 
 ### 0.13.8 -- Sep 21, 2022
 * Add - New documentation structure based on markdown PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)

Dockerfile

@@ -1,13 +1,9 @@
-ARG PY_VER=3.8
-ARG DISTRO=alpine
 ARG IMAGE=djbase
+ARG PY_VER=3.9
+ARG DISTRO=debian
 FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO}
-WORKDIR /main
-COPY --chown=anaconda:anaconda ./requirements.txt ./setup.py \
-    /main/
-COPY --chown=anaconda:anaconda ./datajoint/*.py /main/datajoint/
+COPY --chown=anaconda:anaconda ./setup.py ./datajoint.pub ./requirements.txt /main/
+COPY --chown=anaconda:anaconda ./datajoint /main/datajoint
 RUN \
-    umask u+rwx,g+rwx,o-rwx && \
-    pip install --no-cache-dir . && \
-    rm -R ./*
-CMD ["python"]
+    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
@@ -51,7 +51,7 @@ services:
         condition: service_healthy
   app:
     <<: *net
-    image: datajoint/pydev:${PY_VER}-alpine${ALPINE_VER}
+    image: datajoint/djtest:py${PY_VER}-${DISTRO}
     depends_on:
       fakeservices.datajoint.io:
         condition: service_healthy
@@ -69,23 +69,19 @@ services:
       - PYTHON_USER=dja
       - JUPYTER_PASSWORD=datajoint
       - DISPLAY
-      - COVERALLS_SERVICE_NAME
-      - COVERALLS_REPO_TOKEN
     working_dir: /src
     command:
       - sh
       - -c
       - |
         set -e
-        pip install --user -r test_requirements.txt
+        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
-        coveralls
-        # jupyter notebook
     # ports:
     #   - "8888:8888"
-    user: ${HOST_UID}:${HOST_GID}
+    user: ${HOST_UID}:anaconda
     volumes:
       - .:/src
       - /tmp/.X11-unix:/tmp/.X11-unix:rw

README.md

@@ -128,12 +128,11 @@ the same command as above, but replace `up --build` with `down`.
 
 * Create an `.env` with desired development environment values e.g.
 ``` sh
-PY_VER=3.7
-ALPINE_VER=3.10
+PY_VER=3.9
 MYSQL_VER=5.7
-MINIO_VER=RELEASE.2021-09-03T03-56-13Z
+DISTRO=alpine
+MINIO_VER=RELEASE.2022-01-03T18-22-58Z
 HOST_UID=1000
-HOST_GID=1000
 ```
 * `cp local-docker-compose.yml docker-compose.yml`
 * `docker-compose up -d` (Note configured `JUPYTER_PASSWORD`)

datajoint/diagram.py

@@ -94,7 +94,6 @@ class Diagram(nx.DiGraph):
         """
 
         def __init__(self, source, context=None):
-
             if isinstance(source, Diagram):
                 # copy constructor
                 self.nodes_to_show = set(source.nodes_to_show)
@@ -302,7 +301,6 @@ def _make_graph(self):
             return graph
 
         def make_dot(self):
-
             graph = self._make_graph()
             graph.nodes()
 

datajoint/heading.py

@@ -273,7 +273,6 @@ def _init_from_database(self):
 
         # additional attribute properties
         for attr in attributes:
-
             attr.update(
                 in_key=(attr["in_key"] == "PRI"),
                 database=database,

datajoint/settings.py

@@ -62,7 +62,6 @@
 
 
 class Config(collections.abc.MutableMapping):
-
     instance = None
 
     def __init__(self, *args, **kwargs):

docker-compose-build.yaml

@@ -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=3.9 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"