datajoint · Synicix · Feb 16, 2021 · Feb 16, 2021 · Feb 16, 2021 · Feb 16, 2021
diff --git a/.github/workflows/development.yaml b/.github/workflows/development.yaml
@@ -1,7 +1,9 @@
 name: Development
 on:
-  push:
   pull_request:
+  push:
+    tags:
+      - '*.*.*'
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,27 +17,35 @@ jobs:
       PY_VER: ${{matrix.py_ver}}
       DISTRO: ${{matrix.distro}}
       IMAGE: ${{matrix.image}}
-      HOST_UID: "1001"
       DOCKER_CLIENT_TIMEOUT: "120"
       COMPOSE_HTTP_TIMEOUT: "120"
       AS_SCRIPT: "TRUE"
     steps:
       - uses: actions/checkout@v2
       - name: Compile image
         run: |
-          export DJGUI_API_VERSION=$(cat dj_gui_api_server/version.py | tail -1 | \
-            awk -F\' '{print $2}')
-          docker-compose -f LNX-docker-compose.yaml build
-          IMAGE=$(docker images --filter "reference=datajoint/djgui*" \
+          export PHARUS_VERSION=$(cat pharus/version.py | tail -1 | awk -F\' '{print $2}')
+          export HOST_UID=$(id -u)
+          docker-compose -f docker-compose-build.yaml up --exit-code-from pharus --build
+          IMAGE=$(docker images --filter "reference=datajoint/pharus*" \
             --format "{{.Repository}}")
-          TAG=$(docker images --filter "reference=datajoint/djgui*" --format "{{.Tag}}")
-          docker save "${IMAGE}:${TAG}" | gzip > "djgui_api-py${PY_VER}-${DISTRO}.tar.gz"
+          TAG=$(docker images --filter "reference=datajoint/pharus*" --format "{{.Tag}}")
+          docker save "${IMAGE}:${TAG}" | \
+            gzip > "image-pharus-${PHARUS_VERSION}-py${PY_VER}-${DISTRO}.tar.gz"
+          echo "PHARUS_VERSION=${PHARUS_VERSION}" >> $GITHUB_ENV
       - name: Add image artifact
         uses: actions/upload-artifact@v2
         with:
-          name: ${{format('{0}-py{1}-{2}', 'djgui_api', matrix.py_ver, matrix.distro)}}
-          path: >
-            ${{format('{0}-py{1}-{2}.tar.gz', 'djgui_api', matrix.py_ver, matrix.distro)}}
+          name: image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}}
+          path: "image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-\
+            ${{matrix.distro}}.tar.gz"
+          retention-days: 1
+      - if: matrix.py_ver == '3.8' && matrix.distro == 'alpine'
+        name: Add pip artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: pip-pharus-${{env.PHARUS_VERSION}}
+          path: dist
           retention-days: 1
   test:
     needs: build
@@ -50,56 +60,133 @@ jobs:
       PY_VER: ${{matrix.py_ver}}
       DISTRO: ${{matrix.distro}}
       IMAGE: ${{matrix.image}}
-      HOST_UID: "1001"
       DOCKER_CLIENT_TIMEOUT: "120"
       COMPOSE_HTTP_TIMEOUT: "120"
       AS_SCRIPT: "TRUE"
     steps:
       - uses: actions/checkout@v2
+      - name: Determine package version
+        run: |
+          PHARUS_VERSION=$(cat pharus/version.py | tail -1 | awk -F\' '{print $2}')
+          echo "PHARUS_VERSION=${PHARUS_VERSION}" >> $GITHUB_ENV
       - name: Fetch image artifact
         uses: actions/download-artifact@v2
         with:
-          name: ${{format('{0}-py{1}-{2}','djgui_api', matrix.py_ver, matrix.distro)}}
+          name: image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}}
       - name: Run primary tests
         run: |
-          docker load < "djgui_api-py${PY_VER}-${DISTRO}.tar.gz"
-          export DJGUI_API_VERSION=$(cat dj_gui_api_server/version.py | tail -1 | \
-            awk -F\' '{print $2}')
-          docker-compose -f LNX-docker-compose.yaml up --exit-code-from dj-gui-api-test
-  # publish:
-  #   if: github.event_name == 'push' && github.ref == 'refs/heads/master'
-  #   needs: test
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     matrix:
-  #       include:
-  #         - py_ver: 3.8
-  #           distro: alpine
-  #           image: djbase
-  #   env:
-  #     PY_VER: ${{matrix.py_ver}}
-  #     DISTRO: ${{matrix.distro}}
-  #     IMAGE: ${{matrix.image}}
-  #     DOCKER_USERNAME: ${{secrets.docker_username}}
-  #     DOCKER_PASSWORD: ${{secrets.docker_password}}
-  #   steps:
-  #     - name: Fetch image artifact
-  #       uses: actions/download-artifact@v2
-  #       with:
-  #         name: ${{format('{0}-py{1}-{2}', matrix.conda_ver, matrix.py_ver, matrix.distro)}}
-  #     - name: Publish image
-  #       run: |
-  #         echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
-  #         docker load < "${CONDA_VER}-py${PY_VER}-${DISTRO}.tar.gz"
-  #         IMAGE=$(docker images --filter "reference=datajoint/*" --format "{{.Repository}}")
-  #         TAG=$(docker images --filter "reference=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..."
+          export HOST_UID=$(id -u)
+          docker load < "image-pharus-${PHARUS_VERSION}-py${PY_VER}-${DISTRO}.tar.gz"
+          docker-compose -f docker-compose-test.yaml up --exit-code-from pharus
+  publish-release:
+    if: github.event_name == 'push'
+    needs: test
+    runs-on: ubuntu-latest
+    env:
+      TWINE_USERNAME: ${{secrets.twine_username}}
+      TWINE_PASSWORD: ${{secrets.twine_password}}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Determine package version
+        run: |
+          PHARUS_VERSION=$(cat pharus/version.py | tail -1 | awk -F\' '{print $2}')
+          echo "PHARUS_VERSION=${PHARUS_VERSION}" >> $GITHUB_ENV
+      - name: Fetch pip artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: pip-pharus-${{env.PHARUS_VERSION}}
+      - name: Publish pip release
+        run: python -m twine upload dist/*
+      - name: Get changelog entry
+        id: changelog_reader
+        uses: mindsers/changelog-reader-action@v2
+        with:
+          validation_depth: 10
+          version: ${{steps.tag_name.outputs.current_version}}
+          path: ./CHANGELOG.md
+      - name: Create GH release
+        id: create_gh_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          tag_name: ${{github.ref}}
+          release_name: Release ${{steps.changelog_reader.outputs.version}}
+          body: ${{steps.changelog_reader.outputs.changes}}
+          prerelease: ${{steps.changelog_reader.outputs.status == 'prereleased'}}
+          draft: ${{steps.changelog_reader.outputs.status == 'unreleased'}}
+      - name: Determine pip artifact paths
+        run: |
+          echo "PHARUS_WHEEL_PATH=$(ls dist/pharus-*.whl)" >> $GITHUB_ENV
+          echo "PHARUS_SDIST_PATH=$(ls dist/pharus-*.tar.gz)" >> $GITHUB_ENV
+      - name: Upload pip wheel asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: $${{env.PHARUS_WHEEL_PATH}}
+          asset_name: pip-pharus-${{env.PHARUS_VERSION}}.whl
+          asset_content_type: application/zip
+      - name: Upload pip sdist asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: $${{env.PHARUS_SDIST_PATH}}
+          asset_name: pip-pharus-${{env.PHARUS_VERSION}}.tar.gz
+          asset_content_type: application/zip
+  publish-images:
+    if: github.event_name == 'push'
+    needs: publish-release
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - py_ver: 3.8
+            distro: alpine
+            image: djbase
+    env:
+      PY_VER: ${{matrix.py_ver}}
+      DISTRO: ${{matrix.distro}}
+      IMAGE: ${{matrix.image}}
+      DOCKER_USERNAME: ${{secrets.docker_username}}
+      DOCKER_PASSWORD: ${{secrets.docker_password}}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Determine package version
+        run: |
+          PHARUS_VERSION=$(cat pharus/version.py | tail -1 | awk -F\' '{print $2}')
+          echo "PHARUS_VERSION=${PHARUS_VERSION}" >> $GITHUB_ENV
+      - name: Fetch image artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}}
+      - name: Publish image
+        run: |
+          echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
+          docker load < "image-pharus-${PHARUS_VERSION}-py${PY_VER}-${DISTRO}.tar.gz"
+          IMAGE=$(docker images --filter "reference=datajoint/*" --format "{{.Repository}}")
+          TAG=$(docker images --filter "reference=datajoint/*" --format "{{.Tag}}")
+          docker push "${IMAGE}:${TAG}"
+          docker tag "${IMAGE}:${TAG}" "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
+          docker push "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
+          [ "$PY_VER" == "3.8" ] && [ "$DISTRO" == "alpine" ] \
+                  && docker tag "${IMAGE}:${TAG}" "${IMAGE}:latest" \
+                  && docker push "${IMAGE}:latest" \
+              || echo "skipping 'latest' tag..."
+      - name: Upload image to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{needs.publish-release.steps.create_gh_release.outputs.upload_url}}
+          asset_path: "image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-\
+            ${{matrix.distro}}.tar.gz"
+          asset_name: "image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-\
+            ${{matrix.distro}}.tar.gz"
+          asset_content_type: application/gzip
   # publish-docs:
   #   if: github.event_name == 'push' && github.ref == 'refs/heads/master'
   #   runs-on: ubuntu-latest

diff --git a/.gitignore b/.gitignore
@@ -2,4 +2,7 @@
 *__pycache__
 .vscode
 docker-compose.y*ml
-.coverage
+.coverage
+*.egg-info
+dist
+build
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,13 @@
+# Changelog
+
+Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
+
+## [0.1.0a1] - 2021-02-16
+### Added
+- List schemas method.
+- List tables method.
+- Create, Read, Update, Delete (CRUD) operations for DataJoint table tiers: `dj.Manual`, `dj.Lookup`.
+- Read table records with proper paging and compounding restrictions (i.e. filters).
+- Read table definition method.
+- Support for DataJoint attribute types: `varchar`, `int`, `float`, `datetime`, `date`, `time`, `decimal`, `uuid`.
+- Check dependency utility to determine child table references.
diff --git a/contributing.md → CONTRIBUTING.md b/contributing.md → CONTRIBUTING.md
diff --git a/Dockerfile b/Dockerfile
@@ -4,7 +4,7 @@ ARG IMAGE
 FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO}
 COPY --chown=dja:anaconda ./README.md ./requirements.txt ./setup.py \
     /main/
-COPY --chown=dja:anaconda ./dj_gui_api_server/*.py /main/dj_gui_api_server/
+COPY --chown=dja:anaconda ./pharus/*.py /main/pharus/
 RUN \
     cd /main && \
     pip install . && \
@@ -15,5 +15,12 @@ HEALTHCHECK       \
     --interval=15s \
     CMD           \
         wget --quiet --tries=1 --spider \
-            http://localhost:5000/api/version > /dev/null 2>&1 || exit 1
-CMD ["djgui_api"]
+            http://localhost:${PHARUS_PORT}${PHARUS_PREFIX}/version > /dev/null 2>&1 || exit 1
+ENV PHARUS_PORT 5000
+WORKDIR /main
+
+# development service
+# CMD ["pharus"]
+
+# production service
+CMD ["sh", "-lc", "gunicorn --bind 0.0.0.0:${PHARUS_PORT} pharus.server:app"]
diff --git a/LNX-docker-compose.yaml b/LNX-docker-compose.yaml
diff --git a/README.md b/README.md
@@ -5,39 +5,37 @@
 </p>
 </div>
 
-> :warning: The DJGUI project is still early in its life and the maintainers are currently actively developing with a priority of addressing first critical issues directly related to the deliveries of [Alpha](https://github.com/datajoint/DJ-GUI-API/milestone/1) and [Beta](https://github.com/datajoint/DJ-GUI-API/milestone/2) milestones. Please be advised that while working through our milestones, we may restructure/refactor the codebase without warning until we issue our [Official Release](https://github.com/datajoint/DJ-GUI-API/milestone/3) currently planned as `0.1.0` on `2021-03-31`.
+> :warning: The Pharus project is still early in its life and the maintainers are currently actively developing with a priority of addressing first critical issues directly related to the deliveries of [Alpha](https://github.com/datajoint/pharus/milestone/1) and [Beta](https://github.com/datajoint/pharus/milestone/2) milestones. Please be advised that while working through our milestones, we may restructure/refactor the codebase without warning until we issue our [Official Release](https://github.com/datajoint/pharus/milestone/3) currently planned as `0.1.0` on `2021-03-31`.
 
-# DJ-GUI-API Backend
+# Pharus
 
-Serves as the REST API backend for DJGUI project complimented by [React frontend](https://github.com/datajoint/DJ-GUI-React).
-Built on top of `flask`, `datajoint`, and `pyjwt`.
+A generic REST API server backend for DataJoint pipelines built on top of `flask`, `datajoint`, and `pyjwt`.
 
 Requirements:
 - [Docker](https://docs.docker.com/get-docker/  )
 - [Docker Compose](https://docs.docker.com/compose/install/)
 
 ## Run Locally
 
-- Copy `local-docker-compose.yaml` to `docker-compose.yaml`. This file is untracked so feel free to modify as necessary.
+- Copy a `*-docker-compose.yaml` file corresponding to your usage to `docker-compose.yaml`. This file is untracked so feel free to modify as necessary.
 - Check the first comment which will provide best instruction on how to start the service.
 
-> :warning: The docker-compose file creates a docker network called `dj-gui-api` which is meant to connect the frontend to the backend via reverse proxy for development. Running or installation options currently being considered are [Docker Compose](https://docs.docker.com/compose/install/) and [Electron](https://www.electronjs.org/). Deployment options currently being considered are [Docker Compose](https://docs.docker.com/compose/install/) and [Kubernetes](https://kubernetes.io/docs/tutorials/kubernetes-basics/).
+> :warning: Deployment options currently being considered are [Docker Compose](https://docs.docker.com/compose/install/) and [Kubernetes](https://kubernetes.io/docs/tutorials/kubernetes-basics/).
 
-## Run Tests
+## Run Tests for Development
 
 - Create a `.env` as appropriate for your setup:
 ```shell
-HOST_UID=1000 # Unix UID associated with non-root login
 PY_VER=3.8    # Python version: 3.6|3.7|3.8
 IMAGE=djtest  # Image type:     djbase|djtest|djlab|djlabhub
 DISTRO=alpine # Distribution:   alpine|debian
 AS_SCRIPT=    # If 'TRUE', will not keep container alive but run tests and exit
 ```
-- Navigate to `LNX-docker-compose.yaml` and check first comment which will provide best instruction on how to start the service. Yes, the command is a bit long...
+- Navigate to `test-docker-compose.yaml` and check first comment which will provide best instruction on how to start the service. Yes, the command is a bit long...
 
 ## References
 
-- DJGUI Frontend:
-  - https://github.com/datajoint/DJ-GUI-React
-- Under construction image credits:
+- DataJoint LabBook (a companion frontend)
+  - https://github.com/datajoint/datajoint-labbook
+- Under construction image credits
   - https://www.pngfind.com/mpng/ooiim_under-construction-tape-png-under-construction-transparent-png/
diff --git a/dj_gui_api_server/version.py b/dj_gui_api_server/version.py