Merge pull request #73 from guzman-raphael/alpha-release

Fix Publish: Utilize twine creds in pip publish, fix upload url

Author: Synicix

.github/workflows/development.yaml

@@ -85,6 +85,8 @@ jobs:
     env:
       TWINE_USERNAME: ${{secrets.twine_username}}
       TWINE_PASSWORD: ${{secrets.twine_password}}
+    outputs:
+      release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
     steps:
       - uses: actions/checkout@v2
       - name: Determine package version
@@ -104,7 +106,9 @@ jobs:
         run: |
           export HOST_UID=$(id -u)
           docker load < "image-pharus-${PHARUS_VERSION}-py3.8-alpine.tar.gz"
-          docker-compose -f docker-compose-build.yaml run pharus python -m twine upload dist/*
+          docker-compose -f docker-compose-build.yaml run \
+            -e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} pharus \
+            sh -lc "pip install twine && python -m twine upload dist/*"
       - name: Get changelog entry
         id: changelog_reader
         uses: mindsers/changelog-reader-action@v2
@@ -144,7 +148,7 @@ jobs:
           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
+          asset_content_type: application/gzip
   publish-images:
     if: github.event_name == 'push'
     needs: publish-release
@@ -189,7 +193,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
         with:
-          upload_url: ${{needs.publish-release.steps.create_gh_release.outputs.upload_url}}
+          upload_url: ${{needs.publish-release.outputs.release_upload_url}}
           asset_path: "image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-\
             ${{matrix.distro}}.tar.gz"
           asset_name: "image-pharus-${{env.PHARUS_VERSION}}-py${{matrix.py_ver}}-\

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 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
+## [0.1.0a1] - 2021-02-17
 ### Added
 - List schemas method.
 - List tables method.

README.md

@@ -11,28 +11,50 @@
 
 A generic REST API server backend for DataJoint pipelines built on top of `flask`, `datajoint`, and `pyjwt`.
 
-Requirements:
+Usage and API documentation currently available within method docstrings. See Python's `help(...)` utility.
+
+## Requirements for Preferred Setup
+
 - [Docker](https://docs.docker.com/get-docker/  )
 - [Docker Compose](https://docs.docker.com/compose/install/)
 
-## Run Locally
+## Run Locally w/ Docker
 
 - 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: 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 for Development
+## Run Locally w/ Python
+
+- Set environment variables for port assignment (`PHARUS_PORT`, defaults to 5000) and API route prefix (`PHARUS_PREFIX` e.g. `/api`, defaults to empty string).
+- For development, use CLI command `pharus`. This method supports hot-reloading so probably best coupled with `pip install -e ...`.
+- For production, use `gunicorn --bind 0.0.0.0:${PHARUS_PORT} pharus.server:app`.
+
+## Run Tests for Development w/ Docker
 
 - Create a `.env` as appropriate for your setup:
-```shell
-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
-```
+  ```shell
+  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 `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...
 
+## Run Tests for Development w/ Pytest and Flake8
+
+- Set `pharus` testing environment variables:
+  ```shell
+  PKG_DIR=/opt/conda/lib/python3.8/site-packages/pharus # path to pharus installation
+  TEST_DB_SERVER=example.com:3306 # testing db server address
+  TEST_DB_USER=root # testing db server user (needs CRUD on schemas, tables, users)
+  TEST_DB_PASS=unsecure # testing db server password
+  ```
+- For syntax tests, run `flake8 ${PKG_DIR} --count --select=E9,F63,F7,F82 --show-source --statistics`
+- For pytest integration tests, run `pytest -sv --cov-report term-missing --cov=${PKG_DIR} /main/tests`
+- For style tests, run `flake8 ${PKG_DIR} --count --max-complexity=20 --max-line-length=95 --statistics`
+
 ## References
 
 - DataJoint LabBook (a companion frontend)

docker-compose-build.yaml

@@ -13,7 +13,6 @@ services:
         - IMAGE
     volumes:
       - .:/main
-      - ./requirements_package.txt:/tmp/pip_requirements.txt
     command:
       - sh
       - -lc