Fix docs asset upload issue

.github/workflows/development.yaml

@@ -193,6 +193,15 @@ jobs:
           asset_path: ${{env.PHARUS_SDIST_PATH}}
           asset_name: pip-pharus-${{env.PHARUS_VERSION}}.tar.gz
           asset_content_type: application/gzip
+      - name: Upload deploy docker environment
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: docker-compose-deploy.yaml
+          asset_name: docker-compose-deploy.yaml
+          asset_content_type: application/yaml
   publish-images:
     if: github.event_name == 'push'
     needs: publish-release
@@ -287,7 +296,7 @@ jobs:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
         with:
           upload_url: ${{needs.publish-release.outputs.release_upload_url}}
-          asset_path: docs-static-pharus-${PHARUS_VERSION}.zip
-          asset_name: docs-static-pharus-${PHARUS_VERSION}.zip
+          asset_path: "docs-static-pharus-${{env.PHARUS_VERSION}}.zip"
+          asset_name: "docs-static-pharus-${{env.PHARUS_VERSION}}.zip"
           asset_content_type: application/zip
           # fail_on_unmatched_files: true

CHANGELOG.md

@@ -2,19 +2,19 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.1.0b1] - 2021-03-11
+## [0.1.0b2] - 2021-03-12
 
 ### Fixed
 - Fixed behavior where using list_table with a nonexistent schema_name creates it instead of returning an error message (#65) PR #63
 
 ### Changed
-- Contribution policy to follow directly the general DataJoint Contribution Guideline. (#91) PR #94
+- Contribution policy to follow directly the general DataJoint Contribution Guideline. (#91) PR #94, #95
 
 ### Added
-- Issue templates for bug reports and enhancement requests. PR #94
-- Docker environment for documentation build. (#92) PR #94
-- Add Sphinx-based documentation source and fix parsing issues. (#92) PR #94
-- GitHub Actions automation that publishes on release new docs to release and GitHub Pages. (#92) PR #94
+- Issue templates for bug reports and enhancement requests. PR #94, #95
+- Docker environment for documentation build. (#92) PR #94, #95
+- Add Sphinx-based documentation source and fix parsing issues. (#92) PR #94, #95
+- GitHub Actions automation that publishes on release new docs to release and GitHub Pages. (#92) PR #94, #95
 
 ## [0.1.0b0] - 2021-02-26
 
@@ -50,6 +50,6 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 - Support for DataJoint attribute types: `varchar`, `int`, `float`, `datetime`, `date`, `time`, `decimal`, `uuid`.
 - Check dependency utility to determine child table references.
 
-[0.1.0b1]: https://github.com/datajoint/pharus/compare/0.1.0b0...0.1.0b1
+[0.1.0b2]: https://github.com/datajoint/pharus/compare/0.1.0b0...0.1.0b2
 [0.1.0b0]: https://github.com/datajoint/pharus/compare/0.1.0a5...0.1.0b0
 [0.1.0a5]: https://github.com/datajoint/pharus/releases/tag/0.1.0a5

README.rst

@@ -5,100 +5,49 @@ User Documentation
 
     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``.
 
-``pharus`` is a generic REST API server backend for DataJoint pipelines built on top of ``flask``, ``datajoint``, and ``pyjwt``.
+``pharus`` is a generic REST API server backend for `DataJoint <https://datajoint.io>`_ pipelines built on top of ``flask``, ``datajoint``, and ``pyjwt``.
 
 - `Documentation <https://datajoint.github.io/pharus>`_
-- `Package <https://pypi.org/project/pharus/>`_
+- `PyPi Package <https://pypi.org/project/pharus/>`_
+- `Docker Image <https://hub.docker.com/r/datajoint/pharus>`_
+- `Release <https://github.com/datajoint/pharus/releases/latest>`_
 - `Source <https://github.com/datajoint/pharus>`_
 
-Requirements for Preferred Setup
---------------------------------
+Installation
+------------
+
+If you have not done so already, please install the following dependencies.
 
 - `Docker <https://docs.docker.com/get-docker/>`_
 - `Docker Compose <https://docs.docker.com/compose/install/>`_
 
-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. Idea is to commit anything generic but system/setup dependent should go on 'your' version i.e. local UID/GID, etc.
-- Check the first comment which will provide the best instruction on how to start the service; yes, it is a bit long. Note: Any of the keyword arguments prepended to the ``docker-compose`` command can be safely moved into a dedicated ``.env`` and read automatically if they are not evaluated i.e. ``$(...)``. Below is a brief description of the non-evaluated environment variables:
-
-    .. code-block:: bash
-
-        PY_VER=3.8    # Python version: 3.6|3.7|3.8
-        IMAGE=djtest  # Image type:     djbase|djtest|djlab|djlabhub
-        DISTRO=alpine # Distribution:   alpine|debian
-        AS_SCRIPT=    # If 'TRUE', will not keep container alive but run tests and exit
-
-.. note::
-
-    Deployment options currently being considered are `Docker Compose <https://docs.docker.com/compose/install/>`_ and `Kubernetes <https://kubernetes.io/docs/tutorials/kubernetes-basics/>`_.
-
-Run Locally w/ Python
----------------------
-
-- Set environment variables for port assignment (``PHARUS_PORT``, defaults to 5000) and API route prefix (``PHARUS_PREFIX`` e.g. ``/api``, defaults to empty string).
-- For development, use CLI command ``pharus``. This method supports hot-reloading so probably best coupled with ``pip install -e ...``.
-- For production, use ``gunicorn --bind 0.0.0.0:${PHARUS_PORT} pharus.server:app``.
-
-Run Tests for Development w/ Pytest and Flake8
-----------------------------------------------
-
-- Set ``pharus`` testing environment variables:
-
-    .. code-block:: bash
-
-        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 DDL privilege)
-        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``
+Prerequisites
+-------------
 
-Creating Sphinx Documentation from Scratch
-------------------------------------------
+Download the ``docker-compose-deploy.yaml`` docker environment from the source located `here <https://github.com/datajoint/pharus/releases/latest/download/docker-compose-deploy.yaml>`_.
 
-Recommend the follow to be ran within the ``pharus`` container in ``docs`` Docker Compose environment.
+Running the API server
+----------------------
 
-- Run the following commands and complete the prompts as requested.
+To start the API server, use the command:
 
     .. code-block:: bash
 
-        mkdir docs
-        cd docs
-        sphinx-quickstart
-
-- In ``docs/conf.py`` add to the beginning:
-
-    .. code-block:: python
+        PHARUS_VERSION=0.1.0b2 docker-compose -f docker-compose-deploy.yaml up -d
 
-        import os
-        import sys
-        sys.path.insert(0, os.path.abspath('..'))
-
-- In ``docs/conf.py:extensions`` append ``['sphinx.ext.autodoc', 'sphinxcontrib.httpdomain']``. See ``requirements_docs.txt`` and ``docker-compose-docs.yaml`` for details on documentation dependencies.
-- Run the following to automatically generate the API docs:
+To stop the API server, use the command:
 
     .. code-block:: bash
 
-        sphinx-apidoc -o . .. ../tests/* ../setup.py
-
-- Add ``modules`` within the ``toctree`` directive in ``index.rst``.
-- Build the docs by running:
-
-    .. code-block:: bash
-
-        make html
+        PHARUS_VERSION=0.1.0b2 docker-compose -f docker-compose-deploy.yaml down
 
 References
 ----------
 
+- DataJoint
+
+  - https://datajoint.io
+
 - DataJoint LabBook (a companion frontend)
 
   - https://github.com/datajoint/datajoint-labbook
-
-- Python Tutorial for Flask, Swagger, and Automated docs
-
-  - https://realpython.com/flask-connexion-rest-api/#reader-comments

docker-compose-deploy.yaml

@@ -1,5 +1,5 @@
-# PHARUS_VERSION=0.1.0b1 docker-compose -f docker-compose-deploy.yaml pull
-# PHARUS_VERSION=0.1.0b1 docker-compose -f docker-compose-deploy.yaml up -d
+# PHARUS_VERSION=0.1.0b2 docker-compose -f docker-compose-deploy.yaml pull
+# PHARUS_VERSION=0.1.0b2 docker-compose -f docker-compose-deploy.yaml up -d
 #
 # Intended for production deployment.
 # Note: You must run both commands above for minimal outage

docs/dev_notes.rst

@@ -1,4 +1,98 @@
 General Notes
 =============
 
-Dev docs TBD.
+Requirements for Preferred Setup
+--------------------------------
+
+- `Docker <https://docs.docker.com/get-docker/>`_
+- `Docker Compose <https://docs.docker.com/compose/install/>`_
+
+Run Locally w/ Docker
+---------------------
+
+- Copy the docker environment (i.e. ``*-docker-compose.yaml``) of your choice corresponding to your usage to ``docker-compose.yaml``. This file is untracked so feel free to modify as necessary. Idea is to commit anything generic but system/setup dependent should go on 'your' version i.e. local UID/GID, etc.
+- Check the first header comment which will provide the best instruction on how to start the service; yes, it is a bit long. Note: Any of the keyword arguments prepended to the ``docker-compose`` command can be safely moved into a dedicated ``.env`` and read automatically if they are not evaluated i.e. ``$(...)``. Below is a brief description of the non-evaluated environment variables:
+
+    .. code-block:: bash
+
+        PY_VER=3.8    # Python version: 3.6|3.7|3.8
+        IMAGE=djtest  # Image type:     djbase|djtest|djlab|djlabhub
+        DISTRO=alpine # Distribution:   alpine|debian
+        AS_SCRIPT=    # If 'TRUE', will not keep container alive but run tests and exit
+
+.. note::
+
+    Deployment options currently being considered are `Docker Compose <https://docs.docker.com/compose/install/>`_ and `Kubernetes <https://kubernetes.io/docs/tutorials/kubernetes-basics/>`_.
+
+Run Locally w/ Python
+---------------------
+
+- Set environment variables for port assignment (``PHARUS_PORT``, defaults to 5000) and API route prefix (``PHARUS_PREFIX`` e.g. ``/api``, defaults to empty string).
+- For development, use CLI command ``pharus``. This method supports hot-reloading so probably best coupled with ``pip install -e ...``.
+- For production, use ``gunicorn --bind 0.0.0.0:${PHARUS_PORT} pharus.server:app``.
+
+Run Tests for Development w/ Pytest and Flake8
+----------------------------------------------
+
+- Set ``pharus`` testing environment variables:
+
+    .. code-block:: bash
+
+        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 DDL privilege)
+        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``
+
+Creating Sphinx Documentation from Scratch
+------------------------------------------
+
+Recommend the follow to be ran within the ``pharus`` container in ``docs`` Docker Compose environment.
+
+- Run the following commands and complete the prompts as requested.
+
+    .. code-block:: bash
+
+        mkdir docs
+        cd docs
+        sphinx-quickstart
+
+- In ``docs/conf.py`` add to the beginning:
+
+    .. code-block:: python
+
+        import os
+        import sys
+        sys.path.insert(0, os.path.abspath('..'))
+
+- In ``docs/conf.py:extensions`` append ``['sphinx.ext.autodoc', 'sphinxcontrib.httpdomain']``. See ``requirements_docs.txt`` and ``docker-compose-docs.yaml`` for details on documentation dependencies.
+- Run the following to automatically generate the API docs:
+
+    .. code-block:: bash
+
+        sphinx-apidoc -o . .. ../tests/* ../setup.py
+
+- Add ``modules`` within the ``toctree`` directive in ``index.rst``.
+- Build the docs by running:
+
+    .. code-block:: bash
+
+        make html
+
+References
+----------
+
+- DataJoint
+
+  - https://datajoint.io
+
+- DataJoint LabBook (a companion frontend)
+
+  - https://github.com/datajoint/datajoint-labbook
+
+- Python Tutorial for Flask, Swagger, and Automated docs
+
+  - https://realpython.com/flask-connexion-rest-api/#reader-comments

pharus/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = '0.1.0b1'
+__version__ = '0.1.0b2'