Merge pull request #219 from pbashyal-nmdp/documentation_and_cleanup_for_1.0

Documentation and cleanup for 1.0

Author: mmaiers-nmdp

.github/workflows/black.yml

@@ -6,5 +6,5 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: psf/black@stable

.github/workflows/post-release.yml

@@ -8,10 +8,10 @@ jobs:
     name: Update changelog
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           ref: master
-      - uses: rhysd/changelog-from-release/action@v2
+      - uses: rhysd/changelog-from-release/action@v3
         with:
           file: CHANGELOG.md
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python-tests.yml

@@ -15,9 +15,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.8
     - name: Install dependencies

.github/workflows/pythonpublish.yml

@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
-        python-version: '3.x'
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/mhalagan-nmdp/pyars/issues.
+Report bugs at https://github.com/nmdp-bioinformatics/py-ard/issues.
 
 If you are reporting a bug, please include:
 
@@ -38,14 +38,14 @@ and "help wanted" is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-pyARS could always use more documentation, whether as part of the
-official pyARS docs, in docstrings, or even on the web in blog posts,
+py-ard could always use more documentation, whether as part of the
+official py-ard docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/mhalagan-nmdp/pyars/issues.
+The best way to send feedback is to file an issue at https://github.com/nmdp-bioinformatics/py-ard/issues
 
 If you are proposing a feature:
 
@@ -57,32 +57,40 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `pyars` for local development.
+Ready to contribute? Here's how to set up `py-ard` for local development.
 
-1. Fork the `pyars` repo on GitHub.
+1. Fork the `py-ard` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/pyars.git
+    $ git clone [email protected]:your_name_here/py-ard.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3. Install your local copy into a venv. This is how you set up your fork for local development::
 
-    $ mkvirtualenv pyars
-    $ cd pyars/
-    $ python setup.py develop
+    $ cd py-ard
+    $ make venv
+    $ source venv/bin/activate
+    $ make install
 
 4. Create a branch for local development::
 
     $ git checkout -b name-of-your-bugfix-or-feature
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+5. When you're done making changes, make sure you have a corresponding test, check that all your changes pass flake8 and the tests::
 
-    $ flake8 pyars tests
-    $ python setup.py test or py.test
-    $ tox
+    $ make test
+    $ make lint
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+   To get test runners, you would to have done `make install` earlier.
+
+   To run behavior-driven development (BDD) tests locally via the behave framework, run::
+
+    $ behave
+
+   Run unit-tests::
+
+    $ python -m unittest tests.test_pyard
 
 6. Commit your changes and push your branch to GitHub::
 
@@ -101,14 +109,5 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
-   https://travis-ci.org/mhalagan-nmdp/pyars/pull_requests
+3. The pull request should work for Python 3.8 and higher.
    and make sure that the tests pass for all supported Python versions.
-
-Tips
-----
-
-To run a subset of tests::
-
-
-    $ python -m unittest tests.test_pyars

Dockerfile

@@ -4,16 +4,23 @@ LABEL MAINTAINER="Pradeep Bashyal"
 
 WORKDIR /app
 
+ARG PY_ARD_VERSION=1.0.0rc4
+
 COPY requirements.txt /app
 RUN pip install --no-cache-dir --upgrade pip && \
     pip install --no-cache-dir -r requirements.txt
 
 COPY requirements-deploy.txt /app
 RUN pip install --no-cache-dir -r requirements-deploy.txt
 
+RUN pip install --no-cache-dir py-ard==$PY_ARD_VERSION
+
+RUN pyard-import && \
+    pyard --version && \
+    pyard-status
+
 COPY app.py /app/
 COPY api.py /app/
 COPY api-spec.yaml /app/
-COPY pyard /app/pyard
 
 CMD ["gunicorn", "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm",  "--timeout", "30", "app:app"]

Dockerfile-local

@@ -0,0 +1,19 @@
+FROM python:3.10-slim-buster
+
+LABEL MAINTAINER="Pradeep Bashyal"
+
+WORKDIR /app
+
+COPY requirements.txt /app
+RUN pip install --no-cache-dir --upgrade pip && \
+    pip install --no-cache-dir -r requirements.txt
+
+COPY requirements-deploy.txt /app
+RUN pip install --no-cache-dir -r requirements-deploy.txt
+
+COPY app.py /app/
+COPY api.py /app/
+COPY api-spec.yaml /app/
+COPY pyard /app/pyard
+
+CMD ["gunicorn", "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm",  "--timeout", "30", "app:app"]

HEADER.txt

@@ -1,6 +1,6 @@
 #
-#    pyars pyARS.
-#    Copyright (c) 2018 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#    py-ard
+#    Copyright (c) 2023 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
 #
 #    This library is free software; you can redistribute it and/or modify it
 #    under the terms of the GNU Lesser General Public License as published

Makefile

@@ -101,7 +101,7 @@ docker-build: ## build a docker image for the service
 	docker build -t pyard-service:latest .
 
 docker: docker-build ## build a docker image and run the service
-	docker run --name pyard-service -p 8080:8080 pyard-service:latest
+	docker run --rm --name pyard-service -p 8080:8080 pyard-service:latest
 
 install: clean ## install the package to the active Python's site-packages
 	pip install --upgrade pip