Merge pull request #24 from bcgsc/release/v0.1.0

Release/v0.1.0

Author: elewis2

.github/workflows/gkb_workflows/pytest.yml

@@ -10,20 +10,20 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
     steps:
     - name: checkout
-      uses: actions/checkout@v1
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: install and build
       run: |
         python -m pip install --upgrade pip setuptools
         pip install .[docs]
         pip install markdown_refdocs mkdocs mkdocs-material
-        markdown_refdocs ipr -o docs/reference --link
+        markdown_refdocs pori_python -o docs/reference --link
         mkdocs build
     - name: Deploy
       uses: peaceiris/actions-gh-pages@v3

.github/workflows/publishdevdocs.yml

@@ -1,12 +1,9 @@
 # This workflows will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
-name: upload to pypi
+name: upload to testpypi
 
-on:
-  release:
-    types: [released]
-  workflow_dispatch:
+on: workflow_dispatch
 
 jobs:
   deploy:
@@ -25,8 +22,8 @@ jobs:
         pip install setuptools wheel twine
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        TWINE_USERNAME: ${{ secrets.PYPI_TEST_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_TEST_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel install
-        twine upload dist/*
+        twine upload --repository testpypi dist/*

.github/workflows/publishgkbdevdocs.yml

@@ -6,7 +6,7 @@ name: build
 on:
   push:
     branches:
-      - master
+      - main
       - develop
   pull_request:
 
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3
@@ -32,15 +32,15 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 ipr graphkb --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Check with black
       run: |
         pip install black
-        black --check -S -l 100 ipr graphkb tests
+        black --check -S -l 100 pori_python tests
     - name: Full Tests with pytest
       run: |
         pip list
-        pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov ipr --cov-report term --cov-report xml
+        pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov pori_python --cov-report term --cov-report xml
       env:
         IPR_USER: ${{ secrets.IPR_TEST_USER }}
         IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }}

…/workflows/gkb_workflows/pypipublish.yml .github/workflows/pypitestpublish.yml.github/workflows/gkb_workflows/pypipublish.yml renamed to .github/workflows/pypitestpublish.yml .github/workflows/gkb_workflows/pypipublish.yml renamed to .github/workflows/pypitestpublish.yml

@@ -4,7 +4,7 @@
 name: quick-tests
 
 on:
-  - push
+  push:
 
 jobs:
   build:
@@ -13,7 +13,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.11']
 
     steps:
     - uses: actions/checkout@v3
@@ -29,11 +29,11 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 ipr graphkb --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Check with black
       run: |
         pip install black
-        black --check -S -l 100 ipr graphkb tests
+        black --check -S -l 100 pori_python tests
     - name: Short Tests with pytest
       run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov ipr --cov-report term --cov-report xml
       env:
@@ -43,3 +43,4 @@ jobs:
         GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }}
         EXCLUDE_INTEGRATION_TESTS: 1
         # EXCLUDE_INTEGRATION_TESTS: ${{ matrix.python-version != '3.11' }}
+      if: github.event_name != 'pull_request'

.github/workflows/pytest.yml

@@ -1,15 +1,22 @@
 
-# IPR
+# PORI Python Adaptor
 
-![build](https://github.com/bcgsc/pori_ipr_python/workflows/build/badge.svg) [![PyPi](https://img.shields.io/pypi/v/ipr.svg)](https://pypi.org/project/ipr) [![codecov](https://codecov.io/gh/bcgsc/pori_ipr_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_ipr_python) [![PyPI - Downloads](https://img.shields.io/pypi/dm/ipr)](https://pypistats.org/packages/ipr) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5730671.svg)](https://doi.org/10.5281/zenodo.5730671)
+![build](https://github.com/bcgsc/pori_python/workflows/build/badge.svg) [![codecov](https://codecov.io/gh/bcgsc/pori_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_python)
 
 This repository is part of the [Platform for Oncogenomic Reporting and Interpretation (PORI)](https://bcgsc.github.io/pori/).
 
+This is a python adaptor package for querying the GraphKB API and IPR API.
+
 This python tool takes in variant inputs as tab-delimited files and annotates them using GraphKB.
 The resulting output is uploaded to IPR as a report. Additional report content such as images and
 metadata can be passed to be included in the report upload.
 
-For documentation on how to create reports using this adaptor, see the [main documentation site](https://bcgsc.github.io/pori/) for the platform.
+For documentation on how to create reports using the IPR adaptor, see the [main documentation site](https://bcgsc.github.io/pori/) for the platform. For the GraphKB adaptor, see the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/).
+
+- [Getting Started](#getting-started)
+  - [Install (For developers)](#install-for-developers)
+- [Documentation](#documentation)
+- [Deployment (Publishing)](#deployment-publishing)
 
 ## Getting Started
 
@@ -18,8 +25,8 @@ For documentation on how to create reports using this adaptor, see the [main doc
 clone this repository
 
 ```bash
-git clone https://github.com/bcgsc/pori_ipr_python.git
-cd pori_ipr_python
+git clone https://github.com/bcgsc/pori_python.git
+cd pori_python
 ```
 
 create a virtual environment
@@ -36,67 +43,47 @@ pip install -U pip setuptools
 pip install -e .[dev]
 ```
 
-Run the tests
+Run the tests:
 
-```bash
-pytest tests
-```
+Export usernames, passwords, and set test options.
 
-## Documentation
-
-The user documentation for this tool is hosted with the [main documentation site](https://bcgsc.github.io/pori/).
+Note that IPR tests will try to use the BCGSC production GraphKB API by default.
+If you want to test interaction with a different instance, you will need to
+set the GraphKB variables.
 
-Developers: Any updates to this tool should be edited and reflected in the main site documentation as well.
-
-
-# GraphKB (Python)
-
-![build](https://github.com/bcgsc/pori_graphkb_python/workflows/build/badge.svg) [![PyPi](https://img.shields.io/pypi/v/graphkb.svg)](https://pypi.org/project/graphkb) [![codecov](https://codecov.io/gh/bcgsc/pori_graphkb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_graphkb_python) [![PyPI - Downloads](https://img.shields.io/pypi/dm/graphkb)](https://pypistats.org/packages/graphkb) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5730523.svg)](https://doi.org/10.5281/zenodo.5730523)
-
-This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).
-
-Python adapter package for querying the GraphKB API. See the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/)
-
-- [Getting Started](#getting-started)
-  - [Install (For developers)](#install-for-developers)
-  - [Run Tests](#run-tests)
-- [Generating the Documentation](#generating-the-documentation)
-- [Deployment (Publishing)](#deployment-publishing)
-
-## Getting Started
-
-### Install (For developers)
-
-clone this repository
+Set EXCLUDE vars to 1 if you don't want to run these tests. 
+ONCOKB and BCGSC tests are enabled by default.
 
 ```bash
-git clone https://github.com/bcgsc/pori_graphkb_python
-cd pori_graphkb_python
+export IPR_USER='pori_admin'
+export IPR_PASS='pori_admin'
+export IPR_URL='http://localhost:8081/api'
+export GRAPHKB_USER='pori_admin'
+export GRAPHKB_PASS='pori_admin'
+export GRAPHKB_URL='http://localhost:8080/api'
+EXCLUDE_BCGSC_TESTS = 1
+EXCLUDE_ONCOKB_TESTS = 1
 ```
 
-create a virtual environment
+If you want to run tests that upload reports to a live IPR instance,
+specify the url of the IPR API you want to use and set the test var to 1.
+These tests are disabled by default.
 
 ```bash
-python3 -m venv venv
-source venv/bin/activate
+export IPR_TEST_URL='http://localhost:8081/api'
+INCLUDE_UPLOAD_TESTS = 1
 ```
 
-install the package and its development dependencies
-
 ```bash
-pip install -U pip setuptools
-pip install -e .[dev]
+pytest tests
 ```
 
-### Run Tests
+## Documentation
 
-```bash
-pytest tests
-```
+The user documentation for this tool is hosted with the [main documentation site](https://bcgsc.github.io/pori/).
 
-## Generating the Documentation
+Developers: Any updates to this tool should be edited and reflected in the main site documentation as well.
 
-User documentation for this repository is hosted in the [central PORI repository](https://github.com/bcgsc/pori/)
 
 ## Deployment (Publishing)
 

.github/workflows/quick-pytest.yml

@@ -1,2 +1 @@
-from . import ipr
-from . import graphkb
+from . import graphkb, ipr  # noqa: F401

README.md

@@ -2,7 +2,7 @@
   <body>
     <script src="https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.min.js"></script>
       <div class="mermaid">
-    
+
         classDiagram
           class BasicPosition {
             pos : int
@@ -78,9 +78,9 @@
             untemplatedSeqSize : Optional[int]
           }
           class Statement {
-            conditions : List[OntologyLink]
-            evidence : List[OntologyLink]
-            evidenceLevel : List[OntologyLink]
+            conditions : List[Ontology]
+            evidence : List[Ontology]
+            evidenceLevel : List[Ontology]
             relevance : Union
             source : Union
             sourceId : str
@@ -90,12 +90,12 @@
             displayName : str
             germline : bool
             reference1 : Union
-            reference2 : Optional[OntologyLink]
+            reference2 : Optional[Ontology]
             type : Union
             zygosity : str
           }
           PositionalVariant --|> Variant
-  
+
        </div>
   </body>
 </html>