Automate codecov

.github/workflows/code_coverage.yaml

@@ -0,0 +1,54 @@
+name: Pytest Coverage
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  live-test:
+    name: Test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install basic dependencies
+        run: |
+          pip install --upgrade pip==21.3.0
+          pip install pytest-cov
+          pip install -r requirements.txt
+      - name: Build coverage file
+        run: |
+          python -m pytest --junitxml=pytest.xml --cov=pyrelational tests/ | tee pytest-coverage.txt
+
+      - name: Pytest coverage comment
+        id: coverageComment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
+
+      - name: Check the output coverage
+        run: |
+          echo "Coverage Percantage - ${{ steps.coverageComment.outputs.coverage }}"
+          echo "Coverage Color - ${{ steps.coverageComment.outputs.color }}"
+          echo "Coverage Html - ${{ steps.coverageComment.outputs.coverageHtml }}"
+          echo "Coverage Warnings - ${{ steps.coverageComment.outputs.warnings }}"
+          echo "Coverage Errors - ${{ steps.coverageComment.outputs.errors }}"
+          echo "Coverage Failures - ${{ steps.coverageComment.outputs.failures }}"
+          echo "Coverage Skipped - ${{ steps.coverageComment.outputs.skipped }}"
+          echo "Coverage Tests - ${{ steps.coverageComment.outputs.tests }}"
+          echo "Coverage Time - ${{ steps.coverageComment.outputs.time }}"
+          echo "Not Success Test Info - ${{ steps.coverageComment.outputs.notSuccessTestInfo }}"
+      - name: Create the Badge
+        uses: schneegans/dynamic-badges-action@v1.0.0
+        with:
+          auth: ${{ secrets.GIST_TOKEN }}
+          gistID: 99eba16a0a4fad7eadf98ef938afe38c
+          filename: pytest-coverage-comment.json
+          label: Test Coverage
+          message: ${{ steps.coverageComment.outputs.coverage }}
+          color: ${{ steps.coverageComment.outputs.color }}
+          namedLogo: python

.github/workflows/tests.yaml

@@ -2,9 +2,6 @@ name: tests
 
 # Run this workflow every time a new commit pushed to your repository
 on:
-  push:
-    branches:
-      - main
   pull_request:
 
 jobs:
@@ -13,17 +10,21 @@ jobs:
   # when a job name is not provided
   run-tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+
     name: Tests
     # Name the Job
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ matrix.python-version }}
       - name: Install basic dependencies
         run: |
-          pip install --upgrade pip==21.3.0
+          pip install --upgrade pip
           pip install pytest-cov
           pip install -r requirements.txt
       - name: Test with pytest

README.md

@@ -1,15 +1,8 @@
 # PyRelationAL
 
-<p>
-    <a alt="coverage">
-        <img src="https://img.shields.io/badge/coverage-94%25-green" /></a>
-    <a alt="semver">
-        <img src="https://img.shields.io/badge/semver-0.1.6-blue" /></a>
-    <a alt="documentation" href="https://pyrelational.readthedocs.io/en/latest/index.html">
-        <img src="https://img.shields.io/badge/documentation-online-orange" /></a>
-    <a alt="pypi" href="https://pypi.org/project/pyrelational/">
-        <img src="https://img.shields.io/badge/pypi-online-yellow" /></a>
-</p>
+![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/RelationTherapeutics/99eba16a0a4fad7eadf98ef938afe38c/raw/pytest-coverage-comment.json)
+[![PyPI version](https://badge.fury.io/py/pyrelational.svg)](https://badge.fury.io/py/pyrelational)
+[![Documentation Status](https://readthedocs.org/projects/pyrelational/badge/?version=stable)](https://pyrelational.readthedocs.io/en/stable/?badge=stable)
 
 PyRelationAL is an open source Python library for the rapid and reliable construction of active learning (AL) pipelines and strategies. The toolkit offers a modular design for a flexible workflow that enables active learning with as little change to your models and datasets as possible. The package is primarily aimed at researchers so that they can rapidly reimplement, adapt, and create novel active learning strategies. For more information on how we achieve this you can consult the sections below, our comprehensive docs, or our paper. PyRelationAL is principally designed with PyTorch workflows in mind but can easily be extended to work with other ML frameworks.
 

requirements.txt

@@ -1,20 +1,19 @@
-numpy==1.21.0
-pandas==1.3.5
-pytorch-lightning==1.5.9
-torch==1.9.0
-torchvision==0.10.0
-gpytorch==1.4.0
-scikit-learn==1.0.2
-tabulate==0.8.9
-pre-commit==2.17.0
-black==22.3.0
-pytest==6.2.5
-setuptools==59.5.0
-flake8==4.0.1
-flake8-bugbear==22.1.11
-gpytorch==1.4.0
-pyreadr==0.4.4
-xlrd==2.0.1
-openpyxl==3.0.9
+numpy>=1.22.0
+pandas>=1.3.0
+pytorch-lightning>=1.6
+torch>=1.9.0
+torchvision
+gpytorch
+scikit-learn
+tabulate>=0.7.0
+pre-commit
+black
+pytest
+setuptools
+flake8
+flake8-bugbear
+pyreadr>=0.4.4
+xlrd>=2.0.1
+openpyxl>=3.0.9
 pytest-cov
-protobuf~=3.19.0
+protobuf

setup.py

@@ -8,9 +8,9 @@
 tests_require = ["pytest", "pytest-cov", "mock"]
 
 install_requires = [
-    "numpy>=1.20.0",
+    "numpy>=1.22.0",
     "pandas>=1.3.0",
-    "pytorch-lightning>=1.5",
+    "pytorch-lightning>=1.6",
     "torch>=1.9.0",
     "scikit-learn>=1.0.2",
     "tabulate>=0.7.0",