Merge branch 'develop' into add_doc

.github/workflows/code-cov.yaml

@@ -0,0 +1,64 @@
+name: CI-code-cov
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: 
+      - main
+      - develop
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'  # Specify the Python version you want to use    
+
+    - name: Install Package in Editable Mode with Python Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+        
+    - name: Setup R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: '4.3.2' # Use the R version you prefer
+
+    - name: Install R packages
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        cache: true
+        cache-version: 1
+        dependencies: 'NA'
+        install-pandoc: false
+        packages: |
+          grf
+          causalweight
+          mediation
+
+    - name: Install plmed package          
+      run: |    
+        R -e "pak::pkg_install('ohines/plmed')"
+
+    - name: Install Pytest and Coverage
+      run: |
+        pip install pytest pytest-cov
+
+    - name: Run tests with coverage
+      run: |
+        pytest --cov=med_bench --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/[email protected]
+      with:
+        # token: ${{ secrets.CODECOV_TOKEN }}
+        token: 'e4829e41-01da-4d08-9e04-04443da957e3'
+        slug: judithabk6/med_bench
+

.github/workflows/tests-with-R.yaml

@@ -4,7 +4,9 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: 
+      - main
+      - develop
 
 jobs:
   test:

.github/workflows/tests-without-R.yaml

@@ -4,7 +4,9 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: 
+      - main
+      - develop
 
 jobs:
   test:

.gitignore

@@ -128,4 +128,6 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# DS_STORE files
+src/.DS_Store
 .DS_Store

README.md

@@ -1,3 +1,5 @@
+[![codecov](https://codecov.io/gh/judithabk6/med_bench/graph/badge.svg?token=PASB71N41D)](https://codecov.io/gh/judithabk6/med_bench)
+
 # med_bench
 
 **med_bench** is a Python package designed to wrap the most common estimators for causal mediation analysis in a single framework. We additionally allow for some flexibility in the choice of nuisance parameters models.

setup.py

@@ -23,7 +23,8 @@
         'rpy2>=2.9.4',
         'scipy>=1.5.2',
         'seaborn>=0.11.1',
-        'matplotlib>=3.3.2'
+        'matplotlib>=3.3.2',
+        "pytest"
     ],
     classifiers=[
         'Programming Language :: Python :: 3',