Add coveralls to CI (#1925)

* Add coveralls to CI

* Do not run coverage for docs

* add coveralls badge to README

* add github token for coveralls

* try to set PYTEST_ADDOPTS globally

* Use editable installation in CI for coverage

.github/workflows/ci.yml

@@ -8,6 +8,9 @@ on:
   pull_request:
     branches: [ master ]
 
+env:
+  PYTEST_ADDOPTS: "--cov=numpyro"
+
 jobs:
   lint:
 
@@ -67,14 +70,19 @@ jobs:
         pip install jaxlib
         pip install jax
         pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install .[dev,test]
+        pip install -e .[dev,test]
         pip freeze
     - name: Test with pytest
       run: |
         CI=1 pytest -vs -k "not test_example" --durations=100 --ignore=test/infer/ --ignore=test/contrib/
     - name: Test x64
       run: |
         JAX_ENABLE_X64=1 pytest -vs test/test_distributions.py -k powerLaw
+    - name: Coveralls
+      if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.10'
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
 
 
   test-inference:
@@ -99,7 +107,7 @@ jobs:
         pip install jaxlib
         pip install jax
         pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install .[dev,test]
+        pip install -e .[dev,test]
         pip freeze
     - name: Test with pytest
       run: |
@@ -121,6 +129,11 @@ jobs:
     - name: Test nested sampling
       run: |
         JAX_ENABLE_X64=1 pytest -vs test/contrib/test_nested_sampling.py
+    - name: Coveralls
+      if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.10'
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
 
 
   examples:
@@ -143,8 +156,13 @@ jobs:
         pip install jaxlib
         pip install jax
         pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install .[dev,examples,test]
+        pip install -e .[dev,examples,test]
         pip freeze
     - name: Test with pytest
       run: |
         CI=1 XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs -k test_example
+    - name: Coveralls
+      if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.10'
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -1,4 +1,5 @@
 [![Build Status](https://github.com/pyro-ppl/numpyro/workflows/CI/badge.svg)](https://github.com/pyro-ppl/numpyro/actions)
+[![Coverage Status](https://coveralls.io/repos/github/pyro-ppl/numpyro/badge.svg)](https://coveralls.io/github/pyro-ppl/numpyro)
 [![Documentation Status](https://readthedocs.org/projects/numpyro/badge/?version=latest)](https://numpyro.readthedocs.io/en/latest/?badge=latest)
 [![Latest Version](https://badge.fury.io/py/numpyro.svg)](https://pypi.python.org/pypi/numpyro)
 

setup.py

@@ -66,6 +66,7 @@
             "matplotlib",
             "optax>=0.0.6",
             "pylab-sdk",  # jaxns dependency
+            "pytest-cov",
             "pyyaml",  # flax dependency
             "requests",  # pylab dependency
             "tensorflow_probability>=0.18.0",