Code coverage and a bunch of other packaging updates (#6)

* Update test.yml * Update gitignore * Add coverage to testing * Add pytest coverage requirements * Split out requirement files * Add html and terminal local * Update gitignore * Update CI coverage * Update tolerance a little bit for CI * Change job names * Pin all development versions
blackjax-devs · Jan 30, 2021 · dff5d53 · dff5d53
1 parent e9489dc
commit dff5d53
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Showing 7 changed files with 25 additions and 8 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ jobs:
       matrix:
         python-version: [ '3.7', '3.8', '3.9' ]
 
-    name: Set up Python ${{ matrix.python-version }}
+    name: pytest Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v1
       - name: Set up Python ${{ matrix.python-version }}
@@ -29,4 +29,11 @@ jobs:
 
       - name: Run the tests with pytest
         run: |
-          pytest -n 4 tests 
+          pytest -n 4 -vv --cov=blackjax --cov-report=xml --cov-report=term tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
diff --git a/.gitignore b/.gitignore
@@ -100,3 +100,8 @@ ehthumbs.db
 # Apparently both patterns _have_ to be present on my system.
 # Having both is a nice backup, I guess.
 .ipynb_checkpoints
+
+.idea
+.coverage
+coverage.xml
+coverage
diff --git a/Makefile b/Makefile
@@ -7,7 +7,7 @@ lint:
 	mypy blackjax tests
 
 test:
-	pytest -n 4 tests
+	pytest -n 4 --cov=blackjax --cov-report term --cov-report html:coverage tests
 
 # We launch the package release by tagging the master branch with the package's
 # new version number. The version number is read from `blackjax/__init__.py`

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -18,6 +18,8 @@ pycodestyle==2.6.0
 pyflakes==2.2.0
 pyparsing==2.4.7
 pytest==6.1.2
+pytest-cov==2.11.1 
+pytest-html==3.1.1
 pytest-forked==1.3.0
 pytest-xdist==2.1.0
 regex==2020.11.13

diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,2 @@
+jax==0.2.7
+jaxlib==0.1.57
diff --git a/setup.py b/setup.py
@@ -11,6 +11,9 @@ def read(rel_path):
         return fp.read()
 
 
+INSTALL_REQS = read("requirements.txt").splitlines()
+
+
 def get_version(rel_path):
     """Get the package's version number.
 
@@ -32,8 +35,6 @@ def get_version(rel_path):
     version=get_version("blackjax/__init__.py"),
     description="Flexible and fast inference in Python",
     packages=setuptools.find_packages(),
-    install_requires=[
-        "jax==0.2.7",
-        "jaxlib==0.1.57",
-    ],
+    install_requires=INSTALL_REQS
+   ,
 )
diff --git a/tests/test_hmc.py b/tests/test_hmc.py
@@ -62,4 +62,4 @@ def test_hmc(inv_mass_matrix):
     scale_samples = states.position["scale"][5000:]
 
     assert np.mean(scale_samples) == pytest.approx(1, 1e-1)
-    assert np.mean(coefs_samples) == pytest.approx(3, 1e-1)
+    assert np.mean(coefs_samples) == pytest.approx(3, 2e-1)