Test on oldest supported versions during end-to-end CI (#4374)

* test on oldest supported versions during end-to-end CI

* less strict pin

* try 1.15 pin

* try pinning pandas and scipy too

* only test betabinom if scipy modern enough

* revert sort_conda changes (will do in separate PR)

* generate requirements-dev from py37 env

Author: MarcoGorelli

.codecov.yml

@@ -1,7 +1,7 @@
 codecov:
   require_ci_to_pass: no
   notify:
-      after_n_builds: 9
+      after_n_builds: 16
 
 coverage:
   precision: 2

.github/workflows/arviz_compat.yml

@@ -12,6 +12,7 @@ jobs:
         os: [ubuntu-latest, macos-latest]
         floatx: [float64]
         test-subset:
+          - pymc3/tests/test_distributions.py
           - pymc3/tests/test_distributions_random.py
           - pymc3/tests/test_sampling.py
       fail-fast: false
@@ -27,12 +28,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev-py38.yml has not changed
+          # Increase this value to reset cache if environment-dev-py39.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-dev-py38.yml') }}
+            hashFiles('conda-envs/environment-dev-py39.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -47,18 +48,18 @@ jobs:
             hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: pymc3-dev-py38
+          activate-environment: pymc3-dev-py39
           channel-priority: strict
-          environment-file: conda-envs/environment-dev-py38.yml
+          environment-file: conda-envs/environment-dev-py39.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Install pymc3
         run: |
-          conda activate pymc3-dev-py38
+          conda activate pymc3-dev-py39
           pip install -e .
           python --version
       - name: Install latest arviz
         run: |
-          conda activate pymc3-dev-py38
+          conda activate pymc3-dev-py39
           pip uninstall arviz -y
           pip install git+git://github.com/arviz-devs/arviz.git
       - name: Run tests

.github/workflows/pytest.yml

@@ -70,12 +70,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev-py39.yml has not changed
+          # Increase this value to reset cache if environment-dev-py37.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-dev-py39.yml') }}
+            hashFiles('conda-envs/environment-dev-py37.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -90,18 +90,18 @@ jobs:
             hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: pymc3-dev-py39
+          activate-environment: pymc3-dev-py37
           channel-priority: strict
-          environment-file: conda-envs/environment-dev-py39.yml
+          environment-file: conda-envs/environment-dev-py37.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Install-pymc3
         run: |
-          conda activate pymc3-dev-py39
+          conda activate pymc3-dev-py37
           pip install -e .
           python --version
       - name: Run tests
         run: |
-          conda activate pymc3-dev-py39
+          conda activate pymc3-dev-py37
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1

.github/workflows/windows.yml

@@ -26,12 +26,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if conda-envs/environment-dev-py37.yml has not changed
+          # Increase this value to reset cache if conda-envs/environment-dev-py38.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-dev-py37.yml') }}
+            hashFiles('conda-envs/environment-dev-py38.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -46,15 +46,15 @@ jobs:
             hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: pymc3-dev-py37
+          activate-environment: pymc3-dev-py38
           channel-priority: strict
-          environment-file: conda-envs/environment-dev-py37.yml
+          environment-file: conda-envs/environment-dev-py38.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Install-pymc3
         run: |
-          conda activate pymc3-dev-py37
+          conda activate pymc3-dev-py38
           pip install -e .
           python --version
       - run: |
-          conda activate pymc3-dev-py37
+          conda activate pymc3-dev-py38
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

.pre-commit-config.yaml

@@ -44,7 +44,7 @@ repos:
     - id: conda-env-sort
       additional_dependencies: [pyyaml]
       entry: python scripts/sort_conda_envs.py
-      files: ^conda-envs/
+      files: ^conda-envs/environment-dev-py37\.yml$
       language: python
       name: Sort dependencies in conda envs
       types: [yaml]

conda-envs/environment-dev-py37.yml

@@ -8,13 +8,16 @@ dependencies:
 - libblas=*=*mkl
 - mkl-service
 - nbsphinx>=0.4
+- numpy=1.15
 - numpydoc>=0.9
+- pandas=0.24
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.7
 - recommonmark>=0.4
+- scipy=1.2
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark

pymc3/tests/test_distributions.py

@@ -25,6 +25,8 @@
 
 from numpy import array, exp, inf, log
 from numpy.testing import assert_allclose, assert_almost_equal, assert_equal
+from packaging.version import parse
+from scipy import __version__ as scipy_version
 from scipy import integrate
 from scipy.special import erf, logit
 
@@ -97,6 +99,8 @@
 from pymc3.theanof import floatX
 from pymc3.vartypes import continuous_types
 
+SCIPY_VERSION = parse(scipy_version)
+
 
 def get_lkj_cases():
     """
@@ -1163,6 +1167,9 @@ def test_binomial(self):
 
     # Too lazy to propagate decimal parameter through the whole chain of deps
     @pytest.mark.xfail(condition=(theano.config.floatX == "float32"), reason="Fails on float32")
+    @pytest.mark.xfail(
+        condition=(SCIPY_VERSION < parse("1.4.0")), reason="betabinom is new in Scipy 1.4.0"
+    )
     def test_beta_binomial(self):
         self.checkd(
             BetaBinomial,

requirements.txt

@@ -1,9 +1,9 @@
 arviz>=0.9.0
 dill
 fastprogress>=0.2.0
-numpy>=1.13.0
-pandas>=0.18.0
+numpy>=1.15.0
+pandas>=0.24.0
 patsy>=0.5.1
-scipy>=0.18.1
+scipy>=1.2.0
 theano-pymc==1.0.14
 typing-extensions>=3.7.4

setup.py

@@ -85,5 +85,4 @@ def get_version():
         python_requires=">=3.7",
         install_requires=install_reqs,
         tests_require=test_reqs,
-        test_suite="nose.collector",
     )