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

Author: MarcoGorelli

.github/workflows/arviz_compat.yml

@@ -27,12 +27,12 @@ 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 +47,18 @@ 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

@@ -42,7 +42,7 @@ repos:
       name: Check no tests are ignored
       pass_filenames: false
     - id: conda-env-sort
-      additional_dependencies: [pyyaml]
+      additional_dependencies: [ruamel.yaml]
       entry: python scripts/sort_conda_envs.py
       files: ^conda-envs/
       language: python
@@ -51,7 +51,7 @@ repos:
     - id: pip-from-conda
       additional_dependencies: [pyyaml]
       entry: python scripts/generate_pip_deps_from_conda.py
-      files: ^conda-envs/
+      files: ^conda-envs/environment-dev-py37\.yml$
       language: python
       name: Generate pip dependency from conda
     - id: no-relative-imports

conda-envs/environment-dev-py37.yml

@@ -8,6 +8,7 @@ dependencies:
 - libblas=*=*mkl
 - mkl-service
 - nbsphinx>=0.4
+- numpy=1.13.0
 - numpydoc>=0.9
 - pre-commit>=2.8.0
 - pytest-cov>=2.5

requirements-dev.txt

@@ -4,6 +4,7 @@
 h5py>=2.7
 ipython>=7.16
 nbsphinx>=0.4
+numpy==1.13.0
 numpydoc>=0.9
 pre-commit>=2.8.0
 pytest-cov>=2.5

scripts/sort_conda_envs.py

@@ -7,15 +7,24 @@
 
 import argparse
 
-import yaml
+from pathlib import Path
+from typing import Optional, Sequence
 
-if __name__ == "__main__":
+import ruamel.yaml
+
+yaml = ruamel.yaml.YAML()
+
+
+def main(argv: Optional[Sequence[str]] = None) -> None:
+    """Sort dependencies in conda environment files."""
     parser = argparse.ArgumentParser()
-    parser.add_argument("files", nargs="*")
-    args = parser.parse_args()
-    for file_ in args.files:
-        with open(file_) as fd:
-            doc = yaml.safe_load(fd)
-            doc["dependencies"].sort()
-        with open(file_, "w") as fd:
-            yaml.dump(doc, fd, sort_keys=False)
+    parser.add_argument("paths", nargs="*", type=Path)
+    args = parser.parse_args(argv)
+    for path in args.paths:
+        doc = yaml.load(path)
+        doc["dependencies"].sort()
+        yaml.dump(doc, path)
+
+
+if __name__ == "__main__":
+    main()

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",
     )