Merge pull request #5 from pymc-devs/tests

simplify tests

Author: aloctavodia

.github/workflows/test.yml

@@ -1,140 +1,58 @@
-name: pytest
+name: Run tests
 
 on:
-  pull_request:
   push:
-    branches: [main]
-    paths:
-      - ".github/workflows/*"
-      - "pymc_bart/**"
-      - "setup.py"
-      - "pyproject.toml"
-      - "buildosx"
-      - "conda-envs/**"
-      - "codecov.yml"
+    branches:
+      - main
+  pull_request:
 
 jobs:
-  ubuntu:
+  test:
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [ubuntu-18.04]
-        floatx: [float32, float64]
-      fail-fast: false
-    runs-on: ${{ matrix.os }}
-    env:
-      TEST_SUBSET: ${{ matrix.test-subset }}
-      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
-    defaults:
-      run:
-        shell: bash -l {0}
+        python-version: ["3.8", "3.9", "3.10"]
+
+    name: Set up Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if environment-test-py38.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-test-py38.yml') }}
-      - name: Cache multiple paths
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if requirements.txt has not changed
-          CACHE_NUMBER: 0
         with:
-          path: |
-            ~/.cache/pip
-            $RUNNER_TOOL_CACHE/Python/*
-            ~\AppData\Local\pip\Cache
-          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
-            hashFiles('requirements.txt') }}
-      - uses: conda-incubator/setup-miniconda@v2
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          mamba-version: "*"
-          activate-environment: pymc-test-py38
-          channel-priority: strict
-          environment-file: conda-envs/environment-test-py38.yml
-          use-mamba: true
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - name: Install-pymc
+          channels: conda-forge, defaults
+          channel-priority: true
+          python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+
+      - name: Install pymc_bart
+        shell: bash -l {0}
         run: |
-          conda activate pymc-test-py38
-          pip install -e .
+          conda install pip
+          pip install -r requirements-dev.txt
+          pip install .
           python --version
+          conda list
+          pip freeze
+      - name: Run linters
+        shell: bash -l {0}
+        run: |
+          python -m black pymc_bart --check
+          echo "Success!"
+          # echo "Checking code style with pylint..."
+          # python -m pylint pymc_bart/
       - name: Run tests
+        shell: bash -l {0}
         run: |
-          conda activate pymc-test-py38
-          python -m pytest -vv --cov=pymc_bart --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
-        with:
-          env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
-  windows:
-    strategy:
-      matrix:
-        os: [windows-latest]
-        floatx: [float32, float64]
-      fail-fast: false
-    runs-on: ${{ matrix.os }}
-    env:
-      TEST_SUBSET: ${{ matrix.test-subset }}
-      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
-    defaults:
-      run:
-        shell: cmd
-    steps:
-      - uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if conda-envs/environment-test-py37.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/windows-environment-test-py37.yml') }}
-      - name: Cache multiple paths
-        uses: actions/cache@v2
+          python -m pytest -vv --cov=pymc_bart --cov-report=term --cov-report=xml tests
         env:
-          # Increase this value to reset cache if requirements.txt has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: |
-            ~/.cache/pip
-            $RUNNER_TOOL_CACHE/Python/*
-            ~\AppData\Local\pip\Cache
-          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
-            hashFiles('requirements.txt') }}
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          mamba-version: "*"
-          activate-environment: pymc-test-py37
-          channel-priority: strict
-          environment-file: conda-envs/windows-environment-test-py37.yml
-          use-mamba: true
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - name: Install-pymc
-        run: |
-          conda activate pymc-test-py37
-          pip install -e .
-          python --version
-      - name: Run tests
-        # This job uses a cmd shell, therefore the environment variable syntax is different!
-        # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
-        run: >-
-          conda activate pymc-test-py37 &&
-          python -m pytest -vv --cov=pymc_bart --doctest-modules pymc_bart --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
+          PYTHON_VERSION: ${{ matrix.python-version }}
+
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v1
         with:
-          env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false

buildosx

@@ -0,0 +1,5 @@
+black==22.3.0
+click==8.0.4
+pylint==2.10.2
+pytest-cov>=2.6.1
+pytest>=4.4.0

conda-envs/environment-test-py38.yml

@@ -3,7 +3,7 @@
 import pytest
 from numpy.random import RandomState
 from numpy.testing import assert_almost_equal, assert_array_equal
-from pymc.tests.distributions.util import assert_moment_is_expected
+from pymc.tests.test_distributions_moments import assert_moment_is_expected
 
 import pymc_bart as pmb