TEST: fix workflow tests across OS and add test status badge

mh105 · Jul 20, 2024 · 65a843c · 65a843c
1 parent eba3a93
commit 65a843c
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Showing 6 changed files with 96 additions and 31 deletions.
diff --git a/.github/workflows/pr-pytest-conda.yml b/.github/workflows/pr-pytest-conda.yml
@@ -31,9 +31,10 @@ jobs:
         cache-environment: true
 
     - name: Package install with pip
-      run: |
-        python --version
-        pip install .
+      run: pip install .
+
+    - name: "- Check python version"
+      run: python --version
 
     - name: Lint with flake8
       run: |

diff --git a/.github/workflows/push-pytest-conda.yml b/.github/workflows/push-pytest-conda.yml
@@ -31,9 +31,10 @@ jobs:
         cache-environment: true
 
     - name: Package install with pip
-      run: |
-        python --version
-        pip install .
+      run: pip install .
+
+    - name: "- Check python version"
+      run: python --version
 
     - name: Lint with flake8
       run: |

diff --git a/.github/workflows/release-install-tests.yml b/.github/workflows/release-install-tests.yml
@@ -10,11 +10,11 @@ on:
 
 env:
   PACKAGE_NAME: somata
-  RELEASE_JSON: https://api.github.com/repos/mh105/somata/releases/latest
+  RELEASE_HTTP: https://github.com/mh105/somata/releases/latest
 
 jobs:
-  install-unix:
-    name: install-on-${{ matrix.os }}
+  pip-install:
+    name: pip-install-${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -26,12 +26,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: "Curl the latest release version"
-      run: |
-        latest_version=$(curl -s ${{ env.RELEASE_JSON }} | grep "tag_name" | cut -d '"' -f4 | cut -c2-)
-        echo "latest_version=$latest_version" >> $GITHUB_ENV
-
-    - name: "[Test 1] Create environment for 'pip install' on Unix"
+    - name: "Create environment for 'pip install' on Unix"
       if: runner.os != 'Windows'
       uses: mamba-org/setup-micromamba@v1
       with:
@@ -40,27 +35,38 @@ jobs:
           pip
           cmdstanpy  # avoids having to run 'install_cmdstan' after pip install
 
-    - name: "[Test 1] Create environment for 'pip install' on Windows"
+    - name: "Create environment for 'pip install' on Windows"
       if: runner.os == 'Windows'
       uses: mamba-org/setup-micromamba@v1
       with:
         environment-name: pip_env
         create-args:
           pip
-          cmdstanpy  # avoids having to run 'install_cmdstan' after pip install
+          cmdstanpy
+          numpy<2
           spectrum  # avoids building 'spectrum' on Windows that requires VC++ v14+
 
     - name: "- Pip install ${{ env.PACKAGE_NAME }}"
       run: pip install ${{ env.PACKAGE_NAME }}
 
     - name: "- Pip list"
+      run: pip list
+
+    - name: "- Get the latest release version"
       run: |
         python --version
-        pip list
+        latest_version=$(python -c "import requests; url = '${{ env.RELEASE_HTTP }}'; r = requests.get(url); print(r.url.split('/')[-1])" | awk '{print substr($0, 2)}')
+        if [ -n "$latest_version" ]; then
+          echo "latest_version extracted from GitHub releases: $latest_version"
+          echo "latest_version=$latest_version" >> $GITHUB_ENV
+        else
+          echo "failed to retrieve latest_version."
+          exit 1 
+        fi
 
     - name: "- Verify installed package version"
       run: |
-        installed_version=$(pip show ${{ env.PACKAGE_NAME }} | grep Version | cut -d' ' -f2)
+        installed_version=$(pip show ${{ env.PACKAGE_NAME }} | grep Version | awk '{print $2}')
         if [ "$installed_version" != "${{ env.latest_version }}" ]; then
           echo "Installed version from PyPI ($installed_version) does not match the latest release version on GitHub (${{ env.latest_version }})."
           exit 1
@@ -71,9 +77,22 @@ jobs:
     - name: "- Run tests with pytest"
       run: |
         pip install pytest
-        pytest
+        pytest -vv
 
-    - name: "[Test 2] Install ${{ env.PACKAGE_NAME }} with 'conda create'"
+  conda-install:
+    name: conda-install-${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: "Install ${{ env.PACKAGE_NAME }} with 'conda create'"
       uses: mamba-org/setup-micromamba@v1
       with:
         environment-name: conda_env
@@ -82,10 +101,17 @@ jobs:
           -c conda-forge
           ${{ env.PACKAGE_NAME }}
 
-    - name: "- Micromamba list"
+    - name: "- Get the latest release version"
       run: |
         python --version
-        micromamba list
+        latest_version=$(python -c "import requests; url = '${{ env.RELEASE_HTTP }}'; r = requests.get(url); print(r.url.split('/')[-1])" | awk '{print substr($0, 2)}')
+        if [ -n "$latest_version" ]; then
+          echo "latest_version extracted from GitHub releases: $latest_version"
+          echo "latest_version=$latest_version" >> $GITHUB_ENV
+        else
+          echo "failed to retrieve latest_version."
+          exit 1 
+        fi
 
     - name: "- Verify installed package version"
       run: |
@@ -100,4 +126,4 @@ jobs:
     - name: "- Run tests with pytest"
       run: |
         micromamba install pytest
-        pytest
+        pytest -vv
diff --git a/README.md b/README.md
@@ -8,11 +8,11 @@ Basic state-space models are introduced as class objects for flexible manipulati
 Classical exact and approximate inference algorithms are implemented and interfaced as class methods.
 Advanced neural oscillator modeling techniques are brought together to work synergistically.
 
-[![Release install tests](https://github.com/mh105/somata/actions/workflows/release-install-tests.yml/badge.svg?kill_cache)](https://github.com/mh105/somata/actions/workflows/release-install-tests.yml)
-[![Version](https://img.shields.io/badge/Version-0.5.5-green?kill_cache)](https://github.com/mh105/somata/releases)
-[![Last-Update](https://anaconda.org/conda-forge/somata/badges/latest_release_date.svg?kill_cache)](https://anaconda.org/conda-forge/somata)
-[![License: BSD 3-Clause Clear](https://img.shields.io/badge/License-BSD%203--Clause%20Clear-lightgrey.svg?kill_cache)](https://spdx.org/licenses/BSD-3-Clause-Clear.html)
-[![DOI](https://zenodo.org/badge/556083594.svg?kill_cache)](https://zenodo.org/badge/latestdoi/556083594)
+[![Release install tests](https://github.com/mh105/somata/actions/workflows/release-install-tests.yml/badge.svg)](https://github.com/mh105/somata/actions/workflows/release-install-tests.yml)
+[![Version](https://img.shields.io/badge/Version-0.5.5-green)](https://github.com/mh105/somata/releases)
+[![Last-Update](https://anaconda.org/conda-forge/somata/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/somata)
+[![License: BSD 3-Clause Clear](https://img.shields.io/badge/License-BSD%203--Clause%20Clear-lightgrey.svg)](https://spdx.org/licenses/BSD-3-Clause-Clear.html)
+[![DOI](https://zenodo.org/badge/556083594.svg)](https://zenodo.org/badge/latestdoi/556083594)
 
 ---
 

diff --git a/tests/test__import__numpy_torch.py b/tests/test__import__numpy_torch.py
@@ -0,0 +1,38 @@
+"""
+Author: Mingjian He <[email protected]>
+
+Testing function for importing numpy and torch libraries
+"""
+import torch
+import numpy as np
+
+
+def test_import_numpy_torch(dim=2):
+    """
+    Due to a strange dependency on sys lib5.dll between numpy and torch in
+    macOS(osx-arm64), one must import torch first then numpy to avoid the error:
+        >>> zsh: segmentation fault  python
+
+    This is a very problematic issue because it fails silently without any
+    error message unless the offending function call is asked directly in a
+    python session because it is a system-level error that does not return an
+    error code to parent stacks, leading to all superordinate processes hanging.
+
+    This unit test checks that numpy and torch can be imported without error.
+    Note that we do not want to import within the function as it is executed
+    in runtime during test suite collection such as by pytest.
+    """
+
+    np.random.seed(1)
+    A = np.random.rand(dim, dim)
+    A = A @ A.T + np.eye(dim)
+    _ = np.linalg.inv(A)  # this call depends on lib5.dll
+    A = torch.as_tensor(data=A, dtype=torch.float32)  # does not call lib5.dll
+    _ = torch.linalg.qr(A, mode='complete')  # this call also invokes lib5.dll
+
+    return
+
+
+if __name__ == "__main__":
+    test_import_numpy_torch()
+    print('numpy and torch import test finished without exception.')
diff --git a/tests/test_dp_func.py b/tests/test_dp_func.py
@@ -4,6 +4,7 @@
 Testing functions for exact inference signal processing methods in somata/exact_inferences/dp_func.py
 """
 
+import torch
 import numpy as np
 from codetiming import Timer
 from test_load_data import _load_data  # type: ignore
@@ -195,7 +196,6 @@ def test_inverse(dim=128):
 
 def test_inverse_torch(dim=128, atol=1e-3):
     from somata.exact_inference import inverse_torch
-    import torch
 
     np.random.seed(1)
 
@@ -263,7 +263,6 @@ def test_logdet():
 
 def test_logdet_torch(rtol=1e-3, atol=1e-3):
     from somata.exact_inference import logdet_torch
-    import torch
 
     np.random.seed(1)