Merge pull request #33 from LabForComputationalVision/mac_failing_test

Fix failing tests/notebooks by updating action versions

Author: billbrod

.github/ISSUE_TEMPLATE/bug_report.md

@@ -30,7 +30,7 @@ If applicable, add screenshots to help explain your problem.
 
 **System (please complete the following information):**
  - OS: [e.g. Mac (with version), Ubuntu 18.04]
- - Python version [e.g. 3.7]
+ - Python version [e.g. 3.11]
  - Pyrtools version [e.g. 1.0.1]
 
 **Additional context**

.github/workflows/ci.yml

@@ -17,7 +17,7 @@ jobs:
     outputs:
       notebook: ${{ steps.get-notebooks.outputs.nb }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - id: get-notebooks
         # it's weird to me, but the quotes around \n should *not* be escaped or it breaks
       run: "echo \"nb=$(ls TUTORIALS/*ipynb | jq -R -s -c 'split(\"\\n\")[:-1]')\"\
@@ -27,39 +27,39 @@ jobs:
     needs: [get_notebooks]
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
         notebook: ${{fromJson(needs.get_notebooks.outputs.notebook)}}
       fail-fast: false
     name: Execute notebooks
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
         cache-dependency-path: setup.py
     - name: Setup FFmpeg
-      uses: FedericoCarboni/setup-ffmpeg@v2
+      uses: FedericoCarboni/setup-ffmpeg@v3.1
     - name: Install dependencies
         # nbclient 0.5.5 is the first version that includes jupyter execute
       run: |
         pip install --upgrade --upgrade-strategy eager .
         pip install jupyter ipywidgets
         pip install "nbclient>=0.5.5"
     - name: Run notebooks
-      run: jupyter execute ${{ matrix.notebook }}.ipynb --kernel_name=python3
+      run: jupyter execute ${{ matrix.notebook }} --kernel_name=python3
   tests:
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
       fail-fast: false
     name: Run tests
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install Python 3
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
@@ -80,7 +80,9 @@ jobs:
         # generate the xml file and move it to root dir for codecov
         coverage xml -o ../coverage.xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@858dd794fbb81941b6d60b0dca860878cba60fa9 # v3.1.1
+      uses: codecov/codecov-action@a079530fc142d3d288ddf76321ca0b7fe5b18df5 # v4.4.1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
   all_tutorials_in_docs:
     runs-on: ubuntu-latest
     name: Check that all tutorial notebooks are included in docs
@@ -89,7 +91,7 @@ jobs:
       matrix:
         notebook: ${{fromJson(needs.get_notebooks.outputs.notebook)}}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Check for file
       shell: bash
       run: if [[ -z "$(grep ${{ matrix.notebook }} docs/tutorials/*nblink)" ]] ; then
@@ -98,7 +100,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Check that we don't have any extra nblink files
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Check same number of nblink and notebooks
       shell: bash
       run: |

.github/workflows/deploy.yml

@@ -10,60 +10,60 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
+        os: [macos-latest, ubuntu-latest, windows-latest]
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-      - name: "Build wheels"
-        uses: pypa/cibuildwheel@v2.8.1
-        env:
-          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-          CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
-          CIBW_SKIP: "*musllinux*"
-          CIBW_ARCHS: native
-          CIBW_BUILD_FRONTEND: build
-          CIBW_TEST_COMMAND: "python {project}/TESTS/unitTests.py"
+    - name: Build wheels
+      uses: pypa/cibuildwheel@357b80c11e6e995e6297e86386460ae84cbc5bee # v2.18.1
+      env:
+        CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+        CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
+        CIBW_SKIP: '*musllinux*'
+        CIBW_ARCHS: native
+        CIBW_BUILD_FRONTEND: build
+        CIBW_TEST_COMMAND: python {project}/TESTS/unitTests.py
           # cross-compilation for Apple Silicon:
           # https://cibuildwheel.readthedocs.io/en/stable/faq/#how-to-cross-compile
-          CIBW_ARCHS_MACOS: x86_64 arm64
+        CIBW_ARCHS_MACOS: x86_64 arm64
 
-      - name: "Upload wheel as artifact"
-        uses: actions/upload-artifact@v4
-        with:
-          name: artifact-${{ matrix.os }}-wheel
-          path: "./**/*.whl"
+    - name: Upload wheel as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: artifact-${{ matrix.os }}-wheel
+        path: ./**/*.whl
 
   build-sdist:
     name: Make source distribution
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - run: pipx run build --sdist
 
     - uses: actions/upload-artifact@v4
       with:
         name: artifact-source-dist
-        path: "./**/dist/*.tar.gz"
+        path: ./**/dist/*.tar.gz
 
   deploy:
     needs: [build-wheels, build-sdist]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/checkout@v3
-      - name: Download all artifacts
-        uses: actions/download-artifact@v4
-      - name: Copy artifacts to dist/ folder
-        run: |
-          find . -name 'artifact-*' -exec unzip '{}' \;
-          mkdir -p dist/
-          find . -name '*.tar.gz' -exec mv '{}' dist/ \;
-          find . -name '*.whl' -exec mv '{}' dist/ \;
-      - name: Publish package to test pypi
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+    - uses: actions/checkout@v4
+    - name: Download all artifacts
+      uses: actions/download-artifact@v4
+    - name: Copy artifacts to dist/ folder
+      run: |
+        find . -name 'artifact-*' -exec unzip '{}' \;
+        mkdir -p dist/
+        find . -name '*.tar.gz' -exec mv '{}' dist/ \;
+        find . -name '*.whl' -exec mv '{}' dist/ \;
+    - name: Publish package to test pypi
+      uses: pypa/gh-action-pypi-publish@68e62d4871ad9d14a9d55f114e6ac71f0b408ec0 # v1.8.14
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

README.md

@@ -2,7 +2,7 @@
 
 [![PyPI Version](https://img.shields.io/pypi/v/pyrtools.svg)](https://pypi.org/project/pyrtools/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/LabForComputationalVision/pyrtools/blob/main/LICENSE)
-![Python version](https://img.shields.io/badge/python-3.7|3.8|3.9|3.10-blue.svg)
+![Python version](https://img.shields.io/badge/python-3.8|3.9|3.10|3.11|3.12-blue.svg)
 [![Build Status](https://github.com/LabForComputationalVision/pyrtools/workflows/build/badge.svg)](https://github.com/LabForComputationalVision/pyrtools/actions?query=workflow%3Abuild)
 [![Documentation Status](https://readthedocs.org/projects/pyrtools/badge/?version=latest)](https://pyrtools.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/137527035.svg)](https://zenodo.org/doi/10.5281/zenodo.10161031)

TESTS/unitTests.py

@@ -217,7 +217,7 @@ def test1(self):
         #foo = pointOp(200, 200, img, 5, filt, 0, 1, 0);
         foo = pt.pointOp(img, filt, 0, 1);
         foo = np.reshape(foo,(200,200))
-        self.assertTrue((matImg['foo'] == foo).all())
+        np.testing.assert_allclose(matImg['foo'], foo)
 
 class maxPyrHeightTests(unittest.TestCase):
     def test1(self):
@@ -336,7 +336,7 @@ def test7(self):
         img = plt.imread(op.join(test_data_path, 'lenna-256x256.tif'))
         pyPyr = pt.pyramids.LaplacianPyramid(img)
         recon = pyPyr.recon_pyr()
-        self.assertTrue((matPyr['recon'] == recon).all())
+        np.testing.assert_allclose(matPyr['recon'], recon)
     def test8(self):
         matPyr = scipy.io.loadmat(op.join(matfiles_path, 'buildLpyr8.mat'))
         pyRamp = pt.synthetic_images.ramp(200)
@@ -360,13 +360,13 @@ def test11(self):
         pyRamp = pt.synthetic_images.ramp((200,200))
         pyPyr = pt.pyramids.LaplacianPyramid(pyRamp)
         recon = pyPyr.recon_pyr(levels=[1])
-        self.assertTrue((matPyr['recon'] == recon).all())
+        np.testing.assert_allclose(matPyr['recon'], recon, atol=1e-6)
     def test12(self):
         matPyr = scipy.io.loadmat(op.join(matfiles_path, 'buildLpyr12.mat'))
         pyRamp = pt.synthetic_images.ramp((200,200))
         pyPyr = pt.pyramids.LaplacianPyramid(pyRamp)
         recon = pyPyr.recon_pyr(levels=[0, 2, 4])
-        self.assertTrue((matPyr['recon'] == recon).all())
+        np.testing.assert_allclose(matPyr['recon'], recon, atol=1e-6)
 
 class WpyrTests(unittest.TestCase):
     def test0(self):

docs/index.rst

@@ -4,7 +4,7 @@
 .. |license-shield| image:: https://img.shields.io/badge/license-MIT-yellow.svg
 			    :target: https://github.com/LabForComputationalVision/pyrtools/blob/main/LICENSE
 
-.. |python-version-shield| image:: https://img.shields.io/badge/python-3.7%7C3.8%7C3.9%7C3.10-blue.svg
+.. |python-version-shield| image:: https://img.shields.io/badge/python-3.8%7C3.9%7C3.10%7C3.11%7C3.12-blue.svg
 
 .. |build| image:: https://github.com/LabForComputationalVision/pyrtools/workflows/build/badge.svg
 		     :target: https://github.com/LabForComputationalVision/pyrtools/actions?query=workflow%3Abuild

pyproject.toml

@@ -4,7 +4,7 @@ dynamic = ["version"]
 authors = [{name="Pyrtools authors"}]
 description = "Python tools for multi-scale image processing, including Laplacian pyramids, Wavelets, and Steerable Pyramids."
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Programming Language :: Python :: 3",