Merge pull request #2914 from ericpre/CI_maintenance

Add python 3.10 and fix some tests
hyperspy · Mar 30, 2022 · 2fac7e8 · 2fac7e8
2 parents e56209a + 8e55714
commit 2fac7e8
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Showing 7 changed files with 32 additions and 26 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -18,7 +18,7 @@ jobs:
       upload_url: ${{ steps.create_release.outputs.upload_url }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Create Release
         id: create_release
         uses: actions/create-release@v1
@@ -38,12 +38,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
           python-version: ${{ matrix.python-version }}
@@ -74,7 +74,7 @@ jobs:
           pip install --pre --find-links dist hyperspy[tests]
           pytest --pyargs hyperspy
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./dist/*.whl
 
@@ -94,10 +94,10 @@ jobs:
     needs: create_release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
 
@@ -111,9 +111,9 @@ jobs:
           python -m build --sdist
 
       - name: Build manylinux Python wheels
-        uses: RalfG/python-wheels-manylinux-build@v0.3.3
+        uses: RalfG/python-wheels-manylinux-build@v0.4.2
         with:
-          python-versions: 'cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39'
+          python-versions: 'cp37-cp37m cp38-cp38 cp39-cp39 cp310-cp310'
           build-requirements: 'cython'
 
       - name: Display content dist folder
@@ -127,7 +127,7 @@ jobs:
           pip install --pre --find-links dist hyperspy[tests]
           pytest --pyargs hyperspy
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: |
             ./dist/*-manylinux*.whl

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -16,12 +16,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, windows, macos]
-        PYTHON_VERSION: [3.8, 3.9]
+        PYTHON_VERSION: ['3.8', '3.9']
         PIP_SELECTOR: ['[all, tests]']
         include:
           # test oldest supported version of main dependencies on python 3.6
           - os: ubuntu
-            PYTHON_VERSION: 3.7
+            PYTHON_VERSION: '3.7'
             OLDEST_SUPPORTED_VERSION: true
             DEPENDENCIES: matplotlib==3.1.3 numpy==1.17.1 scipy==1.1 imagecodecs==2020.1.31 tifffile==2020.2.16 dask==2.11.0 distributed==2.11.0 scikit-image==0.15 numba==0.52
             PIP_SELECTOR: '[all, tests, coverage]'
@@ -30,27 +30,30 @@ jobs:
             LABEL: -oldest
           # test minimum requirement
           - os: ubuntu
-            PYTHON_VERSION: 3.8
+            PYTHON_VERSION: '3.8'
             PIP_SELECTOR: '[tests]'
             LABEL: -minimum
           # Run coverage
           - os: ubuntu
-            PYTHON_VERSION: 3.8
+            PYTHON_VERSION: '3.8'
             PIP_SELECTOR: '[all, tests, coverage]'
             PYTEST_ARGS_COVERAGE: --cov=. --cov-report=xml
             LABEL: -coverage
           - os: ubuntu
-            PYTHON_VERSION: 3.7
+            PYTHON_VERSION: '3.7'
+            PIP_SELECTOR: '[all, tests]'
+          - os: ubuntu
+            PYTHON_VERSION: '3.10'
             PIP_SELECTOR: '[all, tests]'
         exclude:
           # redundant build (same as coverage)
           - os: ubuntu
-            PYTHON_VERSION: 3.8
+            PYTHON_VERSION: '3.8'
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
           python-version: ${{ matrix.PYTHON_VERSION }}
@@ -80,7 +83,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ always() }} && ${{ matrix.PYTEST_ARGS_COVERAGE }}
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2
 
   build_doc:
     name: Build doc
@@ -90,7 +93,7 @@ jobs:
       LATEX_DEPS: dvipng latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: ericpre/sphinx-action@latest_sphinx
         with:
@@ -99,7 +102,7 @@ jobs:
           build-command: make html
           docs-folder: doc/
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./doc/_build/html/
           name: doc_build

diff --git a/.github/workflows/tests_extension.yml b/.github/workflows/tests_extension.yml
@@ -27,9 +27,9 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: conda-incubator/setup-miniconda@master
+      - uses: conda-incubator/setup-miniconda@v2
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest

diff --git a/hyperspy/tests/io/test_hdf5.py b/hyperspy/tests/io/test_hdf5.py
@@ -212,7 +212,8 @@ def test_save_long_list(self, tmp_path, file):
         fname = tmp_path / file
         s.save(fname)
         end = time.time()
-        assert end - start < 1.0  # It should finish in less that 1 s.
+        # It should finish in less that 2 s on CI.
+        assert end - start < 2.0  
 
     @zspy_marker
     def test_numpy_only_inner_lists(self, tmp_path, file):

diff --git a/hyperspy/tests/model/test_linear_model.py b/hyperspy/tests/model/test_linear_model.py
@@ -283,7 +283,7 @@ def test_convolved_and_std_error(self):
         lm = m.as_signal()
         std_lm = m.p_std
         diff = linear - lm
-        np.testing.assert_allclose(diff.data.sum(), 0.0)
+        np.testing.assert_allclose(diff.data.sum(), 0.0, atol=3E-7)
         np.testing.assert_allclose(std_linear, std_lm)
 
     def test_nonconvolved(self):
@@ -293,7 +293,7 @@ def test_nonconvolved(self):
         m.fit(optimizer='lm')
         lm = m.as_signal()
         diff = linear - lm
-        np.testing.assert_allclose(diff.data.sum(), 0.0)
+        np.testing.assert_allclose(diff.data.sum(), 0.0, atol=3E-7)
 
 
 class TestWarningSlowMultifit:

diff --git a/setup.py b/setup.py
@@ -403,6 +403,7 @@ def __exit__(self, type, value, traceback):
             "Programming Language :: Python :: 3.7",
             "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
+            "Programming Language :: Python :: 3.10",
             "Development Status :: 4 - Beta",
             "Environment :: Console",
             "Intended Audience :: Science/Research",

diff --git a/upcoming_changes/2914.maintenance.rst b/upcoming_changes/2914.maintenance.rst
@@ -0,0 +1 @@
+Tweak tests tolerance to fix tests failure on aarch64 platform; Add python 3.10 build.