Merge pull request #10 from ericpre/remove_setup.py

Consolidate packaging in `pyproject.toml`
hyperspy · Nov 14, 2023 · 987e6a8 · 987e6a8
2 parents b8c0de6 + 165217d
commit 987e6a8
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Showing 64 changed files with 170 additions and 235 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
diff --git a/.github/workflows/package_and_test.yml b/.github/workflows/package_and_test.yml
@@ -0,0 +1,8 @@
+name: Package & Test
+
+on: [push, pull_request]
+
+jobs:
+  package_and_test:
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/package_and_test.yml@main
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -1,4 +1,8 @@
 name: Release
+# Reusable workflow are not supported with trusted publisher
+# https://github.com/pypa/gh-action-pypi-publish/issues/166
+# copy and paste
+# https://github.com/hyperspy/.github/blob/main/.github/workflows/release_pure_python.yml
 
 # This workflow builds the wheels "on tag".
 # If run from the hyperspy/hyperspy repository, the wheels will be uploaded to pypi ;
@@ -10,76 +14,60 @@ on:
     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
 jobs:
-  build_wheels:
-    name: Build wheels
+  build:
+    name: Build wheel and sdist
     runs-on: ubuntu-latest
-    env:
-      CIBW_TEST_COMMAND: "pytest --pyargs exspy"
-      CIBW_TEST_EXTRAS: "tests"
-
     steps:
-      - uses: actions/checkout@v3
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: wheels
-          path: ./wheelhouse/*.whl
-          if-no-files-found: error
+    - uses: actions/checkout@v4
 
-  make_sdist:
-    name: Make SDist
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
+    - name: Run build
+      run: |
+        pipx run build
 
-    - name: Build SDist
-      run: pipx run build --sdist
+    - name: Display built files
+      run: |
+        ls -shR
+      working-directory: dist
 
     - uses: actions/upload-artifact@v3
       with:
-        path: dist/*.tar.gz
+        path: dist/*
+        name: artifacts
 
   upload_to_pypi:
-    needs: [build_wheels, make_sdist]
+    needs: [build]
     runs-on: ubuntu-latest
+    name: Upload to pypi
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
     - name: Download dist
       uses: actions/download-artifact@v3
       with:
-        name: artifact
-        path: dist
-
-    - name: Download wheels
-      uses: actions/download-artifact@v3
-      with:
-        name: wheels
+        name: artifacts
         path: dist
 
-    - name: Display structure of downloaded files
-      run: ls -R
+    - name: Display downloaded files
+      run: |
+        ls -shR
       working-directory: dist
 
     - uses: pypa/gh-action-pypi-publish@release/v1
-      if: github.repository_owner == 'hyperspy'
+      if: ${{ startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'hyperspy' }}
       # See https://docs.pypi.org/trusted-publishers/using-a-publisher/
 
-  create_release:
-    # TODO: once we are happy with the workflow
-    # setup zenodo to create a DOI automatically
+  create_github_release:
+    # If zenodo is setup to create a DOI automatically on a GitHub release,
+    # this step will trigger the mining of the DOI
     needs: upload_to_pypi
     permissions:
       contents: write
-    name: Create Release
+    name: Create GitHub Release
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Create Release
-        id: create_release
+        if: ${{ startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'hyperspy' }}
         uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -13,13 +13,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, windows, macos]
-        PYTHON_VERSION: ['3.9', '3.10']
+        PYTHON_VERSION: ['3.9', '3.11']
         LABEL: ['']
         include:
           - os: ubuntu
             PYTHON_VERSION: '3.8'
           - os: ubuntu
-            PYTHON_VERSION: '3.11'
+            PYTHON_VERSION: '3.10'
+          - os: ubuntu
+            PYTHON_VERSION: '3.12'
 
     steps:
       - uses: actions/checkout@v3

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -13,6 +13,12 @@ https://holospy.readthedocs.io/en/latest/changes.html
   (`HyperSpy #3082 <https://github.com/hyperspy/hyperspy/issues/3082>`_)
 - Add functionality to fit the :ref:`EELS fine structure <eels.fine_structure>` using components, e.g. :py:class:`hyperspy.api.model.components1D.Gaussian`. (`HyperSpy #3206 <https://github.com/hyperspy/hyperspy/issues/3206>`_)
 - Use reusable workflow from the hyperspy organisation for the doc workflow (`#13 <https://github.com/hyperspy/exspy/pull/13>`_)
+- Consolidate packaging metadata in ``pyproject.toml``. (`#4 <https://github.com/hyperspy/exspy/pull/4>`_, `#10 <https://github.com/hyperspy/exspy/pull/10>`_)
+- Use ``setuptools_scm`` to set holospy version at build time (`#10 <https://github.com/hyperspy/exspy/pull/10>`_)
+- Add package and test workflow (`#10 <https://github.com/hyperspy/exspy/pull/10>`_)
+- Add python 3.12 (`#10 <https://github.com/hyperspy/exspy/pull/10>`_)
+- Add release workflow (`#10 <https://github.com/hyperspy/exspy/pull/10>`_)
+
 
 Initiation (2023-10-28)
 =======================

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,2 @@
+prune exspy/tests/drawing/plot_model
+prune exspy/tests/drawing/plot_spectra_markers
diff --git a/exspy/__init__.py b/exspy/__init__.py
@@ -1,10 +1,23 @@
+from pathlib import Path
+
 from . import components
 from . import data
 from . import models
 from . import signals
 from .misc import material
 from ._defaults_parser import preferences
-from ._version import __version__
+
+
+if Path(__file__).parent.parent.name == "site-packages":  # pragma: no cover
+    # Tested in the "build" workflow on GitHub CI
+    from importlib.metadata import version
+
+    __version__ = version("rosettasciio")
+else:
+    # Editable install
+    from setuptools_scm import get_version
+
+    __version__ = get_version(Path(__file__).parent.parent)
 
 
 __all__ = [

diff --git a/exspy/_version.py b/exspy/_version.py
diff --git a/exspy/components/eels_double_power_law.py b/exspy/components/eels_double_power_law.py
@@ -72,7 +72,7 @@ def __init__(
         left_cutoff=0.0,
         module="numexpr",
         compute_gradients=False,
-        **kwargs
+        **kwargs,
     ):
         super().__init__(
             expression="where(x > left_cutoff, \

diff --git a/exspy/components/volume_plasmon_drude.py b/exspy/components/volume_plasmon_drude.py
@@ -61,7 +61,7 @@ def __init__(
         fwhm=1.5,
         module="numexpr",
         compute_gradients=False,
-        **kwargs
+        **kwargs,
     ):
         super().__init__(
             expression="where(x > 0, intensity * (pe2 * x * fwhm) \

diff --git a/exspy/models/edsmodel.py b/exspy/models/edsmodel.py
@@ -344,7 +344,7 @@ def fit_background(
         end_energy=None,
         windows_sigma=(4.0, 3.0),
         kind="single",
-        **kwargs
+        **kwargs,
     ):
         """
         Fit the background in the energy range containing no X-ray line.
@@ -849,7 +849,7 @@ def get_lines_intensity(
         plot_result=False,
         only_one=True,
         only_lines=("a",),
-        **kwargs
+        **kwargs,
     ):
         """
         Return the fitted intensity of the X-ray lines.

diff --git a/exspy/signals/eds_sem.py b/exspy/signals/eds_sem.py
@@ -312,7 +312,7 @@ def create_model(self, auto_background=True, auto_add_lines=True, *args, **kwarg
             auto_background=auto_background,
             auto_add_lines=auto_add_lines,
             *args,
-            **kwargs
+            **kwargs,
         )
         return model
 

diff --git a/exspy/test/__init__.py → exspy/tests/__init__.py b/exspy/test/__init__.py → exspy/tests/__init__.py
diff --git a/exspy/test/components/__init__.py → exspy/tests/components/__init__.py b/exspy/test/components/__init__.py → exspy/tests/components/__init__.py
diff --git a/exspy/test/components/test_EELSarctan.py → exspy/tests/components/test_EELSarctan.py b/exspy/test/components/test_EELSarctan.py → exspy/tests/components/test_EELSarctan.py
diff --git a/exspy/test/components/test_ceels_cl_edge.py → exspy/tests/components/test_ceels_cl_edge.py b/exspy/test/components/test_ceels_cl_edge.py → exspy/tests/components/test_ceels_cl_edge.py
diff --git a/.../test/components/test_double_power_law.py → ...tests/components/test_double_power_law.py b/.../test/components/test_double_power_law.py → ...tests/components/test_double_power_law.py
diff --git a/...st/components/test_pes_core_line_shape.py → ...ts/components/test_pes_core_line_shape.py b/...st/components/test_pes_core_line_shape.py → ...ts/components/test_pes_core_line_shape.py
diff --git a/exspy/test/components/test_pes_see.py → exspy/tests/components/test_pes_see.py b/exspy/test/components/test_pes_see.py → exspy/tests/components/test_pes_see.py
diff --git a/exspy/test/components/test_pes_voigt.py → exspy/tests/components/test_pes_voigt.py b/exspy/test/components/test_pes_voigt.py → exspy/tests/components/test_pes_voigt.py
diff --git a/...t/components/test_volume_plasmon_drude.py → ...s/components/test_volume_plasmon_drude.py b/...t/components/test_volume_plasmon_drude.py → ...s/components/test_volume_plasmon_drude.py
diff --git a/exspy/test/data/test_data.py → exspy/tests/data/test_data.py b/exspy/test/data/test_data.py → exspy/tests/data/test_data.py
diff --git a/exspy/test/data/test_eelsdb.py → exspy/tests/data/test_eelsdb.py b/exspy/test/data/test_eelsdb.py → exspy/tests/data/test_eelsdb.py
diff --git a/exspy/test/drawing/__init__.py → exspy/tests/drawing/__init__.py b/exspy/test/drawing/__init__.py → exspy/tests/drawing/__init__.py
diff --git a/exspy/test/drawing/data/Cr_L_cl.hspy → exspy/tests/drawing/data/Cr_L_cl.hspy b/exspy/test/drawing/data/Cr_L_cl.hspy → exspy/tests/drawing/data/Cr_L_cl.hspy
diff --git a/exspy/test/drawing/data/Cr_L_ll.hspy → exspy/tests/drawing/data/Cr_L_ll.hspy b/exspy/test/drawing/data/Cr_L_ll.hspy → exspy/tests/drawing/data/Cr_L_ll.hspy
diff --git a/...t_model/test_fit_EELS_convolved_False.png → ...t_model/test_fit_EELS_convolved_False.png b/...t_model/test_fit_EELS_convolved_False.png → ...t_model/test_fit_EELS_convolved_False.png
diff --git a/...ot_model/test_fit_EELS_convolved_True.png → ...ot_model/test_fit_EELS_convolved_True.png b/...ot_model/test_fit_EELS_convolved_True.png → ...ot_model/test_fit_EELS_convolved_True.png
diff --git a/...ussian_EELSSpectrum_False-False-False.png → ...ussian_EELSSpectrum_False-False-False.png b/...ussian_EELSSpectrum_False-False-False.png → ...ussian_EELSSpectrum_False-False-False.png
diff --git a/...aussian_EELSSpectrum_False-False-True.png → ...aussian_EELSSpectrum_False-False-True.png b/...aussian_EELSSpectrum_False-False-True.png → ...aussian_EELSSpectrum_False-False-True.png
diff --git a/...aussian_EELSSpectrum_False-True-False.png → ...aussian_EELSSpectrum_False-True-False.png b/...aussian_EELSSpectrum_False-True-False.png → ...aussian_EELSSpectrum_False-True-False.png
diff --git a/...gaussian_EELSSpectrum_False-True-True.png → ...gaussian_EELSSpectrum_False-True-True.png b/...gaussian_EELSSpectrum_False-True-True.png → ...gaussian_EELSSpectrum_False-True-True.png
diff --git a/...aussian_EELSSpectrum_True-False-False.png → ...aussian_EELSSpectrum_True-False-False.png b/...aussian_EELSSpectrum_True-False-False.png → ...aussian_EELSSpectrum_True-False-False.png
diff --git a/...gaussian_EELSSpectrum_True-False-True.png → ...gaussian_EELSSpectrum_True-False-True.png b/...gaussian_EELSSpectrum_True-False-True.png → ...gaussian_EELSSpectrum_True-False-True.png
diff --git a/...gaussian_EELSSpectrum_True-True-False.png → ...gaussian_EELSSpectrum_True-True-False.png b/...gaussian_EELSSpectrum_True-True-False.png → ...gaussian_EELSSpectrum_True-True-False.png
diff --git a/..._gaussian_EELSSpectrum_True-True-True.png → ..._gaussian_EELSSpectrum_True-True-True.png b/..._gaussian_EELSSpectrum_True-True-True.png → ..._gaussian_EELSSpectrum_True-True-True.png
diff --git a/...t_spectra_markers/test_plot_eds_lines.png → ...t_spectra_markers/test_plot_eds_lines.png b/...t_spectra_markers/test_plot_eds_lines.png → ...t_spectra_markers/test_plot_eds_lines.png
diff --git a/...spectra_markers/test_plot_eels_labels.png → ...spectra_markers/test_plot_eels_labels.png b/...spectra_markers/test_plot_eels_labels.png → ...spectra_markers/test_plot_eels_labels.png
diff --git a/exspy/test/drawing/test_plot_model.py → exspy/tests/drawing/test_plot_model.py b/exspy/test/drawing/test_plot_model.py → exspy/tests/drawing/test_plot_model.py
diff --git a/...test/drawing/test_plot_spectra_markers.py → ...ests/drawing/test_plot_spectra_markers.py b/...test/drawing/test_plot_spectra_markers.py → ...ests/drawing/test_plot_spectra_markers.py
diff --git a/exspy/test/misc/__init__.py → exspy/tests/misc/__init__.py b/exspy/test/misc/__init__.py → exspy/tests/misc/__init__.py
diff --git a/exspy/test/misc/test_eds.py → exspy/tests/misc/test_eds.py b/exspy/test/misc/test_eds.py → exspy/tests/misc/test_eds.py
diff --git a/exspy/test/misc/test_eds_utils.py → exspy/tests/misc/test_eds_utils.py b/exspy/test/misc/test_eds_utils.py → exspy/tests/misc/test_eds_utils.py
diff --git a/exspy/test/misc/test_eels.py → exspy/tests/misc/test_eels.py b/exspy/test/misc/test_eels.py → exspy/tests/misc/test_eels.py
diff --git a/exspy/test/misc/test_gos.py → exspy/tests/misc/test_gos.py b/exspy/test/misc/test_gos.py → exspy/tests/misc/test_gos.py
diff --git a/exspy/test/misc/test_material.py → exspy/tests/misc/test_material.py b/exspy/test/misc/test_material.py → exspy/tests/misc/test_material.py
diff --git a/exspy/test/models/__init__.py → exspy/tests/models/__init__.py b/exspy/test/models/__init__.py → exspy/tests/models/__init__.py
diff --git a/exspy/test/models/test_edsmodel.py → exspy/tests/models/test_edsmodel.py b/exspy/test/models/test_edsmodel.py → exspy/tests/models/test_edsmodel.py
diff --git a/exspy/test/models/test_eelsmodel.py → exspy/tests/models/test_eelsmodel.py b/exspy/test/models/test_eelsmodel.py → exspy/tests/models/test_eelsmodel.py
diff --git a/exspy/test/models/test_linear_model.py → exspy/tests/models/test_linear_model.py b/exspy/test/models/test_linear_model.py → exspy/tests/models/test_linear_model.py
diff --git a/exspy/test/signals/__init__.py → exspy/tests/signals/__init__.py b/exspy/test/signals/__init__.py → exspy/tests/signals/__init__.py
diff --git a/...nescan_simulated_thickness_variation.hspy → ...nescan_simulated_thickness_variation.hspy b/...nescan_simulated_thickness_variation.hspy → ...nescan_simulated_thickness_variation.hspy
diff --git a/...nescan_simulated_thickness_variation.hspy → ...nescan_simulated_thickness_variation.hspy b/...nescan_simulated_thickness_variation.hspy → ...nescan_simulated_thickness_variation.hspy
diff --git a/exspy/test/signals/test_assign_subclass.py → exspy/tests/signals/test_assign_subclass.py b/exspy/test/signals/test_assign_subclass.py → exspy/tests/signals/test_assign_subclass.py
diff --git a/exspy/test/signals/test_binned.py → exspy/tests/signals/test_binned.py b/exspy/test/signals/test_binned.py → exspy/tests/signals/test_binned.py
diff --git a/exspy/test/signals/test_edges_range.py → exspy/tests/signals/test_edges_range.py b/exspy/test/signals/test_edges_range.py → exspy/tests/signals/test_edges_range.py
diff --git a/exspy/test/signals/test_eds_sem.py → exspy/tests/signals/test_eds_sem.py b/exspy/test/signals/test_eds_sem.py → exspy/tests/signals/test_eds_sem.py
diff --git a/exspy/test/signals/test_eds_tem.py → exspy/tests/signals/test_eds_tem.py b/exspy/test/signals/test_eds_tem.py → exspy/tests/signals/test_eds_tem.py
diff --git a/exspy/test/signals/test_eels.py → exspy/tests/signals/test_eels.py b/exspy/test/signals/test_eels.py → exspy/tests/signals/test_eels.py
diff --git a/.../signals/test_kramers_kronig_transform.py → .../signals/test_kramers_kronig_transform.py b/.../signals/test_kramers_kronig_transform.py → .../signals/test_kramers_kronig_transform.py
diff --git a/.../test/test_non-uniform_not-implemented.py → ...tests/test_non-uniform_not-implemented.py b/.../test/test_non-uniform_not-implemented.py → ...tests/test_non-uniform_not-implemented.py