From 4e61945874ce0ada57f09953cfa50c126ef58bd4 Mon Sep 17 00:00:00 2001 From: PrimozGodec Date: Tue, 19 Mar 2024 15:37:40 +0100 Subject: [PATCH 1/4] [CI] User reusable workflow for automated release --- .github/workflows/release.yml | 72 +++-------------------------------- 1 file changed, 5 insertions(+), 67 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2f75d8f..f226213 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -1,74 +1,12 @@ name: Release - on: release: types: [published] - - # Enable manual run workflow_dispatch: jobs: - build_dist_files: - name: Build distribution files - runs-on: ubuntu-20.04 - steps: - - name: Check out the repo - uses: actions/checkout@v2 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - - - name: Install build tool - run: python -m pip install build - - - name: Build sdist and wheel - run: python -m build --sdist --wheel . - - - name: Upload dist files - uses: actions/upload-artifact@v2 - with: - name: dist_files - path: dist/* - - upload_release_assets: - name: Upload Release Assets - needs: [build_dist_files] - runs-on: ubuntu-20.04 - - steps: - - name: Download dist files - id: download_artifact - uses: actions/download-artifact@v2 - with: - name: dist_files - path: ~/downloads - - - name: List downloaded artifacts - run: ls -la ~/downloads - - - name: Upload to release - uses: shogo82148/actions-upload-release-asset@v1.2.3 - with: - upload_url: ${{ github.event.release.upload_url }} - asset_path: ${{ steps.download_artifact.outputs.download-path }}/*.whl - - pypi_publish: - name: PyPI Publish - needs: [upload_release_assets] - runs-on: ubuntu-20.04 - - steps: - - name: Download dist files - uses: actions/download-artifact@v2 - with: - name: dist_files - path: downloads/ - - - name: Publish packages to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} - packages_dir: downloads/ - # repository_url: https://test.pypi.org/legacy/ - # verbose: true + release: + uses: biolab/orange-ci-cd/.github/workflows/release.yml@master + with: + pure-python: true + secrets: inherit From 7cbea82ed8141d7910460f7de1ff9ca41376b476 Mon Sep 17 00:00:00 2001 From: PrimozGodec Date: Tue, 19 Mar 2024 15:57:03 +0100 Subject: [PATCH 2/4] Remove get_column workaround --- orangecontrib/survival_analysis/__init__.py | 17 ----------------- .../tests/test_deprecation.py | 18 ------------------ setup.cfg | 2 +- tox.ini | 6 +++--- 4 files changed, 4 insertions(+), 39 deletions(-) delete mode 100644 orangecontrib/survival_analysis/tests/test_deprecation.py diff --git a/orangecontrib/survival_analysis/__init__.py b/orangecontrib/survival_analysis/__init__.py index 596063e..21fbee4 100644 --- a/orangecontrib/survival_analysis/__init__.py +++ b/orangecontrib/survival_analysis/__init__.py @@ -1,18 +1 @@ -from Orange.data import Table - from .evaluation import scoring # noqa: F401 - -# Remove this when we require Orange 3.34 -if not hasattr(Table, "get_column"): - import scipy.sparse as sp - import numpy as np - - def get_column(self, column): - col, _ = self.get_column_view(column) - if sp.issparse(col): - col = col.toarray().reshape(-1) - if self.domain[column].is_primitive(): - col = col.astype(np.float64) - return col - - Table.get_column = get_column diff --git a/orangecontrib/survival_analysis/tests/test_deprecation.py b/orangecontrib/survival_analysis/tests/test_deprecation.py deleted file mode 100644 index f922304..0000000 --- a/orangecontrib/survival_analysis/tests/test_deprecation.py +++ /dev/null @@ -1,18 +0,0 @@ -import unittest - - -class TestDeprecations(unittest.TestCase): - def test_remove_get_column_workaround(self): - """ - When this tests start to fail: - 1. remove this test - 2. set minimum version of Orange to 3.34 if not set yet - 3. remove workaround from __inint__.py - """ - from datetime import datetime - - self.assertLess(datetime.today(), datetime(2024, 1, 1)) - - -if __name__ == "__main__": - unittest.main() diff --git a/setup.cfg b/setup.cfg index 9b983af..8e8ed9e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -25,7 +25,7 @@ setup_requires = setuptools>=42.0 setuptools-scm install_requires = - Orange3>=3.32.0 + Orange3>=3.34.0 lifelines statsmodels diff --git a/tox.ini b/tox.ini index ef6514d..59effcf 100644 --- a/tox.ini +++ b/tox.ini @@ -22,10 +22,10 @@ deps = {env:PYQT_PYPI_NAME:PyQt5}=={env:PYQT_PYPI_VERSION:5.15.*} {env:WEBENGINE_PYPI_NAME:PyQtWebEngine}=={env:WEBENGINE_PYPI_VERSION:5.15.*} oldest: scikit-learn==1.0.1 - oldest: orange3==3.32.0 + oldest: orange3==3.34.0 # Use newer canvas-core and widget-base to avoid segfaults on windows - oldest: orange-canvas-core==0.1.24 - oldest: orange-widget-base==4.16.1 + oldest: orange-canvas-core==0.1.28 + oldest: orange-widget-base==4.19.0 oldest: pandas==1.3 latest: git+https://github.com/biolab/orange3.git#egg=orange3 latest: git+https://github.com/biolab/orange-canvas-core.git#egg=orange-canvas-core From cfff335a4cd8b6fffbcd15f4b7516a37695032eb Mon Sep 17 00:00:00 2001 From: PrimozGodec Date: Tue, 19 Mar 2024 15:59:13 +0100 Subject: [PATCH 3/4] Add sphinx_rtd_theme to doc extras_require --- setup.cfg | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.cfg b/setup.cfg index 8e8ed9e..ff226a6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -33,6 +33,7 @@ install_requires = doc = sphinx recommonmark + sphinx_rtd_theme test = pytest coverage From 6a0393492ec12d86ad0dafbdd5a6035b700399a9 Mon Sep 17 00:00:00 2001 From: PrimozGodec Date: Tue, 19 Mar 2024 16:24:57 +0100 Subject: [PATCH 4/4] owsurvivalnomogram - Making black happy --- .../widgets/owsurvivalnomogram.py | 30 ++++++++++--------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/orangecontrib/survival_analysis/widgets/owsurvivalnomogram.py b/orangecontrib/survival_analysis/widgets/owsurvivalnomogram.py index 38c4e00..187cc29 100644 --- a/orangecontrib/survival_analysis/widgets/owsurvivalnomogram.py +++ b/orangecontrib/survival_analysis/widgets/owsurvivalnomogram.py @@ -1081,20 +1081,22 @@ def create_nomogram_header_and_body( ) feature_items = [ - DiscreteFeatureItem( - name_item, attr, point, scale_x, name_offset, -scale_x * min_p - ) - if attr.is_discrete - else cont_feature_item_class( - name_item, - attr, - self.data_extremes[i], - self.get_ruler_values( - point.min(), point.max(), scale_x * point.ptp(), False - ), - scale_x, - name_offset, - -scale_x * min_p, + ( + DiscreteFeatureItem( + name_item, attr, point, scale_x, name_offset, -scale_x * min_p + ) + if attr.is_discrete + else cont_feature_item_class( + name_item, + attr, + self.data_extremes[i], + self.get_ruler_values( + point.min(), point.max(), scale_x * point.ptp(), False + ), + scale_x, + name_offset, + -scale_x * min_p, + ) ) for i, attr, name_item, point in zip( attr_inds, attributes, name_items, points