Merge tag '3.36.1' into stable

.github/workflows/build-wheels.yaml

@@ -0,0 +1,138 @@
+name: Build
+
+on:
+  release:
+    types: [published]
+  # Enable manual run
+  workflow_dispatch:
+
+jobs:
+  generate-wheels-matrix:
+    # Create a matrix of all architectures & versions to build.
+    # This enables the next step to run cibuildwheel in parallel.
+    # From https://iscinumpy.dev/post/cibuildwheel-2-10-0/#only-210
+    name: Generate wheels matrix
+    runs-on: ubuntu-latest
+    outputs:
+      include: ${{ steps.set-matrix.outputs.include }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install cibuildwheel
+        # Nb. keep cibuildwheel version pin consistent with job below
+        run: pipx install cibuildwheel==2.14.1
+      - id: set-matrix
+        run: |
+          MATRIX=$(
+            {
+              cibuildwheel --print-build-identifiers --platform linux \
+              | jq -nRc '{"only": inputs, "os": "ubuntu-latest"}' \
+              && cibuildwheel --print-build-identifiers --platform macos \
+              | jq -nRc '{"only": inputs, "os": "macos-latest"}' \
+              && cibuildwheel --print-build-identifiers --platform windows \
+              | jq -nRc '{"only": inputs, "os": "windows-latest"}'
+            } | jq -sc
+          )
+          echo "include=$MATRIX" >> $GITHUB_OUTPUT
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.only }}
+    needs: generate-wheels-matrix
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
+
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: all
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.15.0
+        with:
+          only: ${{ matrix.only }}
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+          name: Orange3-wheels
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+
+      - name: Build sdist (pep517)
+        run: |
+          python -m pip install pep517 numpy cython
+          python -m pep517.build -s .
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v3
+        with:
+          name: Orange3-source
+          path: dist/*.tar.gz
+
+  upload_release_assets:
+    name: Upload Release Assets
+    needs: [ build_wheels ]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags')
+
+    steps:
+      - name: Download bdist files
+        id: download_artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: Orange3-wheels
+          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: [ build_wheels, build_sdist ]
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # this permission is mandatory for trusted publishing
+    if: startsWith(github.ref, 'refs/tags')
+
+    steps:
+      - name: Download bdist files
+        uses: actions/download-artifact@v2
+        with:
+          name: Orange3-wheels
+          path: downloads/
+
+      - name: Download sdist files
+        uses: actions/download-artifact@v2
+        with:
+          name: Orange3-source
+          path: downloads/
+
+      - name: Display structure of downloaded files
+        run: ls -R downloads/
+
+      - name: Publish packages to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages_dir: downloads/

.github/workflows/test.yml

@@ -148,10 +148,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install system dependencies on MacOS
-        run: brew install libomp
-        if: runner.os == 'macOS'
-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

CHANGELOG.md

@@ -4,6 +4,13 @@ Change Log
 [next] - TBA
 ------------
 
+[3.36.1] - 2023-09-22
+--------------------
+##### Bugfixes
+* Distributions: Fix selection output ([#6578](../../pull/6578))
+* Datasets: save selected dataset platform independently ([#6575](../../pull/6575))
+
+
 [3.36.0] - 2023-09-08
 --------------------
 ##### Enhancements
@@ -1822,7 +1829,8 @@ Change Log
 * Initial version based on Python 1.5.2 and Qt 2.3
 
 
-[next]: https://github.com/biolab/orange3/compare/3.35.0..HEAD
+[next]: https://github.com/biolab/orange3/compare/3.36.1..HEAD
+[3.36.1]: https://github.com/biolab/orange3/compare/3.36.0...3.36.1
 [3.36.0]: https://github.com/biolab/orange3/compare/3.35.0...3.36.0
 [3.35.0]: https://github.com/biolab/orange3/compare/3.34.1...3.35.0
 [3.34.1]: https://github.com/biolab/orange3/compare/3.34.0...3.34.1

Orange/projection/freeviz.py

@@ -21,7 +21,7 @@ class FreeViz(LinearProjector):
     projection = FreeVizModel
 
     def __init__(self, weights=None, center=True, scale=True, dim=2, p=1,
-                 initial=None, maxiter=500, alpha=0.1,
+                 initial=None, maxiter=500, alpha=0.1, gravity=None,
                  atol=1e-5, preprocessors=None):
         super().__init__(preprocessors=preprocessors)
         self.weights = weights
@@ -33,6 +33,7 @@ def __init__(self, weights=None, center=True, scale=True, dim=2, p=1,
         self.maxiter = maxiter
         self.alpha = alpha
         self.atol = atol
+        self.gravity = gravity
         self.is_class_discrete = False
         self.components_ = None
 
@@ -50,6 +51,7 @@ def get_components(self, X, Y):
             X, Y, weights=self.weights, center=self.center, scale=self.scale,
             dim=self.dim, p=self.p, initial=self.initial,
             maxiter=self.maxiter, alpha=self.alpha, atol=self.atol,
+            gravity=self.gravity,
             is_class_discrete=self.is_class_discrete)[1].T
 
     @classmethod
@@ -104,7 +106,7 @@ def forces_regression(cls, distances, y, p=1):
         return F
 
     @classmethod
-    def forces_classification(cls, distances, y, p=1):
+    def forces_classification(cls, distances, y, p=1, gravity=None):
         diffclass = scipy.spatial.distance.pdist(y.reshape(-1, 1), "hamming") != 0
         # handle attractive force
         if p == 1:
@@ -120,6 +122,8 @@ def forces_classification(cls, distances, y, p=1):
             F[mask] = 1 / distances[mask]
         else:
             F[mask] = 1 / (distances[mask] ** p)
+        if gravity is not None:
+            F[mask] *= -np.sum(F[~mask]) / np.sum(F[mask]) / gravity
         return F
 
     @classmethod
@@ -180,7 +184,8 @@ def gradient(cls, X, embeddings, forces, embedding_dist=None, weights=None):
         return G
 
     @classmethod
-    def freeviz_gradient(cls, X, y, embedding, p=1, weights=None, is_class_discrete=False):
+    def freeviz_gradient(cls, X, y, embedding, p=1, weights=None,
+                         gravity=None, is_class_discrete=False):
         """
         Return the gradient for the FreeViz [1]_ projection.
 
@@ -214,7 +219,7 @@ def freeviz_gradient(cls, X, y, embedding, p=1, weights=None, is_class_discrete=
         assert X.ndim == 2 and X.shape[0] == y.shape[0] == embedding.shape[0]
         D = scipy.spatial.distance.pdist(embedding)
         if is_class_discrete:
-            forces = cls.forces_classification(D, y, p=p)
+            forces = cls.forces_classification(D, y, p=p, gravity=gravity)
         else:
             forces = cls.forces_regression(D, y, p=p)
         G = cls.gradient(X, embedding, forces, embedding_dist=D, weights=weights)
@@ -234,7 +239,8 @@ def _rotate(cls, A):
 
     @classmethod
     def freeviz(cls, X, y, weights=None, center=True, scale=True, dim=2, p=1,
-                initial=None, maxiter=500, alpha=0.1, atol=1e-5, is_class_discrete=False):
+                initial=None, maxiter=500, alpha=0.1, atol=1e-5, gravity=None,
+                is_class_discrete=False):
         """
         FreeViz
 
@@ -341,6 +347,7 @@ def freeviz(cls, X, y, weights=None, center=True, scale=True, dim=2, p=1,
         step_i = 0
         while step_i < maxiter:
             G = cls.freeviz_gradient(X, y, embeddings, p=p, weights=weights,
+                                     gravity=gravity,
                                      is_class_discrete=is_class_discrete)
 
             # Scale the changes (the largest anchor move is alpha * radius)