Merge pull request #167 from PrimozGodec/reusable-workflows

CI - Reusable workflows

.github/workflows/rebase.yml

@@ -0,0 +1,8 @@
+name: Automatic Rebase
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  rebase:
+    uses: biolab/orange-ci-cd/.github/workflows/rebase-addons.yml@master
+    secrets: inherit

.github/workflows/test.yml

@@ -9,102 +9,5 @@ on:
       - master
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.experimental }}
-    timeout-minutes: 15
-    name: ${{ matrix.name }} (${{ matrix.os }}, ${{ matrix.python-version }})
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-18.04, macos-10.15, windows-2019]
-        python-version: [3.7, 3.8, 3.9]
-        tox_env: [py-orange-released]
-        experimental: [false]
-        name: [Released]
-        include:
-          - os: windows-latest
-            python-version: 3.8
-            tox_env: py-orange-released
-            experimental: true
-            name: Windows10
-          - os: macos-11.0
-            python-version: 3.8
-            tox_env: py-orange-released
-            experimental: true
-            name: Big Sur
-
-          - os: windows-2019
-            python-version: 3.7
-            tox_env: py-orange-oldest
-            experimental: false
-            name: Oldest
-          - os: macos-10.15
-            python-version: 3.7
-            tox_env: py-orange-oldest
-            name: Oldest
-            experimental: false
-          - os: ubuntu-18.04
-            python-version: 3.7
-            tox_env: py-orange-oldest
-            name: Oldest
-            experimental: false
-
-          - os: windows-2019
-            python-version: 3.8
-            tox_env: py-orange-latest
-            experimental: false
-            name: Latest
-          - os: macos-10.15
-            python-version: 3.8
-            tox_env: py-orange-latest
-            experimental: false
-            name: Latest
-          - os: ubuntu-18.04
-            python-version: 3.8
-            tox_env: py-orange-latest
-            experimental: false
-            name: Latest
-
-          - os: windows-2019
-            python-version: 3.9
-            tox_env: py-orange-latest
-            experimental: false
-            name: Latest
-          - os: macos-10.15
-            python-version: 3.9
-            tox_env: py-orange-latest
-            experimental: false
-            name: Latest
-          - os: ubuntu-18.04
-            python-version: 3.9
-            tox_env: py-orange-latest
-            experimental: false
-            name: Latest
-
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade tox
-
-      - name: Test with Tox
-        run: |
-          tox -e ${{ matrix.tox_env }}
-        env:
-          QT_QPA_PLATFORM: offscreen
-
-      - name: Upload code coverage
-        if: |
-          matrix.python-version == '3.8' &&
-          matrix.os == 'ubuntu-18.04' &&
-          matrix.tox_env == 'py-orange-released'
-        run: |
-          pip install codecov
-          codecov
+  test:
+      uses: biolab/orange-ci-cd/.github/workflows/test-addons.yml@master

orangecontrib/geo/__init__.py

@@ -1,4 +1,23 @@
 from os.path import join, dirname
 from Orange.data.table import dataset_dirs
+from Orange.data import Table
+
+
 dataset_dirs.insert(0, join(dirname(__file__), "datasets"))
 del join, dirname, dataset_dirs
+
+
+# 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

orangecontrib/geo/tests/test_utils.py

@@ -1,3 +1,4 @@
+import unittest
 from unittest import TestCase
 
 import numpy as np
@@ -96,3 +97,19 @@ def attrs_for(*attrs, x=None):
         self.assertEqual(attrs_for(d1, c1, c2, lon), (c1, c1))
         self.assertEqual(attrs_for(d1, lon, c1, c2), (lon, lon))
         self.assertEqual(attrs_for(d1, c3, c2, c1), (c3, c3))
+
+
+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()

orangecontrib/geo/utils.py

@@ -56,7 +56,7 @@ def find_lat_lon(data, filter_hidden=False):
     def max_in_col(attr):
         if not data:
             return 0
-        return np.nanmax(np.abs(data.get_column_view(attr)[0].astype(float)))
+        return np.nanmax(np.abs(data.get_column(attr).astype(float)))
 
     if len(cont_vars) == 2:
         if lat_attr is not None:

orangecontrib/geo/widgets/owchoropleth.py

@@ -908,8 +908,7 @@ def get_regions(self, lat_attr, lon_attr, admin):
             dict of region ids matched to their additional info,
             dict of region ids matched to their polygon
         """
-        latlon = np.c_[self.data.get_column_view(lat_attr)[0],
-                       self.data.get_column_view(lon_attr)[0]]
+        latlon = np.c_[self.data.get_column(lat_attr), self.data.get_column(lon_attr)]
         region_info = latlon2region(latlon, admin)
         ids = np.array([region.get('_id') for region in region_info])
         region_info = {info.get('_id'): info for info in region_info}
@@ -931,7 +930,7 @@ def get_grouped(self, lat_attr, lon_attr, admin, attr, agg_func):
             Series of aggregated values
         """
         if attr is not None:
-            data = self.data.get_column_view(attr)[0]
+            data = self.data.get_column(attr)
         else:
             data = np.ones(len(self.data))
 

orangecontrib/geo/widgets/owgeocoding.py

@@ -235,8 +235,8 @@ def decode(self):
                 self.lat_attr not in self.data.domain or
                 self.lon_attr not in self.data.domain):
             return None
-        latlon = np.c_[self.data.get_column_view(self.lat_attr)[0],
-                       self.data.get_column_view(self.lon_attr)[0]]
+        latlon = np.c_[self.data.get_column(self.lat_attr),
+                       self.data.get_column(self.lon_attr)]
         assert isinstance(self.admin, int)
         with self.progressBar(2) as progress:
             progress.advance()
@@ -280,7 +280,7 @@ def _get_data_values(self):
         if self.data is None:
             return None
 
-        values = self.data.get_column_view(self.str_attr)[0]
+        values = self.data.get_column(self.str_attr)
         # no comment
         if self.str_attr.is_discrete:
             values = np.array(self.str_attr.values)[values.astype(np.int16)].astype(str)

orangecontrib/geo/widgets/owgeotransform.py

@@ -33,8 +33,8 @@ def __init__(self, transformer, var_lat, var_lon):
         self.var_lat, self.var_lon = var_lat, var_lon
 
     def __call__(self, data):
-        latitude = data.get_column_view(self.var_lat)[0]
-        longitude = data.get_column_view(self.var_lon)[0]
+        latitude = data.get_column(self.var_lat)
+        longitude = data.get_column(self.var_lon)
         coords = tuple(
             zip(*self.transformer.itransform(zip(latitude, longitude))))
         return coords

orangecontrib/geo/widgets/owmap.py

@@ -155,7 +155,7 @@ def _add_controls(self):
         lat_lon_box = gui.vBox(self.controlArea, box="Layout", spacing=0)
         options = dict(
             labelWidth=75, orientation=Qt.Horizontal, sendSelectedValue=True,
-            valueType=str, contentsLength=14
+            contentsLength=14
         )
 
         gui.comboBox(lat_lon_box, self, 'graph.tile_provider_key', label='Map:',

orangecontrib/geo/widgets/tests/test_owchoropleth.py

@@ -1,3 +1,4 @@
+import unittest
 from unittest.mock import patch
 import numpy as np
 
@@ -118,4 +119,8 @@ def test_no_data(self):
         with self.data.unlocked():
             self.data.X[:] = np.nan
 
-        self.send_signal(self.widget.Inputs.data, self.data)
+        self.send_signal(self.widget.Inputs.data, self.data)
+
+
+if __name__ == "__main__":
+    unittest.main()

orangecontrib/geo/widgets/tests/test_owgeocoding.py

@@ -1,7 +1,5 @@
 # pylint: disable=protected-access
 import unittest
-import numpy as np
-import pandas as pd
 
 from Orange.data import Table, Domain, DiscreteVariable
 from Orange.widgets.tests.base import WidgetTest
@@ -81,4 +79,3 @@ def test_minimum_size(self):
 
 if __name__ == "__main__":
     unittest.main()
-

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{37,38,39}-orange-{oldest, latest, released}
+    orange-{oldest, latest, released}
 skip_missing_interpreters = true
 isolated_build = true
 
@@ -20,8 +20,8 @@ setenv =
     COVERAGE_FILE = {toxinidir}/.coverage
     COVERAGE_RCFILE = {toxinidir}/.coveragerc
 deps =
-    pyqt5==5.12.*
-    pyqtwebengine==5.12.*
+    {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~=0.22.0
     oldest: orange3==3.25.0
     # Use newer canvas-core and widget-base to avoid segfaults on windows