Merge branch 'main' into ordereddict_regression

.github/workflows/build.yaml

@@ -51,10 +51,16 @@ jobs:
           bash ./scripts/build_conda.sh
       - name: conda dev upload
         if: (github.event_name == 'push' && (contains(steps.vars.outputs.tag, 'a') || contains(steps.vars.outputs.tag, 'b') || contains(steps.vars.outputs.tag, 'rc')))
-        run: doit package_upload --token=$CONDA_UPLOAD_TOKEN --label=dev
+        run: |
+          VERSION="$(echo "$(ls dist/*.whl)" | cut -d- -f2)"
+          FILE="$CONDA_PREFIX/conda-bld/noarch/holoviews-$VERSION-py_0.tar.bz2"
+          anaconda --token $CONDA_UPLOAD_TOKEN upload --user pyviz --label=dev $FILE
       - name: conda main upload
         if: (github.event_name == 'push' && !(contains(steps.vars.outputs.tag, 'a') || contains(steps.vars.outputs.tag, 'b') || contains(steps.vars.outputs.tag, 'rc')))
-        run: doit package_upload --token=$CONDA_UPLOAD_TOKEN --label=dev --label=main
+        run: |
+          VERSION="$(echo "$(ls dist/*.whl)" | cut -d- -f2)"
+          FILE="$CONDA_PREFIX/conda-bld/noarch/holoviews-$VERSION-py_0.tar.bz2"
+          anaconda --token $CONDA_UPLOAD_TOKEN upload --user pyviz --label=dev --label=main $FILE
   pip_build:
     name: Build PyPI Packages
     runs-on: 'ubuntu-latest'

.github/workflows/test.yaml

@@ -63,7 +63,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           channel-priority: strict
           channels: pyviz/label/dev,conda-forge,nodefaults
-          envs: "-o flakes -o tests -o examples_tests"
+          envs: "-o flakes -o tests -o examples_tests -o test_ci"
           cache: true
           conda-update: true
         id: install
@@ -109,7 +109,7 @@ jobs:
           name: ui_test_suite
           python-version: ${{ matrix.python-version }}
           channels: pyviz/label/dev,bokeh,conda-forge,nodefaults
-          envs: "-o recommended -o tests -o build"
+          envs: "-o recommended -o tests -o build -o test_ci"
           cache: true
           playwright: true
         id: install
@@ -150,7 +150,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           channel-priority: strict
           channels: pyviz/label/dev,conda-forge,nodefaults
-          envs: "-o tests_core"
+          envs: "-o tests_core -o test_ci"
           cache: true
           conda-update: true
         id: install

examples/conftest.py

@@ -60,12 +60,17 @@ def pytest_runtest_makereport(item, call):
 
     """
     from _pytest.runner import pytest_runtest_makereport
+
     tr = pytest_runtest_makereport(item, call)
 
     if call.excinfo is not None:
-        msg = "Kernel died before replying to kernel_info"
-        if call.excinfo.type == RuntimeError and call.excinfo.value.args[0] == msg:
-            tr.outcome = 'skipped'
-            tr.wasxfail = f"reason: {msg}"
+        msgs = [
+            "Kernel died before replying to kernel_info",
+            "Kernel didn't respond in 60 seconds",
+        ]
+        for msg in msgs:
+            if call.excinfo.type == RuntimeError and call.excinfo.value.args[0] in msg:
+                tr.outcome = "skipped"
+                tr.wasxfail = f"reason: {msg}"
 
     return tr

holoviews/core/data/ibis.py

@@ -23,6 +23,11 @@ def ibis4():
     return ibis_version() >= Version("4.0")
 
 
+@lru_cache
+def ibis5():
+    return ibis_version() >= Version("5.0")
+
+
 class IbisInterface(Interface):
 
     types = ()
@@ -163,16 +168,16 @@ def histogram(cls, expr, bins, density=True, weights=None):
         else:
             # sort_by will be removed in Ibis 5.0
             hist_bins = binned.value_counts().sort_by('bucket').execute()
-
-        for b, v in zip(hist_bins['bucket'], hist_bins['count']):
+        metric_name = 'bucket_count' if ibis5() else 'count'
+        for b, v in zip(hist_bins['bucket'], hist_bins[metric_name]):
             if np.isnan(b):
                 continue
             hist[int(b)] = v
         if weights is not None:
             raise NotImplementedError("Weighted histograms currently "
                                       "not implemented for IbisInterface.")
         if density:
-            hist = hist/expr.count().execute()
+            hist = hist/expr.count().execute()/np.diff(bins)
         return hist, bins
 
     @classmethod

holoviews/operation/element.py

@@ -737,10 +737,16 @@ def _process(self, element, key=None):
 
         # Mask data
         if is_ibis_expr(data):
+            from ..core.data.ibis import ibis5
+
             mask = data.notnull()
             if self.p.nonzero:
                 mask = mask & (data != 0)
-            data = data.to_projection()
+            if ibis5():
+                data = data.as_table()
+            else:
+                # to_projection removed in ibis 5.0.0
+                data = data.to_projection()
             data = data[mask]
             no_data = not len(data.head(1).execute())
             data = data[dim.name]

holoviews/tests/conftest.py

@@ -1,3 +1,5 @@
+import pytest
+
 from panel.tests.conftest import server_cleanup, port, pytest_addoption, pytest_configure, optional_markers  # noqa
 
 
@@ -26,3 +28,15 @@ def pytest_collection_modifyitems(config, items):
     dask.config.set({"dataframe.convert-string": False})
 except Exception:
     pass
+
+
+@pytest.fixture
+def ibis_sqlite_backend():
+    try:
+        import ibis
+    except ImportError:
+        yield None
+    else:
+        ibis.set_backend('sqlite')
+        yield
+        ibis.set_backend(None)

holoviews/tests/operation/test_operation.py

@@ -10,6 +10,11 @@
 except ImportError:
     da = None
 
+try:
+    import ibis
+except ImportError:
+    ibis = None
+
 from holoviews import (HoloMap, NdOverlay, NdLayout, GridSpace, Image,
                        Contours, Polygons, Points, Histogram, Curve, Area,
                        QuadMesh, Dataset, renderer)
@@ -20,6 +25,7 @@
                                          interpolate_curve, decimate)
 
 da_skip = skipIf(da is None, "dask.array is not available")
+ibis_skip = skipIf(ibis is None, "ibis is not available")
 
 
 class OperationTests(ComparisonTestCase):
@@ -179,6 +185,43 @@ def test_dataset_weighted_histogram_dask(self):
         self.assertIsInstance(op_hist.data['y'], da.Array)
         self.assertEqual(op_hist, hist)
 
+    @ibis_skip
+    @pytest.mark.usefixtures('ibis_sqlite_backend')
+    def test_dataset_histogram_ibis(self):
+        df = pd.DataFrame(dict(x=np.arange(10)))
+        t = ibis.memtable(df, name='t')
+        ds = Dataset(t, vdims='x')
+        op_hist = histogram(ds, dimension='x', num_bins=3, normed=True)
+
+        hist = Histogram(([0, 3, 6, 9], [0.1, 0.1, 0.133333]),
+                         vdims=('x_frequency', 'Frequency'))
+        self.assertEqual(op_hist, hist)
+
+    @ibis_skip
+    @pytest.mark.usefixtures('ibis_sqlite_backend')
+    def test_dataset_cumulative_histogram_ibis(self):
+        df = pd.DataFrame(dict(x=np.arange(10)))
+        t = ibis.memtable(df, name='t')
+        ds = Dataset(t, vdims='x')
+        op_hist = histogram(ds, num_bins=3, cumulative=True, normed=True)
+
+        hist = Histogram(([0, 3, 6, 9], [0.3, 0.6, 1]),
+                         vdims=('x_frequency', 'Frequency'))
+        self.assertEqual(op_hist, hist)
+
+    @ibis_skip
+    @pytest.mark.usefixtures('ibis_sqlite_backend')
+    def test_dataset_histogram_explicit_bins_ibis(self):
+        df = pd.DataFrame(dict(x=np.arange(10)))
+        t = ibis.memtable(df, name='t')
+        ds = Dataset(t, vdims='x')
+        op_hist = histogram(ds, bins=[0, 1, 3], normed=False)
+
+        hist = Histogram(([0, 1, 3], [1, 3]),
+                         vdims=('x_count', 'Count'))
+        self.assertEqual(op_hist, hist)
+
+
     def test_points_histogram_bin_range(self):
         points = Points([float(i) for i in range(10)])
         op_hist = histogram(points, num_bins=3, bin_range=(0, 3), normed=True)

setup.py

@@ -39,7 +39,6 @@
     'pillow',
     'plotly >=4.0',
     'dash >=1.16',
-    'codecov',
     'ipython >=5.4.0',
 ]
 
@@ -48,7 +47,7 @@
 # of those.
 extras_require['tests'] = extras_require['tests_core'] + [
     'dask',
-    'ibis-framework != 7.0.0',  # Mapped to ibis-sqlite in setup.cfg for conda
+    'ibis-framework',  # Mapped to ibis-sqlite in setup.cfg for conda
     'xarray >=0.10.4',
     'networkx',
     'shapely',
@@ -60,6 +59,11 @@
     'datashader >=0.11.1',
 ]
 
+extras_require['test_ci'] = [
+    'codecov',
+    "pytest-github-actions-annotate-failures",
+]
+
 extras_require['tests_gpu'] = extras_require['tests'] + [
     'cudf',
 ]