Merge branch 'main' into ci_updates

.github/workflows/test.yaml

@@ -10,6 +10,10 @@ on:
   schedule:
     - cron: '0 14 * * SUN'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pre_commit:
     name: Run pre-commit hooks
@@ -41,7 +45,7 @@ jobs:
             # Bokeh 3 does not support Python 3.7
           - bokeh-version: '3'
             python-version: '3.7'
-    timeout-minutes: 120  # Because slow conda solve on Python 3.7
+    timeout-minutes: 120
     defaults:
       run:
         shell: bash -el {0}
@@ -59,7 +63,7 @@ jobs:
           name: unit_test_suite_bokeh${{ matrix.bokeh-version }}
           python-version: ${{ matrix.python-version }}
           channel-priority: strict
-          channels: pyviz/label/dev,bokeh/label/dev,conda-forge,nodefaults
+          channels: pyviz/label/dev,conda-forge,nodefaults
           envs: "-o flakes -o tests -o examples_tests -o bokeh${{ matrix.bokeh-version }}"
           cache: true
           conda-update: true
@@ -74,20 +78,11 @@ jobs:
           conda activate test-environment
           doit test_unit
       - name: test examples
-        if: matrix.python-version != '3.11'
         run: |
           conda activate test-environment
           mkdir -p ~/.jupyter/
           echo "c.ExecutePreprocessor.startup_timeout=600" >> ~/.jupyter/jupyter_nbconvert_config.py
           doit test_examples
-      - name: test examples - python 3.11
-        # Should be removed when numba support python 3.11
-        if: matrix.python-version == '3.11'
-        run: |
-          conda activate test-environment
-          mkdir -p ~/.jupyter/
-          echo "c.ExecutePreprocessor.startup_timeout=600" >> ~/.jupyter/jupyter_nbconvert_config.py
-          pytest -n auto --dist loadscope --nbval-lax examples/reference/elements
       - name: codecov
         run: |
           conda activate test-environment

.pre-commit-config.yaml

@@ -1,6 +1,7 @@
 # This is the configuration for pre-commit, a local framework for managing pre-commit hooks
 #   Check out the docs at: https://pre-commit.com/
 
+exclude: (\.min\.js$|\.svg$|\.html$)
 default_stages: [commit]
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -25,3 +26,9 @@ repos:
     rev: v0.1.6
     hooks:
       - id: clean-notebook
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli

CHANGELOG.md

@@ -1,3 +1,15 @@
+Version 1.16.0
+==============
+** 2023 **
+
+
+Removed:
+
+- Raise DataError for non-string column names in DataFrame ([#5653](https://github.com/holoviz/holoviews/pull/5653))
+- Remove deprecated tilesources ([#5653](https://github.com/holoviz/holoviews/pull/5653))
+- Removed support for apply_groups for old option groups signature ([#5497](https://github.com/holoviz/holoviews/pull/5497))
+
+
 Version 1.15.4
 ==============
 **January 16, 2023**
@@ -403,7 +415,7 @@ Bug fixes:
 Documentation:
 
 - Updated Large data guide to reflect changes in Datashader and
-  antialising support
+  antialiasing support
   ([#5267](https://github.com/holoviz/holoviews/pull/5267),
   [#5290](https://github.com/holoviz/holoviews/pull/5290))
 
@@ -566,7 +578,7 @@ and @philippjfr for contributing.
 
 Enhancements:
 
-- Reenable `SaveTool` for plots with `Tiles`
+- Re-enable `SaveTool` for plots with `Tiles`
   ([#4922](https://github.com/holoviz/holoviews/pull/4922))
 - Enable dask `TriMesh` rasterization using datashader
   ([#4935](https://github.com/holoviz/holoviews/pull/4935))
@@ -732,7 +744,7 @@ Bug fixes:
   ([#4757](https://github.com/holoviz/holoviews/pull/4757))
 - Do not drop tools in linked selections
   ([#4756](https://github.com/holoviz/holoviews/pull/4756))
-- Fixed access to possibly non-existant key
+- Fixed access to possibly non-existent key
   ([#4742](https://github.com/holoviz/holoviews/pull/4742))
 
 Documentation:
@@ -867,7 +879,7 @@ Bug fixes:
 
 - Improvements to iteration over Series in CuDF data backend
   ([#4624](https://github.com/holoviz/holoviews/pull/4624))
-- Added .values_host calls needed for iteraction in CuDF backend
+- Added .values_host calls needed for iteration in CuDF backend
   ([#4646](https://github.com/holoviz/holoviews/pull/4646))
 - Fixed bug resetting ranges
   ([#4654](https://github.com/holoviz/holoviews/pull/4654))
@@ -1051,7 +1063,7 @@ Bug fixes:
   ([#4337](https://github.com/holoviz/holoviews/pull/4337))
 - Fix color and alpha option on bokeh Arrow plot
   ([#4338](https://github.com/holoviz/holoviews/pull/4338))
-- Fix undefined JS varaibles in various bokeh links
+- Fix undefined JS variables in various bokeh links
   ([#4341](https://github.com/holoviz/holoviews/pull/4341))
 - Fix matplotlib >=3.2.1 deprecation warnings
   ([#4335](https://github.com/holoviz/holoviews/pull/4335))
@@ -1469,7 +1481,7 @@ This is a minor release with a number of important bug fixes and a
 small number of enhancements. Many thanks to our users for reporting
 these issues, and special thanks to our internal developers
 @philippjfr, @jlstevens and @jonmease and external contributors
-incluing @ahuang11 and @arabidopsis for their contributions to the
+including @ahuang11 and @arabidopsis for their contributions to the
 code and the documentation.
 
 Enhancements:
@@ -2381,7 +2393,7 @@ improvements and bug fixes, including streaming and graph support,
 binary transfer of Bokeh data, fast Image/RGB regridding, first-class
 statistics elements and a complete overhaul of the geometry elements.
 
-Particular thanks to all users and contributers who have reported
+Particular thanks to all users and contributors who have reported
 issues and submitted pull requests.
 
 Features:
@@ -2463,7 +2475,7 @@ Version 1.8.4
 =============
 **September 13, 2017**
 
-This bugfix release includes a number of critical fixes for compatiblity
+This bugfix release includes a number of critical fixes for compatibility
 with Bokeh 0.12.9 along with various other bug fixes. Many thanks to our
 users for various detailed bug reports, feedback and contributions.
 

doc/releases.rst

@@ -455,7 +455,7 @@ Bug fixes:
 Documentation:
 
 -  Updated Large data guide to reflect changes in Datashader and
-   antialising support
+   antialiasing support
    (`#5267 <https://github.com/holoviz/holoviews/pull/5267>`__,
    `#5290 <https://github.com/holoviz/holoviews/pull/5290>`__)
 
@@ -622,7 +622,7 @@ and @philippjfr for contributing.
 
 Enhancements:
 
-- Reenable ``SaveTool`` for plots with ``Tiles``
+- Re-enable ``SaveTool`` for plots with ``Tiles``
   (`#4922 <https://github.com/holoviz/holoviews/pull/4922>`_)
 - Enable dask ``TriMesh`` rasterization using datashader
   (`#4935 <https://github.com/holoviz/holoviews/pull/4935>`_)
@@ -793,7 +793,7 @@ Bug fixes:
   (`#4757 <https://github.com/holoviz/holoviews/pull/4757>`__)
 - Do not drop tools in linked selections
   (`#4756 <https://github.com/holoviz/holoviews/pull/4756>`__)
-- Fixed access to possibly non-existant key
+- Fixed access to possibly non-existent key
   (`#4742 <https://github.com/holoviz/holoviews/pull/4742>`__)
 
 Documentation:
@@ -929,7 +929,7 @@ Bug fixes:
 
 - Improvements to iteration over Series in CuDF data backend
   (`#4624 <https://github.com/holoviz/holoviews/pull/4624>`_)
-- Added .values_host calls needed for iteraction in CuDF backend
+- Added .values_host calls needed for iteration in CuDF backend
   (`#4646 <https://github.com/holoviz/holoviews/pull/4646>`_)
 - Fixed bug resetting ranges
   (`#4654 <https://github.com/holoviz/holoviews/pull/4654>`_)
@@ -1130,7 +1130,7 @@ Bug fixes:
   (`#4337 <https://github.com/holoviz/holoviews/pull/4337>`_)
 - Fix color and alpha option on bokeh Arrow plot
   (`#4338 <https://github.com/holoviz/holoviews/pull/4338>`_)
-- Fix undefined JS varaibles in various bokeh links
+- Fix undefined JS variables in various bokeh links
   (`#4341 <https://github.com/holoviz/holoviews/pull/4341>`_)
 - Fix matplotlib >=3.2.1 deprecation warnings
   (`#4335 <https://github.com/holoviz/holoviews/pull/4335>`_)
@@ -1568,7 +1568,7 @@ This is a minor release with a number of important bug fixes and a
 small number of enhancements. Many thanks to our users for reporting
 these issues, and special thanks to our internal developers
 @philippjfr, @jlstevens and @jonmease and external contributors
-incluing @ahuang11 and @arabidopsis for their contributions to the
+including @ahuang11 and @arabidopsis for their contributions to the
 code and the documentation.
 
 Enhancements:
@@ -2499,7 +2499,7 @@ improvements and bug fixes, including streaming and graph support,
 binary transfer of Bokeh data, fast Image/RGB regridding, first-class
 statistics elements and a complete overhaul of the geometry elements.
 
-Particular thanks to all users and contributers who have reported issues
+Particular thanks to all users and contributors who have reported issues
 and submitted pull requests.
 
 Features:
@@ -2582,7 +2582,7 @@ Version 1.8.4
 
 **September 13, 2017**
 
-This bugfix release includes a number of critical fixes for compatiblity
+This bugfix release includes a number of critical fixes for compatibility
 with Bokeh 0.12.9 along with various other bug fixes. Many thanks to our
 users for various detailed bug reports, feedback and contributions.
 

examples/conftest.py

@@ -0,0 +1,32 @@
+import sys
+
+import pandas as pd
+from packaging.version import Version
+
+PD2 = Version(pd.__version__) >= Version("2.0")
+
+collect_ignore_glob = [
+    # Needs selenium, phantomjs, firefox, and geckodriver to save a png picture
+    "user_guide/Plotting_with_Bokeh.ipynb",
+    # Possible timeout error
+    "user_guide/17-Dashboards.ipynb",
+    # Give file not found
+    "user_guide/Plots_and_Renderers.ipynb",
+]
+
+# Numba incompatibility
+if sys.version_info >= (3, 11):
+    collect_ignore_glob += [
+        "user_guide/15-Large_Data.ipynb",
+        "user_guide/16-Streaming_Data.ipynb",
+        "user_guide/Linked_Brushing.ipynb",
+        "user_guide/Network_Graphs.ipynb",
+    ]
+
+# Pandas bug: https://github.com/pandas-dev/pandas/issues/52451
+if PD2 and sys.platform == "win32":
+    collect_ignore_glob += [
+        "gallery/demos/bokeh/point_draw_triangulate.ipynb",
+        "reference/elements/*/TriMesh.ipynb",
+        "user_guide/15-Large_Data.ipynb",
+    ]

examples/gallery/demos/bokeh/bars_economic.ipynb

@@ -34,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', '\\t')\n",
+    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', delimiter='\\t')\n",
     "key_dimensions   = [('year', 'Year'), ('country', 'Country')]\n",
     "value_dimensions = [('unem', 'Unemployment'), ('capmob', 'Capital Mobility'),\n",
     "                    ('gdp', 'GDP Growth'), ('trade', 'Trade')]\n",

examples/gallery/demos/bokeh/dropdown_economic.ipynb

@@ -34,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', '\\t')\n",
+    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', delimiter='\\t')\n",
     "key_dimensions   = [('year', 'Year'), ('country', 'Country')]\n",
     "value_dimensions = [('unem', 'Unemployment'), ('capmob', 'Capital Mobility'),\n",
     "                    ('gdp', 'GDP Growth'), ('trade', 'Trade')]\n",

examples/gallery/demos/bokeh/nyc_radial_heatmap.ipynb

@@ -32,9 +32,9 @@
     "\n",
     "Let's dive into a concrete example, namely the New York - Taxi Data ([For-Hire Vehicle (“FHV”) records](http://www.nyc.gov/html/tlc/html/about/trip_record_data.shtml)). The following data contains hourly pickup counts for the entire year of 2016. \n",
     "\n",
-    "**Considerations**: Thinking about taxi pickup counts, we might expect higher taxi usage during business hours. In addition, public holidays should be clearly distinguishable from regular business days. Furthermore, we might expect high taxi pickup counts during Friday and Saterday nights.\n",
+    "**Considerations**: Thinking about taxi pickup counts, we might expect higher taxi usage during business hours. In addition, public holidays should be clearly distinguishable from regular business days. Furthermore, we might expect high taxi pickup counts during Friday and Saturday nights.\n",
     "\n",
-    "**Design**: In order model the above ideas, we decide to assign days with hourly split to the *radial segments* and week of year to the *annulars*. This will allow to detect daily/hourly periodicity and weekly trends. To get you more familiar with the mapping of segemnts and annulars, take a look at the following radial heatmap:"
+    "**Design**: In order model the above ideas, we decide to assign days with hourly split to the *radial segments* and week of year to the *annulars*. This will allow to detect daily/hourly periodicity and weekly trends. To get you more familiar with the mapping of segments and annulars, take a look at the following radial heatmap:"
    ]
   },
   {
@@ -71,7 +71,7 @@
     "\n",
     "- **Remove annular ticks**: The information about week of year is not very important. Therefore, we hide it via `yticks=None`.\n",
     "- **Custom segment ticks**: Right now, segment labels are given via day and hour. We don't need hourly information and we want every day to be labeled. We can use a tuple here which will be passed to `xticks=(\"Friday\", ..., \"Thursday\")`\n",
-    "- **Add segment markers**: Moreover, we want to aid the viewer in distingushing each day more clearly. Hence, we can provide marker lines via `xmarks=7`.\n",
+    "- **Add segment markers**: Moreover, we want to aid the viewer in distinguishing each day more clearly. Hence, we can provide marker lines via `xmarks=7`.\n",
     "- **Rotate heatmap**: The week starts with Monday and ends with Sunday. Accordingly, we want to rotate the plot to have Sunday and Monday be at the top. This can be done via `start_angle=np.pi*19/14`. The default order is defined by the global sort order which is present in the data. The default starting angle is at 12 o'clock.\n",
     "\n",
     "Let's see the result of these modifications:"
@@ -98,9 +98,9 @@
     "**There are many interesting findings in this visualization:**\n",
     "\n",
     "1. Taxi pickup counts are high between 7-9am and 5-10pm during weekdays which business hours as expected. In contrast, during weekends, there is not much going on until 11am. \n",
-    "2. Friday and Saterday nights clearly stand out with the highest pickup densities as expected. \n",
+    "2. Friday and Saturday nights clearly stand out with the highest pickup densities as expected. \n",
     "3. Public holidays can be easily identified. For example, taxi pickup counts are comparetively low around Christmas and Thanksgiving.\n",
-    "4. Weather phenomena also influence taxi service. There is a very dark blue stripe at the beginning of the year starting at Saterday 23rd and lasting until Sunday 24th. Interestingly, there was one of the [biggest blizzards](https://www.weather.gov/okx/Blizzard_Jan2016) in the history of NYC."
+    "4. Weather phenomena also influence taxi service. There is a very dark blue stripe at the beginning of the year starting at Saturday 23rd and lasting until Sunday 24th. Interestingly, there was one of the [biggest blizzards](https://www.weather.gov/okx/Blizzard_Jan2016) in the history of NYC."
    ]
   }
  ],

examples/gallery/demos/bokeh/scatter_economic.ipynb

@@ -34,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', '\\t')\n",
+    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', delimiter='\\t')\n",
     "key_dimensions   = [('year', 'Year'), ('country', 'Country')]\n",
     "value_dimensions = [('unem', 'Unemployment'), ('capmob', 'Capital Mobility'),\n",
     "                    ('gdp', 'GDP Growth'), ('trade', 'Trade')]\n",

examples/gallery/demos/bokeh/us_unemployment.ipynb

@@ -39,7 +39,7 @@
    "source": [
     "from bokeh.sampledata.unemployment1948 import data\n",
     "\n",
-    "data = pd.melt(data.drop('Annual', 1), id_vars='Year', var_name='Month', value_name='Unemployment')\n",
+    "data = pd.melt(data.drop('Annual', axis=1), id_vars='Year', var_name='Month', value_name='Unemployment')\n",
     "heatmap = hv.HeatMap(data, label=\"US Unemployment (1948 - 2013)\")"
    ]
   },

examples/gallery/demos/matplotlib/bars_economic.ipynb

@@ -35,7 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', '\\t')\n",
+    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', delimiter='\\t')\n",
     "key_dimensions   = [('year', 'Year'), ('country', 'Country')]\n",
     "value_dimensions = [('unem', 'Unemployment'), ('capmob', 'Capital Mobility'),\n",
     "                    ('gdp', 'GDP Growth'), ('trade', 'Trade')]\n",

examples/gallery/demos/matplotlib/dropdown_economic.ipynb

@@ -35,7 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', '\\t')\n",
+    "macro_df = pd.read_csv('http://assets.holoviews.org/macro.csv', delimiter='\\t')\n",
     "key_dimensions   = [('year', 'Year'), ('country', 'Country')]\n",
     "value_dimensions = [('unem', 'Unemployment'), ('capmob', 'Capital Mobility'),\n",
     "                    ('gdp', 'GDP Growth'), ('trade', 'Trade')]\n",