Skip empty sequences when streaming with ndarrays (bokeh#14007)

* Skip empty sequences when streaming with ndarrays * Add NumPy version to bokeh info * Add release notes * Add print_info() utility function equivalent of `bokeh info`
abdulrahman305 · Aug 6, 2024 · 61b87ac · 61b87ac
1 parent 0300cc4
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diff --git a/docs/bokeh/source/docs/dev_guide/creating_issues.rst b/docs/bokeh/source/docs/dev_guide/creating_issues.rst
@@ -74,6 +74,15 @@ Software version info
 
         bokeh info
 
+    or alternatively use:
+
+    .. code-block:: python
+
+        from bokeh.util.info import print_info
+        print_info()
+
+    in your scripts and/or MREs (minimal reproducible examples).
+
     This provides you with a list of the versions of relevant software packages.
     Copy and paste this information into your bug report.
 

diff --git a/docs/bokeh/source/docs/dev_guide/setup.rst b/docs/bokeh/source/docs/dev_guide/setup.rst
@@ -487,14 +487,16 @@ You should see output similar to:
 
 .. code-block:: sh
 
-    Python version      :  3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:46)
-    IPython version     :  7.20.0
-    Tornado version     :  6.1
-    Bokeh version       :  3.0.0dev1+20.g6c394d579
-    BokehJS static path :  /opt/anaconda/envs/test/lib/python3.9/site-packages/bokeh/server/static
-    node.js version     :  v16.12.0
-    npm version         :  7.24.2
-    Operating system    :  Linux-5.11.0-40-generic-x86_64-with-glibc2.31
+    Python version        :  3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
+    IPython version       :  8.19.0
+    Tornado version       :  6.3.3
+    NumPy version         :  2.0.0
+    Bokeh version         :  3.5.1
+    BokehJS static path   :  /opt/anaconda/envs/test/lib/python3.12/site-packages/bokeh/server/static
+    node.js version       :  v20.12.2
+    npm version           :  10.8.2
+    jupyter_bokeh version :  (not installed)
+    Operating system      :  Linux-5.15.0-86-generic-x86_64-with-glibc2.35
 
 Run examples
 ~~~~~~~~~~~~

diff --git a/docs/bokeh/source/docs/releases/3.6.0.rst b/docs/bokeh/source/docs/releases/3.6.0.rst
@@ -0,0 +1,8 @@
+.. _release-3-6-0:
+
+3.6.0
+=====
+
+Bokeh version ``3.6.0`` (??? 2024) is a minor milestone of Bokeh project.
+
+* Improved streaming corner cases and added NumPy to ``bokeh info`` (:bokeh-pull:`14007`)
diff --git a/src/bokeh/command/subcommands/info.py b/src/bokeh/command/subcommands/info.py
@@ -17,13 +17,14 @@
 
 .. code-block:: none
 
-    Python version        :  3.11.3 | packaged by conda-forge | (main, Apr  6 2023, 08:57:19) [GCC 11.3.0]
-    IPython version       :  8.13.2
-    Tornado version       :  6.3
-    Bokeh version         :  3.3.0
-    BokehJS static path   :  /opt/anaconda/envs/test/lib/python3.11/site-packages/bokeh/server/static
-    node.js version       :  v18.16.1
-    npm version           :  9.5.1
+    Python version        :  3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
+    IPython version       :  8.19.0
+    Tornado version       :  6.3.3
+    NumPy version         :  2.0.0
+    Bokeh version         :  3.5.1
+    BokehJS static path   :  /opt/anaconda/envs/test/lib/python3.12/site-packages/bokeh/server/static
+    node.js version       :  v20.12.2
+    npm version           :  10.8.2
     jupyter_bokeh version :  (not installed)
     Operating system      :  Linux-5.15.0-86-generic-x86_64-with-glibc2.35
 
@@ -38,7 +39,7 @@
 
 .. code-block:: none
 
-    /opt/anaconda/envs/test/lib/python3.11/site-packages/bokeh/server/static
+    /opt/anaconda/envs/test/lib/python3.12/site-packages/bokeh/server/static
 
 '''
 
@@ -55,15 +56,11 @@
 #-----------------------------------------------------------------------------
 
 # Standard library imports
-import platform
-import sys
 from argparse import Namespace
 
 # Bokeh imports
-from bokeh import __version__
 from bokeh.settings import settings
-from bokeh.util.compiler import nodejs_version, npmjs_version
-from bokeh.util.dependencies import import_optional
+from bokeh.util.info import print_info
 
 # Bokeh imports
 from ..subcommand import Argument, Subcommand
@@ -76,22 +73,6 @@
     'Info',
 )
 
-#-----------------------------------------------------------------------------
-# Private API
-#-----------------------------------------------------------------------------
-
-def if_installed(version_or_none: str | None) -> str:
-    ''' helper method to optionally return module version number or not installed
-
-    :param version_or_none:
-    :return:
-    '''
-    return version_or_none or "(not installed)"
-
-def _version(module_name: str, attr: str) -> str | None:
-    module = import_optional(module_name)
-    return getattr(module, attr) if module else None
-
 #-----------------------------------------------------------------------------
 # General API
 #-----------------------------------------------------------------------------
@@ -122,21 +103,16 @@ def invoke(self, args: Namespace) -> None:
         if args.static:
             print(settings.bokehjs_path())
         else:
-            newline = '\n'
-            print(f"Python version        :  {sys.version.split(newline)[0]}")
-            print(f"IPython version       :  {if_installed(_version('IPython', '__version__'))}")
-            print(f"Tornado version       :  {if_installed(_version('tornado', 'version'))}")
-            print(f"Bokeh version         :  {__version__}")
-            print(f"BokehJS static path   :  {settings.bokehjs_path()}")
-            print(f"node.js version       :  {if_installed(nodejs_version())}")
-            print(f"npm version           :  {if_installed(npmjs_version())}")
-            print(f"jupyter_bokeh version :  {if_installed(_version('jupyter_bokeh', '__version__'))}")
-            print(f"Operating system      :  {platform.platform()}")
+            print_info()
 
 #-----------------------------------------------------------------------------
 # Dev API
 #-----------------------------------------------------------------------------
 
+#-----------------------------------------------------------------------------
+# Private API
+#-----------------------------------------------------------------------------
+
 #-----------------------------------------------------------------------------
 # Code
 #-----------------------------------------------------------------------------
diff --git a/src/bokeh/core/property/wrappers.py b/src/bokeh/core/property/wrappers.py
@@ -69,13 +69,17 @@ class SomeModel(Model):
     TYPE_CHECKING,
     Any,
     Iterable,
+    MutableSequence,
+    Sequence,
     TypeVar,
 )
 
 # External imports
 import numpy as np
 
 if TYPE_CHECKING:
+    import numpy.typing as npt
+
     from ...document import Document
     from ...document.events import DocumentPatchedEvent
     from ...models.sources import ColumnarDataSource
@@ -303,7 +307,9 @@ def symmetric_difference_update(self, s: Iterable[T]) -> None:
     def update(self, *s: Iterable[T]) -> None:
         super().update(*s)
 
-class PropertyValueDict(PropertyValueContainer, dict):
+T_Val = TypeVar("T_Val")
+
+class PropertyValueDict(PropertyValueContainer, dict[str, T_Val]):
     """ A dict property value container that supports change notifications on
     mutating operations.
 
@@ -377,7 +383,7 @@ def setdefault(self, *args):
     def update(self, *args, **kwargs):
         return super().update(*args, **kwargs)
 
-class PropertyValueColumnData(PropertyValueDict):
+class PropertyValueColumnData(PropertyValueDict[Sequence[Any]]):
     """ A property value container for ColumnData that supports change
     notifications on mutating operations.
 
@@ -435,7 +441,7 @@ def update(self, *args, **kwargs):
         return result
 
     # don't wrap with notify_owner --- notifies owners explicitly
-    def _stream(self, doc: Document, source: ColumnarDataSource, new_data: dict[str, Any],
+    def _stream(self, doc: Document, source: ColumnarDataSource, new_data: dict[str, Sequence[Any] | npt.NDArray[Any]],
             rollover: int | None = None, setter: Setter | None = None) -> None:
         """ Internal implementation to handle special-casing stream events
         on ``ColumnDataSource`` columns.
@@ -468,17 +474,41 @@ def _stream(self, doc: Document, source: ColumnarDataSource, new_data: dict[str,
         # is actually the already updated value. This is because the method
         # self._saved_copy() makes a shallow copy.
         for k in new_data:
-            if isinstance(self[k], np.ndarray) or isinstance(new_data[k], np.ndarray):
-                data = np.append(self[k], new_data[k])
-                if rollover is not None and len(data) > rollover:
-                    data = data[len(data) - rollover:]
+            old_seq = self[k]
+            new_seq = new_data[k]
+
+            if isinstance(old_seq, np.ndarray) or isinstance(new_seq, np.ndarray):
+                # Special case for streaming with empty arrays, to allow this:
+                #
+                # data_source = ColumnDataSource(data={"DateTime": []})
+                # data_source.stream({"DateTime": np.array([np.datetime64("now")]))
+                #
+                # See https://github.com/bokeh/bokeh/issues/14004.
+                if len(old_seq) == 0:
+                    seq = new_seq
+                elif len(new_seq) == 0:
+                    seq = old_seq
+                else:
+                    seq = np.append(old_seq, new_seq)
+
+                if rollover is not None and len(seq) > rollover:
+                    seq = seq[len(seq) - rollover:]
+
                 # call dict.__setitem__ directly, bypass wrapped version on base class
-                dict.__setitem__(self, k, data)
+                dict.__setitem__(self, k, seq)
             else:
-                L = self[k]
-                L.extend(new_data[k])
-                if rollover is not None and len(L) > rollover:
-                    del L[:len(L) - rollover]
+                def apply_rollover(seq: MutableSequence[Any]) -> None:
+                    if rollover is not None and len(seq) > rollover:
+                        del seq[:len(seq) - rollover]
+
+                if isinstance(old_seq, MutableSequence):
+                    seq = old_seq
+                    seq.extend(new_seq)
+                    apply_rollover(seq)
+                else:
+                    seq = [*old_seq, *new_seq]
+                    apply_rollover(seq)
+                    dict.__setitem__(self, k, seq)
 
         from ...document.events import ColumnsStreamedEvent
         self._notify_owners(old, hint=ColumnsStreamedEvent(doc, source, "data", new_data, rollover, setter))

diff --git a/src/bokeh/util/__init__.py b/src/bokeh/util/__init__.py
@@ -60,6 +60,14 @@
 .. automodule:: bokeh.util.hex
   :members:
 
+.. _bokeh.util.info:
+
+``bokeh.util.info``
+----------------------
+
+.. automodule:: bokeh.util.info
+  :members:
+
 .. _bokeh.util.logconfig:
 
 ``bokeh.util.logconfig``

diff --git a/src/bokeh/util/info.py b/src/bokeh/util/info.py
@@ -0,0 +1,85 @@
+#-----------------------------------------------------------------------------
+# Copyright (c) Anaconda, Inc., and Bokeh Contributors.
+# All rights reserved.
+#
+# The full license is in the file LICENSE.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+# Boilerplate
+#-----------------------------------------------------------------------------
+from __future__ import annotations
+
+import logging # isort:skip
+log = logging.getLogger(__name__)
+
+#-----------------------------------------------------------------------------
+# Imports
+#-----------------------------------------------------------------------------
+
+# Standard library imports
+import platform
+import sys
+
+# Bokeh imports
+from bokeh import __version__
+from bokeh.settings import settings
+from bokeh.util.compiler import nodejs_version, npmjs_version
+from bokeh.util.dependencies import import_optional
+
+#-----------------------------------------------------------------------------
+# Globals and constants
+#-----------------------------------------------------------------------------
+
+__all__ = (
+    "print_info",
+)
+
+#-----------------------------------------------------------------------------
+# General API
+#-----------------------------------------------------------------------------
+
+def print_info() -> None:
+    """ Print version information about Bokeh, Python, the operating system
+    and a selected set of dependencies.
+    """
+    # Keep one print() per line, so that users don't have to wait a long
+    # time for all libraries and dependencies to get loaded.
+    newline = '\n'
+    print(f"Python version        :  {sys.version.split(newline)[0]}")
+    print(f"IPython version       :  {_if_installed(_version('IPython', '__version__'))}")
+    print(f"Tornado version       :  {_if_installed(_version('tornado', 'version'))}")
+    print(f"NumPy version         :  {_if_installed(_version('numpy', '__version__'))}")
+    print(f"Bokeh version         :  {__version__}")
+    print(f"BokehJS static path   :  {settings.bokehjs_path()}")
+    print(f"node.js version       :  {_if_installed(nodejs_version())}")
+    print(f"npm version           :  {_if_installed(npmjs_version())}")
+    print(f"jupyter_bokeh version :  {_if_installed(_version('jupyter_bokeh', '__version__'))}")
+    print(f"Operating system      :  {platform.platform()}")
+
+#-----------------------------------------------------------------------------
+# Legacy API
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+# Dev API
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+# Private API
+#-----------------------------------------------------------------------------
+
+def _if_installed(version_or_none: str | None) -> str:
+    """ Return the given version or not installed if ``None``.
+    """
+    return version_or_none or "(not installed)"
+
+def _version(module_name: str, attr: str) -> str | None:
+    """ Get the version of a module if installed.
+    """
+    module = import_optional(module_name)
+    return getattr(module, attr) if module else None
+
+#-----------------------------------------------------------------------------
+# Code
+#-----------------------------------------------------------------------------
diff --git a/tests/unit/bokeh/command/subcommands/test_info.py b/tests/unit/bokeh/command/subcommands/test_info.py
@@ -18,7 +18,6 @@
 
 # Standard library imports
 from os.path import join
-from typing import Any
 
 # Bokeh imports
 from bokeh.command.bootstrap import main
@@ -66,17 +65,18 @@ def test_run(capsys: Capture) -> None:
     main(["bokeh", "info"])
     out, err = capsys.readouterr()
     lines = out.split("\n")
-    assert len(lines) == 10
+    assert len(lines) == 11
     assert lines[0].startswith("Python version")
     assert lines[1].startswith("IPython version")
     assert lines[2].startswith("Tornado version")
-    assert lines[3].startswith("Bokeh version")
-    assert lines[4].startswith("BokehJS static")
-    assert lines[5].startswith("node.js version")
-    assert lines[6].startswith("npm version")
-    assert lines[7].startswith("jupyter_bokeh version")
-    assert lines[8].startswith("Operating system")
-    assert lines[9] == ""
+    assert lines[3].startswith("NumPy version")
+    assert lines[4].startswith("Bokeh version")
+    assert lines[5].startswith("BokehJS static")
+    assert lines[6].startswith("node.js version")
+    assert lines[7].startswith("npm version")
+    assert lines[8].startswith("jupyter_bokeh version")
+    assert lines[9].startswith("Operating system")
+    assert lines[10] == ""
     assert err == ""
 
 def test_run_static(capsys: Capture) -> None:
@@ -85,12 +85,6 @@ def test_run_static(capsys: Capture) -> None:
     assert err == ""
     assert out.endswith(join('bokeh', 'server', 'static') + '\n')
 
-def test__version_missing(ipython: Any) -> None:
-    assert scinfo._version('bokeh', '__version__') is not None
-    assert scinfo._version('IPython', '__version__') is not None
-    assert scinfo._version('tornado', 'version') is not None
-    assert scinfo._version('junk', 'whatever') is None
-
 #-----------------------------------------------------------------------------
 # Private API
 #-----------------------------------------------------------------------------