Merge branch 'master' into coalesce_streams

executablebooks · Sep 19, 2024 · 4744bf0 · 4744bf0
2 parents 289fb8c + db8cedb
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -8,9 +8,15 @@ updates:
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "monthly"
 
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    labels:
+      - "github_actions"
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -8,17 +8,6 @@ on:
   pull_request:
 
 jobs:
-  pre-commit:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.10"
-    - uses: pre-commit/[email protected]
 
   tests:
 
@@ -27,28 +16,33 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
-        sphinx: [">=5.0,<=7.*"]  # Newest Sphinx (any)
-        myst-parser: [">=1.0.0,<=2.*"]  # Newest MyST Parser (any)
+        sphinx: [">=5,<9"]  # Newest Sphinx (any)
+        myst-parser: [">=1,<3"]  # Newest MyST Parser (any)
         include:
           # Just check the other platforms once
           - os: windows-latest
-            python-version: "3.10"
-            sphinx: "~=7.0"
-            myst-parser: ">=2.0"
+            python-version: "3.12"
+            sphinx: "~=8.0"
+            myst-parser: "~=4.0"
           - os: macos-latest
-            python-version: "3.10"
-            sphinx: "~=7.0"
-            myst-parser: ">=2.0"
+            python-version: "3.12"
+            sphinx: "~=8.0"
+            myst-parser: "~=4.0"
           # Oldest known-compatible dependencies
           - os: ubuntu-latest
             python-version: "3.9"
-            sphinx: "~=5.0"
-            myst-parser: "~=1.0.0"
+            sphinx: "==5.0.0"
+            myst-parser: "==1.0.0"
+          # Mid-range dependencies
+          - os: ubuntu-latest
+            python-version: "3.11"
+            sphinx: "==7.0.0"
+            myst-parser: "==2.0.0"
           # Newest known-compatible dependencies
           - os: ubuntu-latest
             python-version: "3.12"
-            sphinx: "~=7.0"
-            myst-parser: "~=2.0.0"
+            sphinx: "==8.0.2"
+            myst-parser: "==4.0.0"
 
     runs-on: ${{ matrix.os }}
 
@@ -91,8 +85,10 @@ jobs:
       # for some reason the tests/conftest.py::check_nbs fixture breaks pytest-cov's cov-report outputting
       # this is why we run `coverage xml` afterwards (required by codecov)
 
+    # TEMPORARY FIX: Disable codecov until we can get it working again
     - name: Upload to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
+      if: false
       with:
         name: myst-nb-pytests
         flags: pytests
@@ -101,7 +97,7 @@ jobs:
   publish:
 
     name: Publish to PyPi
-    needs: [pre-commit, tests]
+    needs: [tests]
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,6 +9,9 @@ exclude: >
       tests/.*\.txt
     )$
 
+ci:
+  autoupdate_schedule: 'monthly'
+
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -39,7 +42,7 @@ repos:
       additional_dependencies:
       - importlib_metadata
       - myst-parser~=2.0.0
-      - "sphinx~=7.0"
+      - "sphinx~=7.3.7"
       - nbclient
       - types-PyYAML
       files: >

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,66 @@
 # Change Log
 
+## v1.1.1 - 2024-06-27
+
+([full changelog](https://github.com/executablebooks/MyST-NB/compare/v1.1.0...6ce30cd41fa82543e0f315ac8bbee82669b0cc82))
+
+### Bugs fixed
+
+- FIX: output metadata overwrites image size for all following images [#609](https://github.com/executablebooks/MyST-NB/pull/609) ([@aeisenbarth](https://github.com/aeisenbarth))
+
+- FIX: remove incorrect license classifier [#603](https://github.com/executablebooks/MyST-NB/pull/603) ([@agoose77](https://github.com/agoose77))
+
+### Maintenance and upkeep improvements
+
+- MAINT: bump version [#614](https://github.com/executablebooks/MyST-NB/pull/614) ([@agoose77](https://github.com/agoose77))
+
+- MAINT: appease mypy [#612](https://github.com/executablebooks/MyST-NB/pull/612) ([@agoose77](https://github.com/agoose77))
+
+- MAINT: fix specs for CI matrix [#611](https://github.com/executablebooks/MyST-NB/pull/611) ([@agoose77](https://github.com/agoose77))
+
+- MAINT: bump version [#592](https://github.com/executablebooks/MyST-NB/pull/592) ([@agoose77](https://github.com/agoose77))
+
+### Documentation improvements
+
+- DOCS: set printoptions to disable modern scalar printing [#613](https://github.com/executablebooks/MyST-NB/pull/613) ([@agoose77](https://github.com/agoose77))
+
+- DOCS: extra comma forgotten [#606](https://github.com/executablebooks/MyST-NB/pull/606) ([@jeertmans](https://github.com/jeertmans))
+
+- DOCS: update shown code to match source [#598](https://github.com/executablebooks/MyST-NB/pull/598) ([@OriolAbril](https://github.com/OriolAbril))
+
+### Contributors to this release
+
+([GitHub contributors page for this release](https://github.com/executablebooks/MyST-NB/graphs/contributors?from=2024-04-12&to=2024-06-27&type=c))
+
+[@aeisenbarth](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Aaeisenbarth+updated%3A2024-04-12..2024-06-27&type=Issues) | [@agoose77](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Aagoose77+updated%3A2024-04-12..2024-06-27&type=Issues) | [@jeertmans](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Ajeertmans+updated%3A2024-04-12..2024-06-27&type=Issues) | [@OriolAbril](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3AOriolAbril+updated%3A2024-04-12..2024-06-27&type=Issues) | [@sstroemer](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Asstroemer+updated%3A2024-04-12..2024-06-27&type=Issues) | [@welcome](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Awelcome+updated%3A2024-04-12..2024-06-27&type=Issues)
+
+
+## v1.1.0 - 2024-04-12
+
+([full changelog](https://github.com/executablebooks/MyST-NB/compare/v1.0.0...9943ec214c35844c4535d0184f7840574fc7ab03))
+
+### Enhancements made
+
+- ENH: pass-through image metadata [#588](https://github.com/executablebooks/MyST-NB/pull/588) ([@flying-sheep](https://github.com/flying-sheep))
+
+### Maintenance and upkeep improvements
+
+- MAINT: bump version [#592](https://github.com/executablebooks/MyST-NB/pull/592) ([@agoose77](https://github.com/agoose77))
+
+- MAINT: use `findall` instead of `traverse` [#585](https://github.com/executablebooks/MyST-NB/pull/585) ([@agoose77](https://github.com/agoose77))
+
+- MAINT: restore default line length [#577](https://github.com/executablebooks/MyST-NB/pull/577) ([@agoose77](https://github.com/agoose77))
+
+### Other merged PRs
+
+- build(deps): bump actions/setup-python from 4 to 5 [#576](https://github.com/executablebooks/MyST-NB/pull/576) ([@dependabot](https://github.com/dependabot))
+
+### Contributors to this release
+
+([GitHub contributors page for this release](https://github.com/executablebooks/MyST-NB/graphs/contributors?from=2023-11-08&to=2024-04-12&type=c))
+
+[@agoose77](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Aagoose77+updated%3A2023-11-08..2024-04-12&type=Issues) | [@cisaacstern](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Acisaacstern+updated%3A2023-11-08..2024-04-12&type=Issues) | [@dependabot](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Adependabot+updated%3A2023-11-08..2024-04-12&type=Issues) | [@flying-sheep](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Aflying-sheep+updated%3A2023-11-08..2024-04-12&type=Issues) | [@ma-sadeghi](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Ama-sadeghi+updated%3A2023-11-08..2024-04-12&type=Issues) | [@peytondmurray](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Apeytondmurray+updated%3A2023-11-08..2024-04-12&type=Issues) | [@PhilipVinc](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3APhilipVinc+updated%3A2023-11-08..2024-04-12&type=Issues) | [@sphuber](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Asphuber+updated%3A2023-11-08..2024-04-12&type=Issues) | [@welcome](https://github.com/search?q=repo%3Aexecutablebooks%2FMyST-NB+involves%3Awelcome+updated%3A2023-11-08..2024-04-12&type=Issues)
+
 
 ## v1.0.0 - 2023-11-08
 

diff --git a/docs/configuration.md b/docs/configuration.md
@@ -129,7 +129,7 @@ Tags are a list of strings under the `tags` key in the cell metadata, e.g.
   "cell_type": "code",
   "source": ["print('hello world')"],
   "metadata": {
-    "tags": ["my-tag1", "my-tag2"],
+    "tags": ["my-tag1", "my-tag2"]
   }
 }
 ```

diff --git a/docs/render/format_code_cells.md b/docs/render/format_code_cells.md
@@ -166,7 +166,7 @@ You can also wrap the output in a [`figure`](https://docutils.sourceforge.io/doc
 ---
 mystnb:
   image:
-    width: 200px
+    width: 300px
     alt: fun-fish
     classes: shadow bg-primary
   figure:

diff --git a/docs/render/glue.md b/docs/render/glue.md
@@ -25,7 +25,7 @@ To glue keys from other notebooks, see {ref}`glue/crossdoc`.
 ## Save variables in code cells
 
 You can use `myst_nb.glue()` to assign the output of a variable to a key of your choice.
-`glue` will store all of the information that is normally used to display that variable (ie, whatever happens when you display the variable by putting it at the end of a cell).
+`glue` will store all of the information that is normally used to display that variable (that is, whatever happens when you display the variable by putting it at the end of a cell).
 Choose a key that you will remember, as you will use it later.
 
 The following code glues a variable inside the notebook:
@@ -54,6 +54,8 @@ We'll hide most of this process below, to focus on the glueing part.
 
 # Simulate some data and bootstrap the mean of the data
 import numpy as np
+np.set_printoptions(legacy="1.25")
+
 import pandas as pd
 import matplotlib.pyplot as plt
 
@@ -135,12 +137,12 @@ These variables can be pasted using one of the roles or directives in the `glue:
 
 ### The `glue` role/directive
 
-The simplest role and directive are `glue` (a.k.a. `glue:any`),
+The simplest role and directive are `glue` (also known as `glue:any`),
 which paste the glued output inline or as a block respectively,
 with no additional formatting.
 Simply add:
 
-````
+````md
 ```{glue} your-key
 ```
 ````
@@ -217,6 +219,27 @@ For example, the following: ``My rounded mean: {glue:text}`boot_mean:.2f` `` wil
 
 My rounded mean: {glue:text}`boot_mean:.2f` (95% CI: {glue:text}`boot_clo:.2f`/{glue:text}`boot_chi:.2f`).
 
+````{warning}
+As of NumPy 2.0, the `text/plain` representation of [NumPy objects has changed](https://numpy.org/devdocs/release/2.0.0-notes.html#representation-of-numpy-scalars-changed).
+Using text formatting with NumPy>=2.0 will give warnings like:
+
+```
+sphinx.errors.SphinxWarning: <filename>:257:Failed to format text/plain data: could not convert string to float: 'np.float64(0.9643970836113095)' [mystnb.glue]
+```
+
+This can be resolved by either formatting the number before glueing or by setting NumPy to use legacy print options, as shown below.
+
+```python
+var = np.float(1.0)
+# Format the variable before glueing
+glue("var_glue", f"{var:.2f}")
+
+# Or set NumPy legacy print options
+np.setprintoptions(legacy="1.25")
+glue("var_glue", var)
+```
+````
+
 +++
 
 ### The `glue:figure` directive

diff --git a/myst_nb/__init__.py b/myst_nb/__init__.py
@@ -1,5 +1,5 @@
 """A docutils/sphinx parser for Jupyter Notebooks."""
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 
 
 def setup(app):

diff --git a/myst_nb/core/read.py b/myst_nb/core/read.py
@@ -68,7 +68,7 @@ def create_nb_reader(
     # we check suffixes ordered by longest first, to ensure we get the "closest" match
     iterator = sorted(readers.items(), key=lambda x: len(x[0]), reverse=True)
     for suffix, (reader, reader_kwargs, commonmark_only) in iterator:
-        if path.endswith(suffix):
+        if Path(path).suffix == suffix:
             if isinstance(reader, str):
                 # attempt to load the reader as an object path
                 reader = import_object(reader)

diff --git a/myst_nb/core/render.py b/myst_nb/core/render.py
@@ -660,7 +660,7 @@ def render_image(self, data: MimeData) -> list[nodes.Element]:
         # TODO backwards-compatible re-naming to image_options?
         image_options = self.renderer.get_cell_level_config(
             "render_image_options", data.cell_metadata, line=data.line
-        )
+        ).copy()
         # Overwrite with metadata stored in output
         image_options.update(
             {

diff --git a/myst_nb/sphinx_ext.py b/myst_nb/sphinx_ext.py
@@ -52,13 +52,16 @@ def sphinx_setup(app: Sphinx):
     for name, default, field in NbParserConfig().as_triple():
         if not field.metadata.get("sphinx_exclude"):
             # TODO add types?
-            app.add_config_value(f"nb_{name}", default, "env", Any)
+            app.add_config_value(f"nb_{name}", default, "env", Any)  # type: ignore[arg-type]
             if "legacy_name" in field.metadata:
                 app.add_config_value(
-                    f"{field.metadata['legacy_name']}", _UNSET, "env", Any
+                    f"{field.metadata['legacy_name']}",
+                    _UNSET,
+                    "env",
+                    Any,  # type: ignore[arg-type]
                 )
     # Handle non-standard deprecation
-    app.add_config_value("nb_render_priority", _UNSET, "env", Any)
+    app.add_config_value("nb_render_priority", _UNSET, "env", Any)  # type: ignore[arg-type]
 
     # generate notebook configuration from Sphinx configuration
     # this also validates the configuration values
@@ -130,7 +133,7 @@ def create_mystnb_config(app):
     """Generate notebook configuration from Sphinx configuration"""
 
     # Ignore type checkers because the attribute is dynamically assigned
-    from sphinx.util.console import bold  # type: ignore[attr-defined]
+    from sphinx.util.console import bold
 
     values = {}
     for name, _, field in NbParserConfig().as_triple():
@@ -227,4 +230,4 @@ def add_per_page_html_resources(
         return
     js_files = NbMetadataCollector.get_js_files(cast(SphinxEnvType, app.env), pagename)
     for path, kwargs in js_files.values():
-        app.add_js_file(path, **kwargs)  # type: ignore
+        app.add_js_file(path, **kwargs)  # type: ignore[arg-type]
diff --git a/tests/notebooks/complex_outputs.ipynb b/tests/notebooks/complex_outputs.ipynb
@@ -280,6 +280,10 @@
       ]
      },
      "metadata": {
+      "image/png": {
+          "width": 432,
+          "height": 288
+      },
       "needs_background": "light"
      },
      "output_type": "display_data"

diff --git a/tests/notebooks/metadata_image_output.ipynb b/tests/notebooks/metadata_image_output.ipynb
diff --git a/tests/test_parser/test_complex_outputs.xml b/tests/test_parser/test_complex_outputs.xml
@@ -130,7 +130,7 @@
                 <container classes="cell_output" nb_element="cell_code_output">
                     <container nb_element="mime_bundle">
                         <container mime_type="image/png">
-                            <image candidates="{'*': '_build/jupyter_execute/16832f45917c1c9862c50f0948f64a498402d6ccde1f3a291da17f240797b160.png'}" height="400" uri="_build/jupyter_execute/16832f45917c1c9862c50f0948f64a498402d6ccde1f3a291da17f240797b160.png">
+                            <image candidates="{'*': '_build/jupyter_execute/16832f45917c1c9862c50f0948f64a498402d6ccde1f3a291da17f240797b160.png'}" height="288" uri="_build/jupyter_execute/16832f45917c1c9862c50f0948f64a498402d6ccde1f3a291da17f240797b160.png" width="432">
                         <container mime_type="text/plain">
                             <literal_block classes="output text_plain" language="myst-ansi" xml:space="preserve">
                                 <Figure size 432x288 with 1 Axes>
@@ -244,7 +244,7 @@
             <container classes="cell_output" nb_element="cell_code_output">
                 <container nb_element="mime_bundle">
                     <container mime_type="image/png">
-                        <image candidates="{'*': '_build/jupyter_execute/8c43e5c8cccf697754876b7fec1b0a9b731d7900bb585e775a5fa326b4de8c5a.png'}" height="400" uri="_build/jupyter_execute/8c43e5c8cccf697754876b7fec1b0a9b731d7900bb585e775a5fa326b4de8c5a.png">
+                        <image candidates="{'*': '_build/jupyter_execute/8c43e5c8cccf697754876b7fec1b0a9b731d7900bb585e775a5fa326b4de8c5a.png'}" uri="_build/jupyter_execute/8c43e5c8cccf697754876b7fec1b0a9b731d7900bb585e775a5fa326b4de8c5a.png">
                     <container mime_type="text/latex">
                         <math_block classes="output text_latex" nowrap="False" number="True" xml:space="preserve">
                             \displaystyle \left(\sqrt{5} i\right)^{\alpha} \left(\frac{1}{2} - \frac{2 \sqrt{5} i}{5}\right) + \left(- \sqrt{5} i\right)^{\alpha} \left(\frac{1}{2} + \frac{2 \sqrt{5} i}{5}\right)

diff --git a/tests/test_render_outputs.py b/tests/test_render_outputs.py
@@ -2,6 +2,7 @@
 import pytest
 
 from myst_nb.core.render import EntryPointError, load_renderer
+from sphinx.util.fileutil import copy_asset_file
 
 
 def test_load_renderer_not_found():
@@ -116,6 +117,24 @@ def test_metadata_image(sphinx_run, clean_doctree, file_regression):
     )
 
 
+@pytest.mark.sphinx_params(
+    "metadata_image_output.ipynb",
+    conf={"nb_execution_mode": "force"},
+)
+def test_metadata_image_output(
+    sphinx_run, clean_doctree, file_regression, get_test_path
+):
+    """Test configuring image attributes to be rendered from cell metadata."""
+    asset_path = get_test_path("example.jpg")
+    copy_asset_file(str(asset_path), str(sphinx_run.app.srcdir))
+    sphinx_run.build()
+    assert sphinx_run.warnings() == ""
+    doctree = clean_doctree(sphinx_run.get_resolved_doctree("metadata_image_output"))
+    file_regression.check(
+        doctree.pformat().replace(".jpeg", ".jpg"), extension=".xml", encoding="utf-8"
+    )
+
+
 @pytest.mark.sphinx_params(
     "metadata_figure.ipynb",
     conf={"nb_execution_mode": "off", "nb_cell_metadata_key": "myst"},