Merge branch 'master' into eval-metadata

executablebooks · Jun 27, 2024 · 498cad5 · 498cad5
2 parents ba91962 + 67f1643
commit 498cad5
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Showing 13 changed files with 151 additions and 36 deletions.
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/action@v3.0.0
 
   tests:
 
@@ -27,28 +16,28 @@ 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,<8"]  # 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"
+            myst-parser: "~=2.0"
           - os: macos-latest
             python-version: "3.10"
             sphinx: "~=7.0"
-            myst-parser: ">=2.0"
+            myst-parser: "~=2.0"
           # 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"
           # Newest known-compatible dependencies
           - os: ubuntu-latest
             python-version: "3.12"
-            sphinx: "~=7.0"
-            myst-parser: "~=2.0.0"
+            sphinx: "==7.0.0"
+            myst-parser: "==2.0.0"
 
     runs-on: ${{ matrix.os }}
 
@@ -91,8 +80,10 @@ 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@v3.1.4
+      if: false
       with:
         name: myst-nb-pytests
         flags: pytests
@@ -101,7 +92,7 @@ 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
@@ -39,7 +39,7 @@ repos:
       additional_dependencies:
       - importlib_metadata
       - myst-parser~=2.0.0
-      - "sphinx~=7.0"
+      - "sphinx~=7.3.7"
       - nbclient
       - types-PyYAML
       files: >

diff --git a/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/myst_nb/core/render.py b/myst_nb/core/render.py
@@ -662,7 +662,7 @@ 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"},

diff --git a/tests/test_render_outputs/test_complex_outputs.xml b/tests/test_render_outputs/test_complex_outputs.xml
@@ -123,7 +123,7 @@
                         plt.ylabel(r'a y label with latex $\alpha$')
                         plt.legend();
                 <container classes="cell_output" nb_element="cell_code_output">
-                    <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">
     <section ids="tables-with-pandas" names="tables\ (with\ pandas)">
         <title>
             Tables (with pandas)
@@ -208,7 +208,7 @@
                     f = y(n)-2*y(n-1/sym.pi)-5*y(n-2)
                     sym.rsolve(f,y(n),[1,4])
             <container classes="cell_output" nb_element="cell_code_output">
-                <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 cell_index="25" cell_metadata="{}" classes="cell" exec_count="7" nb_element="cell_code">
             <container classes="cell_input" nb_element="cell_code_source">
                 <literal_block language="ipython3" linenos="False" xml:space="preserve">

diff --git a/tests/test_render_outputs/test_complex_outputs_latex.xml b/tests/test_render_outputs/test_complex_outputs_latex.xml
@@ -123,7 +123,7 @@
                         plt.ylabel(r'a y label with latex $\alpha$')
                         plt.legend();
                 <container classes="cell_output" nb_element="cell_code_output">
-                    <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">
     <section ids="tables-with-pandas" names="tables\ (with\ pandas)">
         <title>
             Tables (with pandas)
@@ -168,7 +168,7 @@
                     f = y(n)-2*y(n-1/sym.pi)-5*y(n-2)
                     sym.rsolve(f,y(n),[1,4])
             <container classes="cell_output" nb_element="cell_code_output">
-                <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 cell_index="25" cell_metadata="{}" classes="cell" exec_count="7" nb_element="cell_code">
             <container classes="cell_input" nb_element="cell_code_source">
                 <literal_block language="ipython3" linenos="False" xml:space="preserve">

diff --git a/tests/test_render_outputs/test_metadata_image_output.xml b/tests/test_render_outputs/test_metadata_image_output.xml
@@ -0,0 +1,21 @@
+<document source="metadata_image_output">
+    <section ids="output-metadata" names="output\ metadata">
+        <title>
+            Output metadata
+        <container cell_index="1" cell_metadata="{'tags': ['skip-execution']}" classes="cell tag_skip-execution" exec_count="1" nb_element="cell_code">
+            <container classes="cell_input" nb_element="cell_code_source">
+                <literal_block language="ipython3" linenos="False" xml:space="preserve">
+                    # Outputs included with width/height in output metadata,
+                    # cell is not executed
+                    from IPython.display import Image
+                    Image(filename="./example.jpg", width=500, height=100)
+            <container classes="cell_output" nb_element="cell_code_output">
+                <image candidates="{'*': '_build/jupyter_execute/a4c9580c74dacf6f3316a3bd2e2a347933aa4463834dcf1bb8f20b4fcb476ae1.jpg'}" height="100" uri="_build/jupyter_execute/a4c9580c74dacf6f3316a3bd2e2a347933aa4463834dcf1bb8f20b4fcb476ae1.jpg" width="500">
+        <container cell_index="2" cell_metadata="{}" classes="cell" exec_count="1" nb_element="cell_code">
+            <container classes="cell_input" nb_element="cell_code_source">
+                <literal_block language="ipython3" linenos="False" xml:space="preserve">
+                    # No outputs, cell is executed, image should have original size (370, 254)
+                    from IPython.display import Image
+                    Image(filename="./example.jpg")
+            <container classes="cell_output" nb_element="cell_code_output">
+                <image candidates="{'*': '_build/jupyter_execute/a4c9580c74dacf6f3316a3bd2e2a347933aa4463834dcf1bb8f20b4fcb476ae1.jpg'}" uri="_build/jupyter_execute/a4c9580c74dacf6f3316a3bd2e2a347933aa4463834dcf1bb8f20b4fcb476ae1.jpg">