From 873ef4ab00e1d8322a06b91446bd23e90e43b449 Mon Sep 17 00:00:00 2001 From: Andreas Eisenbarth Date: Fri, 28 Jun 2024 13:14:54 +0200 Subject: [PATCH] Initial commit --- .gitignore | 58 + .pdm-python | 1 + .pre-commit-config.yaml | 62 + LICENSE | 29 + MANIFEST.in | 15 + README.md | 27 + docs/conf.py | 60 + docs/development.md | 26 + docs/examples.ipynb | 192 ++ docs/images/example1-jupyter.png | Bin 0 -> 17669 bytes docs/images/example1-myst-nb-json.png | Bin 0 -> 17950 bytes docs/images/example1-myst-nb.png | Bin 0 -> 15080 bytes docs/index.md | 57 + docs/static/custom.css | 12 + myst_nb_json/__init__.py | 201 ++ myst_nb_json/py.typed | 0 myst_nb_json/resources/myst-nb-json.css | 58 + myst_nb_json/resources/myst-nb-json.js | 28 + pdm.lock | 1739 +++++++++++++++++ pyproject.toml | 119 ++ tests/__init__.py | 0 tests/conftest.py | 168 ++ tests/notebooks/json_output.ipynb | 54 + tests/test_interactivity.py | 73 + tests/test_mime_plugin.py | 101 + tests/test_myst_nb.py | 17 + .../test_myst_nb/test_render_json_output.xml | 113 ++ 27 files changed, 3210 insertions(+) create mode 100644 .gitignore create mode 100644 .pdm-python create mode 100644 .pre-commit-config.yaml create mode 100644 LICENSE create mode 100644 MANIFEST.in create mode 100644 README.md create mode 100644 docs/conf.py create mode 100644 docs/development.md create mode 100644 docs/examples.ipynb create mode 100644 docs/images/example1-jupyter.png create mode 100644 docs/images/example1-myst-nb-json.png create mode 100644 docs/images/example1-myst-nb.png create mode 100644 docs/index.md create mode 100644 docs/static/custom.css create mode 100644 myst_nb_json/__init__.py create mode 100644 myst_nb_json/py.typed create mode 100644 myst_nb_json/resources/myst-nb-json.css create mode 100644 myst_nb_json/resources/myst-nb-json.js create mode 100644 pdm.lock create mode 100644 pyproject.toml create mode 100644 tests/__init__.py create mode 100644 tests/conftest.py create mode 100644 tests/notebooks/json_output.ipynb create mode 100644 tests/test_interactivity.py create mode 100644 tests/test_mime_plugin.py create mode 100644 tests/test_myst_nb.py create mode 100644 tests/test_myst_nb/test_render_json_output.xml diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..d1c3669 --- /dev/null +++ b/.gitignore @@ -0,0 +1,58 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# Distribution / packaging +.Python +build/ +dist/ +eggs/ +sdist/ +wheels/ +*.egg-info/ +MANIFEST + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +coverage.xml +*.cover +*.py,cover +.pytest_cache/ + +# Sphinx documentation +docs/_build/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +jupyter_execute diff --git a/.pdm-python b/.pdm-python new file mode 100644 index 0000000..28f4ba0 --- /dev/null +++ b/.pdm-python @@ -0,0 +1 @@ +/home/andreas/software/miniconda3/envs/myst-nb-json/bin/python diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..bf0b925 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,62 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: check-json + files: \.(json)$ + - id: check-yaml + - id: check-toml + - id: check-merge-conflict + - id: end-of-file-fixer + - id: trailing-whitespace + - repo: https://github.com/python/black + rev: 22.3.0 + hooks: + - id: black-jupyter + args: ["--config=pyproject.toml"] + pass_filenames: true + - repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + args: ["--settings-path=pyproject.toml"] + - repo: https://github.com/executablebooks/mdformat + rev: 0.7.14 + hooks: + - id: mdformat + additional_dependencies: + - mdformat-beautysh + - mdformat-black + - mdformat-frontmatter + - mdformat-toc + - mdformat-gfm + args: ["--number", "--wrap", "keep"] + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.10.0 + hooks: + - id: mypy + args: ["--install-types", "--non-interactive"] + additional_dependencies: ["bokeh>=3.3.4", "sphinx>=7.2.6"] + exclude: > + (?x)^( + tests/.*\.py + )$ + - repo: https://github.com/pdm-project/pdm + rev: 2.15.4 + hooks: + - id: pdm-lock-check + - repo: https://github.com/hadialqattan/pycln + rev: v1.3.2 + hooks: + - id: pycln + args: ["--config=pyproject.toml"] + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.4.10 + hooks: + # Run the linter. + - id: ruff + types_or: [python, pyi, jupyter] + # Run the formatter. + - id: ruff-format + types_or: [python, pyi, jupyter] diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..59bb17e --- /dev/null +++ b/LICENSE @@ -0,0 +1,29 @@ +BSD License + +Copyright (c) 2024, Andreas Eisenbarth +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, +are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, this + list of conditions and the following disclaimer in the documentation and/or + other materials provided with the distribution. + +* Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from this + software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. +IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, +INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, +BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY +OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE +OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED +OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..eac4cdd --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,15 @@ +exclude docs +recursive-exclude docs * +exclude tests +recursive-exclude tests *.js *.css +include myst_nb_json/resources/*.js +include myst_nb_json/resources/*.css + +exclude .pre-commit-config.yaml +exclude .readthedocs.yaml + +include LICENSE +include README.md +include AUTHORS.md +include CONTRIBUTING.md +include src/myst_nb_json/py.typed diff --git a/README.md b/README.md new file mode 100644 index 0000000..7a4b017 --- /dev/null +++ b/README.md @@ -0,0 +1,27 @@ +# MyST-NB JSON + +A MIME-type plugin for rendering JSON output from Jupyter notebooks to HTML + +______________________________________________________________________ + +Outputs from Jupyter notebook code cells usually contain representations in one or multiple MIME +types (image, text, ...). IPython provides multiple built-in output types, but not all of them +have a representation for HTML, and fall back to a stringified version of the Python object. + +This is the case for the `application/json` type: + +It is nicely rendered in Jupyter because Jupyter includes a +[JSON renderer](https://github.com/jupyterlab/jupyterlab/tree/7909745d075aceb0cf1099ad53a3174e92b575ae/packages/json-extension), +but MyST-NB can only use IPython's built-ins which display as ``. + +## Jupyter Lab + +![Screenshot of json_dict in Jupyter](./docs/images/example1-jupyter.png) + +## MyST-NB without plugin + +![Screenshot of json_dict in HTML by MyST-NB](./docs/images/example1-myst-nb.png) + +## MyST-NB with myst-nb-json plugin + +![Screenshot of json_dict in HTML with myst-nb-json](./docs/images/example1-myst-nb-json.png) diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..ba7339e --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,60 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +from datetime import datetime +from importlib import metadata + +# Custom constants (no Sphinx configuration) + +REPOSITORY_URL = "https://github.com/aeisenbarth/myst-nb-json" + +# -- Project information --------------------------------------------------------------------------- + +project = "MyST-NB JSON" +author = "Andreas Eisenbarth" + +copyright = f"{datetime.now():%Y}, Andreas Eisenbarth" + +release = version = metadata.version("myst-nb-json") + +# -- General configuration ------------------------------------------------------------------------- + +extensions = ["myst_nb"] + +# List of glob-style patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +# Myst-nb creates a folder "jupyter_execute" and copies notebooks there, which causes recursive +# inclusion, so exclude it. See https://github.com/executablebooks/MyST-NB/issues/129 +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "jupyter_execute"] + +# -- Options for HTML output ----------------------------------------------------------------------- + +html_theme = "sphinx_book_theme" + +html_theme_options = dict( + use_repository_button=True, + use_download_button=False, + repository_provider="gitlab", + repository_url=REPOSITORY_URL, + repository_branch="main", + navigation_with_keys=False, # https://github.com/pydata/pydata-sphinx-theme/issues/1492 + collapse_navbar=False, + show_navbar_depth=1, +) + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["static"] + +# Define custom CSS rules +html_css_files = ["custom.css"] + +# If true, “Created using Sphinx” is shown in the HTML footer. Default is True. +html_show_sphinx = False + +# -- myst_parser / myst_nb ------------------------------------------------------------------------- diff --git a/docs/development.md b/docs/development.md new file mode 100644 index 0000000..95907e6 --- /dev/null +++ b/docs/development.md @@ -0,0 +1,26 @@ +# Development + +1. Clone the repository: + + ```shell + git clone https://github.com/aeisenbarth/myst-nb-json.git + ``` + +2. Install dependencies: + + ```shell + pip install pdm + pdm install + ``` + +3. Run tests: + + ```shell + pdm test + ``` + +4. Build documentation: + + ```shell + pdm docs + ``` diff --git a/docs/examples.ipynb b/docs/examples.ipynb new file mode 100644 index 0000000..aba590b --- /dev/null +++ b/docs/examples.ipynb @@ -0,0 +1,192 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "c095fe2d196b3295", + "metadata": {}, + "source": [ + "# Examples\n", + "\n", + "A JSON-like Python dictionary renders the full Python object as `text/plain` (notice the single quotes)." + ] + }, + { + "cell_type": "code", + "id": "5fa6e511ebe825d8", + "metadata": {}, + "source": [ + "json_dict = {\n", + " \"key1\": \"value1\",\n", + " \"key2\": {\"key21\": 42, \"key22\": True, \"key23\": None},\n", + " \"key3\": [\"a\", \"b\"],\n", + "}\n", + "json_dict" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "33f24ef62f7364da", + "metadata": {}, + "source": [ + "It can be wrapped in an output type, which adds the MIME type `application/json`.\n", + "\n", + "```python\n", + "from IPython.display import JSON\n", + "\n", + "JSON(json_dict)\n", + "```\n", + "\n", + "However, there are two issues with this:\n", + "\n", + "- Now `text/plain` is ``\n", + "\n", + "- `application/json`'s data is the original JSON, and it is left up to renderers how to represent it.\n", + "\n", + "Jupyter Lab renders the following:\n", + "\n", + "![Screenshot of json_dict in Jupyter](./images/example1-jupyter.png)\n", + "\n", + "Whereas MyST-NB renders:\n", + "\n", + "![Screenshot of json_dict in HTML by MyST-NB](./images/example1-myst-nb.png)\n", + "\n", + "With `myst-nb-json`, you should get an interactive rendering similar to Jupyter Lab:\n", + "\n", + "![Screenshot of json_dict in HTML with myst-nb-json](./images/example1-myst-nb-json.png)" + ] + }, + { + "cell_type": "code", + "id": "23be0ec2f8ceb03a", + "metadata": {}, + "source": [ + "from IPython.display import JSON\n", + "\n", + "JSON(json_dict)" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "cde3f57f5dd64638", + "metadata": {}, + "source": [ + "With the `expanded` parameter, you can control how much to show by default:" + ] + }, + { + "cell_type": "code", + "id": "7659e360f770ceab", + "metadata": {}, + "source": [ + "JSON(json_dict, expanded=True)" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "32536237d491e70f", + "metadata": {}, + "source": [ + "With the `root` parameter, you can control the display name:" + ] + }, + { + "cell_type": "code", + "id": "3f85070c626b8d8f", + "metadata": {}, + "source": [ + "JSON(json_dict, root=\"json_dict\")" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "ed652ffb9714f6ae", + "metadata": {}, + "source": "This is also nice for **Pydantic** models! By default, they are rendered as plain text:" + }, + { + "cell_type": "code", + "id": "cfb51d59e132581d", + "metadata": { + "tags": [ + "hide-input" + ] + }, + "source": [ + "from typing import Optional\n", + "from pydantic import BaseModel\n", + "\n", + "\n", + "class Model2(BaseModel):\n", + " key21: int\n", + " key22: bool\n", + " key23: Optional[str]\n", + "\n", + "\n", + "class ExampleModel(BaseModel):\n", + " key1: str\n", + " key2: Model2\n", + " key3: list[str]" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "code", + "id": "b75220850f01881", + "metadata": {}, + "source": [ + "example_model = ExampleModel(**json_dict)\n", + "example_model" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "code", + "id": "ca7cd38c9589f5d5", + "metadata": {}, + "source": [ + "JSON(example_model.model_dump(mode=\"json\"))" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "58c778876c5b43d6", + "metadata": {}, + "source": [ + "As a bonus, MyST-NB has been designed that despite the simplified rendering, when you **select and copy** the text, it will include valid JSON." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.19" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/images/example1-jupyter.png b/docs/images/example1-jupyter.png new file mode 100644 index 0000000000000000000000000000000000000000..d7987a14f3980a2ab87be5fd720f41019984a3d8 GIT binary patch literal 17669 zcmdVCXIN8P*fxljV?m?~3LJxU5$V!ZLKlz{dQp0)QbR{YA%rF%ASHlw5+Fk8p@{S@ zgdUnysi7u7C=)+9?|k!X=EuyB*}0N%?X11_Do?$idlUXrQ<>^I%XJD03My3mFB1SS}k-dvKXF8 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z?w>Y$ffy`h#j0Z_CbIuKLjU#f-;}6@Cw}=$nvoy>!AIKcb$nYhYEWf|N$VpbM#Gg|gw{E=+Dy5MlTmI>`oQ^8?K0hvzf<<#*9S_?5{&;% zBC8^fH0N@B*=b4=0=B53tk*4L_XiW&E~;1kgK;&RHEj(UvH)*6qwU8cj(2(h7DR1+wN!i4P3xVRXy?v)cUY2ji%FV$PkFoTmh%a5DT4YYoiy zP`P*r9w?f4+L)%9QDB8>{||;8nmc#lf3>79jW@|rB!uxa;Eo`{q{|kNBP7>0|cCFvCB5M-*8}C5iIS#^3)J=Zu|v literal 0 HcmV?d00001 diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..49fa753 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,57 @@ +# MyST-NB JSON + +A MIME-type plugin for rendering JSON output from Jupyter notebooks to HTML + +______________________________________________________________________ + +```{toctree} +:hidden: + +examples +development +``` + +Outputs from Jupyter notebook code cells usually contain representations in one or multiple MIME +types (image, text…). IPython provides multiple built-in output types, but not all of them +have a representation for HTML, and fall back to a stringified version of the Python object. + +This is the case for the `application/json` type: + +It is nicely rendered in Jupyter because Jupyter includes a +[JSON renderer](https://github.com/jupyterlab/jupyterlab/tree/7909745d075aceb0cf1099ad53a3174e92b575ae/packages/json-extension), +but MyST-NB can only use IPython's built-ins which display as ``. + +## Installation + +Install the Python package: + +```shell +pip install myst-nb-json +``` + +It registers itself in MyST-NB via entry-points, so it is ready to use. + +## Usage + +1. Wrap output from code cells in the IPython `JSON` class. + + ```python + from IPython.display import JSON + + JSON({"key": "value"}) + ``` + +2. When building documentation with Sphinx, the JSON output will be rendered as interactive tree, + instead of displaying plain text. + + ```shell + sphinx-build -b html docs/ docs/_build + ``` + + Or just the notebook with: + + ```shell + mystnb-docutils-html example.ipynb > example.html + ``` + +For more details, see [examples](./examples.ipynb). diff --git a/docs/static/custom.css b/docs/static/custom.css new file mode 100644 index 0000000..09578d8 --- /dev/null +++ b/docs/static/custom.css @@ -0,0 +1,12 @@ +/* + myst-nb renders cells as div block elements with border. However, output cells are separated by a + gap from their input cells, which makes the notebook more visually cluttered. Remove the gap. +*/ +.cell .cell_input + .cell_output { + margin-top: 0; +} +.cell .cell_input + .cell_output .output { + margin-top: 0; + border-top-left-radius: 0; + border-top-right-radius: 0; +} diff --git a/myst_nb_json/__init__.py b/myst_nb_json/__init__.py new file mode 100644 index 0000000..a6e2330 --- /dev/null +++ b/myst_nb_json/__init__.py @@ -0,0 +1,201 @@ +""" +MimeRenderPlugin for MyST-NB for rendering IPython JSON display type to HTML +""" + +__all__ = ["JsonMimeRenderPlugin"] +__version__ = "0.1.0" + +import json +from collections.abc import Generator, Mapping, Sequence +from functools import cached_property +from importlib.resources import files +from typing import Union, cast + +from docutils import nodes +from myst_nb.core.render import MimeData, MimeRenderPlugin, NbElementRenderer + +JAVASCRIPT_FILE_NAME = "myst-nb-json.js" +CSS_FILE_NAME = "myst-nb-json.css" +CLS_COLLAPSIBLE = "myst-nb-json-collapsible" +CLS_COLLAPSED = "myst-nb-json-collapsed" +CLS_HIDDEN = "myst-nb-json-hidden" +CLS_KEY = "myst-nb-json-key" +CLS_UNSELECTABLE = "myst-nb-json-unselectable" +CLS_VALUE = "myst-nb-json-value" + +ScalarJsonType = Union[str, int, float, bool, None] + +JsonType = Union[Mapping[str, "JsonType"], Sequence["JsonType"], ScalarJsonType] + + +class JsonMimeRenderPlugin(MimeRenderPlugin): + mime_priority_overrides = [("*", "application/json", 1)] + + @staticmethod + def handle_mime( + renderer: NbElementRenderer, data: MimeData, inline: bool + ) -> Union[None, list[nodes.Element]]: + """ + A function that renders a mime type to docutils nodes, or returns None to reject + + Args: + renderer: A class for rendering notebook elements + data: The Notebook output data + inline: Whether the MIME type is displayed inline, e.g. in an interactive Jupyter + notebook. In the context of MyST-NB, content is rendered to a file, so the renderer + should not accept inline content. + + Returns: + A list of docutils nodes, or None if this renderer cannot handle the data + """ + try: + if not inline and data.mime_type == "application/json": + root = data.output_metadata.get(data.mime_type, {}).get("root", "root") + expanded = data.output_metadata.get(data.mime_type, {}).get("expanded", True) + plugin = JsonMimeRenderPlugin() + html = plugin.html(data.content, root=root, expanded=expanded) + return [nodes.raw(text=html, format="html", classes=["output", "text_html"])] + except Exception as e: + import traceback + + print(e) + traceback.print_exc() + return None + + def html(self, jsonable: JsonType, root: str = "root", expanded: bool = False) -> str: + """ + Generate an HTML string for a JSON object + + Args: + jsonable: A JSON-like Python object + root: Optional name to display as key for the JSON value + expanded: Whether to initialize the JSON tree collapsed or expanded + + Returns: + The component's HTML as string + """ + return "".join(self.component(jsonable, root=root, expanded=expanded)) + + def component( + self, jsonable: JsonType, root: str = "root", expanded: bool = False + ) -> Generator[str, None, None]: + """ + Yield HTML fragment strings for a JSON object + + Args: + jsonable: A JSON-like Python object + root: Optional name to display as key for the JSON value + expanded: Whether to initialize the JSON tree collapsed or expanded + + Yields: + HTML strings + """ + yield "
" + yield f"""
  • """ + yield from self.key(root, collapsible=is_nested(jsonable), selectable=False) + yield from self.value(jsonable, expanded=expanded) + yield "
" + yield self.style + yield self.script + yield "
" + + @cached_property + def script(self) -> str: + script_str = (files(__package__) / "resources" / JAVASCRIPT_FILE_NAME).read_text() + return f"" + + @cached_property + def style(self) -> str: + css_str = (files(__package__) / "resources" / CSS_FILE_NAME).read_text() + return f"""""" + + def value( + self, value: JsonType, expanded: bool = False, with_comma: bool = False + ) -> Generator[str, None, None]: + if isinstance(value, Sequence) and not isinstance(value, str) and len(value) > 0: + yield from self.list_value(value, expanded=expanded, with_comma=with_comma) + elif isinstance(value, Mapping) and len(value) > 0: + yield from self.dict_value(value, expanded=expanded, with_comma=with_comma) + else: + yield from self.scalar_value(cast(ScalarJsonType, value), with_comma=with_comma) + + def key( + self, key: Union[str, int], collapsible: bool = False, selectable: bool = True + ) -> Generator[str, None, None]: + classes = CLS_KEY + if collapsible: + classes += " " + CLS_COLLAPSIBLE + if not selectable: + classes += " " + CLS_UNSELECTABLE + yield f"""{self.quote}{key}{self.quote}{self.colon}""" + + def list_value( + self, value: Sequence, expanded: bool = False, with_comma: bool = False + ) -> Generator[str, None, None]: + yield f"""
{self.bracket_open}
    """ + last_index = len(value) - 1 + for index, val in enumerate(value): + is_last = index == last_index + yield f"""
  • """ + # yield from self.key(index, collapsible=is_nested(val), selectable=False) + yield from self.value(val, with_comma=not is_last) + # It would be nicer to add the comma here, but if value yields a block element, + # the comma would be an orphan in the next line below the value. To have it in the same + # line, it needs to be inside the value's block. + yield "
    • " + yield f"
{self.bracket_close}{self.comma if with_comma else ''}
" + + def dict_value( + self, value: Mapping, expanded: bool = False, with_comma: bool = False + ) -> Generator[str, None, None]: + yield f"""
{self.curly_open}
    """ + last_index = len(value.items()) - 1 + for index, (key, val) in enumerate(value.items()): + is_last = index == last_index + yield f"""
  • """ + yield from self.key(key, collapsible=is_nested(val)) + yield from self.value(val, with_comma=not is_last) + # It would be nicer to add the comma here. + yield "
    • " + yield f"
{self.curly_close}{self.comma if with_comma else ''}
" + + def scalar_value( + self, value: ScalarJsonType, with_comma: bool = False + ) -> Generator[str, None, None]: + value_str = json.dumps(value) + yield f"""{value_str}{self.comma if with_comma else ''}""" + + @cached_property + def quote(self): + return f""""""" + + @cached_property + def colon(self): + return f""": """ + + @cached_property + def comma(self): + return f""", """ + + @cached_property + def curly_open(self): + return f"""{""" + + @cached_property + def curly_close(self): + return f"""}""" + + @cached_property + def bracket_open(self): + return f"""[""" + + @cached_property + def bracket_close(self): + return f"""]""" + + +def is_nested(jsonable: JsonType) -> bool: + return ( + (isinstance(jsonable, Sequence) and not isinstance(jsonable, str)) + or isinstance(jsonable, Mapping) + ) and len(jsonable) > 0 diff --git a/myst_nb_json/py.typed b/myst_nb_json/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/myst_nb_json/resources/myst-nb-json.css b/myst_nb_json/resources/myst-nb-json.css new file mode 100644 index 0000000..fd362f4 --- /dev/null +++ b/myst_nb_json/resources/myst-nb-json.css @@ -0,0 +1,58 @@ +div.myst-nb-json-value > ul { + display: inline-block; + list-style: none; + margin: 0; + padding: 0; +} + +li { + padding-left: 1.5em; +} + +li.myst-nb-json-collapsed > div.myst-nb-json-value { + display: none; +} + +span.myst-nb-json-key { + color: #008000; + display: inline-block; + font-weight: bold; + margin: 0px 0.5em 0px 0px; + padding: 0; + user-select: all; +} + +span.myst-nb-json-key.myst-nb-json-collapsible::before { + color: black; + content: "▼"; + display: inline-block; + font-size: 0.75em; + margin-left: -1.25em; + position: relative; + top: -0.15em; + transform: rotateZ(0deg); + transform-origin: 40% 50% 0; + transition: 150ms; + user-select: none; + width: 1.25em; +} + +li.myst-nb-json-collapsed > span.myst-nb-json-key.myst-nb-json-collapsible::before { + transform: rotateZ(-90deg); +} + +span.myst-nb-json-value { + color: #ba2121; + text-indent: -0.5em; + user-select: all; +} + +span.myst-nb-json-hidden { + display: inline-block; + opacity: 0; + width: 0; +} + +.myst-nb-json-unselectable { + user-select: none !important; +} diff --git a/myst_nb_json/resources/myst-nb-json.js b/myst_nb_json/resources/myst-nb-json.js new file mode 100644 index 0000000..409ddf9 --- /dev/null +++ b/myst_nb_json/resources/myst-nb-json.js @@ -0,0 +1,28 @@ +// Script to be embedded inside the component's root HTMLElement +(function (component) { + document.addEventListener('DOMContentLoaded', () => { + const CLASS_KEY = "myst-nb-json-key"; + const CLASS_COLLAPSIBLE = "myst-nb-json-collapsible"; + const CLASS_COLLAPSED = "myst-nb-json-collapsed"; + + let toggleable = Array.from(component.getElementsByTagName("li")); + toggleable.forEach((li) => { + // Find list item elements that contain a nested, collapsible value. + if (li.getElementsByClassName(CLASS_COLLAPSIBLE).length == 0) return; + let key = li.getElementsByClassName(CLASS_KEY)[0]; + let toggleFn = function() { + let isCollapsed = li.classList.contains(CLASS_COLLAPSED); + if (isCollapsed) { + li.classList.remove(CLASS_COLLAPSED); + } else { + li.classList.add(CLASS_COLLAPSED); + } + } + // Make the key element interactive to toggle the list item's collapsed state. + key.addEventListener("click", toggleFn); + key.addEventListener("keydown", (event) => { + if (event.code === "ArrowLeft" || event.code === "ArrowRight" || event.code === "Space") toggleFn() + }); + }); + }); +})(document.currentScript.parentElement); diff --git a/pdm.lock b/pdm.lock new file mode 100644 index 0000000..c83e9be --- /dev/null +++ b/pdm.lock @@ -0,0 +1,1739 @@ +# This file is @generated by PDM. +# It is not intended for manual editing. + +[metadata] +groups = ["default", "dev", "test", "docs"] +strategy = ["cross_platform", "inherit_metadata"] +lock_version = "4.4.2" +content_hash = 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email = "andreas.eisenbarth@embl.de"}, + {name = "Andreas Eisenbarth", email = "andreas.eisenbarth@embl.de"}, +] +description = "Default template for PDM package" +keywords = ["docutils", "sphinx", "json"] +requires-python = "==3.9.*" +classifiers = [ + "Development Status :: 4 - Beta", + "Framework :: Sphinx :: Extension", + "Intended Audience :: Developers", + "License :: OSI Approved :: BSD License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Software Development :: Libraries :: Python Modules", + "Topic :: Text Processing :: Markup", +] +dependencies = [ + "docutils", + "myst-nb>=1.0.0", +] +license = { text = "MIT" } +dynamic = ["version", "readme"] + +[project.optional-dependencies] +dev = [ + "mypy>=1.8.0", + "pre-commit>=3.6.0", + "ruff>=0.1.14", +] +docs = [ + "docutils>=0.21.2", + "ipython>=8.12.0", + "myst-nb>=1.0.0", + "Sphinx>=7.2.6", + "sphinx-book-theme>=1.1.3", +] +test = [ + "ipython>=8.12.0", + "pytest~=7.1", + "pytest-cov>=5.0.0", + "pytest-regressions>=2.5.0", + "selenium~=4.22", + "Sphinx[test]>=7.2.6", # For test dependencies like defusedxml +] +type-hints = ["types-docutils"] + +[project.entry-points."myst_nb.mime_renderers"] +application_json = "myst_nb_json:JsonMimeRenderPlugin" + +[tool.black] +line-length = 100 +target-version = ['py310'] +skip-magic-trailing-comma = true +include = '\.(pyi?|ipynb)$' +exclude = ''' +^/( + ( + \.eggs # exclude a few common directories in the + | \.git # root of the project + | \.mypy_cache + | \.pytest_cache + | build + | dist + ) +)/ +''' + +[tool.isort] +combine_as_imports = true +filter_files = true +line_length = 100 +profile = "black" + +[[tool.mypy.overrides]] +module = [ + "myst_nb.core.render", +] +ignore_missing_imports = true + +[tool.pdm] +distribution = true + +[tool.pdm.version] +source = "file" +path = "myst_nb_json/__init__.py" + +[tool.pdm.scripts] +ruff_check = { cmd = "ruff check myst_nb_json/ docs/ tests/" } +ruff_format_check = { cmd = "ruff format --check myst_nb_json/ docs/ tests/" } +mypy_check = { cmd = "mypy myst_nb_json/" } +lint = { composite = ["ruff_check", "ruff_format_check", "mypy_check"] } +ruff_fix = { cmd = "ruff check --fix-only myst_nb_json/ docs/ tests/" } +ruff_format = { cmd = "ruff format myst_nb_json/ docs/ tests/" } +format = { composite = ["ruff_fix", "ruff_format"] } +test = { cmd = "pytest --cov=myst_nb_json --cov-report=xml --cov-report=term-missing" } +docs = { cmd = "sphinx-build -b html docs/ docs/_build" } + +[tool.pycln] +all = true + +[tool.pytest.ini_options] +minversion = "6.0" +# CLI options: Show extra test summary for all except passed; quiet +addopts = "-ra --quiet --color=yes --code-highlight=yes" +# Directories to be searched for tests to speed up test collection +testpaths = ["tests"] + +[tool.ruff] +line-length = 100 + +[tool.setuptools.dynamic] +version = {attr = "myst_nb_json.__version__"} +readme = {file = "README.md", content-type = "text/markdown"} diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..aad3a14 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,168 @@ +# Source: https://github.com/executablebooks/MyST-NB/blob/master/tests/conftest.py +import json +import os +import re +import uuid +from pathlib import Path + +import pytest +import sphinx +from docutils.nodes import image as image_node +from sphinx import version_info as sphinx_version_info +from sphinx.util.console import nocolor + +pytest_plugins = "sphinx.testing.fixtures" + +TEST_FILE_DIR = Path(__file__).parent.joinpath("notebooks") + + +@pytest.fixture() +def get_test_path(): + def _get_test_path(name): + return TEST_FILE_DIR.joinpath(name) + + return _get_test_path + + +class SphinxFixture: + """A class returned by the ``sphinx_run`` fixture, to run sphinx, + and retrieve aspects of the build. + """ + + def __init__(self, app, filenames): + self.app = app + self.env = app.env + self.files = [os.path.splitext(ff) for ff in filenames] + self.software_versions = ( + f".sphinx{sphinx.version_info[0]}" # software version tracking for fixtures + ) + + def build(self): + """Run the sphinx build.""" + self.app.build() + + def warnings(self): + """Return the stderr stream of the sphinx build.""" + return self.app._warning.getvalue().strip() + + def get_resolved_doctree(self, docname=None): + """Load and return the built docutils.document, after post-transforms.""" + docname = docname or self.files[0][0] + doctree = self.env.get_and_resolve_doctree(docname, self.app.builder) + doctree["source"] = docname + return doctree + + +@pytest.fixture() +def sphinx_params(request): + """Parameters that are specified by 'pytest.mark.sphinx_params' + are passed to the ``sphinx_run`` fixture:: + + @pytest.mark.sphinx_params("name.ipynb", conf={"option": "value"}) + def test_something(sphinx_run): + ... + + The first file specified here will be set as the master_doc + """ + markers = request.node.iter_markers("sphinx_params") + kwargs = {} + if markers is not None: + for info in reversed(list(markers)): + kwargs.update(info.kwargs) + kwargs["files"] = info.args + return kwargs + + +@pytest.fixture() +def sphinx_run(sphinx_params, make_app, tmp_path): + """A fixture to setup and run a sphinx build, in a sandboxed folder. + + The `myst_nb` extension is added by default, + and the first file will be set as the masterdoc + + """ + assert len(sphinx_params["files"]) > 0, sphinx_params["files"] + conf = sphinx_params.get("conf", {}) + buildername = sphinx_params.get("buildername", "html") + + confoverrides = { + "extensions": ["myst_nb"], + "master_doc": os.path.splitext(sphinx_params["files"][0])[0], + "exclude_patterns": ["_build"], + "nb_execution_show_tb": True, + } + confoverrides.update(conf) + + current_dir = os.getcwd() + if "working_dir" in sphinx_params: + base_dir = Path(sphinx_params["working_dir"]) / str(uuid.uuid4()) + else: + base_dir = tmp_path + srcdir = base_dir / "source" + srcdir.mkdir(exist_ok=True) + os.chdir(base_dir) + (srcdir / "conf.py").write_text( + "# conf overrides (passed directly to sphinx):\n" + + "\n".join(["# " + ll for ll in json.dumps(confoverrides, indent=2).splitlines()]) + + "\n" + ) + + for nb_file in sphinx_params["files"]: + nb_path = TEST_FILE_DIR.joinpath(nb_file) + assert nb_path.exists(), nb_path + (srcdir / nb_file).parent.mkdir(exist_ok=True) + (srcdir / nb_file).write_text(nb_path.read_text(encoding="utf-8"), encoding="utf-8") + + nocolor() + + # For compatibility with multiple versions of sphinx, convert pathlib.Path to + # sphinx.testing.path.path here. + if sphinx_version_info >= (7, 2): + app_srcdir = srcdir + else: + from sphinx.testing.path import path + + app_srcdir = path(os.fspath(srcdir)) + app = make_app(buildername=buildername, srcdir=app_srcdir, confoverrides=confoverrides) + + yield SphinxFixture(app, sphinx_params["files"]) + + # reset working directory + os.chdir(current_dir) + + +@pytest.fixture() +def clean_doctree(): + def _func(doctree): + if os.name == "nt": # on Windows file paths are absolute + findall = getattr(doctree, "findall", doctree.traverse) + for node in findall(image_node): # type: image_node + if "candidates" in node: + node["candidates"]["*"] = "_build/jupyter_execute/" + os.path.basename( + node["candidates"]["*"] + ) + if "uri" in node: + node["uri"] = "_build/jupyter_execute/" + os.path.basename(node["uri"]) + return doctree + + return _func + + +@pytest.fixture() +def file_regression(file_regression): + return FileRegression(file_regression) + + +class FileRegression: + ignores = (r"",) + + def __init__(self, file_regression): + self.file_regression = file_regression + + def check(self, data, **kwargs): + return self.file_regression.check(self._strip_ignores(data), **kwargs) + + def _strip_ignores(self, data): + for ig in self.ignores: + data = re.sub(ig, "", data) + return data diff --git a/tests/notebooks/json_output.ipynb b/tests/notebooks/json_output.ipynb new file mode 100644 index 0000000..9b99ec4 --- /dev/null +++ b/tests/notebooks/json_output.ipynb @@ -0,0 +1,54 @@ +{ + "cells": [ + { + "metadata": {}, + "cell_type": "code", + "source": [ + "from IPython.display import JSON\n", + "\n", + "JSON(\n", + " {\n", + " \"key1\": \"value1\",\n", + " \"key2\": {\n", + " \"key21\": \"str\",\n", + " \"key22\": 42,\n", + " \"key23\": 3.14,\n", + " \"key24\": True,\n", + " \"key25\": False,\n", + " \"key26\": None,\n", + " \"key27\": {},\n", + " \"key28\": [],\n", + " },\n", + " \"key3\": [\"str\", 42, 3.14, True, False, None, {}, []],\n", + " },\n", + " root=\"test\",\n", + " expanded=True,\n", + ")" + ], + "id": "initial_id", + "outputs": [], + "execution_count": null + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.19" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tests/test_interactivity.py b/tests/test_interactivity.py new file mode 100644 index 0000000..f124d7d --- /dev/null +++ b/tests/test_interactivity.py @@ -0,0 +1,73 @@ +import re +from collections.abc import Generator + +import pytest +from selenium import webdriver +from selenium.webdriver.chrome.options import Options +from selenium.webdriver.common.by import By +from selenium.webdriver.remote.webdriver import WebDriver + +from myst_nb_json import CLS_COLLAPSED, JsonMimeRenderPlugin + + +@pytest.fixture +def plugin() -> JsonMimeRenderPlugin: + return JsonMimeRenderPlugin() + + +JSON_DATA = { + "key1": "value1", + "key2": { + "key21": "str", + "key22": 42, + "key23": 3.14, + "key24": True, + "key25": False, + "key26": None, + "key27": {}, + "key28": [], + }, + "key3": ["str", 42, 3.14, True, False, None, {}, []], +} + + +@pytest.fixture +def browser() -> Generator[WebDriver]: + # Set up headless Chrome options + chrome_options = Options() + chrome_options.add_argument("--headless") + chrome_options.add_argument("--disable-gpu") + + # Initialize the WebDriver + driver: WebDriver = webdriver.Chrome(options=chrome_options) + yield driver + driver.quit() + + +def test_interactive_collapse_expand(plugin: JsonMimeRenderPlugin, browser: WebDriver): + # Load the HTML string + html_content = plugin.html(JSON_DATA, root="test", expanded=True) + # Hash (in CSS color) causes problems for Selenium Chrome webdriver + html_content = re.sub("#", "#", html_content) + browser.get("data:text/html;charset=utf-8," + html_content) + + # Wait for the JavaScript to execute + browser.implicitly_wait(2) + + text_to_click = "key2" + element_to_click = browser.find_element(By.XPATH, f"//*[contains(text(), '{text_to_click}')]") + value_element = element_to_click.find_element(By.XPATH, "following-sibling::*[1]") + li_element = element_to_click.find_element(By.XPATH, "ancestor::li[1]") + + assert CLS_COLLAPSED not in li_element.get_attribute("class") + assert value_element.value_of_css_property("display") != "none" + + # Collapse + element_to_click.click() + assert CLS_COLLAPSED in li_element.get_attribute("class") + assert value_element.value_of_css_property("display") == "none" + + # Expand + element_to_click.click() + assert CLS_COLLAPSED not in li_element.get_attribute("class") + assert value_element.value_of_css_property("display") != "none" diff --git a/tests/test_mime_plugin.py b/tests/test_mime_plugin.py new file mode 100644 index 0000000..d3dd581 --- /dev/null +++ b/tests/test_mime_plugin.py @@ -0,0 +1,101 @@ +import re + +import pytest + +from myst_nb_json import JsonMimeRenderPlugin + + +@pytest.fixture +def plugin() -> JsonMimeRenderPlugin: + return JsonMimeRenderPlugin() + + +def _strip_xml_attributes(string: str) -> str: + return re.sub(pattern=r"<(?P\w+)(?:\s+[^>]*)>", repl=r"<\g>", string=string) + + +def _strip_xml_whitespace(string: str) -> str: + return re.sub(pattern=r">\s+<", repl="><", string=string) + + +def _strip_xml_tags(string: str) -> str: + return re.sub(pattern=r"<\/?\w+[^>]*>", repl="", string=string) + + +CHAR_to_HTML_ENTITY = { + ">": ">", + "<": "<", + "&": "&", + # These also cause problems, although they should not strictly need escaping + "[": "[", + "]": "]", + "{": "{", + "}": "}", + '"': """, + # Hash (in CSS color) causes problems for Selenium Chrome webdriver + "#": "#", +} +HTML_ENTITY_TO_CHAR = {v: k for k, v in CHAR_to_HTML_ENTITY.items()} + + +def _html_unescape(string: str) -> str: + return re.sub( + pattern=r"&\w+;", + repl=lambda m: HTML_ENTITY_TO_CHAR.get(m.group(), m.group()), + string=string, + ) + + +@pytest.mark.parametrize( + ("value", "expected_xml"), + [ + ("abc", '"abc"'), + (42, "42"), + (3.14, "3.14"), + (True, "true"), + (False, "false"), + (None, "null"), + ], +) +def test_scalar_value(plugin: JsonMimeRenderPlugin, value, expected_xml: str): + actual = "".join(plugin.scalar_value(value)) + # It should produce the expected HTML structure + assert _strip_xml_whitespace(_strip_xml_attributes(actual)) == expected_xml + + +@pytest.mark.parametrize( + ("value", "expected_xml", "expected_text"), + [ + ([], "
[
    ]
    ", "[]"), + ( + ["a", "b"], + '
    [
    • "a",
    • "b"
    ]
    ', + '["a", "b"]', + ), + ], +) +def test_list_value(plugin: JsonMimeRenderPlugin, value, expected_xml: str, expected_text: str): + actual = "".join(plugin.list_value(value)) + # It should produce the expected HTML structure + assert _strip_xml_whitespace(_strip_xml_attributes(actual)) == expected_xml + # It should preserve JSON syntax as user-electable text (even if brackets are not displayed) + assert _html_unescape(_strip_xml_tags(actual)) == expected_text + + +@pytest.mark.parametrize( + ("value", "expected_xml", "expected_text"), + [ + ({}, "
    {
      }
      ", "{}"), + ( + {"k1": "v1", "k2": "v2"}, + '
      {
      • "k1": "v1",
      • "k2": "v2"
      }
      ', + '{"k1": "v1", "k2": "v2"}', + ), + ], +) +def test_dict_value(plugin: JsonMimeRenderPlugin, value, expected_xml: str, expected_text: str): + actual = "".join(plugin.dict_value(value)) + # It should produce the expected HTML structure + assert _strip_xml_whitespace(_strip_xml_attributes(actual)) == expected_xml + # It should preserve JSON syntax as user-electable text (even if braces and quotes are not displayed) + assert _html_unescape(_strip_xml_tags(actual)) == expected_text diff --git a/tests/test_myst_nb.py b/tests/test_myst_nb.py new file mode 100644 index 0000000..198bd33 --- /dev/null +++ b/tests/test_myst_nb.py @@ -0,0 +1,17 @@ +import pytest + +from tests.conftest import clean_doctree, file_regression, get_test_path, sphinx_run # noqa: F401 + + +@pytest.mark.sphinx_params("json_output.ipynb", conf={"nb_execution_mode": "force"}) +def test_render_json_output( + sphinx_run, # noqa: F811 + clean_doctree, # noqa: F811 + file_regression, # noqa: F811 + get_test_path, # noqa: F811 +): + """Test that a cell with JSON output is rendered with the MIME type plugin""" + sphinx_run.build() + assert sphinx_run.warnings() == "" + doctree = clean_doctree(sphinx_run.get_resolved_doctree("json_output")) + file_regression.check(doctree.pformat(), extension=".xml", encoding="utf-8") diff --git a/tests/test_myst_nb/test_render_json_output.xml b/tests/test_myst_nb/test_render_json_output.xml new file mode 100644 index 0000000..c902bec --- /dev/null +++ b/tests/test_myst_nb/test_render_json_output.xml @@ -0,0 +1,113 @@ + + + + + from IPython.display import JSON + + JSON( + { + "key1": "value1", + "key2": { + "key21": "str", + "key22": 42, + "key23": 3.14, + "key24": True, + "key25": False, + "key26": None, + "key27": {}, + "key28": [], + }, + "key3": ["str", 42, 3.14, True, False, None, {}, []], + }, + root="test", + expanded=True, + ) + + +
      • "test":
        {
        • "key1": "value1",
        • "key2":
          {
          • "key21": "str",
          • "key22": 42,
          • "key23": 3.14,
          • "key24": true,
          • "key25": false,
          • "key26": null,
          • "key27": {},
          • "key28": []
          },
        • "key3":
          [
          • "str",
          • 42,
          • 3.14,
          • true,
          • false,
          • null,
          • {},
          • []
          ]
        }