Merge branch 'master' into test-code-figures

Author: agoose77

.github/workflows/tests.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python 3.8
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
     - uses: pre-commit/action@v2.0.0
 
   tests:
@@ -26,15 +26,18 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
-        sphinx: [">=3,<4", ">=4,<5"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        sphinx: [">=5,<6"]
         include:
-          - os: windows-latest
+          - os: ubuntu-latest
             python-version: 3.7
-            sphinx: ">=3,<4"
-          - os: macos-latest
-            python-version: 3.9
             sphinx: ">=4,<5"
+          - os: windows-latest
+            python-version: 3.8
+            sphinx: ">=5,<6"
+          - os: macos-latest
+            python-version: 3.8
+            sphinx: ">=5,<6"
 
     runs-on: ${{ matrix.os }}
 
@@ -59,12 +62,12 @@ jobs:
       # this is why we run `coverage xml` afterwards (required by codecov)
 
     - name: Upload to Codecov
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7 && matrix.sphinx == '>=3,<4' && github.repository == 'executablebooks/MyST-NB'
-      uses: codecov/codecov-action@v1
+      if: github.repository == 'executablebooks/MyST-NB' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
+      uses: codecov/codecov-action@v3
       with:
-        name: myst-nb-pytests-py3.7
+        name: myst-nb-pytests
         flags: pytests
-        file: ./coverage.xml
+        files: ./coverage.xml
         fail_ci_if_error: true
 
   publish:
@@ -74,18 +77,18 @@ jobs:
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v1
-        with:
-          python-version: 3.8
-      - name: Build package
-        run: |
-          pip install wheel
-          python setup.py sdist bdist_wheel
-      - name: Publish
-        uses: pypa/gh-action-pypi-publish@v1.1.0
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_KEY }}
+    - name: Checkout source
+      uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: install flit
+      run: |
+        pip install flit~=3.4
+    - name: Build and publish
+      run: |
+        flit publish
+      env:
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD: ${{ secrets.PYPI_KEY }}

.gitignore

@@ -14,7 +14,6 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
 lib64/
 parts/
 sdist/
@@ -130,9 +129,12 @@ dmypy.json
 .pyre/
 
 # Jupyter Cache
-docs/.jupyter_cache
+.jupyter_cache
 
 # OSX
 .DS_Store
 
 .vscode/
+
+todos.md
+_archive/

.pre-commit-config.yaml

@@ -11,52 +11,48 @@ exclude: >
 
 repos:
 
-  - repo: git://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
     hooks:
-    - id: check-manifest
-      args: [--no-build-isolation]
-      additional_dependencies: [setuptools>=46.4.0]
+    - id: pyupgrade
+      args: [--py37-plus]
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.9.3
+    rev: 5.12.0
     hooks:
     - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 21.9b0
+    rev: 23.3.0
     hooks:
     - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 6.0.0
     hooks:
     - id: flake8
-      additional_dependencies: [flake8-bugbear==21.3.1]
+      additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910-1
+    rev: v1.2.0
     hooks:
     - id: mypy
-      args: [--config-file=setup.cfg]
+      args: [--config-file=pyproject.toml]
       additional_dependencies:
-      - myst-parser~=0.14.0
+      - importlib_metadata
+      - myst-parser~=0.18.0
+      - "sphinx~=5.0"
+      - nbclient
+      - types-PyYAML
       files: >
         (?x)^(
-            myst_nb/parser.py|
+            myst_nb/.+\.py|
         )$
-
-  # this is not used for now,
-  # since it converts myst-nb to myst_nb and removes comments
-  # - repo: https://github.com/asottile/setup-cfg-fmt
-  #   rev: v1.17.0
-  #   hooks:
-  #   - id: setup-cfg-fmt

.readthedocs.yml

@@ -1,7 +1,7 @@
 version: 2
 
 python:
-  version: 3
+  version: "3.8"
   install:
       - method: pip
         path: .

CHANGELOG.md

@@ -1,5 +1,208 @@
 # Change Log
 
+## v0.17.1 - 2022-30-09
+
+[Full changelog](https://github.com/executablebooks/MyST-NB/compare/v0.17.0...v0.17.1)
+
+- 👌 IMPROVE: `hide-output` button (#450)
+  This now uses the same margin color as the cell source and, when the cell source is present, is "connected" to that, to form a single element.
+  See [Hide cell contents](docs/render/hiding.md) for more information.
+
+## v0.17.0 - 2022-29-09
+
+[Full changelog](https://github.com/executablebooks/MyST-NB/compare/v0.16.0...v0.17.0)
+
+- 👌 IMPROVE: Replace sphinx-togglebutton with built-in functionality (#446)
+  This allows for tighter integration with myst-nb:
+
+  - Nicer rendering of the hidden content buttons
+  - Customisation of the hide/show prompts
+
+  See [Hide cell contents](docs/render/hiding.md) for more information.
+
+- 🐛 FIX: Inline exec variables with multiple outputs (#440)
+  Previously, it was assumed that a variable evaluation would only ever create 0 or 1 outputs.
+  Multiple are now allowed.
+
+- 👌 IMPROVE: cache bust changes to CSS (#447)
+- 👌 IMPROVE: Move CSS colors to variables (#448)
+
+## v0.16.0 - 2022-06-13
+
+[Full changelog](https://github.com/executablebooks/MyST-NB/compare/v0.15.0...v0.16.0)
+
+- ⬆️ UPGRADE: Sphinx v5 and drop v3 (see [changelog](https://www.sphinx-doc.org/en/master/changes.html)), myst-parser v0.18 (see [changelog](https://myst-parser.readthedocs.io/en/latest/develop/_changelog.html))
+- ⬆️ UPGRADE: Add Python 3.10 support
+
+## v0.15.0 - 2022-05-05
+
+[Full changelog](https://github.com/executablebooks/MyST-NB/compare/v0.14.0...v0.15.0)
+
+✨ NEW: Add `inline` execution mode and `eval` role/directive, for inserting code variables directly into the text flow of your documentation!
+See [Inline variable evaluation](docs/render/inline.md) for more information.
+
+## v0.14.0 - 2022-04-27
+
+[Full changelog](https://github.com/executablebooks/MyST-NB/compare/v0.13.2...v0.14.0)
+
+This release encompasses a **major** rewrite of the entire library and its documentation, primarily in [#380](https://github.com/executablebooks/MyST-NB/pull/380) and [#405](https://github.com/executablebooks/MyST-NB/pull/405).
+
+### Breaking Changes ‼️
+
+#### Configuration
+
+A number of configuration option names have been changed, such that they now share the `nb_` prefix.
+Most of the deprecated names will be auto-converted at the start of the build, emitting a warning such as:
+
+```
+WARNING: 'jupyter_execute_notebooks' is deprecated for 'nb_execution_mode' [mystnb.config]
+```
+
+`nb_render_priority` has been removed and replaced by `nb_mime_priority_overrides`, which has a different format and is more flexible. See [Outputs MIME priority](docs/render/format_code_cells.md) for more information.
+
+As per the changes in [`myst_parser`](myst:develop/_changelog), the `dollarmath` syntax extension is no longer included by default.
+To re-add this extension, ensure that it is specified in your `conf.py`: `myst_enable_extensions = ["dollarmath"]`.
+
+For cell-level configuration the top-level key `render` has now been deprecated for `mystnb`.
+For example, replace:
+
+````markdown
+```{code-cell}
+---
+render:
+  image:
+    width: 200px
+---
+...
+```
+````
+
+with:
+
+````markdown
+```{code-cell}
+---
+mystnb:
+  image:
+    width: 200px
+---
+...
+```
+````
+
+`render` will currently still be read, if present, and will issue a `[mystnb.cell_metadata_key]` warning.
+
+The `jupyter_sphinx_require_url` and `jupyter_sphinx_embed_url` configuration options are no longer used by this package, and are replaced by `nb_ipywidgets_js`.
+
+See the [configuration section](docs/configuration.md) for more details.
+
+#### Dependencies
+
+The [ipywidgets](https://ipywidgets.readthedocs.io) package has been removed from the requirements.
+If required, please install it specifically.
+
+#### AST structure and rendering plugins
+
+The structure of the docutils AST and nodes produced by MyST-NB has been fully changed, for compatibility with the new [docutils only functionality](docs/docutils.md).
+See [the API documentation](docs/reference/api.rst) for more details.
+
+The renderer plugin system (used by the `myst_nb.renderers` entry point) has also been completely rewritten,
+so any current existing renderers will no longer work.
+There is also now a new `myst_nb.mime_renderers` entry point, to allow for targeted rendering of specific code-cell output MIME types.
+See [Customise the render process](docs/render/format_code_cells.md) for more information.
+
+#### Glue functionality
+
+By default, `glue` roles and directives now only work for keys within the same document.
+To reference glued content in a different document, the `glue:any` directive allows for a `doc` option and `glue:any`/`glue:text` roles allow the (relative) doc path to be added, for example:
+
+````markdown
+```{glue:any} var_text
+:doc: other.ipynb
+```
+
+{glue:text}`other.ipynb::var_float:.2E`
+````
+
+This cross-document functionality is currently restricted to only `text/plain` and `text/html` output MIME types, not images.
+
+See [Embedding outputs as variables](docs/render/glue.md) for more details.
+
+### Dependency changes ⬆️
+
+- Removed:
+  - `ipywidgets`
+  - `jupyter_sphinx`
+  - `nbconvert`
+- Updated:
+  - `Python`: `3.6+ -> 3.7+`
+  - `myst_parser`: [`0.15 -> 0.17`](myst:develop/_changelog)
+  - `jupyter-cache`: [`0.4 -> 0.5`](https://github.com/executablebooks/jupyter-cache/blob/master/CHANGELOG.md)
+  - `sphinx-togglebutton`: [`0.1 -> 0.3`](https://sphinx-togglebutton.readthedocs.io/en/latest/changelog.html)
+
+### New and improved ✨
+
+The following is a non-exhaustive list of new features and improvements, see the rest of the documentation for all the changes.
+
+- Multi-level configuration (global (`conf.py`) < notebook level metadata < cell level metadata)
+  - Plus new config options including: `nb_number_source_lines`, `nb_remove_code_source`, `nb_remove_code_outputs`, `nb_render_error_lexer`, `nb_execution_raise_on_error`, `nb_kernel_rgx_aliases`
+  - See the [configuration section](docs/configuration.md) for more details.
+
+- Added `mystnb-quickstart` and `mystnb-to-jupyter` CLI commands.
+
+- MyST text-based notebooks can now be specified by just:
+
+  ```yaml
+  ---
+  file_format: mystnb
+  kernelspec:
+    name: python3
+  ---
+  ```
+
+  as opposed to the alternative jupytext top-matter.
+  See [Text-based Notebooks](docs/authoring/text-notebooks.md) for more details.
+
+- docutils API/CLI with command line tools, e.g. `mystnb-docutils-html`
+  - Includes `glue` roles and directives
+  - See [single page builds](docs/docutils.md) for more details.
+
+- Parallel friendly (e.g. `sphinx-build -j 4` can execute four notebooks in parallel)
+
+- Page specific loading of ipywidgets JavaScript, i.e. only when ipywidgets are present in the notebook.
+
+- Added raw cell rendering, with the `raw-cell` directive.
+  See [Raw cells authoring](docs/authoring/jupyter-notebooks.md) for more details.
+
+- Added MIME render plugins. See [Customise the render process](docs/render/format_code_cells.md) for more details.
+
+- Better log info/warnings, with `type.subtype` specifiers for warning suppression.
+  See [Warning suppression](docs/configuration.md) for more details.
+
+- Reworked jupyter-cache integration to be easier to use (including parallel execution)
+
+- Added image options to `glue:figure`
+
+- New `glue:md` role/directive includes nested parsing of MyST Markdown.
+  See [Embedding outputs as variables](docs/render/glue.md) for more details.
+
+- Improved `nb-exec-table` directive (includes links to documents, etc)
+
+### Additional Pull Requests
+
+- 👌 IMPROVE: Update ANSI CSS colors by @saulshanabrook in [#384](https://github.com/executablebooks/MyST-NB/pull/384)
+- ✨ NEW: Add `nb_execution_raise_on_error` config by @chrisjsewell in [#404](https://github.com/executablebooks/MyST-NB/pull/404)
+- 👌 IMPROVE: Add image options to `glue:figure` by @chrisjsewell in [#403](https://github.com/executablebooks/MyST-NB/pull/403)
+
+## v0.13.2 - 2022-02-10
+
+This release improves for cell outputs and brings UI improvements for toggling cell inputs and outputs.
+It also includes several bugfixes.
+
+- Add CSS support for 8-bit ANSI colours [#379](https://github.com/executablebooks/MyST-NB/pull/379) ([@thiippal](https://github.com/thiippal))
+- Use configured `nb_render_plugin` for glue nodes [#337](https://github.com/executablebooks/MyST-NB/pull/337) ([@bryanwweber](https://github.com/bryanwweber))
+- UPGRADE: sphinx-togglebutton v0.3.0 [#390](https://github.com/executablebooks/MyST-NB/pull/390) ([@choldgraf](https://github.com/choldgraf))
+
 ## 0.13.1 - 2021-10-04
 
 ✨ NEW: `nb_merge_streams` configuration  [[PR #364](https://github.com/executablebooks/MyST-NB/pull/364)]