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Remove html report (#28)
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‎.github/workflows/pytest.yml‎

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extra_args: --verbose --all-files
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- run: poetry run pytest tests/test_nb_run.py # run without extras
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- run: poetry install -E html
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- run: poetry install
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- run: poetry run pytest --cov-report=xml --cov=src
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- run: poetry run python -m ipykernel install --user --name nbmake
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pytest --nbmake teachopencadd/talktorials/T000_template/talktorial.ipynb \
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- shell: bash -l {0}
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run: |
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pip install './nbmake[html]'
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pip install './nbmake'
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- shell: bash -l {0}
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run: |
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pytest \
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--nbmake \
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--path-output=. \
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-n=auto \
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teachopencadd/talktorials/T000_template/talktorial.ipynb \
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teachopencadd/talktorials/T002_compound_adme/talktorial.ipynb \

‎CONTRIBUTING.MD‎

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## Developing
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### Install local package
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```
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poetry install
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```
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### Activate shell
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```
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poetry shell
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```
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### Run static checks
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```
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pre-commit run --all-files
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pre-commit install
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```
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### Run tests
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```
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pytest
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```

‎README.md‎

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pytest --nbmake **/*ipynb
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```
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**See [docs](https://treebeardtech.github.io/nbmake) for more.**
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<br/>
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<br/>
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## Allow errors and Configure Cell Timeouts
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## See Also
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nbmake is built on top of [nbclient](https://github.com/jupyter/nbclient) and designed to compatible with nbsphinx and jupyter-book.
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* [nbmake-action](https://github.com/treebeardtech/nbmake-action)
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The [jupyter book docs](https://jupyterbook.org/content/execute.html?highlight=allow_error#dealing-with-code-that-raises-errors) have a good description of how to ignore errors -- note that nbmake does not work with the external `_config.yml` configuration file. You must use the notebook JSON metadata field.
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### HTML Report Example
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## Parallelisation
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![HTML Report](docs/screen.png)
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Parallelisation with xdist is experimental upon initial release, but you can try it out:
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```
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pip install pytest-xdist
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pytest --nbmake -n=auto
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```
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It is also possible to parallelise at a CI-level using strategies, see [example](https://github.com/LabForComputationalVision/plenoptic/blob/master/.github/workflows/treebeard.yml)
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## Developing
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### Build Jupyter Books Faster
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Using xdist and the `--overwrite` flag let you build a large jupyter book repo faster:
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### Install local package
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```
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poetry install -E html
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pytest --nbmake --overwrite -n=auto examples
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jb build examples
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```
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## Advice on Usage
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nbmake is best used in a scenario where you use the ipynb files only for development. Consumption of notebooks is primarily done via a docs site, built through jupyter book, nbsphinx, or some other means. If using one of these tools, you are able to write assertion code in cells which will be [hidden from readers](https://jupyterbook.org/interactive/hiding.html).
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### Pre-commit
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Treating notebooks like source files lets you keep your repo minimal. Some tools, such as plotly may drop several megabytes of javascript in your output cells, as a result, stripping out notebooks on pre-commit is advisable:
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### Activate shell
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```
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poetry shell
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# .pre-commit-config.yaml
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repos:
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- repo: https://github.com/kynan/nbstripout
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rev: master
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hooks:
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- id: nbstripout
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```
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### Run static checks
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See https://pre-commit.com/ for more...
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## Disable Nbmake
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Implicitly:
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```
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pre-commit run --all-files
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pre-commit install
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pytest
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```
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### Run tests
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Explicitly:
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```
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pytest
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pytest -p no:nbmake
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```
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## See Also:
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* [nbmake action](https://github.com/treebeardtech/treebeard)
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* [pytest](https://pytest.org/)
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* [jupyter book](https://github.com/executablebooks/jupyter-book)
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* [jupyter cache](https://github.com/executablebooks/jupyter-cache)
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* [MyST-NB](https://github.com/executablebooks/MyST-NB)

‎docs/landing-page.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"nbmake tests notebook documentation and is designed for notebooks which are non-deterministic.\n",
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"See the README for details: \n",
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"\n",
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"Despite being a pytest plugin, nbmake is kernel agnostic. It supports any language."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"\n",
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"## Quickstart\n",
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"\n",
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"```bash\n",
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"pip install pytest nbmake\n",
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"pytest --nbmake\n",
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"```\n",
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"\n",
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"### Output\n",
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"```\n",
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"========================================================================================== test session starts ==========================================================================================\n",
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"platform darwin -- Python 3.7.6, pytest-6.1.2, py-1.9.0, pluggy-0.13.1\n",
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"rootdir: /Users/asdf/git/treebeardtech/nbmake, configfile: pytest.ini\n",
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"plugins: nbmake-0.0.1, xdist-2.1.0, cov-2.10.1, forked-1.3.0\n",
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"collected 1 item \n",
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"\n",
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"landing-page.ipynb . [100%]\n",
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"\n",
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"=========================================================================================== 1 passed in 1.56s ===========================================================================================\n",
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"\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Command Line Options\n",
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"\n",
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"Using the following options you can control how notebooks are executed, and configure CI pipelines"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-input"
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]
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},
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"outputs": [],
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"source": [
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"!pytest -h | grep -A6 'notebook testing'"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Run Only Against IPYNB Files\n",
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"\n",
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"```\n",
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"pytest --nbmake **/*ipynb\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Create an HTML Report\n",
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"\n",
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"To view outputs executed remotely, install jupyter-book:\n",
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"```\n",
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"pip install pytest 'nbmake[html]'\n",
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"```\n",
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"\n",
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"Then specify a path:\n",
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"```\n",
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"pytest --nbmake --path-output=.\n",
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"```\n",
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"\n",
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"### Output\n",
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"```\n",
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"========================================================================================== test session starts ==========================================================================================\n",
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"platform darwin -- Python 3.7.6, pytest-6.1.2, py-1.9.0, pluggy-0.13.1\n",
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"rootdir: /Users/asdf/git/treebeardtech/nbmake, configfile: pytest.ini\n",
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"plugins: nbmake-0.0.1, xdist-2.1.0, cov-2.10.1, forked-1.3.0\n",
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"collected 1 item \n",
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"\n",
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"landing-page.ipynb . [100%]\n",
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"\n",
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"\n",
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"2020-12-11 11:10:48 nbmake building test report at: \n",
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"\n",
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" file:///Users/asdf/git/treebeardtech/nbmake/docs/_build/html/index.html\n",
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"\n",
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"2020-12-11 11:10:50 done.\n",
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"\n",
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"=========================================================================================== 1 passed in 4.26s ===========================================================================================\n",
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"```\n",
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"\n",
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"The report contains only the stripped out and executed notebooks\n",
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"![HTML report](screen.png)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Run and upload report on GitHub Actions using Netlify\n",
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"\n",
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"```yaml\n",
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" - run: pip install pytest 'nbmake[html]'\n",
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" - run: |\n",
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" pytest --nbmake --path-output=.\n",
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" - if: failure()\n",
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" run: |\n",
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" netlify deploy --dir=_build/html --auth=${{ secrets.NETLIFY_TOKEN }} --site=${{ secrets.NETLIFY_SITE_API_ID }}\n",
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"```\n",
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"```\n",
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"...\n",
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"- Waiting for deploy to go live...\n",
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"✔ Deploy is live!\n",
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"\n",
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"Logs: https://app.netlify.com/sites/festive-payne-ce084c/deploys/5fcf58ec72dc52a440dffcd7\n",
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"Website Draft URL: https://5fcf58ec72dc52a440dffcd7--festive-payne-ce084c.netlify.app\n",
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"```\n",
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"\n",
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"Note you can also run the tests using [nbmake-action](https://github.com/treebeardtech/treebeard) for this."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Disable Nbmake\n",
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"\n",
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"Implicitly:\n",
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"```\n",
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"pytest\n",
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"```\n",
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"\n",
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"Explicitly:\n",
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"```\n",
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"pytest -p no:nbmake\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Allow errors and Configure Cell Timeouts\n",
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"\n",
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"nbmake is designed to compatible with jupyter book config (placed in notebook `metadata`, not the global config.yml)\n",
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"\n",
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"See [jupyter book docs](https://jupyterbook.org/content/execute.html?highlight=allow_error#dealing-with-code-that-raises-errors)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Parallelisation\n",
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"\n",
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"Parallelisation with xdist is experimental upon initial release, but you can try it out:\n",
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"```\n",
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"pip install pytest-xdist\n",
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"\n",
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"pytest --nbmake -n=auto\n",
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"```\n",
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"\n",
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"It is also possible to parallelise at a CI-level using strategies, see [example](https://github.com/LabForComputationalVision/plenoptic/blob/master/.github/workflows/treebeard.yml)\n",
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"\n",
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"### Build Jupyter Books Faster\n",
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"\n",
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"Using xdist and the `--overwrite` flag let you build a large jupyter book repo faster:\n",
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"\n",
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"```\n",
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"pytest --nbmake --overwrite -n=auto examples\n",
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"jb build examples\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Advice on Usage\n",
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"\n",
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"nbmake is best used in a scenario where you use the ipynb files only for development. Consumption of notebooks is primarily done via a docs site, built through jupyter book, nbsphinx, or some other means. If using one of these tools, you are able to write assertion code in cells which will be [hidden from readers](https://jupyterbook.org/interactive/hiding.html).\n",
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"\n",
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"### Pre-commit\n",
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"\n",
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"Treating notebooks like source files lets you keep your repo minimal. Some tools, such as plotly may drop several megabytes of javascript in your output cells, as a result, stripping out notebooks on pre-commit is advisable:\n",
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"\n",
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"```\n",
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"# .pre-commit-config.yaml\n",
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"repos:\n",
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" - repo: https://github.com/kynan/nbstripout\n",
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" rev: master\n",
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" hooks:\n",
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" - id: nbstripout\n",
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"```\n",
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"\n",
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"See https://pre-commit.com/ for more..."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Contributing\n",
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"\n",
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"Feedback is the best contribution you can make as a user of this tool. Join the [Slack channel](https://join.slack.com/t/treebeard-entmoot/shared_invite/zt-jyvuqted-xBjnbvlfcu5P2ltBvn1~mg) and bug me (Alex), and raise an [issue](https://github.com/treebeardtech/nbmake/issues), even if you think you are the only person with this problem."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## See Also:\n",
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"\n",
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"* [nbmake action](https://github.com/treebeardtech/treebeard)\n",
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"* [pytest](https://pytest.org/)\n",
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"* [jupyter book](https://github.com/executablebooks/jupyter-book)\n",
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"* [jupyter cache](https://github.com/executablebooks/jupyter-cache)\n",
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"* [MyST-NB](https://github.com/executablebooks/MyST-NB)\n"
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"https://github.com/treebeardtech/nbmake"
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]
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}
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],

‎docs/screen.png‎

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