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Developer README

This file provides details needed by developers to properly create and add new example notebooks to this repository.

Table of Contents

  • Installation
  • Add a new example
  • File layout
  • Running tests
  • Building documentation
  • Preprocessing
  • Copyright headers
  • Notebook names
  • How to create an example
    • Jupyter Notebook file extensions
    • Jupyter Notebook cell tags
    • Jupyter notebook metadata
  • Packaging

Quickstart, skip to sections:

Quickstart, skip to sections:

Installation

Clone the repository from GitHub, set up your Python environment as you usually do, then run pip with the developer requirements:

# to create a conda environment first:
# conda create -n idaes-examples python=3.10; conda activate idaes-examples
pip install -r requirements-dev.txt

The configuration of the installation is stored in pyproject.toml.

Add a new example

Note: Below, notebooks/* refers to the directory idaes_examples/notebooks.

If you want to add an example in an existing section of notebooks/docs, you can run idaesx new to get a guided terminal-based UI that will create a skeleton of the new notebook and add it to the table of contents, and also add all the variations of the notebook (see Notebook Names) and, if git is enabled and found, add and commit them to git. Then you just need to edit your notebook.

If you need to create a new section in notebooks/docs or notebooks/held:

  • add the appropriate subdirectory, e.g. notebooks/docs/fantastic
  • add a section into notebooks/_toc.yml, imitating an existing entry
  • create and populate a notebooks/docs/fantastic/index.md file
  • now you can add your notebook(s) manually, e.g. notebooks/docs/fantastic/my_notebook.ipynb, or use the idaesx new command

File layout

This section describes the internal organization of the example notebooks and supporting files.

Directories

The examples are divided into a few top-level directories.

  • notebooks: All the active/tested Jupyter notebooks and supporting data
    • docs: Examples and tutorials that will be tested and also published in the online documentation.
    • active: Not published but tested against new PRs
    • _dev: Notebooks used as examples for development and testing only.
    • held: Not published and not tested. For the next release (or removal).
  • mod: Supporting Python modules (as a Python package).
    It is usually best to match the name of the Python subpackage with its notebook directory.

For guidance on where to put a new notebook, see the Examples Standards page in the IDAES examples repo wiki.

Running tests

There are two sets of tests in this repo. Which one you run depends in which directory you run tests.

If your current directory is the root of the repository:

  1. pytest .: Runs Python test modules, matching the usual patterns (e.g., *_test.py).
  2. pytest idaes_examples: Runs Jupyter notebook tests. Due to the presence of a special conftest.py file in this directory, Jupyter Notebooks will be preprocessed and then all test notebooks (their filename ending in _test.ipynb) will be executed.

Integration tests

Run integration tests from the top-level (root) directory of the repository. In the root directory, tests are configured by pyproject.toml; see the tool.pytest.ini_options section.

# from the root directory of the repository
pytest idaes_examples

Testing a subset of the notebooks

To test just one notebook, you need to use the name of the test notebook not the source. For example, to test the compressor.ipynb notebook (in the unit_models/operations subdirectory) you need to add -c and the path to the top-level pyproject.toml, which has the pytest configuration, then use the name of the test notebook:

pytest -v idaes_examples/notebooks/docs/unit_models/operations/compressor_test.ipynb

If you want to test several related notebooks, or perhaps just not type the whole notebook filename, you can use the pytest -k flag to test all notebooks whose path matches a string (see pytest docs for details). So, for example, from the top-level directory if you want to test all the docs/unit_models/operations notebooks, you could take advantage of the fact that "operations" appears only in this particular path:

pytest -v idaes_examples -k operations
# will match: 
# docs/unit_models/operations/compressor_test.ipynb
# docs/unit_models/operations/heat_exchanger_0d_test.ipynb
# docs/unit_models/operations/mixer_test.ipynb
# docs/unit_models/operations/heater_test.ipynb
# docs/unit_models/operations/skeleton_unit_test.ipynb
# docs/unit_models/operations/pump_test.ipynb
# docs/unit_models/operations/turbine_test.ipynb

Building documentation

Note: Building the documentation runs all the notebooks. This is very slow, so is not an operation that a developer should perform during their regular workflow. Notebooks should be written with unit tests (see above) that can be run quickly to check correctness and syntax during creation and debugging.

The documentation is built using Jupyterbook. We have written a thin layer around the Jupyterbook executable, which is installed as a command-line program idaesx. To build the documentation, run:

idaesx build

The output will be in idaes_examples/nb/_build/html. As a convenience, you can open that HTML file with the command idaesx view.

Preprocessing notebooks

Preprocessing creates separate copies of the Jupyter notebooks that are used for tests, tutorial exercise and solution, and documentation (see Notebook Names). These (derived) notebooks are also committed and saved in Git.

To re-run the preprocessing, which will update any derived files that are out of date (older than the corresponding *.ipynb file):

idaesx pre

A diagram of how preprocessing relates to notebook usage is shown below:

 ┌───────────────┐
 │               │
 │ example.ipynb │
 │               │
 └──────┬────────┘
        │
        ▼            ┌──────────────────┐     ┌──────┐
 ┌────────────┐  ┌─► │example_test.ipynb├────►│pytest│
 │ preprocess ├──┤   └──────────────────┘     └──────┘
 └──────────┬─┘  │
            │    │   ┌─────────────────┐      ┌───────────┐
            │    └─► │example_doc.ipynb├─────►│jupyterbook│
            │        └─────────────────┘      └───────────┘
            │
            │        ┌─────────────────┐     ┌───────────┐
           ┌┴─┐  ┌──►│example_usr.ipynb├────►│ browse/run│
           │OR├──┤   └─────────────────┘     └───────────┘
           └──┘  │                                ▲
                 │   ┌──────────────────────┐     │
                 │   │example_exercise.ipynb├─────┘
                 └──►│example_solution.ipynb│
                     └──────────────────────┘

Notebook names

Notebooks all have a file name that fits the pattern notebook-name_<ext>.ipynb*. When creating or modifying notebooks, you should always use the version with no extension, i.e. *.ipynb. Other extensions are automatically generated when running tests, building the documentation, and manually running the preprocessing step. See the table of notebook types for details.

How to add a new notebook

There are two main steps to creating a new notebook example.

  1. Add Jupyter Notebook and supporting files
    1. See the standards to figure out the parent directory for the notebook -- usually, it's docs.
    2. Put the notebook in the appropriate subdirectory. If you create a new directory for the notebook, the directory name should be in lowercase with underscores between words. For example: 'docs/machine_learning'.
    3. Notebook filename should be in lowercase with underscores and must end with '.ipynb'. For example: 'my_example.ipynb'.
    4. Add -- in the same directory as the notebook -- any data files or images it needs.
    5. Additional Python modules should be put in an appropriate place under idaes_examples/mod. Then your notebook can write: from idaes_examples.mod.<subpackage> import <bla>
  2. Add Jupyter notebook to the Jupyterbook table of contents in idaes_examples/notebooks/_toc.yml.
    1. The notebook will be a section. If you added a new directory, you will create a new chapter, otherwise it will go under an existing one. See Jupyterbook documentation for more details.
    2. Refer to the notebook as 'path/to/notebook-name_doc' (add the '_doc' and drop the '.ipynb' extension). For example: 'machine_learning/my_example_doc'.
    3. If you created a new directory for this notebook, make sure you add an index.md file to it. See other index.md files for the expected format.

You should test the new notebook and build it locally before pushing the new file, i.e., run pytest and idaesx build. Note that the cache for the documentation will be updated to contain the new output cells, which will modify files in idaes_examples/notebooks/nbcache; these files should also be committed and pushed.

Jupyter Notebook file extensions

Each source Jupyter notebook (ending in '.ipynb') is preprocessed to create additional notebooks which are a copy of the original with some cells (steps in the notebook execution) removed.

Notebook type Description Ends with
source Notebook source .ipynb
testing Run for testing _test.ipynb
exercise Tutorial exercises only _exercise.ipynb
solution Tutorial ex. and solutions _solution.ipynb
documentation Show in documentation _doc.ipynb
user Run by end-users _usr.ipynb

Jupyter Notebook cell tags

Preprocessing uses the feature of Jupyter notebook cell tags to understand which additional notebooks to create.

The following tags are understood by the preprocessing step:

  • testing: Remove this cell, except in the testing notebooks
  • exercise: The presence of this tag means a notebook is a tutorial. Generate an exercise and solution notebook, and keep this cell in both. Remove this cell in the documentation notebook.
  • solution: The presence of this tag means a notebook is a tutorial. Generate an exercise and solution notebook, but remove this cell in the solution notebook; keep the cell in the documentation notebook.
  • noauto: This tag means that this cell should not be run during automated notebook execution. The cell will be removed in testing and documentation notebooks.
  • auto: This tag means that this cell should only be run during automated notebook execution. The cell will be removed in all notebooks except testing and documentation.

All other tags, including the standard Jupyterbook tags for hiding or removing cells, will be ignored.

Cell tags tutorial

An example of these tags, with a tutorial on how to set them, is in the _dev/notebooks/ex/notebook_tags_example. ipynb notebook. In this directory the pre-processed output notebooks have been added to Git so you can see what they look like (without having to run idaesx pre yourself).

You can see the results by building the development notebooks into a documentation tree with idaesx build --dev (from the same directory you would normally run). The output will be in _dev/notebooks/_build/html.

Jupyter notebook metadata

In addition to per-cell tags, the preprocessor also can look at notebook-level metadata. This is currently used for only one purpose: to tell the preprocessor not to generate a 'test' notebook, and thereby to skip the given notebook in the tests. In order to make this happen, either manually edit the notebook source or use the Jupyter notebook "Edit -> Edit Notebook Metadata" menu item to add the following section to the notebook-level metadata:

"idaes": {
   "skip": ["test"]
}

Copyright headers

You can add (and update) copyright headers to Python files and Jupyter Notebooks using the addheader command with the included addheader.yml configuration file:

# first see what would be changed (using -n)
addheader -n -c addheader.yml
# if this is OK, add the headers
addheader -c addheader.yml

All existing notebooks and Python files will be automatically discovered and modified as needed.

Packaging

Instructions to package and distribute the examples as idaes-examples in PyPI. Based on the PyPA packaging projects documentation.

Install dependencies for packaging into your current (virtual) Python environment:

pip install -e .[dev,jb,pkg]

Edit the pyproject.toml file:

  1. Ensure that you have commented out the line under [project.optional-dependencies], in the dev section, that reads "idaes-pse @ git+https://github.com/IDAES/idaes-pse".
  2. Set the release version. You should increment the version for each new release.

Build the distribution:

> python -m build
# Many lines of output later, you should see a message like:
Successfully built idaes_examples-x.y.z.tar.gz and idaes_examples-x.y.z-py3-none-any.whl

If you have not already done so, create an account on testpypi.

Copy your API token from your account. To generate an API token, go to Settings → API Tokens, and selecting Add API Token. You will paste this token in the commands below.

Upload to TestPyPI:

> python -m twine upload --repository testpypi dist/*
Uploading distributions to https://test.pypi.org/legacy/
Enter your username: __token__
Enter your password: {{paste token here}}

Create a new virtual environment and install the package from test.pypi into it:

pip install --extra-index-url https://test.pypi.org/simple/ idaes-examples

If the installation succeeds, you should be able to browse the notebooks using the built-in GUI:

idaesx gui

If it all looks good, you can repeat the Upload step with the real PyPI (you will need to get an account and token, just as for test.pypi.org, above):

> python -m twine upload dist/*
Uploading distributions to https://upload.pypi.org/legacy/
Enter your username: __token__
Enter your password: {{past token here}}

Author: Dan Gunter
Last modified: 13 Mar 2023