Feature/25 integrate notebooks into docu #149
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Important Review skippedAuto reviews are disabled on base/target branches other than the default branch. Please check the settings in the CodeRabbit UI or the You can disable this status message by setting the WalkthroughThe changes primarily enhance the documentation deployment process by updating the workflow configuration, removing outdated pre-commit hooks, and modifying documentation files. Key updates include the installation of Pandoc, integration of Jupyter Notebooks via the Changes
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## dev #149 +/- ##
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Coverage 81.30% 81.30%
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Files 11 11
Lines 551 551
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Actionable comments posted: 2
Outside diff range and nitpick comments (1)
.github/workflows/deploy-docs.yaml (1)
39-43: Simplify directory removal by removing the conditional checkSince
rm -rfwill not raise an error if the directory does not exist, you can simplify the script by removing theifcondition.Apply this diff to simplify the code:
- name: Remove existing nb directory - run: | - if [ -d "docs/source/nb" ]; then - rm -rf docs/source/nb - fi + run: rm -rf docs/source/nb
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Files selected for processing (7)
- .github/workflows/deploy-docs.yaml (1 hunks)
- .pre-commit-config.yaml (0 hunks)
- README.md (1 hunks)
- docs/source/conf.py (2 hunks)
- docs/source/index.rst (1 hunks)
- nb/02_Geo_visualization_example.ipynb (12 hunks)
- pyproject.toml (1 hunks)
Files not reviewed due to no reviewable changes (1)
- .pre-commit-config.yaml
Files skipped from review due to trivial changes (2)
- README.md
- nb/02_Geo_visualization_example.ipynb
Additional comments not posted (4)
docs/source/index.rst (1)
25-35: LGTM!The addition of the notebooks section in the documentation index is correctly formatted, and the entries are properly listed.
docs/source/conf.py (2)
31-31: Addition ofnbsphinxextension is appropriateIncluding
"nbsphinx"in theextensionslist enables Jupyter Notebook support in your Sphinx documentation, which is beneficial for integrating notebooks seamlessly.
40-40: Verify thatnbsphinx_execute = "never"meets your documentation requirementsSetting
nbsphinx_execute = "never"will prevent the execution of code cells during the documentation build process. Consequently, the outputs displayed in the documentation will be those already saved in the notebook files. Ensure that all notebooks have the desired outputs pre-executed and saved to provide a complete and informative documentation experience.pyproject.toml (1)
66-66: Addition ofnbsphinxdependency looks goodThe inclusion of
nbsphinx = "^0.9.5"enhances the documentation by enabling integration of Jupyter Notebooks, aligning with the PR objectives.
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Actionable comments posted: 1
Outside diff range and nitpick comments (3)
docs/source/index.rst (1)
Line range hint
1-58: Consider adding brief descriptions for each notebook entry.To further enhance the usability and clarity of the documentation, consider adding a brief one-line description for each notebook entry in the table of contents. This will give users a quick overview of the purpose and content of each notebook without having to navigate to the actual notebook file.
For example:
nb/00_Setup + Setup and configuration of the pystatis environment nb/01_table + Creating and manipulating tables using pystatis nb/02_Geo_visualization_example + Examples and tutorials for geographical visualizations nb/03_find + Finding and querying data using pystatis nb/04_jobs + Job-related functionalities and workflows nb/05_presentation + Presentation and visualization techniques using pystatisThese brief descriptions will provide users with a quick understanding of what each notebook covers, making it easier for them to identify the notebook that best suits their needs.
docs/source/conf.py (1)
Line range hint
1-58: Consider adding a brief comment about the purpose of thenbsphinxextension.To enhance the maintainability and readability of the configuration file, it would be helpful to add a concise comment explaining the purpose of the
nbsphinxextension. This will provide clarity for future maintainers and contributors.Here's a suggested comment to add above the
nbsphinxextension:extensions = [ + # nbsphinx: Enables integration of Jupyter Notebooks into Sphinx documentation "nbsphinx", "myst_parser", "sphinx.ext.autodoc", "sphinx.ext.autosummary", # used to generate overview tables "sphinx.ext.napoleon", # used for google-style docstrings ].github/workflows/deploy-docs.yaml (1)
39-43: Simplify the directory removal step.Instead of checking for the existence of the directory and then removing it, you can use the
-pflag withrmto remove the directory and its contents only if it exists. This simplifies the step and reduces the number of lines needed.Apply this diff to simplify the directory removal step:
- - name: Remove existing nb directory - run: | - if [ -d "docs/source/nb" ]; then - rm -rf docs/source/nb - fi + - name: Remove existing nb directory if it exists + run: rm -rf docs/source/nb
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Files ignored due to path filters (1)
poetry.lockis excluded by!**/*.lock
Files selected for processing (7)
- .github/workflows/deploy-docs.yaml (1 hunks)
- .pre-commit-config.yaml (0 hunks)
- README.md (1 hunks)
- docs/source/conf.py (2 hunks)
- docs/source/index.rst (1 hunks)
- nb/02_Geo_visualization_example.ipynb (12 hunks)
- pyproject.toml (1 hunks)
Files not reviewed due to no reviewable changes (1)
- .pre-commit-config.yaml
Additional comments not posted (6)
nb/02_Geo_visualization_example.ipynb (1)
7-8: LGTM!The formatting changes enhance the readability and visual structure of the notebook without altering the content or functionality. The addition of underlines beneath titles and section headers improves clarity and emphasis. Removing unnecessary line breaks in markdown cells streamlines the presentation.
Also applies to: 12-14, 41-42, 63-64, 253-259, 307-313, 456-457, 464-465, 679-680, 762-763, 884-890, 1065-1066, 1297-1298, 1311-1312, 1436-1436
docs/source/index.rst (2)
25-35: Excellent addition of the Notebooks section!The new Notebooks section in the documentation index significantly improves the organization and discoverability of the notebooks. The clear categorization and intuitive naming of the notebook entries will greatly benefit users in navigating and locating the relevant notebooks for their needs.
The use of a maximum depth of 2 for the table of contents is also a good choice, as it provides a balance between providing an overview of the available notebooks and maintaining a concise structure.
Overall, this is a valuable enhancement to the documentation structure.
Line range hint
1-58: Verify the notebook file paths and names.Please ensure that the notebook file paths and names mentioned in the table of contents match the actual notebook files in the repository. It's important to double-check that the referenced notebooks exist at the specified locations to avoid broken links or missing content in the documentation.
Run the following script to verify the notebook file paths:
Verification successful
This script will list all .ipynb files in the 'nb' directory, show the list from the documentation, and then compare the two lists. If there are any differences, they will be displayed by the
diffcommand.
Notebook file paths and names verified successfully
The verification process has confirmed that all notebook files mentioned in the table of contents exist in the 'nb' directory, and there are no additional notebooks that are not listed in the documentation. The paths and names in the documentation accurately reflect the actual files in the repository.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the notebook files referenced in the table of contents exist. # Test: Check if each notebook file exists. Expect: All files to be found. notebooks=( "nb/00_Setup.ipynb" "nb/01_table.ipynb" "nb/02_Geo_visualization_example.ipynb" "nb/03_find.ipynb" "nb/04_jobs.ipynb" "nb/05_presentation.ipynb" ) for notebook in "${notebooks[@]}"; do if [ ! -f "$notebook" ]; then echo "Notebook file not found: $notebook" exit 1 fi done echo "All notebook files exist."Length of output: 670
Script:
#!/bin/bash # Description: List all .ipynb files in the 'nb' directory and compare with the documented list # List all .ipynb files in the 'nb' directory echo "Notebooks found in the 'nb' directory:" find nb -name "*.ipynb" | sort echo -e "\nNotebooks listed in the documentation:" cat << EOF nb/00_Setup.ipynb nb/01_table.ipynb nb/02_Geo_visualization_example.ipynb nb/03_find.ipynb nb/04_jobs.ipynb nb/05_presentation.ipynb EOF echo -e "\nComparing the lists:" diff <(find nb -name "*.ipynb" | sort) <(cat << EOF nb/00_Setup.ipynb nb/01_table.ipynb nb/02_Geo_visualization_example.ipynb nb/03_find.ipynb nb/04_jobs.ipynb nb/05_presentation.ipynb EOF )Length of output: 706
docs/source/conf.py (2)
31-31: Excellent addition of thenbsphinxextension!The
nbsphinxextension is a great choice for integrating Jupyter Notebooks into the Sphinx documentation. It allows seamless inclusion and rendering of notebook content within the documentation.
40-40: Good configuration choice fornbsphinx_execute.Setting
nbsphinx_executeto "never" is a wise decision. It ensures that code cells in the notebooks are not executed during the documentation build process. This has several benefits:
- Improved build performance by avoiding unnecessary code execution.
- Eliminates dependencies on the notebook execution environment.
- Ensures consistent documentation generation regardless of potentially variable code.
README.md (1)
198-198: Clarify the prerequisite for building documentation locally.The added text provides clear instructions on the necessity of having
pandocinstalled before running the command to build the documentation locally. It includes a link to the installation instructions and an example command usingcondafor installation.This change improves the clarity and usability of the documentation by explicitly stating the prerequisite.
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Built documentation can be found at https://correlaid.github.io/pystatis/dev/index.html |
* Update dependencies, pre-commit, and add pandoc (instructions) #25 * Update docu creation and deployment workflow for nbsphinx #25 * Update headings for compatibility with nbsphinx/ docu rendering #25 * Incorporate coderabbit suggestions #25 * Update dependencies to fix safety issues for jupyterlab and notebook (not jinja) #25 * Rename notebooks, clean-up headings #25 * Attempt to fix case-sensitivity problem by renaming twice #25 * Attempt to fix case-sensitivity problem by renaming twice #25
Addresses #25
Summary by CodeRabbit
Release Notes
New Features
nbsphinxextension.Documentation
Bug Fixes