[pull] master from ericmjl:master #1
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optimize the git clone using --depth flag in term of size of clone and also in term's of time taken to fetch the files and commit history of whole repository . More detail can be found at blog https://www.atlassian.com/git/tutorials/big-repositories Signed-off-by: Pratik Raj <[email protected]>
* Update pandas from 1.0.3 to 1.0.4 * Update numpy from 1.18.4 to 1.18.5 * Update tqdm from 4.46.0 to 4.46.1
* Update matplotlib from 3.2.1 to 3.2.2 * Update pandas from 1.0.4 to 1.0.5 * Update numpy from 1.18.5 to 1.19.0 * Update scipy from 1.4.1 to 1.5.0
* Update numpy from 1.15.3 to 1.15.4 Former-commit-id: afdbd7516dadb529191f8f72e653df42f5b9f710 * Update matplotlib from 3.0.1 to 3.0.2 * Update matplotlib from 3.0.1 to 3.0.2 Former-commit-id: 945d24135d9dc168dbd9d57d79e9f5e274d9862c * Added link to DataCamp course * Added link to DataCamp course Former-commit-id: 7dbcc2e017892a76077dd743d2ebad52c965d4af * Update nxviz from 0.5.0 to 0.6.0 * Update nxviz from 0.5.0 to 0.6.0 Former-commit-id: dbfc8f79de4085a9920744055ae3cf13ef9c17b1 * Update scipy from 1.1.0 to 1.2.0 * Update scipy from 1.1.0 to 1.2.0 Former-commit-id: d2901678efd102004b28c1f47297904a5c1053f3 * Update python-louvain from 0.11 to 0.13 * Update python-louvain from 0.11 to 0.13 Former-commit-id: 7ccd135189168155147f33161122ade916b57314 * Update tqdm from 4.28.1 to 4.29.0 * Update tqdm from 4.28.1 to 4.29.0 Former-commit-id: fea877262946430bf2f927ec4421166bd8d7629f * Update numpy from 1.15.4 to 1.16.0 * Update numpy from 1.15.4 to 1.16.0 Former-commit-id: 5c0268db9f4dcb7d3c895afa537a1d60ae38a211 * Update tqdm from 4.29.0 to 4.29.1 * Update tqdm from 4.29.0 to 4.29.1 Former-commit-id: 0cf5143e3b7e2d3d658593249660841633e55b31 * Update pandas from 0.23.4 to 0.24.0 * Update pandas from 0.23.4 to 0.24.0 Former-commit-id: 578ae3ec5c74e28833035d715810cf3addb66d39 * Update tqdm from 4.29.1 to 4.30.0 * Update tqdm from 4.29.1 to 4.30.0 Former-commit-id: 408c49d7cc389d3f4b42667ecae452454dc7b9ae * Update pandas from 0.24.0 to 0.24.1 * Update pandas from 0.24.0 to 0.24.1 Former-commit-id: b616e16ca71febdb8b382357c09d549a69b587bc * Update numpy from 1.16.0 to 1.16.1 * Update numpy from 1.16.0 to 1.16.1 Former-commit-id: d1228f64ad94a6c21b97c4a06c39e598f216449f * Update scipy from 1.2.0 to 1.2.1 * Update scipy from 1.2.0 to 1.2.1 Former-commit-id: e140df9b9df001d91e1e0e2c179181b0f185225d * Update tqdm from 4.30.0 to 4.31.1 * Update tqdm from 4.30.0 to 4.31.1 Former-commit-id: e9448355422122ecefff7b540563a8cea7ed20ea * Update matplotlib from 3.0.2 to 3.0.3 * Update matplotlib from 3.0.2 to 3.0.3 Former-commit-id: c7364c46e469a333d64c4c6bed498305fd75fdb8 * Update numpy from 1.16.1 to 1.16.2 * Update numpy from 1.16.1 to 1.16.2 Former-commit-id: 9921b3940869fbec98df6875fcd17c94a1d54edc * Update pandas from 0.24.1 to 0.24.2 * Update pandas from 0.24.1 to 0.24.2 Former-commit-id: 4fd0212d46f43bd716fc838eff826817257295e5 * Update networkx from 2.2 to 2.3 * Update networkx from 2.2 to 2.3 Former-commit-id: bd01d180b955c3437d97effee6c323bc03ca890c * Update nxviz from 0.6.0 to 0.6.1 * Update nxviz from 0.6.0 to 0.6.1 Former-commit-id: 8582326fbb92a96162a153905f5b95e22bb4cef6 * Update numpy from 1.16.2 to 1.16.3 * Update numpy from 1.16.2 to 1.16.3 Former-commit-id: 8d486146fb4ef5572b61ba6f227ef8c6f132b371 * Update matplotlib from 3.0.3 to 3.1.0 * Update matplotlib from 3.0.3 to 3.1.0 Former-commit-id: 8755090b30d4b28a43bcd0c001366dda224c3023 * Update scipy from 1.2.1 to 1.3.0 * Update scipy from 1.2.1 to 1.3.0 Former-commit-id: 7e86377f68e88361588622164de07de35d15ec18 * Update tqdm from 4.31.1 to 4.32.1 * Update tqdm from 4.31.1 to 4.32.1 Former-commit-id: cdc8856d52a657fe8279ad885f06a2beb323b227 * Update numpy from 1.16.3 to 1.16.4 * Update numpy from 1.16.3 to 1.16.4 Former-commit-id: 6ad31740e4cf9ff1d0373c0e289ed57d8af1e5fa * Update tqdm from 4.32.1 to 4.32.2 * Update tqdm from 4.32.1 to 4.32.2 Former-commit-id: f41370384743d84976ab4e36bf737b707ce7fb53 * add ffmpeg to env spec * add ffmpeg to env spec Former-commit-id: 7364f0514109402bb7f4bd87041d4d0f57a3b5e7 * Update matplotlib from 3.1.0 to 3.1.1 * Update matplotlib from 3.1.0 to 3.1.1 Former-commit-id: 4da6add03eb96c72faf7016e51154ce234f17652 * Update pandas from 0.24.2 to 0.25.0 * Update pandas from 0.24.2 to 0.25.0 Former-commit-id: ed65351257a790f22f8a8b5055ee004b11ecb878 * Update numpy from 1.16.4 to 1.17.0 * Update numpy from 1.16.4 to 1.17.0 Former-commit-id: dd31704b753578c763e04715112a5d8f688a1676 * Update pandas from 0.25.0 to 0.25.1 * Update pandas from 0.25.0 to 0.25.1 Former-commit-id: 4e71b7c8631a47f28dca7021ae29cb8cbcdbb7d6 * Update scipy from 1.3.0 to 1.3.1 * Update scipy from 1.3.0 to 1.3.1 Former-commit-id: fa838d58cb766361468d8904ee44b6b880382e96 * Update tqdm from 4.32.2 to 4.35.0 * Update tqdm from 4.32.2 to 4.35.0 Former-commit-id: 9e06be8d617400611b165b22c94bdf98c1585281 * Update numpy from 1.17.0 to 1.17.1 * Update numpy from 1.17.0 to 1.17.1 Former-commit-id: 27090871dce3d379289d5dcbe2f8065429218ad3 * Update numpy from 1.17.1 to 1.17.2 * Update numpy from 1.17.1 to 1.17.2 Former-commit-id: 778399db274598ae278fb7e8552d74d18d10dc82 * Networkx v2 (#133) * Add nbstripout * update to networkx v2 API * install ffmpeg from native ubuntu repo * comment out xvfb * change python to 3.8 * switch to py37 * manual listing of notebooks to execute * Networkx v2 (#133) * Add nbstripout * update to networkx v2 API * install ffmpeg from native ubuntu repo * comment out xvfb * change python to 3.8 * switch to py37 * manual listing of notebooks to execute Former-commit-id: 25d84cf4c06d9a1a020af53e2e9c2a44e2b4905c * Moved notebooks into notebooks directory * Moved notebooks into notebooks directory Former-commit-id: 91c3c5f41c4b7731809d284c9a40a1d495a25ce9 * Add @MridulS to copyright * Add @MridulS to copyright Former-commit-id: 7030d8d2e268c68e034b85b76bdd88d2057de06a * Add jupyter-book to environment spec * Add jupyter-book to environment spec Former-commit-id: 69b5484f9ae4272f84a4eb2a4b521a17abfb5d12 * mkdocs first commit * mkdocs first commit Former-commit-id: ae0ea364fe28845a22e1d65bd30ad04c5159fddd * Sneaking in Python gitignore * Sneaking in Python gitignore Former-commit-id: 01e8e31413cd05ed09bd2d00238113d9fcb2e588 * committing data before moving to another computer * committing data before moving to another computer Former-commit-id: 20a91bf69b0a50b7ce023cdd5302926915ac6198 * finished chapter 1 * finished chapter 1 Former-commit-id: 3211f2a7d2453e5f7fc4d2fb948c65f11ae39c48 * added static site pieces * ran bfg cleaner * took out comment line in .buildpacks * Trigger commit for Dokku * fixed config file name * Switching over to Dockerfile-based deploy * fixed copy error * Added command to activate bash * add dockerignore * Add command to source bashrc * change source cmd * change conda activate to . activate * add diagnostic which conda * modify dockerfile * manually configure path * fixed docker install command' * Add entrypoint for Docker container * Add headers for feedback and supporting * restricted initial setup * removed custom source from environment spec file * fixed Dockerfile * ignoring ipynb_checkpoints * commit to move to different computer * midway commit on hubs chapter * finished up degree centrality * finished hubs (degree centrality) notebook * Added style guide * Add style guide * removed 1st level heading * Moved exercises solution info to correct place Was in "exercises" section, should instead be in "solutions" section. * starting pre-commit * Finished chapter on paths * finished chapter on paths * Fixed missing import in paths notebook. * Finished chapter 6 * Docs for structures * Added docstrings to structures.py - Sneaking in black and isort fix on paths.py * Added docstrings to all paths.py functions * Docstrings added to each of the chapter solutions. * Added mkdocstrings to environment spec * Added solutions API docs This is a pretty neat hack! Use functions to house the answers and then expose them all at once in an API docs page. * Added special CSS for API docs * Upgraded docs with API docs for solutions * Added docstrings to all hubs solutions. * Found out that mkdocstrings borks mknotebooks * started graph io notebook * made output HTML also use overflow * Updated with admonition * added chapter on testing * Add page to learn more stuff * whitespace changes * switching to other computer * Updated "learn more" * Minor phrasing change to index * Commented out advanced topics until it is made * Added comments on first PDF compilation attempt * Finished prototype of PDF compiler Still left to do: - Separate out chapters such that they start on new pages. * configured mkdocs to execute notebooks * added hypothes.is * Finished PDF builder prototype * Adding more chapters in * add NB7 and 8 to mkdocs (#140) h/t @MridulS! * Updated gitignore * Changed port for Makefile * Finished up to 2nd exercise of bipartite notebook * EOD commit 6 May 2020 * Finished bipartite first draft * Update devdocs with render_html function * Added a render_html convenience function * Switched to using render_html * Switched to using render_html for answers to questions * Switched to using render_html for answers to questions * Finished linear algebra draft * Got rid of top level header * Fixed up linear algebra chapter * Started drafting statistical inference on graphs section * Changed bipartite graph figure to matplotlib-generated one. * Changed links to inline ones * Added figure generation code * Finished more prototyping - Page breaks recognized! Amazing! - Reconfigured book content. It's time to put this one into action in the Dockerfile. * Add dev container specification * Add updated stats notebook * Add content to chapter on GOT case study (#146) * initial work on GoT * GOT finsh up * fix for docs build * strip nboutput * add load_data method for GOT data * update dataset * More stats content * Minor update * Finished stats notebook * Add preface * Building Markua collection of files * Adding in test manuscript for leanpub * Removed python script * Testing travis deploy * Deploying whole repo * Now inserting top level markdown header * Trying alternative output directory * Trying a different build structure * Add tabulate to environment * fixed latex output for LFM * Fixed inline LaTeX to LFM LaTeX * Converting pandas head() to to_markdown() * Fixed up images LFM compatibility * preprocessing markdown tables * swap image with new custom image instead of using the one from the article * Fixed issue with long outputs * I think I got markdown tables working finally * set logging level to INFO * Getting rid of more HTML * Getting rid of more HTML * restored cell content * more fixes * Added a few more automated validations * Fixed final table output * Add deploy to main branch * Move Dockerfile into scripts * Changed README * Update index page * moved notebooks into archive * moved tutorial proposals to archive * Moved images to archive * Removed nbstripout commands from Makefile * previewing deploy on jupyterbook branch * Targeting deploys from main branch rather than jupyterbook branch Co-authored-by: pyup-bot <[email protected]> Co-authored-by: Mridul Seth <[email protected]> Co-authored-by: Mridul Seth <[email protected]> Co-authored-by: Mridul Seth <[email protected]>
* first go through for airport notebook * fix load_data link * Use markdown to show notebook execution errors. Make Travis happy
* Fix graphs introduction * Fix goals * Update Makefile with nams custom installation * Add installation instructions for custom package
…nch (#151) * .csv files are needed to propagate changes in datasets to Leanpub branch * correct typo
use markdown for image instead of html tag
add a hackish way to include images on leanpub
make chapters epub friendly
* Update scipy from 1.5.0 to 1.5.1 * Pin mkdocs to latest version 1.1.2 * Pin mkdocs-material to latest version 5.4.0 * Pin pymdown-extensions to latest version 7.1 * Pin mknotebooks to latest version 0.3.6 * Pin ipykernel to latest version 5.3.2
* Update matplotlib from 3.2.2 to 3.3.0 * Update numpy from 1.19 to 1.19.1 * Update numpy from 1.19.0 to 1.19.1 * Update scipy from 1.5.1 to 1.5.2 * Update tqdm from 4.47.0 to 4.48.0 * Update mkdocs-material from 5.4.0 to 5.5.0 * Update ipykernel from 5.3.2 to 5.3.4
* Update pandas from 1.0.5 to 1.1.0 * Update tqdm from 4.48.0 to 4.48.1 * Update mkdocs-material from 5.5.0 to 5.5.2 * Update mknotebooks from 0.3.6 to 0.4.1
* Update matplotlib from 3.3.0 to 3.3.1 * Update networkx from 2.4 to 2.5 * Update pandas from 1.1.0 to 1.1.1 * Update tqdm from 4.48.1 to 4.48.2 * Update mkdocs-material from 5.5.2 to 5.5.8 * Update pymdown-extensions from 7.1 to 8.0
* Provided numerical numberings This should make file browser easier to navigate * Fixed build script * Add auto-push to JupyterCon 2020 repo clone
- Only does this for notebooks - Each notebook's unique binder link is correctly generated to bring a student to a Binder session with that notebook directly
This guarantees that we can use new changes to custom source inside the PRs.
* Built script that adds binder badge to the top of each notebook. - Only does this for notebooks - Each notebook's unique binder link is correctly generated to bring a student to a Binder session with that notebook directly * Configured travis to insert binder links before doing mkdocs build * Ensured that latest version of custom source is installed. This guarantees that we can use new changes to custom source inside the PRs.
- Introduced a new Python notebook focusing on graph structures and algorithms. - Included exercises and solutions for understanding triangles, cliques, and connected components in graphs. - Utilized libraries such as NetworkX and nxviz for graph analysis and visualization.
- Introduced a new Python notebook focusing on graph input/output operations. - Included examples and exercises for handling graph data using NetworkX and pandas. - Provided detailed markdown explanations and code cells for user interaction.
- Introduced a new Python script for practical testing examples. - Included explanations and code snippets for testing invariants, nullity, and boundaries. - Provided guidance on continuous data testing and further reading resources.
- Introduced a new Python notebook for advanced bipartite graph analysis. - Included examples and exercises for understanding bipartite projections and applications. - Utilized libraries such as NetworkX, nxviz, and pandas for graph operations and visualizations.
- Introduced a new notebook focusing on advanced linear algebra topics. - Included examples and exercises on graph theory and matrix operations. - Utilized the Marimo framework for interactive cell-based execution.
- Introduced a new Python script for advanced statistical analysis on graphs. - Included examples and explanations for Erdos-Renyi and Barabasi-Albert graph models. - Provided methods for hypothesis testing and model comparison using Wasserstein distance.
- Introduced a new Python notebook for analyzing Game of Thrones character networks. - Included data loading, network creation, and centrality analysis functionalities. - Added exercises and solutions for community detection and centrality measures.
- Introduced a new Python notebook for analyzing the evolution of the US Airport Network from 1990 to 2015. - Included data loading, network construction, and visualization functionalities. - Added exercises and solutions for exploring network centrality and connectivity.
Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 3 to 6. - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](astral-sh/setup-uv@v3...v6) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
- Introduced a new section titled 'Interesting Papers' to the documentation. - Added a subsection for 'Network Analysis' with a highlighted paper and link.
…equisites notebook for improved clarity and marimo compatibility - Update marimo version from 0.12.2 to 0.14.8 and add script metadata for Python 3.13 and marimo dependency. - Reformat markdown cells for consistent indentation and improved readability. - Refactor the surname search function to use descriptive variable names and move to @app.function for marimo compatibility. - Update test cell to directly use the new function signature and remove unnecessary tuple return.
… from markdown cells for cleaner formatting - Removed the 'r' raw string prefix from all mo.md markdown cells to improve readability and formatting. - Updated the __generated_with version from 0.12.2 to 0.14.8. - No changes to logic or outputs; only markdown formatting was affected.
…or improved readability and output clarity - Dedent all markdown cell content for consistent formatting and easier reading. - Replace direct list slicing of NodeView and EdgeView with print statements to display node and edge samples. - Add and update instructional comments and exercise prompts for clarity. - Hide code in some markdown cells for a cleaner notebook presentation. - Update __generated_with version to 0.14.8.
…tegration in visualization notebook - Update marimo version from 0.13.0 to 0.14.8 for compatibility. - Add hide_code=True to initial app cell for cleaner notebook presentation. - Fix indentation and remove unnecessary r-string markers from markdown cells for better formatting. - Add plt.show() after nx.draw calls to ensure matplotlib figures are displayed. - Remove extra blank lines and trailing whitespace for code cleanliness. - Update markdown content to improve readability and fix minor typos. - Add missing import of plt in relevant cells.
…histogram comparison, and improve exercise structure in hubs notebook - Add matplotlib as a dependency and update marimo version for improved plotting support. - Hide code for introductory and instructional cells to improve notebook readability. - Refactor markdown cells to use dedented triple-quoted strings for better formatting. - Add new interactive exercise cells for ECDF and histogram comparison, including a slider for bin count. - Clarify and expand exercise prompts and solution scaffolding for degree centrality and node order analysis. - Ensure all plotting cells call plt.show() for consistent output in interactive environments. - Improve guidance and structure for user-implemented answers in exercise cells.
…ions, improve structure, and clarify exercises - Update marimo version metadata to 0.14.8. - Add and reorganize markdown cells to clarify the flow of concepts, including node importance, graph traversal, and betweenness centrality. - Improve exercise instructions and add optional/advanced exercise for path visualization. - Refactor markdown for consistency and readability throughout the notebook. - Add comments and minor code clarifications to support new explanations.
… clarity and consistency - Reformat all markdown cells to remove excessive indentation and ensure consistent formatting. - Update markdown headings and blockquotes for better readability. - Add a new discussion question at the end regarding the innovation graph in 2025. - Update some code cells to include plt.show() for plotting functions. - Change nv.circos(G) to nv.arc(G) for graph visualization. - Update dependency comments to include pyprojroot and tqdm. - Bump marimo version in metadata from 0.13.0 to 0.14.9.
…sistent indentation and code style - Updated all markdown cell strings to remove excessive indentation and ensure consistent formatting. - Changed all markdown cell triple-quoted strings to be left-aligned for improved readability and maintainability. - Set hide_code=True for the first app.cell decorator for better notebook presentation. - Bumped __generated_with version from 0.13.0 to 0.14.9.
…proved readability and consistency - Dedent markdown strings in mo.md() calls to remove unnecessary leading whitespace. - Update @app.cell decorators to use hide_code=True for cells that should hide code. - Add missing plt.show() calls after plotting with matplotlib to ensure plots are displayed. - Update __generated_with version from 0.13.0 to 0.14.9. - Add commented dependencies pyprojroot and tqdm to requirements list.
- Add step-by-step quick start guide for installing uv and running notebooks. - Clarify use of the --sandbox flag for isolated environments. - Update website reference for more detailed information.
…notebooks - Replace multiple setup options (Binder, VSCode dev containers, conda, venv) with a single, quick setup guide using uv and marimo. - Provide clear, step-by-step instructions for installing uv, navigating to the notebook directory, and running notebooks with marimo. - Explain the benefits of the new approach, including isolated environments and automatic dependency management. - Remove outdated or redundant setup instructions to reduce confusion and improve onboarding experience.
…th marimo and uv - Create a new notebook file with step-by-step instructions for setting up the environment using uv and marimo. - Explain the purpose of the setup and how the --sandbox flag ensures isolated environments. - Provide clear, beginner-friendly guidance for running notebooks in a reproducible way.
- Introduce 03-goals.py notebook outlining technical and intellectual goals. - List technical takeaways: NetworkX, graph visualization, basic algorithms, and math connections. - Describe intellectual goals: thinking in relationships and developing algorithmic thinking.
…d adjust numbering - Add step to git clone the repository before installing dependencies. - Renumber setup steps to reflect the new order.
…ersion in preface notebook - Update marimo version from 0.9.33 to 0.14.10 in the notebook metadata. - Refactor setup instructions for clarity and step-by-step guidance, including explicit git clone and uv installation steps. - Clarify usage of the --sandbox flag and how to mimic Jupyter behavior in Marimo. - Update function names from __ to _ for consistency and simplicity. - Add script metadata block at the top of the file for dependencies and Python version.
…ebook name - Correct the directory path in the navigation step to point to the actual subdirectory. - Update the notebook run command to use the specific notebook file name instead of a placeholder.
- Replace custom PyPI index configuration with local editable path for 'nams' package in all notebooks. - Update marimo version metadata in 02-networkx-intro.py to 0.14.10. - Add marimo session state file for 02-networkx-intro.py. - Remove extraneous blank lines in some notebook cells for code cleanliness.
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