{"id":19448573,"url":"https://github.com/neurodata/pcc","last_synced_at":"2026-06-13T03:04:43.798Z","repository":{"id":140563241,"uuid":"505533690","full_name":"neurodata/pcc","owner":"neurodata","description":"On the power of comparative connectomics","archived":false,"fork":false,"pushed_at":"2023-06-02T14:20:19.000Z","size":32241,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-02-25T08:54:13.153Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/neurodata.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-06-20T17:20:12.000Z","updated_at":"2022-06-21T13:43:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"ffaf3ac8-6b5e-4168-9acf-740aba7c99b0","html_url":"https://github.com/neurodata/pcc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/neurodata/pcc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fpcc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fpcc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fpcc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fpcc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/neurodata","download_url":"https://codeload.github.com/neurodata/pcc/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurodata%2Fpcc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34270418,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-13T02:00:06.617Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-10T16:27:41.326Z","updated_at":"2026-06-13T03:04:43.777Z","avatar_url":"https://github.com/neurodata.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PCC\n\n[![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](http://docs.neurodata.io/pcc/)\n\n## Abstract \n*Coming soon*\n\n## Repo structure \n- ``.github``: Files specifying how the repo behaves on GitHub.\n- ``data``: Directory to store the raw data. \n- ``docs``: Files to build the documentation website (in the form of a [Jupyter Book](https://jupyterbook.org/intro.html)), talks, and posters.\n- ``overleaf``: Link to an Overleaf document as a git submodule.\n- ``pkg``: A local Python package used for analysis in the Jupyter Notebooks/Python scripts.\n- ``results``: Place to store intermediate outputs, figures, and saved variables. \n- ``sandbox``: Junk scripts not part of the final paper/project.\n- ``scripts``: Python scripts used to do all analyses\n- ``shell``: Shell scripts used to run the entire project, copy results, etc.\n\n## Guide to using the repository\n### Getting the code and setting up an environment\nPrerequisites: `git`, working knowledge of Python and command line tools.\n\n#### Using Poetry\nI recommend using [Poetry](https://python-poetry.org/) to create and manage a \nreproducible environment for running the code for this project. \n- If you don't have it already, [install Poetry](https://python-poetry.org/docs/#installation) following their linked instructions.\n- Navigate to a directory where you want to store the project, and clone this repo: \n   ```\n   git clone https://github.com/neurodata/pcc\n   ```\n- (TEMPORARY) Clone the sister repository, `giskard`:\n  ```\n  git clone https://github.com/bdpedigo/giskard.git\n  ```\n  - Note: once the code is stable, this will be replaced by an install from PyPI\n- Enter the newly cloned directory:\n  ```\n  cd pcc\n  ```\n- Create a Poetry environment:\n  - Note: this requires that you have a Python 3.9 installation on your machine. It is\n    possible that the code for this project will run with other versions of Python,\n    but I haven't tested it. To check if you have Python 3.9, you can do: \n    ```\n    which python3.9\n    ```\n    If the result says `python3.9 not found` then you'll need to get a 3.9 interpreter\n    on your machine. Common ways to install an interpreter are via\n    [python.org](https://www.python.org/downloads/), [brew](https://docs.brew.sh/Homebrew-and-Python), or \n    [conda](https://anaconda.org/anaconda/python).\n  - After you have ensured you have a Python 3.9 installation, do:\n    ```\n    poetry env use python3.9\n    ```\n  - For me, the output looks like\n     ```\n    Creating virtualenv pcc in /Users/bpedigo/bilateral-test/pcc/.venv\n    Using virtualenv: /Users/bpedigo/bilateral-test/pcc/.venv\n    ```\n  \n- To activate the new environment, do \n  ```\n  source .venv/bin/activate\n  ```\n  - If you need to deactivate this environment, just type `deactivate`\n\n#### Using `pip`\n*Coming soon*\n\n### Getting the data \n*Coming soon*\n\n### Running the code\n- Make sure your virtual environment from the last section is active.\n- Now you should be able to run any individual python files like normal, for example: \n  ```\n  python ./pcc/scripts/er_unmatched_test.py\n  ```\n- Instead of running as a Python file, you can also easily convert a Python file to a\n  notebook, execute it, and have it included in the documentation folder for rendering\n  as a Jupyter Book. To do so, use the `make_notebook.sh` script and pass in the name of \n  the python file (without the `.py` file extension):\n  ```\n  sh ./pcc/shell/make_notebook er_unmatched_test\n  ```\n  If you'd like to build that individual notebook and then rebuild the documentation,\n  just add the `-b` argument to the same script:\n  ```\n  sh ./pcc/shell/make_notebook -b er_unmatched_test\n  ```\n- You can also build and run all notebooks which are essential to the final paper via\n  the `make_project.sh` script: \n  ```\n  sh ./pcc/shell/make_project.sh\n  ```\n\n### Building the documentation Jupyter Book\nThe notebooks associated with this project are assembled into a\n[Jupyter Book](https://jupyterbook.org/). \n- To build the documentation, do:\n  ```\n  jb build ./pcc/docs\n  ```\n- You can then view the locally built HTML by pasting the produced link into your\n  browser. For me, the built index is stored at `./pcc/docs/_build/html/index.html`\n\n\n## Questions about the code or paper \nPlease get in touch! You are welcome to [make an issue](https://github.com/neurodata/pcc/issues/new)\nor email me at bpedigo@jhu.edu.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurodata%2Fpcc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneurodata%2Fpcc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurodata%2Fpcc/lists"}