{"id":19592896,"url":"https://github.com/soedinglab/csgraph_mod","last_synced_at":"2025-06-21T07:34:38.152Z","repository":{"id":76717885,"uuid":"71791822","full_name":"soedinglab/csgraph_mod","owner":"soedinglab","description":"Modification of the scipy csgraph class to allow tracking of the visited nodes","archived":false,"fork":false,"pushed_at":"2019-08-02T14:16:13.000Z","size":1433,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-01-09T06:51:22.875Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/soedinglab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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":"2016-10-24T13:28:03.000Z","updated_at":"2019-08-02T14:16:15.000Z","dependencies_parsed_at":null,"dependency_job_id":"cea2dcbc-85b5-439f-af5a-47f96f8b67b5","html_url":"https://github.com/soedinglab/csgraph_mod","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fcsgraph_mod","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fcsgraph_mod/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fcsgraph_mod/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fcsgraph_mod/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/soedinglab","download_url":"https://codeload.github.com/soedinglab/csgraph_mod/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240867429,"owners_count":19870405,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":"2024-11-11T08:37:19.428Z","updated_at":"2025-02-26T14:16:07.710Z","avatar_url":"https://github.com/soedinglab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"### `csgraph_mod`\n\nWe have modified the implementation of Dijkstra's algorithm contained in the [csgraph](https://docs.scipy.org/doc/scipy/reference/sparse.csgraph.html) module for compressed sparse graph routines to return a list of visited nodes. We use this package to help us construct a minimal spanning tree between single-cell transcriptomes. For more information about this, please refer to the [MERLoT manuscript](https://www.biorxiv.org/content/early/2018/02/08/261768).\n\n### Installation\n\n`csgraph_mod` can be installed using the `pip` package manager or any `pip`-compatible package manager:\n\n    git clone https://github.com/soedinglab/csgraph_mod.git\n    cd csgraph_mod/\n    pip install .\n\n### Dependencies\n\n`csgraph_mod` was developed and tested in [Python 3.5](https://www.python.org/downloads/release/python-350/) and [3.6](https://www.python.org/downloads/release/python-360/). While older Python 3 versions should work, there is no guarantee that they will. Installation requires:\n\n* [`numpy`](www.numpy.org)\n* [`scipy`](https://www.scipy.org/)\n* [`cython`](http://cython.org/)\n\n### Known problems\n\n#### Missing `numpy` headers\n\nIn some cases (especially on Mac computers), the installer may complain that it cannot find some `numpy` headers:\n\n    fatal error: 'numpy/arrayobject.h' file not found\n\nIn this case, try exporting the headers yourself. Run `export CFLAGS=\"-I \u003cpython_loc\u003e/site-packages/numpy/core/include $CFLAGS\"`, where `\u003cpython_loc\u003e` is the directory where python is installed - something like `/usr/local/lib/python3.6`.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fcsgraph_mod","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsoedinglab%2Fcsgraph_mod","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fcsgraph_mod/lists"}