{"id":18524268,"url":"https://github.com/mdanalysis/pmda","last_synced_at":"2025-04-12T23:08:01.877Z","repository":{"id":57453723,"uuid":"106346721","full_name":"MDAnalysis/pmda","owner":"MDAnalysis","description":"Parallel algorithms for MDAnalysis","archived":false,"fork":false,"pushed_at":"2024-08-02T17:48:40.000Z","size":7033,"stargazers_count":31,"open_issues_count":37,"forks_count":23,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-04-12T23:07:56.504Z","etag":null,"topics":["analysis","dask","mdanalysis","molecular-dynamics","parallel"],"latest_commit_sha":null,"homepage":"https://www.mdanalysis.org/pmda/","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/MDAnalysis.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG","contributing":".github/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":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-09T23:46:26.000Z","updated_at":"2024-12-24T13:07:21.000Z","dependencies_parsed_at":"2024-11-10T22:21:11.683Z","dependency_job_id":"c2438ce9-ae0e-450c-8eba-478d6adbfad4","html_url":"https://github.com/MDAnalysis/pmda","commit_stats":{"total_commits":201,"total_committers":11,"mean_commits":"18.272727272727273","dds":0.5671641791044777,"last_synced_commit":"e6ac508338b1e6513eab15eadc37e3ec5356cb17"},"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpmda","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpmda/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpmda/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpmda/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/pmda/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248643004,"owners_count":21138355,"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":["analysis","dask","mdanalysis","molecular-dynamics","parallel"],"created_at":"2024-11-06T17:40:20.939Z","updated_at":"2025-04-12T23:08:01.845Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"==============================================\n  PMDA - Parallel Molecular Dynamics Analysis\n==============================================\n\n|build| |cov| |PRwelcome| |zenodo| |conda|\n\nReady to use analysis and buildings blocks to write parallel analysis algorithms\nusing MDAnalysis_ with dask_.\n\n.. warning::\n   This project is **alpha software** and not API stable. It will and\n   should rapidly evolve to test different approaches to implementing\n   parallel analysis in a seamless and intuitive fashion.\n\n\nFor example, run a rmsd analysis on all available cores:\n\n.. code:: python\n\n   import MDAnalysis as mda\n   from pmda import rms\n\n   u = mda.Universe(top, traj)\n   ref = mda.Universe(top, traj)\n\n   rmsd_ana = rms.RMSD(u.atoms, ref.atoms).run(n_jobs=-1)\n\n   print(rmsd_ana.rmsd)\n\n\nBy default PMDA use the multiprocessing scheduler of dask_. This is sufficient\nif you want to run your simulation on a single machine. If your analysis takes\na very long time (\u003e30 min) you can also spread it to several nodes using the\ndistributed_ scheduler. To do this you can pass a ``scheduler`` keyword\nargument to the ``run`` method.\n\nTo write your own parallel algorithms you can subclass the\n``pmda.parallel.ParallelAnalysisBase`` class.\n\n\nLicense and source code\n=======================\n\nPMDA is released under the `GNU General Public License, version 2`_ (see the\nfiles AUTHORS and LICENSE for details).\n\nSource code is available in the public GitHub repository\nhttps://github.com/MDAnalysis/pmda/.\n\n       \nInstallation\n============\n\nInstall a release with ``pip``\n------------------------------\n\nThe latest release is available from https://pypi.org/project/pmda/\nand can be installed with pip_\n\n.. code-block:: sh\n\n   pip install --upgrade pmda\n\t\t\n\n   \nDevelopment version from source\n-------------------------------\n\nTo install the latest development version from source, run\n\n.. code-block:: sh\n\n  git clone git@github.com:MDAnalysis/pmda.git\n  cd pmda\n  python setup.py install\n\n \nGetting help\n============\n\n*Help* is also available through the *MDAnalysis mailing list*\n\n     https://groups.google.com/group/mdnalysis-discussion\n\nPlease report *bugs and feature requests* for PMDA through the `Issue\nTracker`_.\n\n\n\nContributing\n============\n\nPMDA welcomes new contributions. Please drop by the `MDAnalysis developer\nmailing list`_ to discuss and ask questions.\n\nTo contribute code, submit a *pull request* against the master branch in the\n`PMDA repository`_.\n\n\nCitation\n========\n\nIf you use PMDA in published work please cite [Fan2019]_.\n\n.. [Fan2019] Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers,\n\t     Michael Gecht, and Oliver Beckstein. PMDA --- Parallel Molecular Dynamics\n\t     Analysis. In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe,\n\t     editors, Proceedings of the 18th Python in Science Conference,\n\t     pages 134-142, Austin, TX, 2019.\n\t     doi: `10.25080/Majora-7ddc1dd1-013`_\t     \n\n.. _MDAnalysis: https://www.mdanalysis.org\n.. _dask: https://dask.pydata.org/en/latest/\n.. _distributed: https://distributed.readthedocs.io/\n.. _`Issue tracker`: https://github.com/MDAnalysis/pmda/issues\n.. _`PMDA repository`: https://github.com/MDAnalysis/pmda/\n.. _pip: https://pip.pypa.io/en/stable/\n.. _`GNU General Public License, version 2`:\n   https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html\n.. _`MDAnalysis developer mailing list`:\n   https://groups.google.com/group/mdnalysis-devel\n.. _`10.25080/Majora-7ddc1dd1-013`:\n   https://doi.org/10.25080/Majora-7ddc1dd1-013\n   \n.. |build| image:: https://travis-ci.org/MDAnalysis/pmda.svg?branch=master\n    :alt: Build Status\n    :target: https://travis-ci.org/MDAnalysis/pmda\n\n.. |cov| image:: https://codecov.io/gh/MDAnalysis/pmda/branch/master/graph/badge.svg\n   :alt: Coverage\n   :target: https://codecov.io/gh/MDAnalysis/pmda\n\n.. |zenodo| image:: https://zenodo.org/badge/106346721.svg\n   :alt: DOI\n   :target: https://zenodo.org/badge/latestdoi/106346721\n\n.. |conda| image:: https://anaconda.org/conda-forge/pmda/badges/version.svg\n   :alt: conda release\n   :target: https://anaconda.org/conda-forge/pmda\n\n.. |PRwelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square\n   :alt: PRs welcome\n   :target: http://makeapullrequest.com\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fpmda","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fpmda","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fpmda/lists"}