{"id":35317686,"url":"https://github.com/pepkit/pephubclient","last_synced_at":"2026-04-01T23:01:49.878Z","repository":{"id":69876966,"uuid":"511972031","full_name":"pepkit/pephubclient","owner":"pepkit","description":"A tool to provide Python and CLI interface and Python API for PEPhub.","archived":false,"fork":false,"pushed_at":"2026-03-18T18:47:09.000Z","size":353,"stargazers_count":3,"open_issues_count":10,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-03-28T00:42:39.796Z","etag":null,"topics":["bioinformatics","command-line-tool","project","python"],"latest_commit_sha":null,"homepage":"https://pephub.databio.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pepkit.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-07-08T17:16:40.000Z","updated_at":"2026-03-18T18:51:58.000Z","dependencies_parsed_at":"2023-02-28T23:00:20.827Z","dependency_job_id":"c86f8ac9-3e00-4c31-9e10-98692e152997","html_url":"https://github.com/pepkit/pephubclient","commit_stats":null,"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"purl":"pkg:github/pepkit/pephubclient","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pepkit%2Fpephubclient","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pepkit%2Fpephubclient/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pepkit%2Fpephubclient/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pepkit%2Fpephubclient/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pepkit","download_url":"https://codeload.github.com/pepkit/pephubclient/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pepkit%2Fpephubclient/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31292782,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-01T21:15:39.731Z","status":"ssl_error","status_checked_at":"2026-04-01T21:15:34.046Z","response_time":53,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","command-line-tool","project","python"],"created_at":"2025-12-30T18:43:12.180Z","updated_at":"2026-04-01T23:01:49.871Z","avatar_url":"https://github.com/pepkit.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1 align=\"center\"\u003ePEPHubClient\u003c/h1\u003e\n\n[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)\n![Run pytests](https://github.com/pepkit/pephubclient/workflows/Run%20pytests/badge.svg)\n[![pypi-badge](https://img.shields.io/pypi/v/pephubclient?color=%2334D058)](https://pypi.org/project/pephubclient)\n[![pypi-version](https://img.shields.io/pypi/pyversions/pephubclient.svg?color=%2334D058)](https://pypi.org/project/pephubclient)\n[![Coverage](https://coverage-badge.samuelcolvin.workers.dev/pepkit/pephubclient.svg)](https://coverage-badge.samuelcolvin.workers.dev/redirect/pepkit/pephubclient)\n[![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/pepkit/pephubclient)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n\n\n`PEPHubClient` is a tool to provide Python API and CLI for [PEPhub](https://pephub.databio.org).\n\n\n---\n\n**Documentation**: \u003ca href=\"https://pep.databio.org/\" target=\"_blank\"\u003ehttps://pep.databio.org\u003c/a\u003e\n\n**Source Code**: \u003ca href=\"https://github.com/pepkit/pephubclient\" target=\"_blank\"\u003ehttps://github.com/pepkit/pephubclient\u003c/a\u003e\n\n---\n\n## Installation\nTo install `pepdbagent` use this command: \n```\npip install pephubclient\n```\nor install the latest version from the GitHub repository:\n```\npip install git+https://github.com/pepkit/pephubclient.git\n```\n\n---\n\n### `pephubclient` features: \n1) `push` (upload) projects)\n2) `pull` (download projects)\n\nAdditionally, our client supports pephub authorization.\nThe authorization process is based on pephub device authorization protocol.\nTo upload projects or to download private projects, user must be authorized through pephub.\n\nIf you want to use your own pephub instance, you can specify it by setting `PEPHUB_BASE_URL` environment variable.\ne.g. `export PEPHUB_BASE_URL=https://pephub.databio.org/` (This is original pephub instance)\n\nTo login, use the `login` argument; to logout, use `logout`.\n\n----\n```text\n$ phc --help\n                                                                                                                   \n Usage: pephubclient [OPTIONS] COMMAND [ARGS]...                                                                   \n                                                                                                                   \n╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮\n│ --version             -v                                                                                        │\n│ --install-completion            Install completion for the current shell.                                       │\n│ --show-completion               Show completion for the current shell, to copy it or customize the              │\n│                                 installation.                                                                   │\n│ --help                          Show this message and exit.                                                     │\n╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯\n╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────╮\n│ login               Login to PEPhub                                                                             │\n│ logout              Logout                                                                                      │\n│ pull                Download and save project locally.                                                          │\n│ push                Upload/update project in PEPhub                                                             │\n╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯\n```\n\n```text\n$ phc pull --help\n                                                                                                                   \n Usage: pephubclient pull [OPTIONS] PROJECT_REGISTRY_PATH                                                          \n                                                                                                                   \n Download and save project locally.                                                                                \n                                                                                                                   \n╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮\n│ *    project_registry_path      TEXT  [default: None] [required]                                                │\n╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯\n╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮\n│ --force    --no-force      Overwrite project if it exists. [default: no-force]                                  │\n│ --help                     Show this message and exit.                                                          │\n╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯\n```\n\n```text\n$ phc push --help\n                                                                                                                   \n Usage: pephubclient push [OPTIONS] CFG                                                                            \n                                                                                                                   \n Upload/update project in PEPhub                                                                                   \n                                                                                                                   \n╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮\n│ *    cfg      TEXT  Project config file (YAML) or sample table (CSV/TSV)with one row per sample to constitute   │\n│                     project                                                                                     │\n│                     [default: None]                                                                             │\n│                     [required]                                                                                  │\n╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯\n╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮\n│ *  --namespace                        TEXT  Project namespace [default: None] [required]                        │\n│ *  --name                             TEXT  Project name [default: None] [required]                             │\n│    --tag                              TEXT  Project tag [default: None]                                         │\n│    --force         --no-force               Force push to the database. Use it to update, or upload project.    │\n│                                             [default: no-force]                                                 │\n│    --is-private    --no-is-private          Upload project as private. [default: no-is-private]                 │\n│    --help                                   Show this message and exit.                                         │\n╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯\n\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpepkit%2Fpephubclient","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpepkit%2Fpephubclient","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpepkit%2Fpephubclient/lists"}