pydatapipeline

Python Implementation of the FAIR Data Pipeline API

https://github.com/fairdatapipeline/pydatapipeline

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
2 of 8 committers (25.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary

Keywords from Contributors

mesh interactive

Last synced: 6 months ago · JSON representation

Repository

Python Implementation of the FAIR Data Pipeline API

Basic Info

Host: GitHub
Owner: FAIRDataPipeline
License: gpl-3.0
Language: Python
Default Branch: main
Homepage: https://www.fairdatapipeline.org/pyDataPipeline/
Size: 6.15 MB

Statistics

Stars: 6
Watchers: 2
Forks: 1
Open Issues: 8
Releases: 10

Created over 4 years ago · Last pushed 10 months ago

Metadata Files

Readme License Codemeta Zenodo

README.md

pyDataPipeline

Welcome to pyDataPipeline a Python api to interact with the Fair Data Pipeline.

Full documention of the pyDataPipeline is avaialable at https://www.fairdatapipeline.org/pyDataPipeline/

Installation

pyDataPipeline can be installed from PyPi: pip3 install data-pipeline-api

Or from the Repository: ``` git clone https://github.com/FAIRDataPipeline/pythonFDP.git

git checkout dev

pip3 install -e . ``` NB. PyDataPipeline requires Python3.

Example submission_script

Assume FDPCONFIGDIR, storage_locations and objects have been set by CLI tool

``` import os import fairdatapipeline as pipeline

token = os.environ['FDPLOCALTOKEN'] configdir = os.environ['FDPCONFIGDIR'] configpath = os.path.join(configdir, 'config.yaml') scriptpath = os.path.join(config_dir, 'script.sh')

handle = pipeline.initialise(token, configpath, scriptpath)

pipeline.finalise(token, handle)

```

SEIRS Model Example

The SEIRS Model Example is available at: https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html

Owner

Name: FAIR Data Pipeline
Login: FAIRDataPipeline
Kind: organization

Website: https://www.fairdatapipeline.org
Repositories: 22
Profile: https://github.com/FAIRDataPipeline

CodeMeta (codemeta.json)

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  "type": "SoftwareSourceCode",
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        "type": "Organization",
        "name": "University of Glasgow"
      },
      "email": "ryan.field@glasgow.ac.uk",
      "familyName": "Field",
      "givenName": "Ryan"
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    {
      "id": "https://orcid.org/0000-0002-4971-2346",
      "type": "Person",
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        "name": "The University of Sheffield"
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      "familyName": "Reddyhoff",
      "givenName": "Dennis"
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      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "The University of Sheffield"
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        "name": "United Kingdom Atomic Energy Authority"
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      "familyName": "Zarebski",
      "givenName": "Kristian"
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  ],
  "codeRepository": "git+https://github.com/FAIRDataPipeline/pyDataPipeline.git",
  "dateCreated": "2021-06-29",
  "dateModified": "2024-08-05",
  "datePublished": "2021-10-04",
  "description": "Python implementation of the data pipeline API for the FAIR Data Pipeline.",
  "downloadUrl": "https://github.com/FAIRDataPipeline/pyDataPipeline/archive/refs/tags/v0.8.0.tar.gz",
  "identifier": "10.5281/zenodo.5548002",
  "isPartOf": "https://www.fairdatapipeline.org",
  "keywords": [
    "FAIR",
    "Data Pipeline",
    "API"
  ],
  "license": "https://spdx.org/licenses/GPL-3.0-or-later",
  "name": "pyDataPipeline",
  "operatingSystem": [
    "Linux",
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  "programmingLanguage": "Python 3",
  "schema:releaseNotes": "Full change log: https://github.com/FAIRDataPipeline/pyDataPipeline/compare/v0.7.13...v0.8.0",
  "version": "0.8.0",
  "contIntegration": "https://github.com/FAIRDataPipeline/pyDataPipeline/actions",
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  "developmentStatus": "active",
  "issueTracker": "https://github.com/FAIRDataPipeline/pyDataPipeline/issues"
}

GitHub Events

Total

Release event: 1
Watch event: 1
Delete event: 10
Issue comment event: 24
Push event: 16
Pull request event: 18
Create event: 6

Last Year

Release event: 1
Watch event: 1
Delete event: 10
Issue comment event: 24
Push event: 16
Pull request event: 18
Create event: 6

Committers

Last synced: 11 months ago

All Time

Total Commits: 252
Total Committers: 8
Avg Commits per committer: 31.5
Development Distribution Score (DDS): 0.357

Past Year

Commits: 17
Committers: 2
Avg Commits per committer: 8.5
Development Distribution Score (DDS): 0.118

Top Committers

Name	Email	Commits
Ryan J Field	R****d	162
DennisReddyhoff	d**f@s**k	42
bruvio	b**a@p**e	26
dependabot[bot]	4****]	13
bruvio	b**a@p**m	4
Richard Reeve	g**t@r**t	2
Kristian Zarębski	k**i@u**k	2
soniamitchell	s**l@g**k	1

Committer Domains (Top 20 + Academic)

glasgow.ac.uk: 1 ukaea.uk: 1 richardreeve.net: 1 pm.me: 1 sheffield.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 18
Total pull requests: 96
Average time to close issues: 2 months
Average time to close pull requests: 3 months
Total issue authors: 6
Total pull request authors: 7
Average comments per issue: 1.94
Average comments per pull request: 2.49
Merged pull requests: 39
Bot issues: 0
Bot pull requests: 68

Past Year

Issues: 0
Pull requests: 7
Average time to close issues: N/A
Average time to close pull requests: 4 days
Issue authors: 0
Pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 1.29
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 5

View more stats

Top Authors

Issue Authors

DennisReddyhoff (8)
bobturneruk (5)
kzscisoft (2)
richardreeve (1)
bruvio (1)
RyanJField (1)

Pull Request Authors

dependabot[bot] (75)
RyanJField (13)
bruvio (10)
kzscisoft (3)
richardreeve (2)
soniamitchell (1)
bobturneruk (1)

Top Labels

Issue Labels

enhancement (3) help wanted (1) more info needed (1)

Pull Request Labels

dependencies (75) enhancement (6)

Packages

Total packages: 1
Total downloads:
- pypi 34 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 16
Total maintainers: 3

pypi.org: data_pipeline_api

Python api to interact with the Fair Data Pipeline

Homepage: https://www.fairdatapipeline.org/
Documentation: https://data_pipeline_api.readthedocs.io/
License: GNU General Public License v3.0
Latest release: 0.9.0
published over 1 year ago

Versions: 16
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 34 Last month

Rankings

Dependent packages count: 10.5%

Downloads: 25.8%

Average: 31.9%

Dependent repos count: 59.3%

Maintainers (3)

richardreeve ryanjfield bruvio

Last synced: 7 months ago

Dependencies

.github/workflows/gh-pages.yaml actions

actions/checkout v2 composite
actions/checkout master composite
actions/setup-python v2 composite
ad-m/github-push-action master composite
sphinx-notes/pages master composite

.github/workflows/pyDataPipeline.yaml actions

actions/checkout v2 composite
actions/setup-python v2 composite
codecov/codecov-action v2 composite
snok/install-poetry v1 composite

pyproject.toml pypi

Sphinx ^4.3.2 develop
black ^22.1 develop
flake8 ^4.0.1 develop
isort ^5.10.1 develop
mypy ^0.931 develop
poetry ^1.1.6 develop
pre-commit ^2.17.0 develop
pytest ^7.0.0 develop
pytest-cov ^3.0.0 develop
pytest-dependency ^0.5.1 develop
pytest-mock ^3.7.0 develop
sphinx-rtd-theme ^1.0.0 develop
PyYAML ^6.0
h5py ^3.6.0
matplotlib ^3.5.1
python ^3.7.1,<3.11
requests ^2.27.1
scipy ^1.7.3

docs/requirements.txt pypi

sphinx-rtd-theme >=1.0.0

.github/workflows/dependabot.yml actions