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Open Source Science

https://github.com/clinical-genomics/hermes

Communication layer between CG and the pipelines.

https://github.com/clinical-genomics/hermes

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Communication layer between CG and the pipelines.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 11
  • Forks: 0
  • Open Issues: 7
  • Releases: 97
Created over 5 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing Codeowners

README.md

Hermes

Tests codecovCodeFactorCode style: black

Hermes :postal_horn: is a package to handle the communication between workflows and CG.

The name Hermes comes from greek mythology, he was considered to be the messenger between the humans and the gods, feel free to interpret that as you like:). Hermes was moving swiftly between the worlds aided by his winged sandals.

Local Installation

Pypi

pip install cg-hermes

Github

Install poetry

git clone https://github.com/Clinical-Genomics/cg-hermes poetry install

Contributing

Please check out our guide for contributing to Hermes.

Deployment

  1. See DEPLOYMENT.md

Usage

Deliverables

Each workflow specifies its output, or result files, in some way. CG wants to have this input in a certain way to know how to fetch files from housekeeper etc. Hermes is used to convert the deliverables specification from the workflow to the CG format so that CG safely can store the information without parsing different files in different ways.

Also, this is the place where workflow developers can communicate around tags, what to deliver etc without understanding how CG works.

Starting workflows

I think it would be a good idea to have Hermes starting the workflows as well as it is the workflow developers who know this best, following the reasoning above.

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

GitHub Events

Total
  • Create event: 24
  • Release event: 11
  • Issues event: 5
  • Delete event: 11
  • Member event: 1
  • Issue comment event: 32
  • Push event: 61
  • Pull request review comment event: 4
  • Pull request review event: 17
  • Pull request event: 22
Last Year
  • Create event: 24
  • Release event: 11
  • Issues event: 5
  • Delete event: 11
  • Member event: 1
  • Issue comment event: 32
  • Push event: 61
  • Pull request review comment event: 4
  • Pull request review event: 17
  • Pull request event: 22

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 23
  • Total pull requests: 134
  • Average time to close issues: 3 months
  • Average time to close pull requests: 17 days
  • Total issue authors: 12
  • Total pull request authors: 17
  • Average comments per issue: 2.35
  • Average comments per pull request: 1.66
  • Merged pull requests: 110
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 25
  • Average time to close issues: N/A
  • Average time to close pull requests: 12 days
  • Issue authors: 2
  • Pull request authors: 6
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.24
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ivadym (5)
  • henrikstranneheim (4)
  • Mropat (3)
  • ChrOertlin (2)
  • fellen31 (2)
  • jemten (1)
  • raysloks (1)
  • moonso (1)
  • mathiasbio (1)
  • karlnyr (1)
  • ashwini06 (1)
  • mikaell (1)
Pull Request Authors
  • ivadym (30)
  • henrikstranneheim (26)
  • rannick (16)
  • Mropat (15)
  • fevac (10)
  • jemten (6)
  • moonso (5)
  • mathiasbio (4)
  • sofstam (4)
  • hassanfa (4)
  • talnor (3)
  • sylvinite (3)
  • raysloks (3)
  • ChrOertlin (2)
  • islean (1)
Top Labels
Issue Labels
Effort S (4) Urgency M (3) Gain L (3) Urgency S (3) Gain M (2) cancer-in-weekly-production (1) discuss (1) Enhancement (1) Urgency L (1) raredisease (1) Effort M (1) on-hold (1) Gain S (1)
Pull Request Labels
Enhancement (12) security (2)

Dependencies

.github/workflows/build_and_publish.yml actions
  • abatilo/actions-poetry v2.1.6 composite
  • actions/checkout v2.6.0 composite
  • actions/setup-python v4.3.1 composite
.github/workflows/bumpversion.yml actions
  • Clinical-Genomics/bump2version-ci v3 composite
.github/workflows/tests.yml actions
  • abatilo/actions-poetry v2.1.6 composite
  • actions/checkout v2.6.0 composite
  • actions/setup-python v4.3.1 composite
  • codecov/codecov-action v3.1.1 composite
poetry.lock pypi
  • atomicwrites 1.4.0 develop
  • attrs 20.3.0 develop
  • colorama 0.4.4 develop
  • coverage 5.5 develop
  • future 0.18.2 develop
  • importlib-metadata 3.7.3 develop
  • jinja2 2.11.3 develop
  • joblib 1.0.1 develop
  • livereload 2.6.3 develop
  • lunr 0.5.8 develop
  • markdown 3.3.4 develop
  • markupsafe 1.1.1 develop
  • mkdocs 1.1.2 develop
  • more-itertools 8.7.0 develop
  • nltk 3.5 develop
  • packaging 20.9 develop
  • pluggy 0.13.1 develop
  • py 1.10.0 develop
  • pyparsing 2.4.7 develop
  • pytest 5.4.3 develop
  • pytest-cov 2.11.1 develop
  • regex 2021.3.17 develop
  • six 1.15.0 develop
  • tornado 6.1 develop
  • tqdm 4.59.0 develop
  • wcwidth 0.2.5 develop
  • zipp 3.4.1 develop
  • bump2version 1.0.1
  • cgmodels 0.10.3
  • click 7.1.2
  • coloredlogs 14.3
  • humanfriendly 9.1
  • pydantic 1.8.1
  • pyreadline 2.1
  • pyyaml 5.4.1
  • tabulate 0.8.9
  • typer 0.3.2
  • typing-extensions 3.7.4.3
pyproject.toml pypi
  • mkdocs ^1.1.2 develop
  • pytest ^5.2 develop
  • pytest-cov ^2.10.1 develop
  • bump2version ^1.0.1
  • cgmodels ^0.10.3
  • coloredlogs ^14.0
  • pydantic ^1.7.3
  • python ^3.7
  • pyyaml ^5.3.1
  • tabulate ^0.8.7
  • typer ^0.3.2
  • typing-extensions ^3.7.4