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https://github.com/biocypher/project-planning

Demo use case for BioChatter: scheduling of project work

https://github.com/biocypher/project-planning

Science Score: 13.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Demo use case for BioChatter: scheduling of project work

Basic Info
  • Host: GitHub
  • Owner: biocypher
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 70.3 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 11
  • Releases: 0
Created almost 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

GitHub Project Planning

This repo implements a BioCypher pipeline that grabs all issues on a GitHub Projects board that simulates a collaborative team (available here). The pipeline builds a knowledge graph of issues, categories, assigned team members, and annotations on the issues, and then provides access to an LLM assistant that summarises tasks performed in the previous iteration of the project for the group and each individual. Further, the web app provides a planning tab that analyses tasks in next iterations of the project and provides suggestions for task prioritisation and collaboration, again for the group and each individual.

Usage

[!IMPORTANT] The knowledge graph build stage requires a GitHub token to access the GitHub API, BIOCYPHER_GITHUB_PROJECT_TOKEN, in the environment. If you don't have access to this token, the KG build will fail. You can see an online version of the app here.

The docker-compose.yml file contains the necessary services to run the pipeline. To start the pipeline, run:

bash git clone https://github.com/biocypher/project-planning.git cd project-planning docker-compose up -d

The pipeline will build, import, and deploy the knowledge graph, and then start the app service. The KG is available at http://localhost:7474 and the app is available at http://localhost:8051.

This standard pipeline runs a non-password-protected Neo4j instance. To run a password-protected instance (with ports open to the web), run:

bash docker-compose -f docker-compose-password.yml up -d

Authentification settings are configured in the docker-compose-password.yml

Knowledge Graph

The build procedure is orchestrated by BioCypher. The central script is create_knowledge_graph.py, which is responsible for calling the adapter to fetch data from the GitHub API and building the KG. You can run it locally with:

bash poetry install poetry run python create_knowledge_graph.py

Owner

  • Name: biocypher
  • Login: biocypher
  • Kind: organization

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 21
  • Total pull requests: 0
  • Average time to close issues: less than a minute
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.38
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 21
  • Pull requests: 0
  • Average time to close issues: less than a minute
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.38
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • slobentanzer (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/calculate_schedule.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
docker-compose.yml docker
  • docker.io/slobentanzer/biocypher-base 1.1.1
poetry.lock pypi
  • appdirs 1.4.4
  • biocypher 0.5.19
  • certifi 2023.7.22
  • charset-normalizer 3.2.0
  • colorama 0.4.6
  • colorlog 6.7.0
  • idna 3.4
  • isodate 0.6.1
  • more-itertools 10.1.0
  • neo4j 4.4.11
  • neo4j-utils 0.0.7
  • networkx 3.1
  • numpy 1.25.2
  • pandas 2.0.3
  • pyparsing 3.1.1
  • python-dateutil 2.8.2
  • pytz 2023.3
  • pyyaml 6.0.1
  • rdflib 6.3.2
  • requests 2.31.0
  • six 1.16.0
  • stringcase 1.2.0
  • tabulate 0.9.0
  • toml 0.10.2
  • treelib 1.6.4
  • tzdata 2023.3
  • urllib3 2.0.4
pyproject.toml pypi
  • biocypher ^0.5.16
  • python <3.13,>=3.10
  • requests ^2.28.2
  • tabulate ^0.9.0
docker-compose-password.yml docker
  • biocypher/base 1.2.0
  • biocypher/biochatter-light 0.6.10
  • neo4j 4.4-enterprise