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‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: bug
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior.
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Code snippets**
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If applicable, code snippets to reproduce this behavior.
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: enhancement
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context about the feature request here.

‎.github/workflows/run_tests.yml

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# This is a basic workflow to help you get started with Actions
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name: Run tests
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the master branch
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push:
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branches: [ master ]
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pull_request:
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types: [opened, synchronize, reopened]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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types: trigger-run-tests
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "build"
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build:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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name: setup python environment
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with:
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python-version: 3.7
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- name: Install dependencies
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run: |
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pip install -r requirements.txt
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pip install pytest pytest-cov
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- name: Setup Neo4j Docker
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run: |
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docker run --detach --name kgx-neo4j-unit-test -p 8484:7474 -p 8888:7687 --env NEO4J_AUTH=neo4j/test neo4j:3.5.19
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docker run --detach --name kgx-neo4j-integration-test -p 7474:7474 -p 7687:7687 --env NEO4J_AUTH=neo4j/test neo4j:3.5.19
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docker ps -a
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- name: Wait
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uses: jakejarvis/wait-action@master
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with:
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time: '45s'
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- name: Run tests
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run: |
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coverage erase
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pytest --cov=kgx --cov-report xml:coverage.xml tests/*
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coverage combine --append || true
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coverage report
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coverage xml
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- name: SonarCloud Scan
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uses: SonarSource/sonarcloud-github-action@master
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
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SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

‎CHANGELOG.md

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# Changelog
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## 1.0.0b0 - (2021-03-11)
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- Fixed caching bug in RdfSource
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- Fixed bug when setting 'provided_by' for a source
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## 1.0.0a0 - (2021-03-04)
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- Added Source implementation for reading from various data stores
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- Added Sink implementation for writing to various data stores
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- Added a simplified Transformer that is agnostic
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- Refactor KGX to make use of Sources and Sinks
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- Added ability to stream graphs (Thanks to @gregr for the inspiration)
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## 0.5.0 - (2021-02-23)
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- This is the final release on the 0.x.x
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- Added ability to assign a default category in SssomTransformer when the incoming category is invalid
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- Added the ability to generate different types of graph summary reports
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## 0.4.0 - (2021-02-08)
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- Fixed a bug in NtTransformer when parsing malformed triples
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- Added a transformer for parsing SSSOM
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- Added ability to fold predicates to node properties
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- Added ability to unfold node properties to predicates
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- Added ability to remove singleton nodes from a graph
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- Fixed bug in KGX CLI transform operation that prevented stack trace from showing up
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- Unified the way predicates are parsed across different transformers
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- Added ability to annotate edges with OWLStar vocabulary in RdfOwlTransformer
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## 0.3.1 - (2021-01-20)
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- Fixed a bug that led to import errors
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- Fixed column ordering when exporting CSV/TSV
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- Added ability to generate a TRAPI knowledge map for a graph
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- Fixed bug in ObographJsonTransformer when inferring node category
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## 0.3.0 - (2020-12-21)
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- Added Graph API to KGX
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- Added compatibility to Biolink Model 1.4.0
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- Added the ability to facet on node and edge properties for graph-summary CLI operation
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- Fixed a bug where source name defined in YAML was not being used for graph name
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## 0.2.4 - (2020-11-25)
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- Fixed bug when handling empty elements returned from bmt
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- Fixed bug in CLI when setting property types in RdfTransformer
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- Fixed bug when reifying edges on export in RdfTransformer
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## 0.2.3 - (2020-11-04)
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- Updated requirements.txt
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- Added a Dockerfile
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## 0.2.2 - (2020-11-04)
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- Made get_toolkit method configurable
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- Use proper input format when parsing OWL via CLI
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- Switched default parsing format from CSV to TSV
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- Fixed bug with spawning processes when transforming source
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- Fixed parsing of xrefs from from OBOGraph JSON
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## 0.2.1 - (2020-11-04)
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## 0.2.0 - (2020-10-20)
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- Improved clique merge operation and addded support for strict and relaxed mode
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- Fixed a major bug while merging lists during graph merge operation
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- Fixed a bug in neo4j-download CLI
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- Updated the merge and transform YAML format
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- Added support for parsing and exporting jsonlines
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- KGX now assigns UUID for edges that don't have and id
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- Updated documentation
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## 0.1.0 - (2020-09-10)
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- Initial release

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at [email protected]. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq

‎CONTRIBUTING.md

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# Contributing Guidelines
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Welcome contributors! KGX is a open-source project built for addressing the challenges of working knowledge graphs and
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its various serializations. We welcome your suggestions, discussions and contributions to this project.
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## Getting started
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Before you get started please be sure to review the [Contributing Guidelines](CONTRIBUTING.md) and the [Code of Conduct](CODE_OF_CONDUCT.md).
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### Developing
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Take a look at the project's [README.md](README.md) for instructions on setting up a dev environment. We recommend using
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Python `venv` for setting up your virtual environment.
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In addition, you can find the technical documentation at [kgx.readthedocs.io](https://kgx.readthedocs.io/)
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#### Coding Styles
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We try to conform to [PEP-8](https://www.python.org/dev/peps/pep-0008/) style guidelines, but we do not enforce
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them yet. This might changes in the future.
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But we do recommend [NumPy-style docstrings](https://python-sprints.github.io/pandas/guide/pandas_docstring.html)
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for any method you write. This facilitates automated generation of documentation.
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### Testing
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All tests are located in [tests](tests/) folder.
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For running tests, we use `pytest`.
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## Discussion
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If you run into any issues or find certain functionality not documented/explained properly then feel free to
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raise a ticket in the project's [issue tracker](https://github.com/NCATS-Tangerine/kgx/issues).
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There are issue templates to capture certain types of issues.
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## First Time Contributors
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We appreciate your enthusiasm and welcome contributions to this project.
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## How to Submit Changes
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We recommend using GitHub Fork and Pull workflow which involves the following principles,
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### Principle 1: Work from a personal fork
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Prior to adopting the workflow, a developer will perform a one-time setup to create a personal Fork of the repository
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and will subsequently perform their development and testing on a task-specific branch within their forked repository.
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This forked repository will be associated with that developer's GitHub account, and is distinct from the main (upstream)
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repository.
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### Principle 2: Commit to personal branches of that fork
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Changes will never be committed directly to the master branch on the main repository. Rather, they will be composed
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as branches within the developer's forked repository, where the developer can iterate and refine their code prior to
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submitting it for review.
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### Principle 3: Propose changes via pull request of personal branches
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Each set of changes will be developed as a task-specific branch in the developer's forked repository, and then a pull
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request will be created to develop and propose changes to the shared repository. This mechanism provides a way for
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developers to discuss, revise and ultimately merge changes from the forked repository into the main repository.
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### Principle 4: Delete or ignore stale branches, but don't recycle merged ones
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Once a pull request has been merged, the task-specific branch is no longer needed and may be deleted or ignored.
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It is bad practice to reuse an existing branch once it has been merged. Instead, a subsequent branch and pull-request
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cycle should begin when a developer switches to a different coding task.
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You may create a pull request in order to get feedback, but if you wish to continue working on the branch,
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so state with "DO NOT MERGE YET" in the PR title OR mark the pull request as a Draft OR label the pull request
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with a 'Do Not Merge' label.
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## How to Report a Bug
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We recommend making a new ticket for each bug that you encounter while working with KGX. Please be sure to provide
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sufficient context for a bug you are reporting. There are [Issue Templates](https://github.com/NCATS-Tangerine/kgx/issues/new/choose)
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that you can use as a starting point.
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## How to Request an Enhancement
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We welcome request for enhancements and you can make these requestes via the issue tracker. Please be sure to provide
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sufficient context to what the enhancement is trying to address, its utility, and how it's likely to be useful to you
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and the broader community.
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## Core Developer Guidelines
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Core developers should follow these rules when processing pull requests:
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- All PRs should originate from a fork
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- Always wait for tests to pass before merging PRs
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- Use "Squash and merge" to merge PRs
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‎LICENSE

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Copyright (c) 2019, Biomedical Data Translator Consortium
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of
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its contributors may be used to endorse or promote products
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derived from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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