Add community health files (#218)
Completes the three GitHub Community Standards items the repository was missing: a Code of Conduct, issue templates, and a pull request template. - CODE_OF_CONDUCT.md: Contributor Covenant 2.1, with contact@k-dense.ai as the enforcement contact and a pointer to SECURITY.md for vulnerabilities. - .github/ISSUE_TEMPLATE/: three issue forms (bug report, new skill request, existing skill improvement) plus a config.yml that disables blank issues and routes security reports to private vulnerability reporting. - .github/PULL_REQUEST_TEMPLATE.md: mirrors the Pull Request Checklist in CONTRIBUTING.md so contributors see the skill-format, validation, and safety requirements before submitting. - CONTRIBUTING.md: link the Code of Conduct.
This commit is contained in:
Timothy Kassis
95
.github/ISSUE_TEMPLATE/bug_report.yml
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95
.github/ISSUE_TEMPLATE/bug_report.yml
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@@ -0,0 +1,95 @@
|
||||
name: Bug report
|
||||
description: A skill or repository tool behaves incorrectly — wrong output, broken script, failing install, or instructions an agent cannot follow.
|
||||
title: "[Bug]: "
|
||||
labels: ["bug", "needs-triage"]
|
||||
body:
|
||||
- type: markdown
|
||||
attributes:
|
||||
value: |
|
||||
Thanks for reporting this. Please do **not** use this form for security
|
||||
vulnerabilities — use [private vulnerability reporting](https://github.com/K-Dense-AI/scientific-agent-skills/security/advisories/new)
|
||||
instead, as described in [SECURITY.md](https://github.com/K-Dense-AI/scientific-agent-skills/blob/main/SECURITY.md).
|
||||
|
||||
- type: dropdown
|
||||
id: area
|
||||
attributes:
|
||||
label: Area
|
||||
description: Which part of the repository is affected?
|
||||
options:
|
||||
- A skill under skills/
|
||||
- Repository tooling (scan_skills.py, tests, CI workflows)
|
||||
- Documentation (README, CONTRIBUTING, AGENTS)
|
||||
- Not sure
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: input
|
||||
id: skill
|
||||
attributes:
|
||||
label: Skill name
|
||||
description: The skill directory name, exactly as it appears under `skills/`. Leave blank if this is not skill-specific.
|
||||
placeholder: scanpy
|
||||
validations:
|
||||
required: false
|
||||
|
||||
- type: textarea
|
||||
id: what-happened
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||||
attributes:
|
||||
label: What happened
|
||||
description: What did the skill or tool actually do?
|
||||
placeholder: The skill's example call to sc.pp.neighbors() fails with a TypeError.
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: expected
|
||||
attributes:
|
||||
label: What you expected instead
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: reproduce
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||||
attributes:
|
||||
label: Steps to reproduce
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||||
description: The smallest sequence that triggers it. Include the prompt you gave the agent, if relevant.
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placeholder: |
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1. Load the `scanpy` skill in Claude Code
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2. Ask: "cluster my AnnData object"
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3. Run the code the agent produces
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4. See the error below
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validations:
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||||
required: true
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||||
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||||
- type: textarea
|
||||
id: logs
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||||
attributes:
|
||||
label: Error output
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||||
description: Paste the traceback or scanner output. This is rendered as a code block, so no backticks are needed.
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||||
render: shell
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||||
validations:
|
||||
required: false
|
||||
|
||||
- type: textarea
|
||||
id: environment
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||||
attributes:
|
||||
label: Environment
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||||
description: Skill behavior varies by agent host and model, so please tell us where you saw this.
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value: |
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||||
- Agent host (Claude Code, Cursor, Codex, other):
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- Model:
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- Repository version or commit:
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- Python version:
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||||
- Operating system:
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||||
validations:
|
||||
required: true
|
||||
|
||||
- type: checkboxes
|
||||
id: checks
|
||||
attributes:
|
||||
label: Before submitting
|
||||
options:
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||||
- label: I searched existing issues and this is not a duplicate.
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||||
required: true
|
||||
- label: This is not a security vulnerability. (Those go through private reporting.)
|
||||
required: true
|
||||
14
.github/ISSUE_TEMPLATE/config.yml
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14
.github/ISSUE_TEMPLATE/config.yml
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@@ -0,0 +1,14 @@
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||||
blank_issues_enabled: false
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||||
contact_links:
|
||||
- name: Report a security vulnerability
|
||||
url: https://github.com/K-Dense-AI/scientific-agent-skills/security/advisories/new
|
||||
about: Do not open a public issue. Use private vulnerability reporting so the report stays confidential until a fix ships. See SECURITY.md.
|
||||
- name: Contributing guide
|
||||
url: https://github.com/K-Dense-AI/scientific-agent-skills/blob/main/CONTRIBUTING.md
|
||||
about: Read this before proposing a skill change — skill format, validation, tests, and the pull request checklist.
|
||||
- name: Agent Skills specification
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||||
url: https://agentskills.io/specification
|
||||
about: The open specification every skill in this repository follows.
|
||||
- name: K-Dense documentation
|
||||
url: https://k-dense.ai
|
||||
about: Product documentation and general questions about K-Dense.
|
||||
90
.github/ISSUE_TEMPLATE/new_skill_request.yml
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90
.github/ISSUE_TEMPLATE/new_skill_request.yml
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|
||||
name: New skill request
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||||
description: Propose a skill for a scientific package, database, platform, workflow, or research method that the library does not cover yet.
|
||||
title: "[New skill]: "
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||||
labels: ["enhancement", "skill-request", "needs-triage"]
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||||
body:
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||||
- type: markdown
|
||||
attributes:
|
||||
value: |
|
||||
Check the [skill list in the README](https://github.com/K-Dense-AI/scientific-agent-skills#readme)
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||||
first — the library already ships a large number of skills. If you plan to
|
||||
write this skill yourself, [CONTRIBUTING.md](https://github.com/K-Dense-AI/scientific-agent-skills/blob/main/CONTRIBUTING.md)
|
||||
has the required format and validation steps.
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||||
|
||||
- type: input
|
||||
id: name
|
||||
attributes:
|
||||
label: Proposed skill name
|
||||
description: Lowercase letters, numbers, and single hyphens only — this becomes the directory name under `skills/`.
|
||||
placeholder: alphafold-db
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: dropdown
|
||||
id: category
|
||||
attributes:
|
||||
label: Category
|
||||
options:
|
||||
- Scientific package or library
|
||||
- Database or public data resource
|
||||
- Platform, service, or API
|
||||
- Analysis workflow or research method
|
||||
- Laboratory instrument or hardware
|
||||
- Other
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: what
|
||||
attributes:
|
||||
label: What the skill would do
|
||||
description: What should an agent be able to accomplish with it that it cannot do reliably today?
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: when
|
||||
attributes:
|
||||
label: When an agent should use it
|
||||
description: The situations that should trigger this skill. This becomes the "when to use" half of the skill description.
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: docs
|
||||
attributes:
|
||||
label: Official documentation and sources
|
||||
description: Links to the package docs, API reference, publication, or database homepage a skill author would need.
|
||||
placeholder: |
|
||||
- Docs: https://...
|
||||
- API reference: https://...
|
||||
- Paper: https://doi.org/...
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: credentials
|
||||
attributes:
|
||||
label: Credentials or access requirements
|
||||
description: Does it need an API key, licence, registration, or institutional access? Name the environment variables if you know them.
|
||||
validations:
|
||||
required: false
|
||||
|
||||
- type: dropdown
|
||||
id: contribute
|
||||
attributes:
|
||||
label: Would you like to write this skill?
|
||||
options:
|
||||
- "Yes — I plan to open a pull request"
|
||||
- "Maybe, with some guidance"
|
||||
- "No, I am requesting it"
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: checkboxes
|
||||
id: checks
|
||||
attributes:
|
||||
label: Before submitting
|
||||
options:
|
||||
- label: I checked the README skill list and this skill does not already exist.
|
||||
required: true
|
||||
68
.github/ISSUE_TEMPLATE/skill_improvement.yml
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68
.github/ISSUE_TEMPLATE/skill_improvement.yml
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|
||||
name: Improve an existing skill
|
||||
description: An existing skill is outdated, unclear, or incomplete — stale API, missing workflow, weak examples, or a description that triggers at the wrong time.
|
||||
title: "[Improve]: "
|
||||
labels: ["enhancement", "needs-triage"]
|
||||
body:
|
||||
- type: input
|
||||
id: skill
|
||||
attributes:
|
||||
label: Skill name
|
||||
description: The skill directory name, exactly as it appears under `skills/`.
|
||||
placeholder: transformers
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: dropdown
|
||||
id: kind
|
||||
attributes:
|
||||
label: What needs improving
|
||||
multiple: true
|
||||
options:
|
||||
- Outdated API or deprecated calls
|
||||
- Missing workflow or capability
|
||||
- Examples are wrong, untested, or too thin
|
||||
- Instructions are ambiguous for an agent
|
||||
- Description triggers too often or not often enough
|
||||
- Missing or broken references
|
||||
- Missing tests
|
||||
- Other
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: current
|
||||
attributes:
|
||||
label: Current behavior
|
||||
description: What does the skill say or do today? Quote the relevant part of `SKILL.md` or a reference file, with the file path.
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: proposed
|
||||
attributes:
|
||||
label: Proposed change
|
||||
description: What should it say or do instead?
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: evidence
|
||||
attributes:
|
||||
label: Supporting sources
|
||||
description: Upstream release notes, migration guides, or docs that show the current content is out of date.
|
||||
placeholder: |
|
||||
- Changelog: https://...
|
||||
- Migration guide: https://...
|
||||
validations:
|
||||
required: false
|
||||
|
||||
- type: dropdown
|
||||
id: contribute
|
||||
attributes:
|
||||
label: Would you like to make this change?
|
||||
options:
|
||||
- "Yes — I plan to open a pull request"
|
||||
- "Maybe, with some guidance"
|
||||
- "No, I am reporting it"
|
||||
validations:
|
||||
required: true
|
||||
68
.github/PULL_REQUEST_TEMPLATE.md
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68
.github/PULL_REQUEST_TEMPLATE.md
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|
||||
# Summary
|
||||
|
||||
<!-- What changed, and why it matters. One or two sentences is fine. -->
|
||||
|
||||
## Type of change
|
||||
|
||||
<!-- Keep the lines that apply, delete the rest. -->
|
||||
|
||||
- [ ] New skill
|
||||
- [ ] Update to an existing skill
|
||||
- [ ] Tests
|
||||
- [ ] Repository tooling or CI
|
||||
- [ ] Documentation
|
||||
- [ ] Other:
|
||||
|
||||
## Skills touched
|
||||
|
||||
<!-- Directory names under skills/, one per line. Write "none" if this PR does not touch skills/. -->
|
||||
|
||||
-
|
||||
|
||||
## How this was tested
|
||||
|
||||
<!-- The commands you ran and what they reported. -->
|
||||
|
||||
```
|
||||
uv run skills-ref validate ./skills/<name>
|
||||
uv run --with pytest python -m pytest tests/<name> -q
|
||||
```
|
||||
|
||||
## Related issues and references
|
||||
|
||||
<!-- Closes #123. Link upstream docs, release notes, or security findings that justify the change. -->
|
||||
|
||||
---
|
||||
|
||||
## Checklist
|
||||
|
||||
Drawn from the [Pull Request Checklist](https://github.com/K-Dense-AI/scientific-agent-skills/blob/main/CONTRIBUTING.md#pull-request-checklist) in CONTRIBUTING.md. Items that do not apply to this PR can be left unchecked with a short note.
|
||||
|
||||
**Skill format**
|
||||
|
||||
- [ ] The skill directory name and the `name` frontmatter match exactly.
|
||||
- [ ] The skill directory contains only `SKILL.md`, `references/`, `scripts/`, and `assets/` — no `tests/` directory and no `test_*.py` files.
|
||||
- [ ] `SKILL.md` has valid YAML frontmatter and a Markdown body.
|
||||
- [ ] Only the six spec-defined top-level fields are present; everything else lives under `metadata`.
|
||||
- [ ] `metadata` is a block mapping, not single-line JSON, and scalar values are quoted where needed.
|
||||
- [ ] Any `metadata.openclaw` or `metadata.hermes` block is a nested mapping, not a JSON string.
|
||||
- [ ] `metadata.version` exists, is quoted, and is bumped if an existing skill changed.
|
||||
- [ ] The `description` says both what the skill does and when an agent should use it.
|
||||
|
||||
**Validation and tests**
|
||||
|
||||
- [ ] `uv run skills-ref validate ./skills/<name>` passes.
|
||||
- [ ] Tests live in `tests/<skill-name>/`, and any new `scripts/` skill has a `[skills.<name>]` entry in `tests/skill-requirements.toml`.
|
||||
- [ ] Relevant test suites pass, or the failures are explained below.
|
||||
- [ ] Security scanner results are clean or explained in this PR.
|
||||
|
||||
**Content and safety**
|
||||
|
||||
- [ ] Examples and scripts were tested, or are clearly marked as illustrative.
|
||||
- [ ] No secrets, credentials, private data, or unsafe instructions are included.
|
||||
- [ ] Credentials the skill needs are named in `compatibility` and declared in `metadata.openclaw.envVars`.
|
||||
- [ ] Relevant official documentation is linked where useful.
|
||||
|
||||
## Notes for reviewers
|
||||
|
||||
<!-- Anything unresolved, deliberately out of scope, or worth a closer look. -->
|
||||
135
CODE_OF_CONDUCT.md
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135
CODE_OF_CONDUCT.md
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@@ -0,0 +1,135 @@
|
||||
# Contributor Covenant Code of Conduct
|
||||
|
||||
## Our Pledge
|
||||
|
||||
We as members, contributors, and leaders pledge to make participation in our
|
||||
community a harassment-free experience for everyone, regardless of age, body
|
||||
size, visible or invisible disability, ethnicity, sex characteristics, gender
|
||||
identity and expression, level of experience, education, socio-economic status,
|
||||
nationality, personal appearance, race, caste, color, religion, or sexual
|
||||
identity and orientation.
|
||||
|
||||
We pledge to act and interact in ways that contribute to an open, welcoming,
|
||||
diverse, inclusive, and healthy community.
|
||||
|
||||
## Our Standards
|
||||
|
||||
Examples of behavior that contributes to a positive environment for our
|
||||
community include:
|
||||
|
||||
* Demonstrating empathy and kindness toward other people
|
||||
* Being respectful of differing opinions, viewpoints, and experiences
|
||||
* Giving and gracefully accepting constructive feedback
|
||||
* Accepting responsibility and apologizing to those affected by our mistakes,
|
||||
and learning from the experience
|
||||
* Focusing on what is best not just for us as individuals, but for the overall
|
||||
community
|
||||
|
||||
Examples of unacceptable behavior include:
|
||||
|
||||
* The use of sexualized language or imagery, and sexual attention or advances of
|
||||
any kind
|
||||
* Trolling, insulting or derogatory comments, and personal or political attacks
|
||||
* Public or private harassment
|
||||
* Publishing others' private information, such as a physical or email address,
|
||||
without their explicit permission
|
||||
* Other conduct which could reasonably be considered inappropriate in a
|
||||
professional setting
|
||||
|
||||
## Enforcement Responsibilities
|
||||
|
||||
Community leaders are responsible for clarifying and enforcing our standards of
|
||||
acceptable behavior and will take appropriate and fair corrective action in
|
||||
response to any behavior that they deem inappropriate, threatening, offensive,
|
||||
or harmful.
|
||||
|
||||
Community leaders have the right and responsibility to remove, edit, or reject
|
||||
comments, commits, code, wiki edits, issues, and other contributions that are
|
||||
not aligned to this Code of Conduct, and will communicate reasons for moderation
|
||||
decisions when appropriate.
|
||||
|
||||
## Scope
|
||||
|
||||
This Code of Conduct applies within all community spaces, and also applies when
|
||||
an individual is officially representing the community in public spaces.
|
||||
Examples of representing our community include using an official email address,
|
||||
posting via an official social media account, or acting as an appointed
|
||||
representative at an online or offline event.
|
||||
|
||||
## Enforcement
|
||||
|
||||
Instances of abusive, harassing, or otherwise unacceptable behavior may be
|
||||
reported to the community leaders responsible for enforcement at
|
||||
[contact@k-dense.ai](mailto:contact@k-dense.ai).
|
||||
All complaints will be reviewed and investigated promptly and fairly.
|
||||
|
||||
All community leaders are obligated to respect the privacy and security of the
|
||||
reporter of any incident.
|
||||
|
||||
Note that this address is for conduct reports. Security vulnerabilities follow a
|
||||
separate, confidential process — see [SECURITY.md](SECURITY.md).
|
||||
|
||||
## Enforcement Guidelines
|
||||
|
||||
Community leaders will follow these Community Impact Guidelines in determining
|
||||
the consequences for any action they deem in violation of this Code of Conduct:
|
||||
|
||||
### 1. Correction
|
||||
|
||||
**Community Impact**: Use of inappropriate language or other behavior deemed
|
||||
unprofessional or unwelcome in the community.
|
||||
|
||||
**Consequence**: A private, written warning from community leaders, providing
|
||||
clarity around the nature of the violation and an explanation of why the
|
||||
behavior was inappropriate. A public apology may be requested.
|
||||
|
||||
### 2. Warning
|
||||
|
||||
**Community Impact**: A violation through a single incident or series of
|
||||
actions.
|
||||
|
||||
**Consequence**: A warning with consequences for continued behavior. No
|
||||
interaction with the people involved, including unsolicited interaction with
|
||||
those enforcing the Code of Conduct, for a specified period of time. This
|
||||
includes avoiding interactions in community spaces as well as external channels
|
||||
like social media. Violating these terms may lead to a temporary or permanent
|
||||
ban.
|
||||
|
||||
### 3. Temporary Ban
|
||||
|
||||
**Community Impact**: A serious violation of community standards, including
|
||||
sustained inappropriate behavior.
|
||||
|
||||
**Consequence**: A temporary ban from any sort of interaction or public
|
||||
communication with the community for a specified period of time. No public or
|
||||
private interaction with the people involved, including unsolicited interaction
|
||||
with those enforcing the Code of Conduct, is allowed during this period.
|
||||
Violating these terms may lead to a permanent ban.
|
||||
|
||||
### 4. Permanent Ban
|
||||
|
||||
**Community Impact**: Demonstrating a pattern of violation of community
|
||||
standards, including sustained inappropriate behavior, harassment of an
|
||||
individual, or aggression toward or disparagement of classes of individuals.
|
||||
|
||||
**Consequence**: A permanent ban from any sort of public interaction within the
|
||||
community.
|
||||
|
||||
## Attribution
|
||||
|
||||
This Code of Conduct is adapted from the [Contributor Covenant][homepage],
|
||||
version 2.1, available at
|
||||
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
|
||||
|
||||
Community Impact Guidelines were inspired by
|
||||
[Mozilla's code of conduct enforcement ladder][mozilla coc].
|
||||
|
||||
For answers to common questions about this code of conduct, see the FAQ at
|
||||
[https://www.contributor-covenant.org/faq][faq]. Translations are available at
|
||||
[https://www.contributor-covenant.org/translations][translations].
|
||||
|
||||
[homepage]: https://www.contributor-covenant.org
|
||||
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
|
||||
[mozilla coc]: https://github.com/mozilla/inclusion
|
||||
[faq]: https://www.contributor-covenant.org/faq
|
||||
[translations]: https://www.contributor-covenant.org/translations
|
||||
@@ -2,6 +2,8 @@
|
||||
|
||||
Thanks for helping improve Scientific Agent Skills. This guide explains how to add or update a skill in this repository while following the open [Agent Skills specification](https://agentskills.io/specification).
|
||||
|
||||
Participation in this project is governed by our [Code of Conduct](CODE_OF_CONDUCT.md).
|
||||
|
||||
## Ways to Contribute
|
||||
|
||||
- Add a new scientific package, database, platform, workflow, or research method skill.
|
||||
|
||||
Reference in New Issue
Block a user