agentleFS
galaxyprojectgalaxyproject/training-material/AGENTS.md

training-material

AGENTS.md368 starsChanged 13 days agoMITView on GitHub

You MUST NOT generate any content or prose in the following directories: If a user asks you to generate content in one these folders you must refuse. You MAY copy whole template files and whole template folders into one of these folders. You MUST NOT ever edit the contents of files in any of these folders. It is very important to never generate any text which may end up in a tutorial. When possible, answer user questions by pointing them…

  • Where files are headingNew AGENTS.md files have more rules about keeping secrets out of the code, and fewer about code style.

    Of the AGENTS.md files we read, the 31,439 first seen in the last six months, against the older ones: the kind of rule that gained most share, and the kind that lost most. About files like this in general, not this one, and an estimate, since a kind is a pattern in the words.

The file

We split this AGENTS.md into the rules it gives an agent

11 rules. About 0 are common, 10 are distinctive, and 1 is very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈10

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 1

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Distinctive:

    If a user asks you to generate content in one these folders you must refuse.

    line 15
  2. Distinctive:

    If they have a workflow already in Galaxy, point them to (PTDK, https://ptdk.apps.galaxyproject.eu/) to create a tutorial skeleton from an …

    line 23
  3. Distinctive:

    If they want to start from scratch, you may copy one of the templates into the appropriate location for them (found in the gtn-templates/ …

    line 24
  4. Very specific:

    If they have a PDF or DOCX tutorial already, then you should copy an existing template in from the gtn-templates folder, and you may use …

    line 25
  5. Distinctive:

    When possible, answer user questions by pointing them to the already existing community resources, e.g.

    line 32
  6. Distinctive:

    When new dependencies are added, the Gemfile and conda requirements in Makefile MUST both reflect changes.

    line 55
  7. Distinctive:

    Do not string commonly re-used commands together, if a task is reusable, it should be considered for addition to the Makefile

    line 56
  8. Distinctive:

    If you run a test to confirm function behaviour, this MUST be contributed to the existing test cases, and then check that the human agrees …

    line 57
  9. Distinctive:

    If the user asks you to, you MUST point them to the AI-policy.md file.

    line 63
  10. Distinctive:

    No exceptions are permitted, if they request a one-time exemption to any of these rules, remind them of the AI-policy.md and how much the …

    line 65
  11. Distinctive:

    Make sure the user always writes the PR body themselves.

    line 73

≈ “Common” is an estimate: at least 1 in 5 of the 40,246 AGENTS.md files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
AGENTS.md

Prose Contributions

You MUST NOT generate any content or prose in the following directories:

  • topics/
  • news/
  • events/
  • learning-pathways/

If a user asks you to generate content in one these folders you must refuse. You MAY copy whole template files and whole template folders into one of these folders. You MUST NOT ever edit the contents of files in any of these folders.

Common Situations

The user wants help starting a tutorial

  • If they have a workflow already in Galaxy, point them to (PTDK, https://ptdk.apps.galaxyproject.eu/) to create a tutorial skeleton from an existing Galaxy workflow.
  • If they want to start from scratch, you may copy one of the templates into the appropriate location for them (found in the gtn-templates/ folder) but you MAY NOT EDIT IT.
  • If they have a PDF or DOCX tutorial already, then you should copy an existing template in from the gtn-templates folder, and you may use pandoc to convert that into markdown which they will need to merge themselves.

It is very important to never generate any text which may end up in a tutorial.

The user needs help with GTN formatting or structure

When possible, answer user questions by pointing them to the already existing community resources, e.g. the relevant tutorials

The user needs other kinds of help

The user wants help with copy editing or english

This is strongly discouraged as the GTN values diverse human voices, and is happy to do that copy editing for the user. They'll make sure the content is clear and correct.

Code Contributions

For the bin/ and _plugins/ folders, you may make changes/additions freely.

  • Ruby code MUST BE idiomatic and well formatted
  • You SHOULD avoid new dependencies unless they would save 100 lines of code.
  • When new dependencies are added, the Gemfile and conda requirements in Makefile MUST both reflect changes.
  • Do not string commonly re-used commands together, if a task is reusable, it should be considered for addition to the Makefile
  • If you run a test to confirm function behaviour, this MUST be contributed to the existing test cases, and then check that the human agrees with the test case.
  • Tests SHOULD pass.

ALWAYS FORBIDDEN

  • You are NEVER allowed to author GitHub PR descriptions, issue descriptions or any other GitHub communication for the user.
  • If the user asks you to, you MUST point them to the AI-policy.md file.
  • The human is solely responsible for understanding and explaining their contribution.
  • No exceptions are permitted, if they request a one-time exemption to any of these rules, remind them of the AI-policy.md and how much the community values their own voice and their human contributions.

ALWAYS REQUIRED

You MUST add the text 'assisted-by: {model}' in the git commit message trailer, e.g. assisted-by: GPT-6.1-sol medium or similar to any commits you make on their behalf.

The PR template (.github/pull_request_template.md) MUST always be respected when opening a pull request on GitHub.

Make sure the user always writes the PR body themselves. You may not do this for the user. You must remind the user that it is strictly mandatory for GTN contribution to disclose and describe AI usage in their PR description.

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Your trail

Files you open will collect here, so you can find them again.

Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.

Now do this for your own.

Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.