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📝 Add a tutorial for parsing pipeline configs with FROM keys #4

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Description

This PR adds a tutorial for "Parsing minified pipelines (FROM: key)"

Technical details

  • Since an existing tutorial uses cpac (the commandline wrapper) and this one uses C-PAC (the core software), and those two packages can't be installed in the same environment, this PR also moves the cpac installation into a wrapper Jupyter kernel and installs C-PAC in a core Jupyter kernel
  • The core and bash kernels aren't working in Binder with this PR, but we haven't been linking to them yet anyway. They're findable, but not easily, and they do work locally for me 🤷. I vote we merge this and open an issue instead of holding this one up.
  • This PR also adds a :octocat: workflow intended to:
    • cache a Binder build so it'll be quicker to load on mybinder.org/v2/gh/FCP-INDI/C-PAC_tutorials.git/main?labpath=FROM%2Findex.ipynb (once this is merged)
      name: Cache branch Binder build
      on: [push]
      jobs:
      Create-MyBinderOrg-Cache:
      runs-on: ubuntu-latest
      steps:
      - name: Cache Binder build on mybinder.org
      uses: jupyterhub/repo2docker-action@master
      with:
      NO_PUSH: true
      MYBINDERORG_TAG: ${{ github.event.ref }}
    • comment a link to open the tutorials repo on mybinder.org when a PR is (re)opened
      name: Link PR to Binder
      on:
      pull_request:
      types: [opened, reopened]
      jobs:
      Create-Binder-Badge:
      runs-on: ubuntu-latest
      steps:
      - name: comment on PR with Binder link
      uses: actions/github-script@v1
      with:
      github-token: ${{secrets.GITHUB_TOKEN}}
      script: |
      var BRANCH_NAME = process.env.BRANCH_NAME;
      github.issues.createComment({
      issue_number: context.issue.number,
      owner: context.repo.owner,
      repo: context.repo.repo,
      body: `[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/${context.repo.owner}/${context.repo.repo}/${BRANCH_NAME}) :point_left: Launch a binder notebook on this branch`
      })
      env:
      BRANCH_NAME: ${{ github.event.pull_request.head.ref }}

Live Binder

launch Binder

Checklist

  • My pull request has a descriptive title (not a vague title like Update index.md).
  • My pull request targets the main branch of the repository.
  • My commit messages follow best practices.
  • My code follows the established code style of the repository.
  • I added tests for the changes I made (if applicable).
  • I updated the changelog.
  • I added or updated documentation (if applicable).
  • I tried running the project locally and verified that there are no visible errors.

Developer Certificate of Origin

Developer Certificate of Origin
Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.


Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
    have the right to submit it under the open source license
    indicated in the file; or

(b) The contribution is based upon previous work that, to the best
    of my knowledge, is covered under an appropriate open source
    license and I have the right under that license to submit that
    work with modifications, whether created in whole or in part
    by me, under the same open source license (unless I am
    permitted to submit under a different license), as indicated
    in the file; or

(c) The contribution was provided directly to me by some other
    person who certified (a), (b) or (c) and I have not modified
    it.

(d) I understand and agree that this project and the contribution
    are public and that a record of the contribution (including all
    personal information I submit with it, including my sign-off) is
    maintained indefinitely and may be redistributed consistent with
    this project or the open source license(s) involved.

@shnizzedy shnizzedy added documentation Improvements or additions to documentation tutorial labels Sep 20, 2024
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Binder 👈 Launch a binder notebook on this branch

@shnizzedy shnizzedy requested a review from a team September 20, 2024 20:49
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