👷 Automate lite integration and regression tests

[shnizzedy]

Fixes

Related to #1211 (comment) by @shnizzedy

Description

• Updates GitHub Actions workflows to run integration and regression tests automatically
  • on pull requests,
  • when [run reg-suite lite] is included in a commit message,
    or
  • manually from https://github.com/shnizzedy/C-PAC/actions/workflows/regtest.yaml (once .github/workflows/regtest.yaml is merged into main)

Technical details

• SSOTs

  C-PAC/CPAC/utils/io.py

  Lines 24 to 37 in 9ea31ec

  	def load_yaml(
  	path: Path | str, desc: str = "YAML file", encoding="utf8"
  	) -> dict | list | str:
  	"""Try to load a YAML file to a Python object."""
  	path = Path(path).absolute()
  	try:
  	with path.open("r", encoding=encoding) as _yaml:
  	result = safe_load(_yaml)
  	except FileNotFoundError as error:
  	raise error
  	except Exception as error:
  	msg = f"{desc} is not in proper YAML format. Please check {path}"
  	raise YAMLError(msg) from error
  	return result

• Lints modified code.

Tests

New automated regression tests!

After we merge

• 👽️ Remove deprecated xlink XML prefix C-PAC_regression_dashboard#2,
• 👔 Move creation of correlations.json to cpac-correlations CLI CPAC_regtest_pack#12,
• 👔 Build interactive SVG, build a PNG from that interactive SVG, include the PNG in automated comment C-PAC_regression_dashboard#3,
• 👔 Restructure automated integration and regression testing flow childmindresearch/C-PAC_slurm_testing#2,
• 🔖 Set canonincal dependencies + initial version and CHANGELOG C-PAC_regression_dashboard#4, and
• 🔖 Set canonincal dependencies + initial version and CHANGELOG childmindresearch/C-PAC_slurm_testing#3,

we can update the secrets in this repo's ACCESS environment and then try to run the tests from this PR.

Screenshots

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop 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]

This last run died somewhere short of posting the comment, but it did get far enough to generate

[shnizzedy]

There are some changes in CPAC/pipeline/cpac_runner.py, but iirc those changes are just SSOTing

C-PAC/CPAC/utils/io.py

Lines 24 to 37 in c96f3bb

	def load_yaml(
	path: Path | str, desc: str = "YAML file", encoding="utf8"
	) -> dict | list | str:
	"""Try to load a YAML file to a Python object."""
	path = Path(path).absolute()
	try:
	with path.open("r", encoding=encoding) as _yaml:
	result = safe_load(_yaml)
	except FileNotFoundError as error:
	raise error
	except Exception as error:
	msg = f"{desc} is not in proper YAML format. Please check {path}"
	raise YAMLError(msg) from error
	return result

and a little linting, and everything else in this PR is infrastructure, nothing that touches C-PAC itself.