chore: update GitHub Actions versions and replace archived ruff action

[ganow]

Summary

• Updated actions/checkout from v3/v4 → v6 and actions/setup-python from v4 → v6 across all workflows (ci.yml, lint.yml, test_old.yml)
• Replaced the archived chartboost/ruff-action@v1 with the official astral-sh/ruff-action@v3 in lint.yml
• Updated MishaKav/pytest-coverage-comment from v1.1.47 → v1.7.2 and unpinned pytest-github-actions-annotate-failures to always use the latest version

Background

chartboost/ruff-action is now a public archive and no longer maintained. Continuing to use it risks breakage as the repo will not receive security patches or updates.

Test plan

• CI workflow runs successfully on Python 3.8–3.11
• Lint job uses astral-sh/ruff-action@v3 without errors → The lint job fails, but this is not due to a configuration error in the workflow; it is simply the result of a lint error, so there is no issue.
• Type-check job completes with updated action versions → The type-check job also fails, but this is intended as same as above

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
bdpy/bdata
bdata.py	399	195	51%	79, 104, 109, 113, 118, 122, 132–134, 190, 233–239, 252–262, 276–277, 310, 314, 318–356, 405–411, 419–420, 425–426, 443–450, 468–469, 475, 508, 539, 548, 560, 589–598, 610, 625, 661, 683–691, 696–729, 738, 750–757, 761–767, 771–799, 803–824, 828–862, 866–868, 872–874, 878–887
featureselector.py	64	12	81%	62–67, 69–74
metadata.py	67	1	99%	84
utils.py	113	37	67%	71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
datastore.py	107	85	21%	59–75, 90–93, 97–98, 102–113, 116–119, 122–127, 131–132, 137–158, 190–197, 222–259, 262–265
features.py	298	165	45%	31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
kvs.py	177	13	93%	21, 24, 114, 118, 127–131, 171, 173, 185, 254, 282
pd.py	9	5	44%	25–27, 43–44
sparse.py	67	7	90%	29, 52–58, 74, 109, 123
utils.py	12	12	0%	3–18
bdpy/dataset
utils.py	45	45	0%	3–98
bdpy/distcomp
distcomp.py	92	18	80%	33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
caffe.py	60	60	0%	4–129
bdpy/dl/torch
base.py	43	24	44%	31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
dataset.py	74	74	0%	1–195
models.py	333	226	32%	148–169, 297–316, 327–331, 345–350, 442–494, 515–517, 528–587, 611–614, 625–684, 708–711, 722–771, 790–793, 804–853, 872–875
torch.py	121	55	55%	188–225, 228, 231–243, 246–281
bdpy/dl/torch/domain
core.py	46	2	96%	47, 63
feature_domain.py	24	1	96%	30
image_domain.py	81	3	96%	91, 94, 257
bdpy/evals
metrics.py	95	45	53%	49–53, 82–112, 130–142, 151–152, 157, 172–179
bdpy/feature
feature.py	30	2	93%	69–70
bdpy/fig
__init__.py	5	5	0%	6–10
draw_group_image_set.py	90	90	0%	3–182
fig.py	88	88	0%	16–164
makeplots2.py	263	263	0%	1–608
makeplots.py	336	336	0%	1–729
tile_images.py	59	59	0%	1–193
bdpy/ml
crossvalidation.py	59	27	54%	47–48, 113–114, 117–118, 138, 164–196
learning.py	315	97	69%	9, 47–48, 52, 56, 63, 95–108, 113–129, 132, 162–174, 188–213, 297, 313, 317–319, 322–323, 333, 343–344, 349–350, 360–368, 371–372, 380, 415–422, 443, 456, 464, 473, 505–507, 546, 559, 562, 571, 580, 585, 606
model.py	140	120	14%	29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
searchlight.py	16	13	19%	32–51
bdpy/mri
fmriprep.py	497	451	9%	25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862
glm.py	40	36	10%	46–95
image.py	24	19	21%	29–54
load_epi.py	28	18	36%	36–50, 56–63, 82–88
load_mri.py	19	16	16%	16–36
roi.py	248	217	12%	37–100, 165–235, 241–314, 320–387, 399–466, 473–499
spm.py	158	139	12%	26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
__init__.py	1	1	0%	1
openneuro.py	210	210	0%	1–329
bdpy/pipeline
config.py	36	2	94%	37–38
bdpy/preproc
interface.py	52	16	69%	111–123, 148–157
preprocessor.py	129	69	47%	35, 44, 112–114, 121–128, 138–189, 196–227
select_top.py	23	1	96%	55
bdpy/recon
utils.py	55	55	0%	4–146
bdpy/recon/torch
icnn.py	161	161	0%	15–478
bdpy/recon/torch/modules
critic.py	44	2	95%	58, 132
encoder.py	29	1	97%	29
generator.py	72	5	93%	47, 52, 68, 128, 309
latent.py	34	3	91%	16, 21, 32
optimizer.py	22	9	59%	8–26
bdpy/recon/torch/task
inversion.py	88	15	83%	11–16, 22, 40, 45, 50, 57, 62, 67, 72, 96, 210, 225
bdpy/stats
corr.py	43	3	93%	57, 68, 102
bdpy/task
callback.py	71	4	94%	114, 161, 166, 234
core.py	16	1	94%	50
bdpy/util
info.py	47	36	23%	19–79
utils.py	36	8	78%	60, 116–121, 140–142
TOTAL	5998	3683	39%

Tests	Skipped	Failures	Errors	Time
209	0 💤	1 ❌	0 🔥	16.470s ⏱️

[KenyaOtsuka]

I reviewed the PR and left a couple of comments. Could you please update the PR accordingly?

[KenyaOtsuka]

astral-sh/ruff-action@v3 runs on Node.js 20, and the current GitHub Actions lint job shows a Node.js 20 deprecation warning.
astral-sh/ruff-action@v4 is already available and runs on Node.js 24, so I think we should use v4 instead of v3.

[ganow]

Thank you for the suggestion. Updated to astral-sh/ruff-action@v4 in cba6698. → changed the version specification to v4.0.0 in bd5a1ea since the major version tag still does not exist

[KenyaOtsuka]

test_old.yml does not seem to be exercised by the current PR checks.

Could you confirm that this workflow still works as intended after this change?

I am particularly concerned that it still uses ubuntu-20.04, since the GitHub-hosted Ubuntu 20.04 runner image has been retired:
https://github.blog/changelog/2025-01-15-github-actions-ubuntu-20-runner-image-brownout-dates-and-other-breaking-changes/

[ganow]

Thank you for the suggestion. Addressed in fc17758:

• Replaced ubuntu-20.04 with ubuntu-22.04 to avoid the retired runner image.
• Also renamed the trigger branch from test_old to maintenance/legacy. The prefix clarifies that this branch is for maintaining legacy Python support, and decouples the branch name from specific version numbers (e.g., feat/py36+ looked like a feature branch, and the supported version range may change over time).

The workflow itself has not been run in this PR since it only fires on pushes to the trigger branch. I will verify it works as intended after this PR is merged.

[KenyaOtsuka]

Thanks for addressing my comments.
The updates look good to me.

Python 3.8 test is currently failing, but this is not caused by this PR, so I think it is fine.

[ganow]

@KenyaOtsuka I confirmed that test_old CI works appropriately in https://github.com/KamitaniLab/bdpy/actions/runs/25806577703

Note that, actions/setup-python does not support Python 3.6.x on runners from ubuntu-22.04 onward, so I split the 3.6.x tests into a separate job and changed the workflow so that those tests are run inside a Docker container. In any case, we plan to drop support for 3.6.x and 3.7.x themselves in the near future, so this is only a temporary action.

Please see commit a770e6e for the actual changes.