⬆️ Upgrade dependencies for 1.8.6

[shnizzedy]

Fixes

Resolves #1673 by @shnizzedy

Description

• C-PAC/CHANGELOG.md

  Lines 19 to 71 in 6efb38d

  	### Changed
  	- Adds checksum steps to `curl`d steps in Docker build process (for standard and `lite` images)
  	- Makes in-container root directory writable by all
  	### Added dependency
  	- `dc`
  	### Removed dependencies
  	- `bids-validator`
  	- `Node`
  	- `NVM`
  	- `simplejson`
  	- `wxpython`
  	- `yamlordereddictloader`
  	### Upgraded dependencies
  	- `AFNI` 21.1.00 'Domitian' → 23.0.07 'Commodus'
  	- `ANTs` 2.3.3 'Leptomyrmex' → 2.4.3 'Emplastus'
  	- `boto3` 1.7.37 → 1.26.91
  	- `click` 6.7 → 8.1.3
  	- `configparser` 3.7.4 → 5.3.0
  	- `FSL` 5.0.10 (5.0.9) → 6.0.6 (6.0.4:ddd0a010c)
  	- `future` 0.16.0 → 0.18.3
  	- `ICA-AROMA` 0.4.3-beta → 0.4.4-beta
  	- `INDI-Tools` 0.0.7@`main` → 0.0.7@`998c246`
  	- `joblib` 1.0.1 → 1.2.0
  	- `matplotlib` 3.1.3 → 3.7.1
  	- `networkx` 2.4 → 3.1
  	- `nibabel` 3.0.1 → 5.0.1
  	- `nilearn` 0.4.1 → 0.10.0
  	- `nipype` 1.5.1 → 1.8.6
  	- `numpy` 1.21.0 → 1.24.2
  	- `pandas` 1.0.5 → 1.5.3
  	- `patsy` 0.5.0 → 0.5.3
  	- `prov` 1.5.2 → 2.0.0
  	- `psutil` 5.6.6 → 5.9.4
  	- `pybids` 0.15.1 → 0.15.6
  	- `PyPEER` 1.0@`main` → 1.1@`6965d2b`
  	- `Python` 3.7.13 → 3.10.10 (holding back from 3.11 for `sdcflows`, `torch`, and `torchvision`)
  	- `python-dateutil` 2.7.3 → 2.8.2
  	- `PyYAML` 5.4 → 6.0
  	- `requests` 2.21.0 → 2.28.2
  	- `scipy` 1.6.3 → 1.10.1
  	- `sdcflows` 2.0.5 → 2.4.0
  	- `torch` 1.2.0+cu92 → 1.13.1
  	- `torchvision` 0.4.0+cu92 → 0.14.1
  	- `traits` 4.6.0 → 6.3.2
  	- `voluptuous` 0.12.0 → 0.13.1
  	- `wb_command` neurodebian latest → 1.5.0

• Fixes CI bugs and improves CI flow.
• Updates dev versioning to match PEP440

Technical details

• Refactors workflows from workflow_dispatch triggers to workflow_call triggers so event data persists through the run
• Adds ability to rebuild specific stages with [rebuild $STAGE_NAME] in commit message (with )
  • Now we can see which existing staging images in each stage are determined to be rebuilt, like
  • 32,290 of the added lines are just adding a copy of get-pip.py to the repo

Screenshots

Actions before refactor

↓

↓

Actions partially refactored

Actions refactored

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 (📝 Document multistage builds fcp-indi.github.io#300; https://github.com/FCP-INDI/C-PAC/blob/c7fa153f955afa1defc28d652888746edb9c0dfc/.github/README.md).
• 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.

[nx10]

For reference singularity fails on CircleCI with

SINGULARITYENV_COVERAGE_FILE=.coverage.singularity${VARIANT} singularity exec -B $PWD:/code cpac-singularity-image${VARIANT}.sif /code/dev/circleci_data/test_in_image.sh

FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Exited with code exit status 255

I tried different versions of singularity but can not get this to go away.
The images are confirmed working locally/manually so this might be a CircleCI issue.

[amygutierrez]

When using this image to run C-PAC, I get the following error:

FileNotFoundError: File /usr/share/fsl/6.0/data/atlases/HarvardOxford/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz does not exist!

Looks like that file doesn't exist in fsl 6.0

Singularity> pwd
/usr/share/fsl/6.0/data/atlases/HarvardOxford
Singularity> ls
HarvardOxford-cort-maxprob-thr0-1mm.nii.gz   HarvardOxford-cort-maxprob-thr50-1mm.nii.gz  HarvardOxford-sub-maxprob-thr0-1mm.nii.gz   HarvardOxford-sub-maxprob-thr50-1mm.nii.gz  labels
HarvardOxford-cort-maxprob-thr0-2mm.nii.gz   HarvardOxford-cort-maxprob-thr50-2mm.nii.gz  HarvardOxford-sub-maxprob-thr0-2mm.nii.gz   HarvardOxford-sub-maxprob-thr50-2mm.nii.gz  relabel
HarvardOxford-cort-maxprob-thr25-1mm.nii.gz  HarvardOxford-cort-prob-1mm.nii.gz           HarvardOxford-sub-maxprob-thr25-1mm.nii.gz  HarvardOxford-sub-prob-1mm.nii.gz
HarvardOxford-cort-maxprob-thr25-2mm.nii.gz  HarvardOxford-cort-prob-2mm.nii.gz           HarvardOxford-sub-maxprob-thr25-2mm.nii.gz  HarvardOxford-sub-prob-2mm.nii.gz

[shnizzedy]

For reference singularity fails on CircleCI with

SINGULARITYENV_COVERAGE_FILE=.coverage.singularity${VARIANT} singularity exec -B $PWD:/code cpac-singularity-image${VARIANT}.sif /code/dev/circleci_data/test_in_image.sh

FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Exited with code exit status 255

I tried different versions of singularity but can not get this to go away. The images are confirmed working locally/manually so this might be a CircleCI issue.

Disabled the Singularity tests and made a new issue

---

When using this image to run C-PAC, I get the following error:

FileNotFoundError: File /usr/share/fsl/6.0/data/atlases/HarvardOxford/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz does not exist!

Looks like that file doesn't exist in fsl 6.0

Singularity> pwd
/usr/share/fsl/6.0/data/atlases/HarvardOxford
Singularity> ls
HarvardOxford-cort-maxprob-thr0-1mm.nii.gz   HarvardOxford-cort-maxprob-thr50-1mm.nii.gz  HarvardOxford-sub-maxprob-thr0-1mm.nii.gz   HarvardOxford-sub-maxprob-thr50-1mm.nii.gz  labels
HarvardOxford-cort-maxprob-thr0-2mm.nii.gz   HarvardOxford-cort-maxprob-thr50-2mm.nii.gz  HarvardOxford-sub-maxprob-thr0-2mm.nii.gz   HarvardOxford-sub-maxprob-thr50-2mm.nii.gz  relabel
HarvardOxford-cort-maxprob-thr25-1mm.nii.gz  HarvardOxford-cort-prob-1mm.nii.gz           HarvardOxford-sub-maxprob-thr25-1mm.nii.gz  HarvardOxford-sub-prob-1mm.nii.gz
HarvardOxford-cort-maxprob-thr25-2mm.nii.gz  HarvardOxford-cort-prob-2mm.nii.gz           HarvardOxford-sub-maxprob-thr25-2mm.nii.gz  HarvardOxford-sub-prob-2mm.nii.gz

Rebuilt the staging images, added a test to make sure that file's in each final image at $FSLDIR/data/atlases/HarvardOxford/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz (it passes)