Code

⬆️ Upgrade dependencies for 1.8.6#1916

Code

Merged

e-kenneally merged 159 commits intodevelopFCP-INDI/C-PAC:developfrom upgrade/pythonFCP-INDI/C-PAC:upgrade/pythonCopy head branch name to clipboardJun 20, 2023

+34,408-1,068

Commits

Commits on Dec 15, 2022

• 📝 Document Python and package versions

  shnizzedy

  committed
  fdae016

• 🚸 Add versioning report to CLI version command

  shnizzedy

  committed
  28acec6

• ⬆️ Upgrade Python to 3.11; remove miniconda dependency

  shnizzedy

  committed
  c9d4a6b

• 📄 Update license disclosure

  shnizzedy

  committed
  fa36e9d

• ⬆️ Upgrade ldd/glibc for Python 3.11

  shnizzedy

  committed
  d04ef62

Commits on Feb 15, 2023

• ⬆️ Upgrade Python 3.7.13 → 3.10.6

  Show description for dd45308
  shnizzedy

  committed
  dd45308

Commits on Mar 1, 2023

• 👽 Upgrade GPG signing for Neurodebian sources

  shnizzedy

  committed
  dcab725

Commits on Mar 15, 2023

• :arrow-up: Upgrade AFNI 21.1.00 'Domitian' → 23.0.07 'Commodus'

  Show description for c9bc551
  shnizzedy

  committed
  c9bc551

• 🔖 Update version to 1.8.6.dev (⬆️ Upgrade Python 3.7.13 → 3.10.6

  Show description for 6a96cd8
  

  ChildMindInstituteCNL

  authored and

  shnizzedy

  committed
  6a96cd8

• 🔊 Log "$GITHUB_OUTPUT"

  shnizzedy

  committed
  31b1b4f

• 👷 Add missing environment variable for check

  shnizzedy

  committed
  b738538

• 👷 Add missing ids

  shnizzedy

  committed
  44e4ae0

• 👷 Add missing condition

  shnizzedy

  committed
  66b3738

• ⏪ Revert changes to Ubunutu Dockerfiles

  shnizzedy

  committed
  e34352e

• 👷 Clear up space for Ubuntu build stage

  shnizzedy

  committed
  291fb2d

• 👽 Use buildx imagetools instead of manifest

  shnizzedy

  committed
  241cde2

• 🔀 Merge main into upgrade/python

  shnizzedy

  committed
  5c1e6e6

• fixup! :arrow-up: Upgrade AFNI 21.1.00 'Domitian' → 23.0.07 'Commodus'

  shnizzedy

  committed
  c4109cc

Commits on Mar 16, 2023

• fixup! 🔀 Merge main into upgrade/python

  shnizzedy

  committed
  f34da2d

• 🔖 Update version to 1.8.6.dev (fixup! 🔀 Merge main into upgrade/python)

  ChildMindInstituteCNL

  committed
  a896dd7

• 👽 Remove deprecated keyword 'warn' from matplotlib.use call

  shnizzedy

  committed
  f8a8d51

Commits on Mar 17, 2023

• ⬆️ Upgrade PyPEER 1.0@main → 1.1@6965d2b

  shnizzedy

  committed
  6ae9587

Commits on Mar 20, 2023

• ⬆️ Upgrade connectome_workbench @ 1.5.0

  shnizzedy

  committed
  7e753d8

• Merge \document-gh-actions\ into \upgrade/python\

  shnizzedy

  committed
  ca23c4b

Commits on Mar 21, 2023

• ➖ Remove wxpython dependency

  shnizzedy

  committed
  5f24aec

Commits on Mar 22, 2023

• 👷 Add "[rebuild ${stage}]" functionality

  Show description for 4ada7c2
  

  shnizzedy

  and

  amygutierrez

  committed
  4ada7c2

• 👷 Fail build if any stages fail

  Show description for 31bcafd
  

  shnizzedy

  and

  Yann Thomas-Gérard

  committed
  31bcafd

• :log: Include SHA and base ref in build stages run name

  shnizzedy

  committed
  f221b0b

• 👷 ⬆️ Upgrade actions/checkout@v3 ← v2

  shnizzedy

  committed
  8682556

• 👷 Put commit message & SHA in build stages run name

  Show description for bf70869
  shnizzedy

  committed
  bf70869

• 👷 Always check tag

  shnizzedy

  committed
  521c049

• 👷 Pass event commit through to build-stages workflow

  Show description for 9ed8fd6
  shnizzedy

  committed
  9ed8fd6

• 👷 Make run-name a URL

  shnizzedy

  committed
  d5c6df9

• ⬆️ Upgrade FSL 6.0.6 ← 5.0.10

  shnizzedy

  committed
  0c43ec2

• 🚨 Lint CHANGELOG

  shnizzedy

  committed
  5545cb7

• 👽 Replace Sibz/[email protected] with gdonati78/[email protected]

  shnizzedy

  committed
  248fdb0

Commits on Mar 23, 2023

• fixup! ⬆️ Upgrade FSL 6.0.6 ← 5.0.10

  shnizzedy

  committed
  251b83d

• 👷 Add parens in workflow conditionals

  shnizzedy

  committed
  22dcb38

• 👷 workflow_dispatch → workflow_call

  Show description for 22c61ec
  

  shnizzedy

  and

  amygutierrez

  committed
  22c61ec

• 👷 Add missing not_yet_exists condition

  shnizzedy

  committed
  f7193bf

• 👷 📝 Update flow

  shnizzedy

  committed
  3fc1e02

• 👷 Drop custom check

  Show description for 5cd356f
  shnizzedy

  committed
  5cd356f

• ⚗️ Debug

  shnizzedy

  committed
  3c8080d

• 👷 Always set $BASE_REFS as an array

  shnizzedy

  committed
  2ca7ad7

• 👷 Remove fromJson call

  shnizzedy

  committed
  5d9cc31

• ✏️ GITHUB_OUTPUT~~S~~

  shnizzedy

  committed
  ca80520

• ✏️ Replace "s

  shnizzedy

  committed
  062e64c

• ⏪ Revert 5d9cc31

  shnizzedy

  committed
  a515f5c

• 👷 Make base_refs a stringified JSON Array

  shnizzedy

  committed
  7839890

• 👷 Name workflow jobs

  Show description for 24d499f
  shnizzedy

  committed
  24d499f

Commits on Mar 27, 2023

• 👷 Replace explicit input with inherited input

  shnizzedy

  committed
  65a03a6

• 👷 Run build_and_test on build_stages completion

  Show description for 7a9905c
  shnizzedy

  committed
  7a9905c

• 👷 workflow_run → workflow_call

  Show description for c7fa153
  shnizzedy

  committed
  c7fa153

• 📦 [rebuild FSL.5.0.9-5.neurodebian-xenial]

  shnizzedy

  committed
  5c3ccc9

• 👷📦♻️ Refactor installing C-PAC resources into FSL

  shnizzedy

  committed
  118e1ee

• 🔊 Echo base_refs output

  shnizzedy

  committed
  cdae4d6

• 👷 Use jq to set $base_refs

  Show description for 6071e24
  shnizzedy

  committed
  6071e24

• 👷 mkdir -p necessary directories

  Show description for dd9d80b
  shnizzedy

  committed
  dd9d80b

• 📦 Rebuild FSL

  Show description for 7d602b1
  shnizzedy

  committed
  7d602b1

Commits on Mar 28, 2023

• 👷 ♻️ Refactor to reduce number of calls

  shnizzedy

  committed
  41377fa

• 👷 🔊 Log phases

  shnizzedy

  committed
  ea282af

• 👷 Connect rebuild outputs

  Show description for 4395a48
  shnizzedy

  committed
  4395a48

• 👷 Allow base rebuild with or without 'base-' prefix

  shnizzedy

  committed
  33a1bba

• 👷 Inspect all necessary stages

  shnizzedy

  committed
  ca1cca1

• 👷 Inherit secrets

  shnizzedy

  committed
  a62da40

Commits on Mar 29, 2023

• 👽 Update command names (_ → -) for click upgrade

  shnizzedy

  committed
  a7911c1

• 👽 Change deprecated get_data to get_fdata

  Show description for 670da67
  shnizzedy

  committed
  670da67

• 👽 Remove lambda call for now-already-decoded-string

  shnizzedy

  committed
  e5eb7d5

• 👽 Replace deprecated np.int with int

  shnizzedy

  committed
  eac4406

• ✅ Add z_score to test for create_cwas

  shnizzedy

  committed
  9873fbd

• 📦 Remove duplicate env setting

  shnizzedy

  committed
  337c9e1

• ⬆️ Upgrade ANTs 2.3.3 → 2.4.3

  shnizzedy

  committed
  6a439a1

• 👽 Replace deprecated get_header method with header attribute

  shnizzedy

  committed
  deefab7

• 📦 Build ANTs as root

  shnizzedy

  committed
  674dec3

• 👽 Replace deprecated get_affine method with affine attribute

  shnizzedy

  committed
  45aed34

• 📝 Add ANTs upgrade to CHANGELOG

  shnizzedy

  committed
  b4f007f

• 🐛 Handle no z-score case for #1787

  shnizzedy

  committed
  7bd4afa

• ✅ Make click tests backwards compatible

  Show description for a23c491
  shnizzedy

  committed
  a23c491

• 👷 🚧 Test lite build before upgrading FreeSurfer

  shnizzedy

  committed
  736ebcc

• 👷 Maximize build space iff we're going to build

  shnizzedy

  committed
  a6c1263

Commits on Mar 30, 2023

• 👷 ⬆️ Upgrade docker/build-push-action

  Show description for d6cf562
  shnizzedy

  committed
  d6cf562

• 👷 ⚗️ 🔊 ♻️

  shnizzedy

  committed
  815a38b

• 👷 Resequence build prep

  shnizzedy

  committed
  064c924

• 👷 Move into $GITHUB_WORKSPACE

  shnizzedy

  committed
  b67da6d

• 👷 Maximize space first

  shnizzedy

  committed
  daf0a31

• ⏪ Revert 37c06c1

  shnizzedy

  committed
  a71f9d9

• 👷 Build standard from lite

  shnizzedy

  committed
  a689b8e

• 👷 ⚗️ Try to build bases without caches

  shnizzedy

  committed
  a726109

• 📦 Build FSL from scratch

  shnizzedy

  committed
  f58f849

• 👷 Rebuild FSL & bases

  Show description for 9873bc5
  shnizzedy

  committed
  9873bc5

• 👷 Rebuild standard

  Show description for 8c52a63
  shnizzedy

  committed
  8c52a63

• ✅ Handle semver without patch

  shnizzedy

  committed
  52ed96c

• 👷 🚧 Try FreeSurfer upgrade

  shnizzedy

  committed
  11d6ed0

• 📦 Fix FSL environment variables

  shnizzedy

  committed
  fa94fc4

Commits on Mar 31, 2023

• 📦

  Show description for 7f25d81
  shnizzedy

  committed
  7f25d81

• 👷 Shift bottleneck

  shnizzedy

  committed
  aaecae5

• 👷 Use workflow_call to call smoke tests

  shnizzedy

  committed
  eee4c18

• 👷 Plumb in [rebuild standard]

  shnizzedy

  committed
  118046e

• 👷 Specify use this ref's version of local workflows

  shnizzedy

  committed
  a8f45e3

• ⏪ Revert a8f45e3

  shnizzedy

  committed
  a111d0c

• fixup! 👷 Use workflow_call to call smoke tests

  shnizzedy

  committed
  a9fb576

• fixup! 👷 Plumb in [rebuild standard]

  shnizzedy

  committed
  1d71ba8

• 📦 MSM already in lite

  Show description for 19a0ef3
  shnizzedy

  committed
  19a0ef3

• 👷 Rebuild FreeSurfer

  Show description for 70f5574
  shnizzedy

  committed
  70f5574

Commits on Apr 2, 2023

• 👷 [rebuild standard]

  shnizzedy

  committed
  e9ae79a

Commits on Apr 4, 2023

• ⬇️ Revert FreeSurfer

  shnizzedy

  committed
  f0f4b66

• 👷 [rebuild standard]

  shnizzedy

  committed
  aacbf86

• 👷 [rebuild FSL.5.0.10-bionic]

  Show description for ac3299e
  shnizzedy

  committed
  ac3299e

• ⬆️ Upgrade ICA-AROMA 0.4.3-beta → 0.4.4-beta

  shnizzedy

  committed
  601e0db

Commits on Apr 7, 2023

• 📌 Pin upgraded Python requirements

  shnizzedy

  committed
  32fcadd

• 📌 Unpin in info.py

  Show description for 4490a9f
  shnizzedy

  committed
  4490a9f

Commits on Apr 10, 2023

• 🔀 Merge develop-1.8.6 into upgrade/python

  shnizzedy

  committed
  5e97404

• 🔀 Restore develop-1.8.6 changes

  Show description for 27b9220
  

  shnizzedy

  and

  nx10

  committed
  27b9220

• 🔒 Add md5sum checks for 1.8.6 installation steps

  Show description for 7e1dc5a
  shnizzedy

  committed
  7e1dc5a

• 💡 Add source URL to preamble comments

  Show description for 593781a
  shnizzedy

  committed
  593781a

Commits on Apr 11, 2023

• 🚚 Move README to not override root README on GH

  shnizzedy

  committed
  94edb57

• 📦 Set C3D path

  Show description for 07727fd
  shnizzedy

  committed
  07727fd

Commits on Apr 12, 2023

• 📌 Update Nipype version check

  shnizzedy

  committed
  79ee970

• ⬆️ Upgrade networkx to 3.1

  Show description for d951119
  shnizzedy

  committed
  d951119

• ♻️ Update Nipype version check and automate future updates of said check

  shnizzedy

  committed
  a380ded

• 👷 [rebuild Ubuntu.Python3.10-bionic-non-free]

  shnizzedy

  committed
  8897877

Commits on Apr 13, 2023

• ⬆️ Upgrade networkx to 3.1

  Show description for cf7cbe1
  shnizzedy

  committed
  cf7cbe1

• 🔒 Replace md5 with sha384 for Dockerfile checksums

  Show description for 4b8c780
  shnizzedy

  committed
  4b8c780

• 👷 🐛 Fix rebuild-phase-three logic

  Show description for 4434741
  shnizzedy

  committed
  4434741

• ⬆️ Upgrade nipype to 1.8.6

  Show description for c9528ac
  shnizzedy

  committed
  c9528ac

Commits on Apr 14, 2023

• 🔒️ Add sha384sum checks for 1.8.6 installation steps (#1922)

  shnizzedy

  authored
  9a7e028

• ➕ Install dc for FSL6

  Show description for 79e1be3
  shnizzedy

  committed
  79e1be3

• 🔒 Make in-container root directory writable by all

  shnizzedy

  committed
  6efb38d

• 👽 Change cbar_mode="None" to cbar_mode=None for matplotlib upgrade

  shnizzedy

  committed
  76ecf6c

• 🚨 Check equality, not identity

  shnizzedy

  committed
  dbd6990

Commits on Apr 17, 2023

• 👽 PEP440

  shnizzedy

  committed
  fd8086d

• 🔖 Update version to 1.8.6.dev1 (👽 PEP440)

  ChildMindInstituteCNL

  committed
  248d409

• 📦 [rebuild Ubuntu.bionic-non-free]

  shnizzedy

  committed
  cc90131

• 📦 Update variant bases

  Show description for 459a878
  shnizzedy

  committed
  459a878

Commits on Apr 18, 2023

• ✅ Handle different versions of importlib

  Show description for d179ef9
  shnizzedy

  committed
  d179ef9

Commits on Apr 21, 2023

• 👷 [rebuild ABCD-HCP]

  shnizzedy

  committed
  6f747ce

Commits on Apr 24, 2023

• 👷 Upgrade Circle executor

  shnizzedy

  committed
  6cee7c5

• 👷 Don't reinstall Python if it already exists on the runner

  shnizzedy

  authored
  668ab59

Commits on May 22, 2023

• ⬆️ Bump requests from 2.21.0 to 2.31.0

  Show description for eef4e73
  dependabot[bot]

  authored
  eef4e73

Commits on Jun 5, 2023

• Merge branch 'develop' into upgrade/python

  nx10

  committed
  edd433f

• Switch CircleCI to apptainer/singularity and upgrd

  nx10

  committed
  ef75014

Commits on Jun 6, 2023

• CircleCI switch to singularity orb

  nx10

  committed
  a3da6ad

• Empty Commit

  nx10

  committed
  adbd563

• Revert "CircleCI switch to singularity orb"

  Show description for 744abac
  nx10

  committed
  744abac

• CircleCI singularity

  nx10

  committed
  6c28b22

• Copy cpac resources to FSL atlases directory

  nx10

  committed
  8714f10

• Fix FSL atlas paths

  nx10

  committed
  27b350b

• FSL atlas dir permissions

  nx10

  committed
  faeb2c8

Commits on Jun 15, 2023

• Merge branch 'upgrade/python' into dependabot/pip/requests-2.31.0

  shnizzedy

  authored
  c5d4ec7

• 📦 Rebuild FSL staging images

  Show description for a0b2215
  shnizzedy

  committed
  a0b2215

• ✏️ Fix typo

  Show description for a4677fe
  shnizzedy

  committed
  a4677fe

• 📦 Make symlinks real in FSL 5.0.9-5 installation

  Show description for a635d88
  shnizzedy

  committed
  a635d88

Commits on Jun 16, 2023

• fixup! 👷 Inherit secrets

  shnizzedy

  committed
  78e749d

• fixup! fixup! 👷 Inherit secrets

  shnizzedy

  committed
  de0b163

• 📦 Rebuild base images

  Show description for ac2c445
  shnizzedy

  committed
  ac2c445

• 📦 Dedupe realized symlinks

  Show description for e48a25d
  shnizzedy

  committed
  e48a25d

• 👷 Disable Circle Singularity tests

  Show description for c7ce58a
  shnizzedy

  committed
  c7ce58a

• ⬆️ Bump requests from 2.21.0 to 2.31.0 (#1939)

  shnizzedy

  authored
  cb986d7

• ✅ Check for HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz

  shnizzedy

  committed
  ade61a3