News Story: DNP is a good open-source citizen

[gdevenyi]

Lets document all the work we do on projects that aren't ours

[gdevenyi]

Gabriel A. Devenyi (@gdevenyi)

162 pull request(s) across 49 upstream project(s) since 2021-06-18 (merged: 107 · open: 31 · closed-unmerged: 24). Excludes DouglasNeuroInformatics, CoBrALab, and gdevenyi's own personal repos.

BIC-MNI/minc-toolkit-v2 — 32 PR(s), 22 merged

• [merged] #144 — Fix MANPATH so that system man pages still work.
• [merged] #154 — Fixes for 22.04 build
• [merged] #172 — Update README.md
• [merged] #177 — Update BuildNIFTI.cmake to nifti_clib v3.0.0
• [closed] #178 — Disable libarchive test suite in superbuild to fix duplicate test CMake Error
• [merged] #179 — Update BuildOpenJPEG.cmake from v2.3.0 to v2.5.4
• [merged] #180 — Update libjpeg-turbo from 1.5.90 to 3.1.4.1
• [merged] #181 — Fix linking of dcm2mnc with libarchive during static linking
• [merged] #182 — Updated oobicpl
• [merged] #183 — Update FFTW to 3.3.11
• [merged] #184 — Update OpenBLAS to 0.3.33
• [closed] #185 — Update PCRE to 8.45
• [merged] #186 — Swap zlib for zlib-ng 2.3.3 (ZLIB_COMPAT mode)
• [merged] #187 — Switch liblbfgs to upstream chokkan source
• [closed] #188 — BLAS: support generic providers and fix dead detection path
• [open] #189 — Add GitHub Actions release pipeline (.deb / .rpm / .pkg / source tarball)
• [merged] #190 — ITK: bump from v4.13.3 release to release-4.14 branch tip
• [merged] #191 — Swap zlib for zlib-ng 2.3.3 (ZLIB_COMPAT mode)
• [merged] #192 — Update libjpeg-turbo from 1.5.90 to 3.1.4.1
• [merged] #193 — Update OpenBLAS to 0.3.33
• [open] #194 — Update FFTW to 3.3.11
• [merged] #195 — Switch liblbfgs to upstream chokkan source
• [merged] #196 — Drop vendored PCRE; oobicpl uses C++ std::regex
• [closed] #197 — ITKv4: build C sources with -std=gnu17 for C23 compilers
• [closed] #198 — Guard lsb_release for RPM package naming (Fedora)
• [open] #199 — PatchElastix: set CMP0033/CMP0007 to NEW for CMake 4.x
• [open] #200 — C3D + HDF5: CMake 4 policy floor and clang implicit-decl
• [merged] #201 — FFTW: don't force x86 SSE/SSE2 on Apple Silicon
• [open] #202 — Sync submodules to merged develop-1.9.18 tips
• [merged] #203 — HDF5: update 1.10.6 -> 1.10.11
• [merged] #204 — libarchive: disable iconv (macOS undefined _iconv)
• [merged] #205 — ITK: bump release-4.14 pin to cae3eb9 (modern-toolchain fixes)

Mouse-Imaging-Centre/RMINC — 17 PR(s), 14 merged

• [merged] #326 — Merge develop
• [closed] #328 — Fix deprecations
• [closed] #329 — Deprecation updates
• [merged] #330 — Deprecation updates
• [merged] #341 — Fix failing tests
• [merged] #342 — Add Docker-based test infrastructure
• [merged] #343 — Update docs
• [merged] #344 — Preserve input class and attributes in EffectSize functions
• [merged] #345 — Fix registry_name typo in qMincApplyParallel (Add consulting development services #12)
• [merged] #346 — Pass filename to sprintf in minc.isReadable warning (add syn tech #30)
• [merged] #347 — Report failing element's error in failing_mclapply/mcmapply (add new posts, mdx, and animated logo #22)
• [merged] #348 — Fix mincGetWorldVoxel rounding (#316)
• [merged] #349 — Free buffers and handles unconditionally in minc2_model (fix date format #28)
• [merged] #351 — Replace std::bind1st with lambda for C++17 compatibility
• [open] #352 — Fix makeMICeDefsHierachical for R >= 4.2 (closes #335)
• [merged] #353 — [DOC] Update README and modernize pkgdown documentation site
• [merged] #354 — [DOC] Fix broken GitHub Pages build (Jekyll/Liquid error)

ANTsX/ANTs — 12 PR(s), 10 merged

• [merged] #1382 — Update to newest ITK hash
• [merged] #1526 — Enable MINC support by default
• [merged] #1591 — Fix: don't repeat N4 every iteration
• [merged] #1712 — Refactor antsTransformInfo to add some error handling and compute determinant
• [merged] #1751 — ENH: Add Ubuntu 24.04
• [closed] #1820 — BUG: Fix segmentation fault for TranslationTransform in antsTransformInfo
• [merged] #1963 — ENH: Upgrade VTK from v8.1.1 to v9.6.0 and modernize build
• [merged] #1969 — ENH: Deduplicate image reads in antsRegistration multi-stage registration.
• [merged] #1970 — ENH: Deduplicate all image reads in antsRegistration
• [merged] #1976 — DOC: Update all command-line help to correspond to code
• [merged] #1977 — BUG: Fix segfault when mask file does not exist (NOMASK)
• [closed] #1978 — ENH: Add shrink factors, smoothing sigmas, and max iterations to diagnostic log headers

Mouse-Imaging-Centre/MRIcrotome — 12 PR(s), 2 merged

• [merged] #24 — Add documentation and README.
• [open] #28 — Fix multi-overlay crash (subscript out of bounds)
• [open] #29 — Export defaultCol/defaultRCol and improve overlay docs
• [open] #30 — Improve error messages for invalid volume inputs
• [open] #31 — Decouple slice indicator rendering from legends
• [open] #32 — Fix legend labels going off plot
• [open] #33 — Use quantiles for automatic range defaults
• [open] #34 — Add interpolate parameter to overlay for sharp label boundaries
• [open] #35 — Add labels parameter to contours() for contouring label regions
• [open] #36 — Add maskBounds() helper for computing slice bounds from a mask
• [open] #37 — Add side parameter to addtitle() for controlling title placement
• [merged] #38 — Document native pipe (|>) compatibility

InsightSoftwareConsortium/ITK — 10 PR(s), 7 merged

• [closed] #2626 — ENH: Switch to zlib-ng for modern maintained zlib codebase
• [merged] #2630 — ENH: Update to NIFTILIB3.0.1
• [merged] #2632 — ENH: Ignore more bulk changes for git blame
• [merged] #3339 — BUG: Fix failing isAffine check due to insuffcient precision in calculations
• [closed] #4160 — ENH: Add TransformMINC to default modules
• [merged] #4230 — BUG: Fix incorrectly specified expected result in itkIOTransformMINCTest
• [merged] #4864 — BUG: Fix incorrect reading of MINC2 files, convert RAS coordinates to LPS
• [closed] #6201 — Minimal build changes to enable modern building of v4.13
• [merged] #6248 — BUG: Fix check for including old cmake documentation code
• [merged] #6437 — COMP: Fix spFactor.c K&R prototypes for C23 compilers (GCC 15+/16)

BIC-MNI/libminc — 5 PR(s), 2 merged

• [closed] #142 — Comprensive fixes of warnings and static analysis bugs
• [closed] #143 — Fix all compiler warnings (gcc-15/clang-19), static analysis, and valgrind issues
• [merged] #144 — Fix false positive in minc2-leak-test on macOS
• [merged] #145 — Fix uninitialized memory reads found by valgrind
• [open] #146 — gcc-15 -fanalyzer fixes

BIC-MNI/xdisp — 5 PR(s), 2 merged

• [closed] #5 — Build fixes for modern GCC (C23 default, stricter pointer types)
• [merged] #6 — EZWGL: fix K&R int (*)() decls for GCC 15 / C23 compatibility
• [closed] #7 — EZWGL: extend K&R OldErrorHandler typedef fix to remaining 8 files
• [closed] #8 — C23 build fixes: EZWGL/olgx K&R + handler.c XFindContext (combined)
• [merged] #9 — xdisp: modern-toolchain build fixes (C23, handler.c, EZWGL/olgx)

scilus/containers-scilus — 5 PR(s), 4 merged

• [merged] #39 — Update to 2013-era x86-64 optimizations
• [merged] #40 — Add antsRegistration_affine_SyN.sh to ants container.
• [merged] #43 — Update antsRegistration_affine_SyN.sh version to 1.2
• [closed] #44 — Update antsRegistration_affine_SyN.sh version to 1.3
• [merged] #45 — Update antsRegistration_affine_SyN.sh version to 1.3

Worklenz/worklenz — 4 PR(s), 3 merged

• [merged] #20 — Fix docker-compose
• [merged] #141 — Fix use of deprecated mc command for bucket creation
• [merged] #142 — Generate random passwords in update-docker-env.sh
• [open] #143 — Make postgres container use backend .env file for user/pass/db_name

nighres/nighres — 4 PR(s), 3 merged

• [merged] #169 — Create requirements.txt
• [merged] #170 — Add conda environment.
• [closed] #171 — Switch to using git submodules to maintain version stability
• [merged] #172 — Add a github workflow for testing build

BIC-MNI/minc-tools — 3 PR(s), 3 merged

• [merged] #124 — Fixes for minccalc to build with gcc-15
• [merged] #125 — Rename fdiv to safe_div to avoid conflict with fdiv from system mathcalls-narrow.h
• [merged] #126 — Fix old-style k&r shadow define

VANDAlab/Preprocessing_Pipeline — 3 PR(s), 3 merged

• [merged] #2 — Convert all affine registrations to ANTs
• [merged] #3 — Switch to anlm from nlm for denoising
• [merged] #4 — Update Singularity definition

freesurfer/freesurfer — 3 PR(s), 3 merged

• [merged] #1299 — Enhancements for mri_synthstrip Docker builds
• [merged] #1323 — Add procps to containers to enable nextflow use
• [merged] #1386 — Split cpu and gpu dockerfiles for synthmorph

marwanhawari/stew — 3 PR(s), 0 merged

• [open] #89 — Fix test fixtures for updated GitHub API data
• [open] #90 — Improve automatic and manual asset selection
• [open] #93 — fix: recreate tmp dir before each package upgrade

nf-neuro/modules — 3 PR(s), 2 merged

• [merged] #153 — Switch synthstrip to upstream minimal contianer, add gpu support
• [open] #282 — Implementation of antsRegistration_affine_SyN.sh for registration
• [merged] #370 — Update the CLI podman dev containers to use th development version of scilus

wheelybird/luminary — 3 PR(s), 1 merged

• [closed] #142 — Fix variable for username regex
• [closed] #143 — Complete renaming of POSIX_REGEX to USERNAME_REGEX
• [merged] #144 — Fix typo in extra attribute for README

BIC-MNI/mni_autoreg — 2 PR(s), 2 merged

• [merged] #28 — Fix builds for >gcc10
• [merged] #30 — reversedef: drop duplicate get_volume_XYZV_indices definition

fdechaumont/LiveMouseTracker — 2 PR(s), 2 merged

• [merged] #2 — Add comprehensive README and AGENTS.md
• [merged] #4 — Sync AGENTS.md with README.md: add tracking pipeline, detection params, schema fixes, build/deploy steps

franckferman/LastLog-Audit — 2 PR(s), 0 merged

• [closed] #1 — Fix line endings
• [closed] #2 — Fix python shebang to modernized version

frankyeh/DSI-Studio — 2 PR(s), 2 merged

• [merged] #64 — Build Ubuntu Packages
• [merged] #66 — Add Docker containers to build master

vik16nathan/allen_connectome_qc — 2 PR(s), 2 merged

• [merged] #4 — Copilot/review code best practices
• [merged] #7 — Copilot/evaluate scripts for best practices

BIC-MNI/BEaST — 1 PR(s), 0 merged

• [open] #14 — Bump CMake minimum to 3.5; drop CMP0003 OLD policy

BIC-MNI/oobicpl — 1 PR(s), 1 merged

• [merged] #5 — Replace PCRE dependency with C++ std::regex

BrkRaw/brkraw — 1 PR(s), 1 merged

• [merged] #67 — Don't round header affine

ChristianGaser/cat12 — 1 PR(s), 1 merged

• [merged] #37 — Fix hard-coded SPM directory for Poster

Crivaledaz/Mattermost-LDAP — 1 PR(s), 0 merged

• [closed] #89 — Return the displayName from LDAP so users have proper names

McIntosh-Lab/PLS — 1 PR(s), 0 merged

• [open] #7 — Add changes for modern MATLAB

Mouse-Imaging-Centre/minc-stuffs — 1 PR(s), 0 merged

• [open] #51 — Fix perl shebangs

Mouse-Imaging-Centre/pyminc — 1 PR(s), 1 merged

• [merged] #41 — Take advantage of MINC_TOOLKIT variable to find library to load

NIST-MNI/patch_morphology — 1 PR(s), 1 merged

• [merged] #8 — CMake 4 compat: drop CMP0003 OLD

Rodent-Cognition-Core/CBAS — 1 PR(s), 1 merged

• [merged] #159 — Update README.md

VANDAlab/BISON — 1 PR(s), 1 merged

• [merged] #1 — Update packaging and documentation

VANDAlab/BISON-WMH — 1 PR(s), 1 merged

• [merged] #3 — Update packaging and README

bids-standard/bids-website — 1 PR(s), 1 merged

• [merged] #680 — Add libBIDS.sh to tools.yml

cli-guidelines/cli-guidelines — 1 PR(s), 1 merged

• [merged] #91 — Add more argument parsing libraries

clinivance/platform — 1 PR(s), 1 merged

• [merged] #7 — Bundle compiled static web into upstream caddy container

conda-forge/libitk-feedstock — 1 PR(s), 1 merged

• [merged] #83 — Enable MINC file format and transforms

conda-forge/r-seuratdisk-feedstock — 1 PR(s), 0 merged

• [open] #2 — Update version and syncronize dependencies

conda-forge/rstudio-feedstock — 1 PR(s), 1 merged

• [merged] #1 — Fix version specification to include build # count

defencore/gpd-pocket-3-linux — 1 PR(s), 1 merged

• [merged] #1 — Fix path

getredash/redash — 1 PR(s), 1 merged

• [merged] #5687 — Fix hard-coding of amd64 platform, make ARM build work.

loz-hurst/lmod-platform-detection — 1 PR(s), 0 merged

• [open] #1 — Switch to /etc/os-release for detecting versions

mamba-org/ansible-role-micromamba — 1 PR(s), 1 merged

• [merged] #9 — Add bash profile script to enable micromamba activate

nbafrank/uvr — 1 PR(s), 0 merged

• [open] #116 — Use rstudio/r-builds portable builds for R installation on all platforms

neuralabc/neuralabc_ansible — 1 PR(s), 0 merged

• [open] #22 — Modernize Ansible infrastructure: FQCN, role reorganization, and best practices

requarks/wiki — 1 PR(s), 1 merged

• [merged] #5066 — Fix typo spelling of distinguished

rstudio/reticulate — 1 PR(s), 1 merged

• [merged] #1771 — Add direct check for micromamba and mamba executables, adjust preferred ordering

spinicist/QUIT — 1 PR(s), 0 merged

• [open] #46 — Add more ubuntu build runs for CI

ucl-pond/pySuStaIn — 1 PR(s), 0 merged

• [open] #84 — Low-impact performance optimizations for all SuStaIn classes

[gdevenyi]

David Roper (@david-roper)

3 pull request(s) across 3 upstream project(s) since 2021-06-18 (merged: 2 · open: 1 · closed-unmerged: 0). Excludes DouglasNeuroInformatics, CoBrALab, and david-roper's own personal repos.

Rodent-Cognition-Core/CBAS — 1 PR(s), 1 merged

• [merged] #164 — fix headers in readme file

nipoppy/nipoppy — 1 PR(s), 1 merged

• [merged] #264 — Implement RABIES

xpl/printable-characters — 1 PR(s), 0 merged

• [open] #5 — Add mongolian vowel separator

[gdevenyi]

Josh Unrau (@joshunrau)

14 pull request(s) across 11 upstream project(s) since 2021-06-18 (merged: 5 · open: 1 · closed-unmerged: 8). Excludes DouglasNeuroInformatics, CoBrALab, and joshunrau's own personal repos.

FelixHenninger/lab.js — 3 PR(s), 0 merged

• [closed] #219 — Fix TypeScript Build
• [closed] #223 — Vite example
• [closed] #224 — Libary build

jspsych/jsPsych — 2 PR(s), 1 merged

• [merged] #3384 — improve randomization typing
• [open] #3389 — Add eslint and stricter TypeScript rules for jspsych package

BIC-MNI/minc-toolkit — 1 PR(s), 0 merged

• [closed] #61 — add deprecation warning

BIC-MNI/minc-toolkit-v2 — 1 PR(s), 0 merged

• [closed] #165 — add note for install on arm mac

Gilles86/pymp2rage — 1 PR(s), 0 merged

• [closed] #4 — fixed typo in license

HiDeoo/starlight-typedoc — 1 PR(s), 0 merged

• [closed] #58 — add i18n support

RedBearAK/Toshy — 1 PR(s), 0 merged

• [closed] #87 — add xf86-input-evdev as arch dep

clinivance/platform — 1 PR(s), 1 merged

• [merged] #6 — implement postgres

nestjs/swagger — 1 PR(s), 1 merged

• [merged] #2487 — fix: issue where custom assets are not injected in html

neurobagel/old-query-tool — 1 PR(s), 1 merged

• [merged] #105 — [ENH]: add breakpoints

prisma/web — 1 PR(s), 1 merged

• [merged] #5515 — add --dev flag to bun install command

[gdevenyi]

Cian Monnin (@CMonnin)

7 pull request(s) across 6 upstream project(s) since 2021-06-18 (merged: 6 · open: 1 · closed-unmerged: 0). Excludes DouglasNeuroInformatics, CoBrALab, and CMonnin's own personal repos.

nf-neuro/modules — 2 PR(s), 2 merged

• [merged] #347 — Magetbrain
• [merged] #361 — add terminal-based dev environment as alternative to devcontainers

UNFmontreal/Dcm2Bids — 1 PR(s), 1 merged

• [merged] #357 — ==[FIX]== OS level timeout in check_github_latest()

jspsych/jsPsych — 1 PR(s), 1 merged

• [merged] #3408 — Update plugin-development.md

jspsych/jspsych-contrib — 1 PR(s), 0 merged

• [open] #143 — feature: text to speech with button response and keboard response

nf-core/configs — 1 PR(s), 1 merged

• [merged] #964 — added some clusters including trillium and updated some resources to …

nipoppy/nipoppy — 1 PR(s), 1 merged

• [merged] #869 — [DOC] Fix typo in command-line interface example

[gdevenyi]

Thomas Beaudry (@thomasbeaudry)

2 pull request(s) across 1 upstream project(s) since 2021-06-18 (merged: 2 · open: 0 · closed-unmerged: 0). Excludes DouglasNeuroInformatics, CoBrALab, and thomasbeaudry's own personal repos.

netdata/netdata — 2 PR(s), 2 merged

• [merged] #16286 — Apcupsd selftest metric
• [merged] #16361 — Add a apcupsd status code metric

[CMonnin]

@CMonnin
Nipoppy configuration files for freesurfer 8.1.0 pipeline
https://zenodo.org/records/18488207
Nipoppy configuration files for mideface 8.1.0 pipeline
https://zenodo.org/records/18435700