Neurodocker

🐛 Bug Fix

- FIX use --transform in freesurfer's template to generalize across freesurfer versions to strip leading `freesurfer/` folder [626](https://github.com/ReproNim/neurodocker/pull/626) ([mvdoc](https://github.com/mvdoc))
- FIX remove comment from freesurfer env line [622](https://github.com/ReproNim/neurodocker/pull/622) ([mvdoc](https://github.com/mvdoc))
- FIX add default header and entrypoint to docker and singularity files [623](https://github.com/ReproNim/neurodocker/pull/623) ([mvdoc](https://github.com/mvdoc))
- [BOT] update pre-commit hooks [627](https://github.com/ReproNim/neurodocker/pull/627) ([Remi-Gau](https://github.com/Remi-Gau) [github-actions[bot]](https://github.com/github-actions[bot]))
- Fix typo of "softwares" [624](https://github.com/ReproNim/neurodocker/pull/624) ([yarikoptic](https://github.com/yarikoptic))
- [BOT] update pre-commit hooks [621](https://github.com/ReproNim/neurodocker/pull/621) ([Remi-Gau](https://github.com/Remi-Gau) [github-actions[bot]](https://github.com/github-actions[bot]))

Authors: 4

- [github-actions[bot]](https://github.com/github-actions[bot])
- Matteo Visconti di Oleggio Castello ([mvdoc](https://github.com/mvdoc))
- Remi Gau ([Remi-Gau](https://github.com/Remi-Gau))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

💥 Breaking Change

- Bump actions/checkout from 3 to 4 [582](https://github.com/ReproNim/neurodocker/pull/582) ([dependabot[bot]](https://github.com/dependabot[bot]))
- Bump actions/checkout from 3 to 4 [573](https://github.com/ReproNim/neurodocker/pull/573) ([dependabot[bot]](https://github.com/dependabot[bot]))
- Bump actions/stale from 5 to 8 [560](https://github.com/ReproNim/neurodocker/pull/560) ([dependabot[bot]](https://github.com/dependabot[bot]))
- Bump actions/checkout from 2 to 3 [557](https://github.com/ReproNim/neurodocker/pull/557) ([dependabot[bot]](https://github.com/dependabot[bot]))
- Bump actions/setup-python from 2 to 4 [556](https://github.com/ReproNim/neurodocker/pull/556) ([dependabot[bot]](https://github.com/dependabot[bot]))

🐛 Bug Fix

- [BOT] update pre-commit hooks [616](https://github.com/ReproNim/neurodocker/pull/616) ([Remi-Gau](https://github.com/Remi-Gau) [github-actions[bot]](https://github.com/github-actions[bot]))
- [BOT] update pre-commit hooks [614](https://github.com/ReproNim/neurodocker/pull/614) ([Remi-Gau](https://github.com/Remi-Gau) [github-actions[bot]](https://github.com/github-actions[bot]))
- make scripts executable after build [615](https://github.com/ReproNim/neurodocker/pull/615) ([stebo85](https://github.com/stebo85))
- [BOT] update pre-commit hooks [613](https://github.com/ReproNim/neurodocker/pull/613) ([Remi-Gau](https://github.com/Remi-Gau) [github-actions[bot]](https://github.com/github-actions[bot]))
- Use HTTPS for NeuroDebian APT listing urls [612](https://github.com/ReproNim/neurodocker/pull/612) ([TheChymera](https://github.com/TheChymera))
- [BOT] update pre-commit hooks [610](https://github.com/ReproNim/neurodocker/pull/610) ([Remi-Gau](https://github.com/Remi-Gau) [github-actions[bot]](https://github.com/github-actions[bot]))
- [FIX] Update branch in update_precommit_hooks.yml [609](https://github.com/ReproNim/neurodocker/pull/609) ([Remi-Gau](https://github.com/Remi-Gau))
- [ENH] package with hatchling and switch to pyproject.toml [607](https://github.com/ReproNim/neurodocker/pull/607) ([Remi-Gau](https://github.com/Remi-Gau))
- [MAINT] update linting config and CI [604](https://github.com/ReproNim/neurodocker/pull/604) ([Remi-Gau](https://github.com/Remi-Gau))
- fixed flake8 errors from 597 [598](https://github.com/ReproNim/neurodocker/pull/598) ([Vbitz](https://github.com/Vbitz))
- Added "--add" command line option to add tar files as docker layers. [597](https://github.com/ReproNim/neurodocker/pull/597) ([Vbitz](https://github.com/Vbitz))
- added versions to Library PATH [593](https://github.com/ReproNim/neurodocker/pull/593) ([stebo85](https://github.com/stebo85))
- update matlabmcr [592](https://github.com/ReproNim/neurodocker/pull/592) ([stebo85](https://github.com/stebo85))
- [FIX] add url bids validator [591](https://github.com/ReproNim/neurodocker/pull/591) ([Remi-Gau](https://github.com/Remi-Gau))
- [DOC] add list of supported software [587](https://github.com/ReproNim/neurodocker/pull/587) ([Remi-Gau](https://github.com/Remi-Gau))
- [ENH] add templates bids_validator [586](https://github.com/ReproNim/neurodocker/pull/586) ([Remi-Gau](https://github.com/Remi-Gau))
- [MAINT] test build jq [589](https://github.com/ReproNim/neurodocker/pull/589) ([Remi-Gau](https://github.com/Remi-Gau))
- [ENH] test on python 3.12 [588](https://github.com/ReproNim/neurodocker/pull/588) ([Remi-Gau](https://github.com/Remi-Gau))
- Update fsl.yaml [583](https://github.com/ReproNim/neurodocker/pull/583) ([stebo85](https://github.com/stebo85))
- [DOC] update doc [569](https://github.com/ReproNim/neurodocker/pull/569) ([Remi-Gau](https://github.com/Remi-Gau))
- [ENH] implement more recent mrtrix version [579](https://github.com/ReproNim/neurodocker/pull/579) ([Remi-Gau](https://github.com/Remi-Gau))
- Update examples.rst [578](https://github.com/ReproNim/neurodocker/pull/578) ([stebo85](https://github.com/stebo85))
- added FSL interactivity note [576](https://github.com/ReproNim/neurodocker/pull/576) ([stebo85](https://github.com/stebo85))
- Include FSL license auto-yes example [575](https://github.com/ReproNim/neurodocker/pull/575) ([stebo85](https://github.com/stebo85))
- [MAINT] Update stale.yml [577](https://github.com/ReproNim/neurodocker/pull/577) ([Remi-Gau](https://github.com/Remi-Gau))
- [FIX] install the proper dependencies for doc build [574](https://github.com/ReproNim/neurodocker/pull/574) ([Remi-Gau](https://github.com/Remi-Gau))
- [DOC] auto doc main CLI [463](https://github.com/ReproNim/neurodocker/pull/463) ([Remi-Gau](https://github.com/Remi-Gau))
- [FIX] use local var for software name in bootstrap workflow [572](https://github.com/ReproNim/neurodocker/pull/572) ([Remi-Gau](https://github.com/Remi-Gau))
- [FIX] use env variable in bootstrap workflow [571](https://github.com/ReproNim/neurodocker/pull/571) ([Remi-Gau](https://github.com/Remi-Gau))
- [INFRA] add possibility to only build a single workflow [570](https://github.com/ReproNim/neurodocker/pull/570) ([Remi-Gau](https://github.com/Remi-Gau))
- [MAINT] test build of conda as part of the bootstrap workflow [566](https://github.com/ReproNim/neurodocker/pull/566) ([Remi-Gau](https://github.com/Remi-Gau))
- [MAINT] minimize file changes that can trigger the bootstrap workflow [564](https://github.com/ReproNim/neurodocker/pull/564) ([Remi-Gau](https://github.com/Remi-Gau))
- set python version for format job [563](https://github.com/ReproNim/neurodocker/pull/563) ([stebo85](https://github.com/stebo85))
- Add mamba option to miniconda [562](https://github.com/ReproNim/neurodocker/pull/562) ([Shotgunosine](https://github.com/Shotgunosine))
- [MAINT] remove oldest distro in automated build testing [559](https://github.com/ReproNim/neurodocker/pull/559) ([Remi-Gau](https://github.com/Remi-Gau))
- [MAINT] split format checking and testing in CI [554](https://github.com/ReproNim/neurodocker/pull/554) ([Remi-Gau](https://github.com/Remi-Gau))
- [MAINT] Simplify type annotations [551](https://github.com/ReproNim/neurodocker/pull/551) ([Remi-Gau](https://github.com/Remi-Gau))
- apply isort and all pre-commit hooks [549](https://github.com/ReproNim/neurodocker/pull/549) ([Remi-Gau](https://github.com/Remi-Gau))
- Mcr bug [471](https://github.com/ReproNim/neurodocker/pull/471) ([stebo85](https://github.com/stebo85))
- Add codespell: config, pre-commit, workflow + 1 typo fixed [544](https://github.com/ReproNim/neurodocker/pull/544) ([yarikoptic](https://github.com/yarikoptic) [stebo85](https://github.com/stebo85))
- added freesurfer 7.3.2 [547](https://github.com/ReproNim/neurodocker/pull/547) ([stebo85](https://github.com/stebo85))
- add fsl 6.0.7.1 [543](https://github.com/ReproNim/neurodocker/pull/543) ([stebo85](https://github.com/stebo85))
- added freesurfer 7.4.1 [542](https://github.com/ReproNim/neurodocker/pull/542) ([hjbockholt](https://github.com/hjbockholt))
- Fixing my update for mcr2023a [540](https://github.com/ReproNim/neurodocker/pull/540) ([dnkennedy](https://github.com/dnkennedy))
- Update matlabmcr.yaml [539](https://github.com/ReproNim/neurodocker/pull/539) ([dnkennedy](https://github.com/dnkennedy))
- Update years to have full range of years of the project [534](https://github.com/ReproNim/neurodocker/pull/534) ([yarikoptic](https://github.com/yarikoptic))
- Update cat [533](https://github.com/ReproNim/neurodocker/pull/533) ([stebo85](https://github.com/stebo85))

⚠️ Pushed to `master`

- Change name of parent directory ([kaczmarj](https://github.com/kaczmarj))

🏠 Internal

- Upgrade intuit auto to 11.1.6 (most recent) [617](https://github.com/ReproNim/neurodocker/pull/617) ([yarikoptic](https://github.com/yarikoptic))

🔩 Dependency Updates

- Bump actions/setup-python from 4 to 5 [594](https://github.com/ReproNim/neurodocker/pull/594) ([dependabot[bot]](https://github.com/dependabot[bot]))
- Bump actions/stale from 8 to 9 [595](https://github.com/ReproNim/neurodocker/pull/595) ([dependabot[bot]](https://github.com/dependabot[bot]))

Authors: 11

- [dependabot[bot]](https://github.com/dependabot[bot])
- [github-actions[bot]](https://github.com/github-actions[bot])
- David Kennedy ([dnkennedy](https://github.com/dnkennedy))
- Dylan Nielson ([Shotgunosine](https://github.com/Shotgunosine))
- H. Jeremy Bockholt ([hjbockholt](https://github.com/hjbockholt))
- Horea Christian ([TheChymera](https://github.com/TheChymera))
- Jakub Kaczmarzyk ([kaczmarj](https://github.com/kaczmarj))
- Joshua Scarsbrook ([Vbitz](https://github.com/Vbitz))
- Remi Gau ([Remi-Gau](https://github.com/Remi-Gau))
- Steffen Bollmann ([stebo85](https://github.com/stebo85))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🐛 Bug Fix

- Afni missing dependencies for suma [512](https://github.com/ReproNim/neurodocker/pull/512) ([stebo85](https://github.com/stebo85))
- modifying value for entry point to allow -arg or --arg [515](https://github.com/ReproNim/neurodocker/pull/515) ([djarecka](https://github.com/djarecka) [kaczmarj](https://github.com/kaczmarj))
- Mcr missing deb libxp6 [526](https://github.com/ReproNim/neurodocker/pull/526) ([stebo85](https://github.com/stebo85))
- NEW: Add support for FSL version 6.0.6 onwards [527](https://github.com/ReproNim/neurodocker/pull/527) ([ghisvail](https://github.com/ghisvail))
- Enable build of docs with Sphinx 6 [525](https://github.com/ReproNim/neurodocker/pull/525) ([ghisvail](https://github.com/ghisvail))
- Add FSL version 6.0.5.2 [523](https://github.com/ReproNim/neurodocker/pull/523) ([ghisvail](https://github.com/ghisvail))
- Update ants.yaml [521](https://github.com/ReproNim/neurodocker/pull/521) ([araikes](https://github.com/araikes) [kaczmarj](https://github.com/kaczmarj))
- [FIX] fix link to build dashboard [517](https://github.com/ReproNim/neurodocker/pull/517) ([Remi-Gau](https://github.com/Remi-Gau))
- Update cli.rst [514](https://github.com/ReproNim/neurodocker/pull/514) ([sooyounga](https://github.com/sooyounga) [djarecka](https://github.com/djarecka))
- updated version tags and added latest tag clarification to docs [516](https://github.com/ReproNim/neurodocker/pull/516) ([sooyounga](https://github.com/sooyounga))
- Minc install from deb and rpm [509](https://github.com/ReproNim/neurodocker/pull/509) ([stebo85](https://github.com/stebo85))
- fix: repo info ([satra](https://github.com/satra))
- [INFRA] test docker builds in CI [487](https://github.com/ReproNim/neurodocker/pull/487) ([Remi-Gau](https://github.com/Remi-Gau) [pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]) [satra](https://github.com/satra))
- do not install sphinx 6.x [505](https://github.com/ReproNim/neurodocker/pull/505) ([kaczmarj](https://github.com/kaczmarj))
- add bad versions to et file [502](https://github.com/ReproNim/neurodocker/pull/502) ([satra](https://github.com/satra))
- [TESTS] check black style in github actions [501](https://github.com/ReproNim/neurodocker/pull/501) ([kaczmarj](https://github.com/kaczmarj))

⚠️ Pushed to `master`

- Update README.md ([djarecka](https://github.com/djarecka))
- add workflow token ([satra](https://github.com/satra))
- add commit agent ([satra](https://github.com/satra))
- add all changed files ([satra](https://github.com/satra))
- Update bootstrap.yml ([satra](https://github.com/satra))
- simplify git commit ([satra](https://github.com/satra))
- allow writing actions ([satra](https://github.com/satra))
- remove on demand ([satra](https://github.com/satra))
- fix docs build ([satra](https://github.com/satra))
- fix: syntax ([satra](https://github.com/satra))
- testing sphinx build ([satra](https://github.com/satra))

📝 Documentation

- changed base image for AFNI to fedora:35 [520](https://github.com/ReproNim/neurodocker/pull/520) ([stebo85](https://github.com/stebo85) [kaczmarj](https://github.com/kaczmarj))

Authors: 9

- [araikes](https://github.com/araikes)
- [pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot])
- Dorota Jarecka ([djarecka](https://github.com/djarecka))
- Ghislain Vaillant ([ghisvail](https://github.com/ghisvail))
- Jakub Kaczmarzyk ([kaczmarj](https://github.com/kaczmarj))
- Remi Gau ([Remi-Gau](https://github.com/Remi-Gau))
- Satrajit Ghosh ([satra](https://github.com/satra))
- Sooyoung Ahn ([sooyounga](https://github.com/sooyounga))
- Steffen Bollmann ([stebo85](https://github.com/stebo85))

---

🐛 Bug Fix

- fix the types in --copy and --entrypoint [500](https://github.com/ReproNim/neurodocker/pull/500) ([kaczmarj](https://github.com/kaczmarj))
- add long_description to setup.cfg [465](https://github.com/ReproNim/neurodocker/pull/465) ([kaczmarj](https://github.com/kaczmarj))
- [FIX] add regression test for 498 [499](https://github.com/ReproNim/neurodocker/pull/499) ([Remi-Gau](https://github.com/Remi-Gau))

Authors: 2

- Jakub Kaczmarzyk ([kaczmarj](https://github.com/kaczmarj))
- Remi Gau ([Remi-Gau](https://github.com/Remi-Gau))

---

🐛 Bug Fix

- FIX: skip minification tests on M1/M2 macs and run them otherwise [497](https://github.com/ReproNim/neurodocker/pull/497) ([kaczmarj](https://github.com/kaczmarj))
- Add/ants24x [473](https://github.com/ReproNim/neurodocker/pull/473) ([araikes](https://github.com/araikes) [kaczmarj](https://github.com/kaczmarj))

Authors: 2

- [araikes](https://github.com/araikes)
- Jakub Kaczmarzyk ([kaczmarj](https://github.com/kaczmarj))

---

🐛 Bug Fix

- fix: auto setup [496](https://github.com/ReproNim/neurodocker/pull/496) ([satra](https://github.com/satra))
- enh: add release workflow [495](https://github.com/ReproNim/neurodocker/pull/495) ([satra](https://github.com/satra))
- remove empty lines [488](https://github.com/ReproNim/neurodocker/pull/488) ([satra](https://github.com/satra))
- FIX: --version output in containers [493](https://github.com/ReproNim/neurodocker/pull/493) ([kaczmarj](https://github.com/kaczmarj))
- fix: remove py 3.7 and add apptainer 1.1.5 [490](https://github.com/ReproNim/neurodocker/pull/490) ([satra](https://github.com/satra))
- fix: adjust optionEatAll for click >= 8 [492](https://github.com/ReproNim/neurodocker/pull/492) ([satra](https://github.com/satra))
- update pre-commit [482](https://github.com/ReproNim/neurodocker/pull/482) ([Remi-Gau](https://github.com/Remi-Gau))

⚠️ Pushed to `master`

- fix: install mypy stubs ([satra](https://github.com/satra))
- fix: mypy configuration ([satra](https://github.com/satra))

Authors: 3

- Jakub Kaczmarzyk ([kaczmarj](https://github.com/kaczmarj))
- Remi Gau ([Remi-Gau](https://github.com/Remi-Gau))
- Satrajit Ghosh ([satra](https://github.com/satra))