New feature release in the 25.1 series.
This release introduces a new TemplateFlowClient class that provides the
functionality previously exposed in templateflow.api.
templateflow.api is now a thin wrapper around a global instance of TemplateFlowClient,
so existing code using templateflow.api should continue to work as before.
These changes allow multiple independent clients to coexist in the same Python process, as well as defer loading of data from the filesystem until it is requested, significantly improving import time.
- RF: Factor TemplateFlow into Cache and Client classes (#149)
- FIX: Error on missing S3 files, do not write error data to disk (#148)
Patch release to update templateflow skeleton.
Patch release to escape special characters when fetching data from S3.
- FIX: Quote s3 path to handle special characters (#147)
Patch release containing a fix for get queries including the "+" character.
- FIX: Allow plus signs in 'to' and 'from' entities (#146)
Patch release containing fixes to transform names in two templates.
Minor release including updated templates.
- FIX: Fix crash in templateflow get when matching one file (#140)
- MAINT: Update Python support, datalad and git-annex deps (#143)
Patch release containing one bugfix and updating the default skeleton.
- FIX: Avoid directory clobber during zip extraction (#131)
- MAINT: Overdue updates and revision of CircleCI (#136)
Release recalled because it was uploaded in a stale status of the client.
Minor release including a new command line interface for the Client.
- ENH: Add a command line interface (#123)
- MAINT: Update DataLad's pinned version (#128)
- MAINT: Revise failing Pypi deployment and
twine check(#127) - MAINT: Generate a requirements file with
testdependencies (#125) - MAINT: Add codespell and make it fix some typos (#121)
- MAINT: Revise code style according to ruff (#124)
- MAINT: Add license header in all Python files (#122)
- MAINT: Migrate to hatchling packaging (#120)
- MAINT: Run ruff and address some issues (#119)
- MAINT: Finalize migration of package build to PEP517/8 (#117)
Minor release updating PyBIDS's configuration to enable new entities that allow the selection of recently added FreeSurfer's surface parcellations in templateflow/tpl-fsaverage#5.
- ENH: Add seg-<label> and scale-<number> entities (#114)
Minor release to update skeleton to include recently added templates.
- CI: Add manual trigger, bump action versions (#113)
Minor release including support for Python 3.12.
Python 3.7 support has been removed.
- FIX: Use Path.as_posix() and f-strings to build correct URLs on Windows (#107)
- MNT: Python 3.12 support, drop Python 3.7 and pkg_resources (#109)
Minor release including additional API features and an updated skeleton.
- FIX: Preempt
BIDSLayoutfrom indexing dot-folders (#99) - ENH: Make sure existing
layout.get_*are not bubbled in (#102) - ENH: Allow access to PyBIDS' magic
get_*(#101) - ENH: Add an
api.ls()function to list (without getting) files (#97) - MAINT: Discontinue legacy docker runners of CircleCI (#104)
- MAINT: Rotate CircleCI secrets and setup up org-level context (#103)
- MAINT: Fix docs build environment in CircleCI (#96)
Patch release updating the S3 skeleton to include the fixed version of tpl-MouseIn.
Minor release including the feedback received through peer-review of the preprint. Please note that this release is supported by Python +3.7.
- FIX: Normalize extensions for leading dot & update doctests to new resources (#92)
- ENH: Add a
wipe()utility to clear up the cache (#91) - DOC: Update notebooks submodule (#94)
- MAINT: Drop Python 3.6 (#93)
Patch release with a substantially documentation update, as well as usage improvements. Additionally, new surface meshes were added for the fsLR template.
- DOC: Substantial update and re-structuring to the documentation (#77) (#79)
- FIX: layout is
Nonewhen PyBIDS not correctly installed (#72) - FIX: Drop
doi2biband query doi.org directly (#76) - MAINT: Pin
setuptools >=45, new dependency as ofsetuptools_scm>=6.0.1(#73)
Patch release with improvements to the template fetching experience. With thanks to Lea Waller for the contribution.
- FIX: Use
BIDSLayoutIndexerwhen initiatingBIDSLayout(#61) - FIX: Display correct units when downloading templates (#63)
- FIX: GitHub Actions build (#64)
- ENH: Add option to raise exception on empty
getqueries (#57) - ENH: Ensure templates layout is re-indexed when updated (#59)
Release 0.7.0 was withdrawn because of inconsistencies in deployment.
Patch release including an updated PyBIDS configuration file for the PyBIDS 0.11.x series.
- FIX: Include leading dots in extensions (#56)
Patch release including some minimal improvements to package building and CI.
- MAINT: Some additional distribution improvements (#51)
Patch release to generate and distribute wheels.
- MAINT: Run
black(#50) - MAINT: Distribute wheel + Revise CI framework (#49)
Minor release in preparation of a new CalVer versioning following the lead of fMRIPrep.
This release contains a fair amount of maintenance work to ensure synchronicity with the TemplateFlow Archive (https://github.com/templateflow/templateflow). These maintenance actions drive the development towards establishing a peer-reviewed, lightweight template submission protocol. The release includes an update mechanism, enabling users of the S3-backed mode of operation (default) to update their local Archive structure without reinstalling the client. This feature is enabled by default on import time, to disable it make sure you export TEMPLATEFLOW_AUTOUPDATE=off.
With thanks to Yarik for a datalad-related bug-fix.
With thanks to V. Fonov for contributing with the new tpl-MNI152NLin2009cSym.
- FIX: Provide path to the dataset as
datasetargument (#48) - ENH: Run an automatic S3-skeleton update on import by default (#45)
- ENH: Update the internal index of TemplateFlow (#40)
- ENH: Automatic generation of template citations (#35)
- MAINT: Set-up a GitHub action to test installation alternatives (see #23).
- MAINT: Migrate to
setuptools_scm(#42) - MAINT: Run
blackon the whole tree (#41) - MAINT: Transfer the burden of keeping the S3-skeleton updated over to the archive (#39)
Patch release in the 0.5 series, adding a soft brainmask for numerical stability in
floating-point rounding of atlas-based brain-extraction methods using the
MNI152NLin2009cAsym template.
Patch of the new 0.5.x series, including a new rodent template
and file fixes for fsaverage and fsLR templates.
With thanks to E. MacNicol for contributing the new tpl-WHS.
- MAINT: Drop Python 3.5 (#36)
This release has been removed and should not be used.
Patch release including a bugfix, adding a DataLad pin, and making PyBIDS pin more flexible.
- MAINT: Update PyBIDS pin and DataLad pin
- FIX: Density key (#31)
First release after a deep revision of the tests and the continuous integration setup. Also includes minor reliability improvements over the previous release and some bugfixes.
- MAINT: Testing Automatically update CHANGES after merge (51988f8) (#27)
- MAINT: Enable code coverage collection (#25)
- MAINT: Switch to a
setup.cfg-style of installation (#24) - FIX: Check and update
$HOMEif needed with every installation (#20) - FIX: Do not merge branches into master when pushing back skell (#19)
- FIX: Commit newly generated S3 skeletons back to repo (#17)
- FIX: Add
extensionentity for selection (#16) @effigies
- MAINT: Use PyBIDS 0.9.x (#15) @effigies
- ENH: Add
MNIInfanttemplate.
- ENH: Added
MNIPediatricAsymtemplate. - ENH: Updated spec to allow several cohorts (
cohort-).
- ENH: Added the Schaefer 2018 atlas) to
MNI152NLin6Asym. - ENH: Mapped the Schaefer atlas and the Harvard-Oxford atlas into
MNI152NLin2009cAsym.
- ENH: Added FSL's Harvard-Oxford template to
MNI152NLin6Asym.
- ENH: New release including bugfixes for
MNI152NLin2009cAsym(particularly https://github.com/templateflow/tpl-MNI152NLin2009cAsym/commit/6e6d5915c7d8055d4af5efbf5e5457a0ab3246b9)
- ENH: Finish adding
MNI152NLin6Symafter curation of NIfTI volumes and exporting to S3.
- ENH: Add volumetric data to the
fsLRtemplate. - ENH: Rename the segmentation of subcortical structures to be consistent with the new files.
- ENH: New release to include the new
MNI152NLin6Asymtemplate (the default MNI template of FSL).
- FIX: Update TemplateFlow skeleton to include
tpl-fsaverage/tpl-fsaverage_dseg.tsv, after TemplateFlow update.
- FIX:
api.get- robuster fetcher algorithm (allows S3 download on DL repos) and better error messages (#10)
- FIX: Require environment variable to use DataLad (#8)
- ENH: Testing a better
.zenodo.jsonsettings.
- ENH: First minimally functional TemplateFlow client release.
Hotfix release to retrieve correct version when pip installed.
- MAINT: Add a
.zenodo.jsonfile.
- ENH: Datalad-free alternative for TemplateFlow (#7)
- ENH: Use a BIDSLayout to index TemplateFlow (#6)
- ENH: Add a
get_metadatautility
- ENH: Add
api.templates()+ one doctest
- ENH: Add one doctest
- ENH: First functional release