Changes

1.3.0-dev.2 (2023-10-31)

Bug Fixes

  • Dockerfile: update nodejs to 18 as bids-validator failed to build (c4d6aac)

Features

  • bids/dataset.py: add arguments to datalad create_siblings to make it more robust (4851724)

1.3.0-dev.1 (2023-08-04)

Bug Fixes

  • handle datasets not datalad-managed for import / edit commands (a1a4bde)

  • set git user name and email used by Datalad ops (de489e2)

Features

  • add dataset and project commands / methods to release a version (c295ff6)

  • add dataset.publish and dataset.clone commands and corresponding functions (bd9d270)

1.2.0 (2023-07-14)

Bug Fixes

  • conftest.py: change permissions on .git repositories in Datalad datasets at the beginning of the tests (bc1bf4b)

  • make changes in Datalad-related code that make tests working (5b7989e)

  • use absolute path when creating nested datalad dataset (355ce0c)

Features

  • add versioning module file with tags-related functions (9e85674)

  • bids.dataset: add Datalad’s create() and save() methods (0aee9e1)

  • cli/run.py: add commands to inerface with tags / branches of Datalad datasets (e299d00)

  • Dockerfile: install git and git-annex in Docker container image (d8fe0dd)

  • Dockerfile: install recent standalone version of git-annex provided by Datalad (32136cf)

  • handlers.dataset: call datalad create() and save() methods (ebb7cc8)

  • handlers.participants: call Datalad’s create() and save() methods (08d86c9)

  • handlers.project: call Datalad’s create() and save() methods (08d1adf)

  • install pytest-order in Dockerfile and test config of setup.cfg (23732c3)

  • setup.cfg: add datalad-neuroimaging extension (509e668)

  • write release text block in CHANGES of BIDS dataset at version tag creation (37f4f33)

1.2.0-dev.2 (2023-07-14)

Features

  • write release text block in CHANGES of BIDS dataset at version tag creation (37f4f33)

1.2.0-dev.1 (2023-07-14)

Bug Fixes

  • conftest.py: change permissions on .git repositories in Datalad datasets at the beginning of the tests (bc1bf4b)

  • make changes in Datalad-related code that make tests working (5b7989e)

  • use absolute path when creating nested datalad dataset (355ce0c)

Features

  • add versioning module file with tags-related functions (9e85674)

  • bids.dataset: add Datalad’s create() and save() methods (0aee9e1)

  • cli/run.py: add commands to inerface with tags / branches of Datalad datasets (e299d00)

  • Dockerfile: install git and git-annex in Docker container image (d8fe0dd)

  • Dockerfile: install recent standalone version of git-annex provided by Datalad (32136cf)

  • handlers.dataset: call datalad create() and save() methods (ebb7cc8)

  • handlers.participants: call Datalad’s create() and save() methods (08d86c9)

  • handlers.project: call Datalad’s create() and save() methods (08d1adf)

  • install pytest-order in Dockerfile and test config of setup.cfg (23732c3)

  • setup.cfg: add datalad-neuroimaging extension (509e668)

1.1.1 (2023-06-15)

Bug Fixes

  • docs/CHANGES.md: clean duplicated version change logs (35e33f4)

1.1.0 (2023-06-15)

Bug Fixes

  • .gitlab-ci.yml: add github to list of known ssh hosts (9ce3ae9)

  • .gitlab-ci.yml: inverse order of steps and make sure we work with updated branch in deploy-release (144aca1)

  • .gitlab-ci.yml: review ssh key for github push (b5a6f66)

  • .gitlab-ci.yml: use ssh instead of https for github push in deploy-release (23bc34a)

  • comment codecov check (3d685b7)

  • handlers.project: changes to make all tests passed (4d6a126)

  • handlers.project: correct way to extract input paths and create intermediate dirs for doc import (c44fb70)

  • Makefile: update image tag (ee91f2a)

Features

  • add new project module with draft of methods supporting the HIP collab space (0aa717b)

  • add PNG images for logos of dataHIPy package (412ca28)

  • bids.dataset: add methods to support the creation of an initial BIDS dataset (8b95bcc)

  • cli.run: add new commands to the commandline interface (47e9702)

  • handlers.project: add environments folder to project structure (d387507)

  • handlers.project: create initial documents directory structure with “clinical”, “reports”, “protocols”, “other” folders (e9feeae)

  • handlers.project: implement methods supporting the creation and population of collab projects (71d79bf)

  • handlers.project: print info at start and end with “SUCCESS” message in main methods (c35a49a)

  • write JSON dataset summary in project methods (17b96a3)

1.0.1 (2023-03-02)

Bug Fixes

  • remove orcid from .zenodo.json (865335e)

1.0.0 (2023-03-02)

Bug Fixes

  • add dedicated bids_manager module with method to remove AcquisitionDate from ieeg json files created by BIDS_Manager (ed26784)

  • add print to get_version.py (f83f9e1)

  • add versioneer in docs/requirements.txt (7fb67a3)

  • better handle the insertion of the SEEG information into the indexed content (a299d73)

  • bids/utils/update_with_participants_info: handle case when participants.tsv is empty (9e20468)

  • bids/utils: better handle bids dataset and schema version in get_bidsdataset_content() (6e8fd0e)

  • change regex in from field of semantic release replace plugin (8f843be)

  • correct how version tags are generated and used in Makefile (ade139b)

  • generation of list of participant groups (dd48a3a)

  • import resource_filename from pkg_resources in bids/utils.py (082a7f9)

  • Makefile: replace / and _ in branch name of docker tag (128d54b)

  • Makefile: review how to normalize the tag (a912511)

  • paths in github action yaml file (5963d50)

  • remove AcquisitionDate from ieeg json files created by BIDS_Manager (1bbf98c)

  • replace sub.create by sub.import in VALID_COMMANDS of scripts/main.py (b791593)

  • review how to insert the year release_date that was causing troubles in get_version.py (cc9852e)

  • review imports of bids_manager to allow sphinx argparse to generate the documentation of the parser in usage.rst (86e5960)

  • set “id” in dataset content to be indexed (ea765b9)

  • Set “n/a” values as null in dataset json content to make elasticsearch happy indexing it (dcf3abf)

  • update main doc only if master and dev branches are updated (c52af1d)

  • update regex for replacement of version (96c1128)

Features

  • add BIDS_VERSION to bids.const (a986cce)

  • add get_subject_bidsfile_info in bids.utils to handle this task with pybids (65b7d25)

  • add methods to create the json summarizing bids datasets for indexing (f54d291)

  • add original pybids bids.json config file (5687d17)

  • bids_utils: extract additional ChannelCount fields in get_bidsdataset_content (9e23ebf)

  • bids_utils: use asyncio to generate asynchronously the indexed content of multiple datasets (edcf742)

  • check the validity of the value given to –command parser’s argument (e2b3f14)

  • create function to get dataset size in bids/utils.py (680ffc3)

  • Dockerfile: install bids-validator npm package from our fork on dev-hip branch (85f9afd)

  • fixed build and tag name for backward compatibility (93e81a0)

  • get dataset content to be indexed for all at once (a397b00)

  • handle CT in sub_import() of participants.py using our modified BIDS Manager fork (4552e8c)

  • implement function to create BIDSLayout object with custom config to handle CT (fea0b72)

  • install pybids and pandas in docker (8d3f7e0)

  • make adjustment of bids dataset content (15008ad)

  • Makefile: use BuildKit for docker build (fa0b55b)

  • perform test and code coverage with pytest and pytest-cov (8a89db1)

  • validate with bids-validator and put outputs into the dataset’s JSON to be indexed (c1bcd79)

Reverts

  • change back to from: version = “.*” for semrel replace plugin (ea516e1)

1.0.0-dev.2 (2023-03-02)

Bug Fixes

  • change regex in from field of semantic release replace plugin (8f843be)

  • review how to insert the year release_date that was causing troubles in get_version.py (cc9852e)

  • update main doc only if master and dev branches are updated (c52af1d)

  • update regex for replacement of version (96c1128)

Reverts

  • change back to from: version = “.*” for semrel replace plugin (ea516e1)

1.0.0-dev.1 (2023-02-26)

Bug Fixes

  • add dedicated bids_manager module with method to remove AcquisitionDate from ieeg json files created by BIDS_Manager (ed26784)

  • add print to get_version.py (f83f9e1)

  • add versioneer in docs/requirements.txt (7fb67a3)

  • better handle the insertion of the SEEG information into the indexed content (a299d73)

  • bids/utils/update_with_participants_info: handle case when participants.tsv is empty (9e20468)

  • bids/utils: better handle bids dataset and schema version in get_bidsdataset_content() (6e8fd0e)

  • correct how version tags are generated and used in Makefile (ade139b)

  • generation of list of participant groups (dd48a3a)

  • import resource_filename from pkg_resources in bids/utils.py (082a7f9)

  • Makefile: replace / and _ in branch name of docker tag (128d54b)

  • Makefile: review how to normalize the tag (a912511)

  • paths in github action yaml file (5963d50)

  • remove AcquisitionDate from ieeg json files created by BIDS_Manager (1bbf98c)

  • replace sub.create by sub.import in VALID_COMMANDS of scripts/main.py (b791593)

  • review imports of bids_manager to allow sphinx argparse to generate the documentation of the parser in usage.rst (86e5960)

  • set “id” in dataset content to be indexed (ea765b9)

  • Set “n/a” values as null in dataset json content to make elasticsearch happy indexing it (dcf3abf)

Features

  • add BIDS_VERSION to bids.const (a986cce)

  • add get_subject_bidsfile_info in bids.utils to handle this task with pybids (65b7d25)

  • add methods to create the json summarizing bids datasets for indexing (f54d291)

  • add original pybids bids.json config file (5687d17)

  • bids_utils: extract additional ChannelCount fields in get_bidsdataset_content (9e23ebf)

  • bids_utils: use asyncio to generate asynchronously the indexed content of multiple datasets (edcf742)

  • check the validity of the value given to –command parser’s argument (e2b3f14)

  • create function to get dataset size in bids/utils.py (680ffc3)

  • Dockerfile: install bids-validator npm package from our fork on dev-hip branch (85f9afd)

  • fixed build and tag name for backward compatibility (93e81a0)

  • get dataset content to be indexed for all at once (a397b00)

  • handle CT in sub_import() of participants.py using our modified BIDS Manager fork (4552e8c)

  • implement function to create BIDSLayout object with custom config to handle CT (fea0b72)

  • install pybids and pandas in docker (8d3f7e0)

  • make adjustment of bids dataset content (15008ad)

  • Makefile: use BuildKit for docker build (fa0b55b)

  • perform test and code coverage with pytest and pytest-cov (8a89db1)

  • validate with bids-validator and put outputs into the dataset’s JSON to be indexed (c1bcd79)