Changelog

0.4.8

• BasePrepare: introduced launchcontainers/prepare/base_prepare.py with a BasePrepare base class shared by all prepare pipelines. Provides basedir / bidsdir properties and the write_example_config / _example_config_dict classmethod pair so every subclass can auto-generate an annotated lc_config_example.yaml without duplicating boilerplate.

• GLMPrepare now subclasses BasePrepare. Removed the redundant basedir / bidsdir properties and replaced the @staticmethod write_example_config with @classmethod _example_config_dict.

• GLMPrepare — Word-Center (WC) mode: new output_bids and output_bids_dir properties. When is_WC=True the prepare workflow writes all outputs (events TSVs, BIDS bold symlinks, fMRIprep bold symlinks, and their JSON sidecars) into a separate BIDS-mirrored directory tree rooted at <basedir>/<output_bids> (e.g. BIDS_WC/), including a derivatives/<fmriprep_analysis_name>/ sub-tree.

• Symlinks now include JSON sidecars: both gen_bids_bold_symlinks and gen_fmriprep_bold_symlinks create a matching .json symlink alongside every NIfTI / GIFTI symlink.

• Mapping TSV moved to vistadisplog dir: PRFPrepare.parse_prf_mat now writes sub-<sub>_ses-<ses>_desc-mapping_PRF_acqtime.tsv to the vistadisplog source directory instead of the BIDS func/ directory. GLMPrepare._load_mapping_tsv reads from the same location.

• Bug fix: run_glm_prepare was not forwarding the layout argument to run_prf_glm_prepare, causing an AttributeError: 'NoneType' object has no attribute 'get' at runtime.

• Type annotations: added TYPE_CHECKING guard in glm_prepare.py for pandas.DataFrame and bids.BIDSLayout; all public wrapper functions now carry full type signatures.

• Docs: added tutorial sub-pages prepare_glm.rst, prepare_dwi.rst, prepare_ret.rst under the Tutorial section. Rewrote extending.rst to document the actual BasePrepare pattern with step-by-step guidance. Updated configuration.rst container_specific section and api.rst fMRI-GLM preparation section.

0.4.7

• Logging: replaced ad-hoc output redirection with a structured logging architecture. log_setup.py now provides _LoggingConsole, a Rich Console subclass that auto-forwards every console.print() call to a Python logging.Logger. Two log files are written per CLI command and copied into the analysis directory on completion:

  • <cmd>_<timestamp>.log — all messages (DEBUG and above)

  • <cmd>_<timestamp>.err — warnings and errors only

• gen_jobscript package: replaced the single gen_launch_cmd.py module with a gen_jobscript/ package. The orchestrator (__init__.py) routes to per-type command builders:

  • gen_container_cmd.py — Apptainer/Singularity containers (existing logic)

  • gen_matlab_cmd.py — MATLAB script launcher (stub, raises NotImplementedError)

  • gen_py_cmd.py — Python script launcher (stub, raises NotImplementedError)

• clusters/local.py: renamed job_scheduler.py to local.py. Added launch_serial() and launch_parallel() functions controlled by the new launch_mode yaml key. Each subprocess now runs inside bash -l so that module load commands work correctly. Parallel mode supports a mem_per_job memory ceiling enforced via resource.setrlimit on each worker process.

• host_options.local yaml keys updated: launch_mode (serial / parallel), max_workers (concurrent container limit), mem_per_job (per-worker memory cap). Old Dask-era keys (njobs, memory_limit, threads_per_worker) are no longer used.

0.4.6

• Added GLMPreparer and BasePreparer abstract class hierarchy for analysis-based (fMRI) pipelines.

• Introduced PREPARER_REGISTRY for zero-touch extension of new analysis types.

• cli.py: two-path dispatch — legacy DWI path untouched; new registry path for analysis-based pipelines.

• Added glm_specific config section and glm_config_template.yaml.

0.4.3

• Improved temporal proximity matching for sbref↔bold pairing (180-second window).

• Fixed DWI file mapping for PA/AP direction naming.

• Fixed datetime parsing for ISO timestamp formats in scans.tsv validation.

• Fixed bidirectional file matching to always produce _dwi.nii.gz suffixes.

0.4.0

• Initial public release of the lc CLI with prepare, run, qc, copy_configs, gen_subses, and create_bids subcommands.

• SLURM (DIPC) and SGE (BCBL) scheduler support.

• Container-based pipeline support: anatrois, freesurferator, rtppreproc, rtp-pipeline, rtp2-preproc, rtp2-pipeline.