chore(main): release 0.2.0

[github-actions]

🤖 I have created a release beep boop

0.2.0 (2025-11-28)

Features

• add annotation-image-segmentation matching and feature consolidation (16df635)
• add average version of CCC measurement results (dd4713c)
• add Bland-Altman plotting (3e04ee1)
• add click command (c51b316)
• add click command (7078b1d)
• add click functionality (c5e6b85)
• add code for running MIT (bc63778)
• add code for running MIT (bc63778)
• add config file for CPTAC-HNSCC to run MIT (97df925)
• add config files for additional CPTAC datasets (762b8c7)
• add config files for CPTAC-PDA and NSCLC-Radiogenomics (5e0c3ff)
• add confirmation of annotation-segmentation match and visualization (299f34e)
• add default file names to create_rvr_measurements (7b437ba)
• add directory setting command to get damply to work (ea5ba90)
• add function to process entire dataset of SRs (017beba)
• add handling of duplicate annotation measurements and non-existant nifti files (c6f8415)
• add handling of no short axis measurements and two or more nifti segmentations mapping to one series instance UID (5a1f38d)
• add image processing bash script and corresponding config file (8ef0c00)
• add list of patient IDs from CCC that overlap with available segmentations (fd25771)
• add matching annotations to segmentation script (aa0b8ab)
• add more robust handling for multiple nifti segmentations in get_nifti_locs (a43038a)
• add more robust search for RTSTRUCT DICOM files (1238743)
• add MR compatibility (0ea0dc6)
• add multiple tumour matching and additional file info outputs (28c238d)
• add nifti file paths to matched csv output file (63828ad)
• add paired t-test and additional PyRadiomic features for analysis (aa06dbf)
• add pixi task for mit (6e1c3e0)
• add pixi task for running sr_testing (62cbb16)
• add pyradiomics feature consolidation script (16398d2)
• add RECIST vs PyRadiomics t-tests for matched data (0a0267f)
• add relative measurement difference TOST (604cd1e)
• add roi match map to autopipeline call (61cf718)
• add roi match map to config file (05007e8)
• add saving of figures (975231b)
• add Snakemake setup for running med-imagetools (cd42418)
• add task to run med-imagetools via snakemake pipeline (7ff8054)
• add usage documentation (f484227)
• add usage documentation (f484227)
• add visualizations for RECIST vs PyRadiomics measurement data (2372519)
• added SR scrape testing script (70267d1)
• calculate relative measurement difference (e9b7216)
• code used for medsam2 evaluation of RADCURE oral cavity segmentations for ICHNO 2026 (88e496e)
• evaluation metrics script (ed29d45)
• exploration of highdicom for SR metadata extraction (67217d6)
• ignore example files in ruff check (4dd9e56)
• ignore internal dataset config files (f71a12d)
• ignore snakemake output files (dbd9f6c)
• ignore vscode files (582373f)
• notebook to explore image-mask-annotation overlap (43ac1ca)
• plotting and stats for RECIST vs. PyRadiomics diameters (dbc7479)
• pull annotation scraping script from kaitlyn (d7c39fb)
• remove need for annotation DICOM path definition (b736115)
• script with functions to calculate segmentation geometry for comparison between ground truth and predictions (44f4e93)
• trying out highdicom and imgtools for SR processing (d2f8643)

Bug Fixes

• add click option for dataset_name (8b8b012)
• add specific error messages when no matches found (d2c0aa2)
• correct image modality for CCRCC (7f250cd)
• correct image modality for CPTAC-HNSCC (a22a8b6)
• handle missing nifti paths (6092e35)
• indentation and file path errors in create_rvr_measurements (1be7110)
• matched dataframe has proper nifti path names instead of just index number (fdf365f)
• moved block in BA analysis so variables get defined properly (af6ce0e)
• previous commit for RMD had missing calculations which are now included (ffffd40)

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