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Merge branch 'bids-standard:master' into master
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‎.gitignore‎

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venv3.11/
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.idea/*
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.pytest_cache/*
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build/*
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*.egg-info

‎README.md‎

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@@ -34,6 +34,8 @@ Camille Maumet ([@cmaumet](https://github.com/cmaumet)) and Satrajit Ghosh ([@sa
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- Cyril Regan ([@cyril-data](https://github.com/cyril-data))<a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=cyril-data" title="Code">💻</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/pulls?q=is%3Apr+reviewed-by%3Acyril-data" title="Reviewed Pull Requests">👀</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=cyril-data" title="Documentation">📖</a>
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<a href="https://github.com/bids-standard/BEP028_BIDSprov/issues?q=author%3Acyril-data" title="Bug reports">🐛</a>
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- Boris Clénet ([@bclenet](https://github.com/bclenet))<a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=bclenet" title="Code">💻</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=bclenet" title="Documentation">📖</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/issues?q=author%3Abclenet" title="Bug reports">🐛</a>
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This project follows the
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[all-contributors](https://github.com/all-contributors/all-contributors)
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specification. Contributions of any kind welcome!
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[New features (to be included)](new_features.md)
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## Run parsers on the SPM, FSL and AFNI data
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## Using the code
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### Visualize your BIDSprov data
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To visualize your BIDSprov data, perform the following steps :
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1. [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) the code inside a `BEP028_BIDSprov` directory, and cd into this directory :
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```shell
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git clone [email protected]:bids-standard/BEP028_BIDSprov.git
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cd BEP028_BIDSprov
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```
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3. install the `bids_prov` python package :
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```shell
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pip install .
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```
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4. you should be able to launch the visualizer on your .jsonld files with the command `bids_prov_visualizer`
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```shell
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bids_prov_visualizer --input_file graph.jsonld --output_file graph.png
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bids_prov -h
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usage: bids_prov_visualizer [-h] --input_file INPUT_FILE [--output_file OUTPUT_FILE]
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options:
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-h, --help show this help message and exit
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--input_file INPUT_FILE
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input BIDSprov data as a .jsonld file
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--output_file OUTPUT_FILE
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output .png file showing BIDSprov graph
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```
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### Run parsers on the SPM, FSL and AFNI data
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To obtain data in **bids-prov format**, you can use the developed parsers.
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* [Tutorial](https://github.com/bids-standard/BEP028_BIDSprov/blob/master/bids_prov/README.md)

‎bids_prov/visualize.py‎

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viz_jsonld11(jsonld11, output_file)
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if __name__ == "__main__":
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def entry_point():
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""" A command line tool for the visualize module """
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parser = argparse.ArgumentParser()
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parser.add_argument("--input_file", type=str, default="res.jsonld", help="data jsonld file ")
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parser.add_argument("--output_file", type=str, default="res.png", help="output dir where results are written")
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parser.add_argument("--input_file", type=str, help="input BIDSprov data as a .jsonld file ", required=True)
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parser.add_argument("--output_file", type=str, default="output_graph.png", help="output .png file showing BIDSprov graph")
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opt = parser.parse_args()
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main(opt.input_file, output_file=opt.output_file, omit_details=True)
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# >> python -m bids_prov.visualize --input_file ./res_temp.jsonld --output_file res.png
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if __name__ == "__main__":
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entry_point()

‎examples/from_parsers/context_2024_10_08_13h43m16s.txt‎

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Date : 2024_10_08_13h43m16s
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Processing files...
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file= nidmresults-examples/afni_alt_onesided_proc.sub_001
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file= nidmresults-examples/afni_alt_onesided_proc.sub_001
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file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
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file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
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file= nidmresults-examples/afni_clustconn_18_proc.sub_001
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file= nidmresults-examples/afni_clustconn_18_proc.sub_001
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file= nidmresults-examples/afni_clustconn_26_proc.sub_001
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file= nidmresults-examples/afni_clustconn_26_proc.sub_001
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file= nidmresults-examples/afni_con_f_proc.sub_001
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file= nidmresults-examples/afni_con_f_proc.sub_001
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file= nidmresults-examples/afni_default_proc.sub_001
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file= nidmresults-examples/afni_default_proc.sub_001
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file= nidmresults-examples/afni_gam_proc.sub_001
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file= nidmresults-examples/afni_gam_proc.sub_001
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file= nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
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file= nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
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file= nidmresults-examples/afni_hrf_tent_proc.sub_001
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file= nidmresults-examples/afni_hrf_tent_proc.sub_001
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file= nidmresults-examples/afni_other_template_proc.sub_001
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file= nidmresults-examples/afni_other_template_proc.sub_001
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file= nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
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file= nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
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file= nidmresults-examples/afni_thr_clustunck10_proc.sub_001
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file= nidmresults-examples/afni_thr_clustunck10_proc.sub_001
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file= nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
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file= nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
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file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
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file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
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file= nidmresults-examples/fsl_con_f_multiple_report_log.html
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file= nidmresults-examples/fsl_con_f_report_log.html
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file= nidmresults-examples/fsl_contrast_mask_report_log.html
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file= nidmresults-examples/fsl_default_report_log.html
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file= nidmresults-examples/fsl_full_examples001_report_log.html
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file= nidmresults-examples/fsl_gamma_basis_report_log.html
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file= nidmresults-examples/fsl_gaussian_report_log.html
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file= nidmresults-examples/fsl_group_btw_report_log.html
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file= nidmresults-examples/fsl_group_ols_report_log.html
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file= nidmresults-examples/fsl_group_wls_report_log.html
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file= nidmresults-examples/fsl_hrf_fir_report_log.html
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file= nidmresults-examples/fsl_hrf_gammadiff_report_log.html
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file= nidmresults-examples/fsl_motion_reg_der_report_log.html
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file= nidmresults-examples/fsl_motion_reg_report_log.html
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file= nidmresults-examples/fsl_thr_clustfwep05_report_log.html
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file= nidmresults-examples/fsl_thr_voxelfwep05_report_log.html
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file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
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file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
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file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
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file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
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file= nidmresults-examples/narps_do_13_view_zoom.tcsh
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file= nidmresults-examples/narps_do_13_view_zoom.tcsh
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file= nidmresults-examples/spm_2_t_test_batch.m
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file= nidmresults-examples/spm_HRF_informed_basis_batch.m
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file= nidmresults-examples/spm_con_f_batch.m
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file= nidmresults-examples/spm_conjunction_batch.m
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file= nidmresults-examples/spm_contrast_mask_batch.m
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file= nidmresults-examples/spm_covariate_batch.m
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file= nidmresults-examples/spm_default_batch.m
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file= nidmresults-examples/spm_explicit_mask_batch.m
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file= nidmresults-examples/spm_group_ols_batch.m
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file= nidmresults-examples/spm_group_wls_batch.m
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file= nidmresults-examples/spm_hrf_fir_batch.m
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file= nidmresults-examples/spm_non_sphericity_batch.m
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file= nidmresults-examples/spm_partial_conjunction_batch.m
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file= nidmresults-examples/spm_temporal_derivative_batch.m
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file= nidmresults-examples/spm_thr_clustfwep05_batch.m
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file= nidmresults-examples/spm_thr_clustunck10_batch.m
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file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
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file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
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file= nidmresults-examples/spm_thr_voxelunct4_batch.m
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End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:02.150151

‎pyproject.toml‎

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[build-system]
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requires = ["poetry-core"]
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build-backend = "poetry.core.masonry.api"
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[tool.poetry]
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name = "bids_prov"
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authors = [
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"Camille Maumet",
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"Satrajit Ghosh",
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"Stefan Appelhoff",
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"Chris Markiewicz",
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"Yaroslav Halchenko",
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"Jean-Baptiste Poline",
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"Rémi Adon",
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"Hermann Courteille",
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"Thomas Betton",
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"Cyril Regan",
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"Boris Clénet"
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]
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description = "BIDS extension proposal 28 : BIDS Provenance"
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version = "0.1.0"
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readme = "README.md"
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requires-python = ">=3.10, <3.11"
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license = "CC-BY-4.0"
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classifiers = [
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"Intended Audience :: Science/Research",
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"Programming Language :: Python :: 3",
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"Topic :: Scientific/Engineering",
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"Topic :: Scientific/Engineering :: Medical Science Apps."
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]
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include = ["bids_prov/visualize.py"]
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exclude = ["bids_prov*"]
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[tool.poetry.dependencies]
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python = "^3.10.0"
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beautifulsoup4 = "^4.12.3"
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boutiques = "^0.5.26"
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click = "^8.1.7"
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deepdiff = "^7.0.1"
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graphviz = "^0.20.3"
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rdflib = "^7.0.0"
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rdflib-jsonld = "^0.6.2"
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prov = "^2.0.0"
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pydot = "^2.0.0"
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pyld = "^2.0.4"
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pyyaml = "^6.0.1"
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requests = "^2.32.3"
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[tool.poetry.group.dev.dependencies]
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black = "^24.4.2"
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markdownify = "^0.12.1"
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pre-commit = "^3.7.1"
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pytest-cov = "^5.0.0"
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[tool.poetry.scripts]
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bids_prov_visualizer = "bids_prov.visualize:entry_point"

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