diff --git a/.gitignore b/.gitignore index 336385a09..95e4fe37a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +docs/generated/ cubids/_version.py *.DS_Store diff --git a/cubids/data/references.bib b/cubids/data/references.bib new file mode 100644 index 000000000..e69de29bb diff --git a/cubids/metadata_merge.py b/cubids/metadata_merge.py index f3decd19a..e46879b30 100644 --- a/cubids/metadata_merge.py +++ b/cubids/metadata_merge.py @@ -304,6 +304,7 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level, is_long """Find unique sets of Key/Param groups across subjects. This writes out the following files: + - _AcqGrouping.tsv: A tsv with the mapping of subject/session to acquisition group. - _AcqGrouping.json: A data dictionary for the AcqGrouping.tsv. diff --git a/docs/api.rst b/docs/api.rst index b4d81eac6..f42f71c20 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -25,17 +25,17 @@ API :toctree: generated/ :template: function.rst - cubids.workflows.validate - cubids.workflows.bids_sidecar_merge - cubids.workflows.group - cubids.workflows.apply - cubids.workflows.datalad_save - cubids.workflows.undo - cubids.workflows.copy_exemplars - cubids.workflows.add_nifti_info - cubids.workflows.purge - cubids.workflows.remove_metadata_fields - cubids.workflows.print_metadata_fields + workflows.validate + workflows.bids_sidecar_merge + workflows.group + workflows.apply + workflows.datalad_save + workflows.undo + workflows.copy_exemplars + workflows.add_nifti_info + workflows.purge + workflows.remove_metadata_fields + workflows.print_metadata_fields ********************************************** @@ -48,11 +48,11 @@ API :toctree: generated/ :template: function.rst - cubids.metadata_merge.check_merging_operations - cubids.metadata_merge.merge_without_overwrite - cubids.metadata_merge.merge_json_into_json - cubids.metadata_merge.get_acq_dictionary - cubids.metadata_merge.group_by_acquisition_sets + metadata_merge.check_merging_operations + metadata_merge.merge_without_overwrite + metadata_merge.merge_json_into_json + metadata_merge.get_acq_dictionary + metadata_merge.group_by_acquisition_sets *********************************** @@ -65,8 +65,8 @@ API :toctree: generated/ :template: function.rst - cubids.validator.build_validator_call - cubids.validator.build_subject_paths - cubids.validator.run_validator - cubids.validator.parse_validator_output - cubids.validator.get_val_dictionary + validator.build_validator_call + validator.build_subject_paths + validator.run_validator + validator.parse_validator_output + validator.get_val_dictionary diff --git a/docs/conf.py b/docs/conf.py index 9da1b27fb..124af6f2f 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -73,7 +73,7 @@ # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] -source_suffix = ".rst" +source_suffix = {".rst": "restructuredtext"} # The master toctree document. master_doc = "index" @@ -171,13 +171,10 @@ _python_doc_base = "https://docs.python.org/" + _python_version_str intersphinx_mapping = { "python": (_python_doc_base, None), - "numpy": ("https://numpy.org/doc/stable/", (None, "./_intersphinx/numpy-objects.inv")), - "scipy": ( - "https://docs.scipy.org/doc/scipy/reference", - (None, "./_intersphinx/scipy-objects.inv"), - ), - "sklearn": ("https://scikit-learn.org/stable", (None, "./_intersphinx/sklearn-objects.inv")), - "matplotlib": ("https://matplotlib.org/", (None, "https://matplotlib.org/objects.inv")), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None), + "sklearn": ("https://scikit-learn.org/stable", None), + "matplotlib": ("https://matplotlib.org/stable/", None), "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), "pybids": ("https://bids-standard.github.io/pybids/", None), "nibabel": ("https://nipy.org/nibabel/", None), diff --git a/docs/contributing.rst b/docs/contributing.rst new file mode 100644 index 000000000..3bdd7dc21 --- /dev/null +++ b/docs/contributing.rst @@ -0,0 +1 @@ +.. include:: ../CONTRIBUTING.rst \ No newline at end of file diff --git a/docs/faq.rst b/docs/faq.rst new file mode 100644 index 000000000..edf1e5cfe --- /dev/null +++ b/docs/faq.rst @@ -0,0 +1,29 @@ +========================== +Frequently Asked Questions +========================== + + +-------------------------------------- +Does CuBIDS work on all BIDS datasets? +-------------------------------------- + +CuBIDS relies on many hardcoded rules and data types, +so it may not work on all BIDS datasets. +Some datatypes, such as EEG or iEEG, are not yet supported, +nor are some configurations of supported datatypes, such as multi-echo fMRI. + +If you encounter an issue, please open an issue on the CuBIDS GitHub repository. + + +----------------------------------------------------- +How do the developers determine what features to add? +----------------------------------------------------- + +CuBIDS is primarily developed to curate large-scale datasets in order to be used by the PennLINC team. +This means that we will naturally prioritize features that are useful to us. +However, we are always open to suggestions and contributions from the community, +and will of course consider features that do not directly benefit us. + +If you want to request support for a new modality or niche data feature, +please open an issue on the CuBIDS GitHub repository. +We are more likely to add support for a new feature if you can point us toward a dataset that we can use to test it. diff --git a/docs/index.rst b/docs/index.rst index 3a9d5b9d4..6f8fa7c0b 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -13,8 +13,7 @@ Contents usage cli example - ../CONTRIBUTING - ../AUTHORS - ../HISTORY + contributing + faq glossary api diff --git a/docs/usage.rst b/docs/usage.rst index 4696221c6..25b3dba77 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -110,7 +110,7 @@ but it keeps track of every file's assignment to Entity and Parameter Groups. .. _acqgrouptsv: Modifying Entity and Parameter Group Assignments ---------------------------------------------- +------------------------------------------------ Sometimes we see that there are important differences in acquisition parameters within a Entity Set. If these differences impact how a pipeline will process the data,