Reorganize packaging and hopefully fix tests (#267)

* Reorganize packaging for project.

* Update CITATION.cff

* Reorganize the tests.

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update Dockerfile

Update Dockerfile

Update Dockerfile

Update Dockerfile

Update Dockerfile

Update Dockerfile

Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update.

* this is exhausting

* Try this.

* Update config.yml

* Revert "Update config.yml"

This reverts commit 4214b47.

* Revert "Try this."

This reverts commit 1415387.

* Try installing before getting version.

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* I hate linux.

* Update config.yml

* Update config.yml

* Update.

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

Update.

Update config.yml

Update config.yml

Update config.yml

* Revert "Update config.yml"

This reverts commit b74d382.

* Update config.yml

* Update config.yml

* Streamline CircleCI config with @mattcieslak.

* Update config.yml

* Update config.yml

* Update lint.yml

* Update.

* Update config.yml

* Update config.yml

* Update config.yml

* Update.

* Update config.yml

* Update lint.yml

* Update lint.yml

* Update.

* Update lint.yml

* Fix misspellings.

* Block datalad 0.17.3.

* Update pyproject.toml

* Update tests.

* Update .readthedocs.yml

.github/workflows/lint.yml

@@ -7,7 +7,6 @@ on:
 jobs:
   lint:
     runs-on: ubuntu-latest
-
     steps:
     - name: Set up environment
       uses: actions/checkout@v3
@@ -16,11 +15,12 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.7'
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         pip install flake8 flake8-absolute-import flake8-black flake8-docstrings \
         flake8-isort flake8-pyproject flake8-unused-arguments \
-        flake8-use-fstring pep8-naming
+        flake8-use-fstring pep8-naming \
+        codespell tomli
     - name: Run linters
       run: python -m flake8 cubids

.gitignore

@@ -1,3 +1,4 @@
+cubids/_version.py
 *.DS_Store
 
 # Byte-compiled / optimized / DLL files

.readthedocs.yml

@@ -1,5 +1,13 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+sphinx:
+  configuration: docs/conf.py
+
 python:
   install:
     - method: pip

AUTHORS.rst

@@ -12,6 +12,6 @@ Contributors
 
 * Tinashe Tapera <tinashe.tapera at pennmedicine dot upenn .edu>
 
-Principle Investigator 
------------------------
+Principal Investigator
+----------------------
 * Theodore Satterthwaite <theodore.satterthwaite at pennmedicine dot upenn .edu>

CITATION.cff

@@ -0,0 +1,107 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: >-
+  Curation of BIDS (CuBIDS)
+message: If you use this software, please cite it using the metadata from this file, as well as the NeuroImage paper (doi:10.1016/j.neuroimage.2022.119609).
+type: software
+authors:
+  - given-names: Sydney
+    family-names: Covitz
+    affiliation: University of Pennsylvania
+    orcid: 'https://orcid.org/0000-0002-7430-4125'
+  - given-names: Tinashe M.
+    family-names: Tapera
+  - given-names: Azeez
+    family-names: Adebimpe
+    affiliation: University of Pennsylvania
+    orcid: 'https://orcid.org/0000-0001-9049-0135'
+  - given-names: Aaron F.
+    family-names: Alexander-Bloch
+    affiliation: University of Pennsylvania
+  - given-names: Maxwell
+    family-names: Bertolero
+    orcid: 'https://orcid.org/0000-0002-2691-3698'
+    affiliation: University of Pennsylvania
+  - given-names: Eric
+    family-names: Feczko
+  - given-names: Alexandre R.
+    family-names: Franco
+  - given-names: Raquel E.
+    family-names: Gur
+  - given-names: Ruben C.
+    family-names: Gur
+  - given-names: Timothy
+    family-names: Hendrickson
+  - given-names: Audrey
+    family-names: Houghton
+  - given-names: Kahini
+    family-names: Mehta
+  - given-names: Kristin
+    family-names: Murtha
+    affiliation: University of Pennsylvania
+  - given-names: Anders J.
+    family-names: Perrone
+  - given-names: Tim
+    family-names: Robert-Fitzgerald
+  - given-names: Jenna M.
+    family-names: Schabdach
+  - given-names: Russell T.
+    family-names: Shinohara
+  - given-names: Jacob W.
+    family-names: Vogel
+  - given-names: Chenying
+    family-names: Zhao
+  - given-names: Damien A.
+    family-names: Fair
+  - given-names: Michael
+    family-names: Milham
+  - given-names: Matthew
+    family-names: Cieslak
+    email: [email protected]
+    affiliation: University of Pennsylvania
+    orcid: 'https://orcid.org/0000-0002-1931-4734'
+  - given-names: Taylor
+    family-names: Salo
+    email: [email protected]
+    affiliation: University of Pennsylvania
+    orcid: 'https://orcid.org/0000-0001-9813-3167'
+  - given-names: Theodore
+    family-names: Satterthwaite
+    affiliation: University of Pennsylvania
+    orcid: 'https://orcid.org/0000-0001-7072-9399'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.6514881
+    description: The Zenodo DOI
+  - type: doi
+    value: 10.1016/j.neuroimage.2022.119609
+    description: The NeuroImage journal article
+repository-code: 'https://github.com/PennLINC/CuBIDS'
+url: 'https://cubids.readthedocs.io'
+abstract: >-
+  The Brain Imaging Data Structure (BIDS) is a specification accompanied by a software
+  ecosystem that was designed to create reproducible and automated workflows for processing
+  neuroimaging data.
+  BIDS Apps flexibly build workflows based on the metadata detected in a dataset.
+  However, even BIDS valid metadata can include incorrect values or omissions that result in
+  inconsistent processing across sessions.
+  Additionally, in large-scale, heterogeneous neuroimaging datasets,
+  hidden variability in metadata is difficult to detect and classify.
+  To address these challenges, we created a Python-based software package titled
+  “Curation of BIDS” (CuBIDS), which provides an intuitive workflow that helps users validate
+  and manage the curation of their neuroimaging datasets.
+  CuBIDS includes a robust implementation of BIDS validation that scales to large samples and
+  incorporates DataLad- a version control software package for data- as an optional dependency
+  to ensure reproducibility and provenance tracking throughout the entire curation process.
+  CuBIDS provides tools to help users perform quality control on their images' metadata and
+  identify unique combinations of imaging parameters.
+  Users can then execute BIDS Apps on a subset of participants that represent the full range of
+  acquisition parameters that are present, accelerating pipeline testing on large datasets.
+keywords:
+  - BIDS
+  - Neuroimaging
+license: MIT
+version: 1.0.2
+date-released: '2023-09-07'

cubids/cli.py

@@ -763,32 +763,26 @@ def cubids_copy_exemplars():
         "bids_dir",
         type=Path,
         action="store",
-        help=(
-            "path to the root of a BIDS dataset. "
-            "It should contain sub-X directories and "
-            "dataset_description.json."
-        ),
+        help="path to the root of a BIDS dataset. "
+        "It should contain sub-X directories and "
+        "dataset_description.json.",
     )
     parser.add_argument(
         "exemplars_dir",
         type=Path,
         action="store",
-        help=(
-            "absolute path to the root of a BIDS dataset "
-            "containing one subject from each Acquisition Group. "
-            "It should contain sub-X directories and "
-            "dataset_description.json."
-        ),
+        help="absolute path to the root of a BIDS dataset "
+        "containing one subject from each Acquisition Group. "
+        "It should contain sub-X directories and "
+        "dataset_description.json.",
     )
     parser.add_argument(
         "exemplars_tsv",
         type=Path,
         action="store",
-        help=(
-            "absolute path to the .tsv file that lists one "
-            "subject from each Acqusition Group "
-            "(*_AcqGrouping.tsv from the cubids-group output)"
-        ),
+        help="absolute path to the .tsv file that lists one "
+        "subject from each Acquisition Group "
+        "(*_AcqGrouping.tsv from the cubids-group output)",
     )
     parser.add_argument(
         "--use-datalad", action="store_true", help="check exemplar dataset into DataLad"
@@ -797,11 +791,9 @@ def cubids_copy_exemplars():
         "--min-group-size",
         action="store",
         default=1,
-        help=(
-            "minimum number of subjects an Acquisition Group "
-            "must have in order to be included in the exemplar "
-            "dataset "
-        ),
+        help="minimum number of subjects an Acquisition Group "
+        "must have in order to be included in the exemplar "
+        "dataset ",
         required=False,
     )
     # parser.add_argument('--include-groups',

cubids/cubids.py

@@ -219,7 +219,7 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
         """Apply changes documented in the edited summary tsv and generate the new tsv files.
 
         This function looks at the RenameKeyGroup and MergeInto
-        columns and modifies the bids datset according to the
+        columns and modifies the bids dataset according to the
         specified changs.
 
         Parameters
@@ -825,7 +825,7 @@ def get_param_groups_from_key_group(self, key_group):
         if ret == "erroneous sidecar found":
             return "erroneous sidecar found"
 
-        # add modality to the retun tuple
+        # add modality to the return tuple
         l_ret = list(ret)
         l_ret.append(modality)
         tup_ret = tuple(l_ret)

cubids/metadata_merge.py

@@ -15,7 +15,7 @@
 def check_merging_operations(action_tsv, raise_on_error=False):
     """Check that the merges in an action tsv are possible.
 
-    To be mergable the
+    To be mergeable the
     """
     actions = pd.read_table(action_tsv)
     ok_merges = []