Merge pull request #379 from yarikoptic/bf-codespell

Make codespell happy again: afile -> f, ignore typoed line in CHANGELOG

.codespellrc

@@ -1,5 +1,6 @@
 [codespell]
 skip = .git,*.pdf,*.svg,*.js,*.ttl
+ignore-regex = Splitted.*is not a word
 # Commun - abbreviation in publication venue
 # nd - some css within .rst
 # Groth - name

README.rst

@@ -42,6 +42,26 @@ your user space and use the pull request GitHub feature to submit code for
 review. Please provide a reasonably detailed description of what was changed
 and why in the pull request.
 
+To establish development environment, we recommend to install the
+clone of this repository in development mode with development tools
+installed via
+
+.. code:: bash
+
+ $ pip install -e .[devel]
+
+We also recommend using
+`pre-commit <https://github.com/pre-commit/pre-commit>`_ for ensuring
+that your contributions would conform our conventions for code quality
+etc. You can enable ``pre-commit`` by running once in your clone
+
+.. code:: bash
+
+ $ pre-commit install
+
+which would then ensure that all commits would be subject to `black
+<https://pypi.org/project/black/>`_ code reformatting etc.
+
 Reporting Issues or Problems
 ============================
 If you encounter a bug, you can directly report it in the issues section.

setup.cfg

@@ -56,6 +56,9 @@ install_requires =
 tools =
  matplotlib
  seaborn
+devel =
+ pytest
+ pre-commit
 
 [options.packages.find]
 where = src

src/nidm/experiment/Project.py

@@ -130,7 +130,6 @@ def add_dataelements(self, dataelement):
  # dataelement.add_attributes({pm.QualifiedName(pm.Namespace("dct", Constants.DCT), 'isPartOf'): self})
  return True
 
-
  def __str__(self):
  return "NIDM-Experiment Project Class"
 

src/nidm/experiment/Query.py

@@ -1356,11 +1356,11 @@ def OpenGraph(file):
 
  BLOCKSIZE = 65536
  hasher = hashlib.md5()
- with open(file, "rb") as afile:
- buf = afile.read(BLOCKSIZE)
+ with open(file, "rb") as f:
+ buf = f.read(BLOCKSIZE)
  while len(buf) > 0:
  hasher.update(buf)
- buf = afile.read(BLOCKSIZE)
+ buf = f.read(BLOCKSIZE)
  digest = hasher.hexdigest()
 
  pickle_file = f"{tempfile.gettempdir()}/rdf_graph.{digest}.pickle"

src/nidm/experiment/tools/bidsmri2nidm.py

@@ -28,12 +28,12 @@
  Project,
  Session,
 )
+from nidm.experiment.Core import getUUID
 from nidm.experiment.Utils import (
  add_attributes_with_cde,
  addGitAnnexSources,
  map_variables_to_terms,
 )
-from nidm.experiment.Core import getUUID
 
 
 def getRelPathToBIDS(filepath, bids_root):
@@ -231,7 +231,13 @@ def addbidsignore(directory, filename_to_add):
 
 
 def addimagingsessions(
- bids_layout, subject_id, session, participant, directory, collection, img_session=None
+ bids_layout,
+ subject_id,
+ session,
+ participant,
+ directory,
+ collection,
+ img_session=None,
 ):
  """
  This function adds imaging acquistions to the NIDM file and deals with BIDS structures potentially having
@@ -992,15 +998,15 @@ def bidsmri2project(directory, args):
  provgraph = project.getGraph()
  collection = provgraph.collection(Constants.NIIRI[getUUID()])
  # 7/22/23 add type as bids:Dataset
- collection.add_attributes({PROV_TYPE: QualifiedName(
-  Namespace("bids", Constants.BIDS), "Dataset"
-  )})
+ collection.add_attributes(
+ {PROV_TYPE: QualifiedName(Namespace("bids", Constants.BIDS), "Dataset")}
+ )
 
  # if there are git annex sources then add them
  num_sources = addGitAnnexSources(obj=project.get_uuid(), bids_root=directory)
  # else just add the local path to the dataset
- #if num_sources == 0:
-  # 7/22/23 - modified to add location attribute to collection of acquisition objects
+ # if num_sources == 0:
+ # 7/22/23 - modified to add location attribute to collection of acquisition objects
  # collection.add_attributes({Constants.PROV["Location"]: "file:/" + directory})
 
  # add various attributes if they exist in BIDS dataset description file
@@ -1163,7 +1169,7 @@ def bidsmri2project(directory, args):
  acq_entity = AssessmentObject(acquisition=acq)
 
  # Modified 7/22/23 to add acq_entity to collection
- provgraph.hadMember(collection,acq_entity)
+ provgraph.hadMember(collection, acq_entity)
 
  # create participant dictionary indexed by subjid to get agen UUIDs for later use
  participant[subjid] = {}
@@ -1490,7 +1496,7 @@ def bidsmri2project(directory, args):
  )
  # else just add the local path to the dataset
  # 7/22/23 commented out to not add local source if no gitAnnex source found
- #if num_sources == 0:
+ # if num_sources == 0:
  # acq_entity.add_attributes(
  # {Constants.PROV["Location"]: "file:/" + tsv_file}
  # )
@@ -1527,7 +1533,7 @@ def bidsmri2project(directory, args):
  )
  # else just add the local path to the dataset
  # 7/22/23 commented out so local source file isn't stored if no gitAnnex sources
- #if num_sources == 0:
+ # if num_sources == 0:
  # json_entity.add_attributes(
  # {Constants.PROV["Location"]: "file:/" + data_dict}
  # )