From 1a9dfdbebb07ebdff6067a65c985063ec47c46bc Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Fri, 5 Sep 2025 18:33:47 +0100
Subject: [PATCH 01/28] added intial tests for Context class

---
 tests/test_context.py | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/tests/test_context.py b/tests/test_context.py
index 0cc6c45..f9df20b 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -41,3 +41,32 @@ def test_fileparts(examples, schema):
         suffix='T1w',
         extension='.nii',
     )
+
+def test_context(examples, schema):
+
+    tree = FileTree.read_from_filesystem(examples / 'synthetic')
+    ds = context.Dataset(tree, schema)
+    T1w = tree / 'sub-01' / 'ses-01' / 'anat' / 'sub-01_ses-01_T1w.nii'
+
+    file_context = context.Context(T1w, ds)
+
+    assert file_context.schema == schema
+    assert file_context.dataset == ds
+    assert file_context.entiities == {'sub': '01', 'ses': '01'}
+    assert file_context.path == '/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii'
+    assert file_context.datatype == 'anat'
+    assert file_context.suffix == 'T1w'
+    assert file_context.extension == '.nii'
+    assert file_context.modality == 'mri'
+    assert file_context.size == 352
+
+    ## Tests for:
+    #  subject
+    #  sidecar
+    #  associations
+    #  columns
+    #  json
+    #  gzip
+    #  nifti_header
+    #  ome
+    #  tiff

From 2db6ba9a2cdefbf9a582cf2a3e55df3f73437d91 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Fri, 5 Sep 2025 18:34:07 +0100
Subject: [PATCH 02/28] Context class WIP

---
 src/bids_validator/context.py | 75 +++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 7b940a1..80e4d8f 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -298,3 +298,78 @@ def from_file(cls, file: FileTree, schema: Namespace) -> t.Self:
             suffix=suffix,
             extension=extension,
         )
+
+@attrs.define
+class Context:
+
+    file: FileTree
+    dataset: Dataset
+    schema: Namespace = attrs.field(init=False)
+    file_parts: FileParts = attrs.field(init=False)
+
+    def __attrs_post_init__(self):
+        self.schema = self.dataset.schema
+        self.file_parts = FileParts.from_file(self.file, self.schema)
+    
+    @property
+    def path(self) -> str:
+        return self.file_parts.path
+    
+    @property
+    def entiities(self) -> dict[str, str] | None:
+        return self.file_parts.entities
+    
+    @property
+    def datatype(self) -> str | None:
+        return self.file_parts.datatype
+
+    @property
+    def suffix(self) -> str | None:
+        return self.file_parts.suffix
+
+    @property
+    def extension(self) -> str | None:
+        return self.file_parts.extension
+    
+    @property
+    def modality(self) -> str | None:
+        modalities = self.schema.rules.modalities
+        for mod_name, mod_dtypes in modalities.items():
+            if self.datatype in mod_dtypes.datatypes:
+                return mod_name
+    
+    @property
+    def size(self) -> int:
+        return self.file.direntry.stat().st_size
+    
+    @property
+    def subject(self) -> ctx.Subject | None:
+        return ctx.Subject()
+
+    @property
+    def associations(self) -> ctx.Associations:
+        return ctx.Associations()
+
+    @property
+    def columns(self) -> None:
+        pass
+
+    @property
+    def json(self) -> None:
+        pass
+
+    @property
+    def gzip(self) -> None:
+        pass
+
+    @property
+    def nifti_header(self) -> None:
+        pass
+
+    @property
+    def ome(self) -> None:
+        pass
+
+    @property
+    def tiff(self) -> None:
+        pass

From 5cc92f5ba06c3065162f257746e2eb4511bd25bb Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Mon, 8 Sep 2025 23:38:18 +0100
Subject: [PATCH 03/28] PR feedback changes

---
 src/bids_validator/context.py | 25 ++++++++++++++++---------
 tests/test_context.py         |  6 +++---
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 80e4d8f..27db178 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -304,21 +304,24 @@ class Context:
 
     file: FileTree
     dataset: Dataset
-    schema: Namespace = attrs.field(init=False)
     file_parts: FileParts = attrs.field(init=False)
 
     def __attrs_post_init__(self):
-        self.schema = self.dataset.schema
         self.file_parts = FileParts.from_file(self.file, self.schema)
-    
+
+    @property
+    def schema(self) -> Namespace:
+        """The BIDS specification schema."""
+        return self.dataset.schema
+
     @property
     def path(self) -> str:
         return self.file_parts.path
-    
+
     @property
-    def entiities(self) -> dict[str, str] | None:
+    def entities(self) -> dict[str, str] | None:
         return self.file_parts.entities
-    
+
     @property
     def datatype(self) -> str | None:
         return self.file_parts.datatype
@@ -330,18 +333,18 @@ def suffix(self) -> str | None:
     @property
     def extension(self) -> str | None:
         return self.file_parts.extension
-    
+
     @property
     def modality(self) -> str | None:
         modalities = self.schema.rules.modalities
         for mod_name, mod_dtypes in modalities.items():
             if self.datatype in mod_dtypes.datatypes:
                 return mod_name
-    
+
     @property
     def size(self) -> int:
         return self.file.direntry.stat().st_size
-    
+
     @property
     def subject(self) -> ctx.Subject | None:
         return ctx.Subject()
@@ -373,3 +376,7 @@ def ome(self) -> None:
     @property
     def tiff(self) -> None:
         pass
+
+    @property
+    def sidecar(self) -> None:
+        pass
diff --git a/tests/test_context.py b/tests/test_context.py
index f9df20b..f8e72db 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -50,9 +50,9 @@ def test_context(examples, schema):
 
     file_context = context.Context(T1w, ds)
 
-    assert file_context.schema == schema
-    assert file_context.dataset == ds
-    assert file_context.entiities == {'sub': '01', 'ses': '01'}
+    assert file_context.schema is schema
+    assert file_context.dataset is ds
+    assert file_context.entities == {'sub': '01', 'ses': '01'}
     assert file_context.path == '/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii'
     assert file_context.datatype == 'anat'
     assert file_context.suffix == 'T1w'

From 0d427f4402058be0abd39648843f84c810fbb7b8 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Mon, 8 Sep 2025 23:43:14 +0100
Subject: [PATCH 04/28] add missing docstrings

---
 src/bids_validator/context.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 27db178..d7f8622 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -299,8 +299,10 @@ def from_file(cls, file: FileTree, schema: Namespace) -> t.Self:
             extension=extension,
         )
 
+
 @attrs.define
 class Context:
+    """A context object that creates context for file on access."""
 
     file: FileTree
     dataset: Dataset
@@ -316,26 +318,32 @@ def schema(self) -> Namespace:
 
     @property
     def path(self) -> str:
+        """Path of the current file."""
         return self.file_parts.path
 
     @property
     def entities(self) -> dict[str, str] | None:
+        """Entities parsed from the current filename."""
         return self.file_parts.entities
 
     @property
     def datatype(self) -> str | None:
+        """Datatype of current file, for examples, anat."""
         return self.file_parts.datatype
 
     @property
     def suffix(self) -> str | None:
+        """Suffix of current file."""
         return self.file_parts.suffix
 
     @property
     def extension(self) -> str | None:
+        """Extension of current file including initial dot."""
         return self.file_parts.extension
 
     @property
     def modality(self) -> str | None:
+        """Modality of current file, for examples, MRI."""
         modalities = self.schema.rules.modalities
         for mod_name, mod_dtypes in modalities.items():
             if self.datatype in mod_dtypes.datatypes:
@@ -343,40 +351,50 @@ def modality(self) -> str | None:
 
     @property
     def size(self) -> int:
+        """Length of the current file in bytes."""
         return self.file.direntry.stat().st_size
 
     @property
     def subject(self) -> ctx.Subject | None:
+        """Properties and contents of the current subject."""
         return ctx.Subject()
 
     @property
     def associations(self) -> ctx.Associations:
+        """Associated files, indexed by suffix, selected according to the inheritance principle."""
         return ctx.Associations()
 
     @property
     def columns(self) -> None:
+        """TSV columns, indexed by column header, values are arrays with column contents."""
         pass
 
     @property
     def json(self) -> None:
+        """Contents of the current JSON file."""
         pass
 
     @property
     def gzip(self) -> None:
+        """Parsed contents of gzip header."""
         pass
 
     @property
     def nifti_header(self) -> None:
+        """Parsed contents of NIfTI header referenced elsewhere in schema."""
         pass
 
     @property
     def ome(self) -> None:
+        """Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files."""
         pass
 
     @property
     def tiff(self) -> None:
+        """TIFF file format metadata."""
         pass
 
     @property
     def sidecar(self) -> None:
+        """Sidecar metadata constructed via the inheritance principle."""
         pass

From 72dbbeb7f87d8ae6f7b66b1e37363fe16d28cd1b Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Tue, 9 Sep 2025 00:05:38 +0100
Subject: [PATCH 05/28] add and use global mapping for datatype to modality

---
 src/bids_validator/context.py | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index d7f8622..ecb31a1 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -46,6 +46,18 @@ class ValidationError(Exception):
     """TODO: Add issue structure."""
 
 
+_DATATYPE_MAP = {}
+
+
+def datatype_to_modality(datatype: str, schema: Namespace) -> str:
+    """Generate a global map for datatype to modality."""
+    global _DATATYPE_MAP
+    if not _DATATYPE_MAP:
+        for mod_name, mod_dtypes in schema.rules.modalities.items():
+            _DATATYPE_MAP |= dict.fromkeys(mod_dtypes['datatypes'], mod_name)
+    return _DATATYPE_MAP[datatype]
+
+
 @cache
 def load_tsv(file: FileTree, *, max_rows=0) -> Namespace:
     """Load TSV contents into a Namespace."""
@@ -130,14 +142,7 @@ def dataset_description(self) -> Namespace:
     @cached_property
     def modalities(self) -> list[str]:
         """List of modalities found in the dataset."""
-        result = set()
-
-        modalities = self.schema.rules.modalities
-        for datatype in self.datatypes:
-            for mod_name, mod_dtypes in modalities.items():
-                if datatype in mod_dtypes.datatypes:
-                    result.add(mod_name)
-
+        result = {datatype_to_modality(datatype, self.schema) for datatype in self.datatypes}
         return list(result)
 
     @cached_property
@@ -344,10 +349,7 @@ def extension(self) -> str | None:
     @property
     def modality(self) -> str | None:
         """Modality of current file, for examples, MRI."""
-        modalities = self.schema.rules.modalities
-        for mod_name, mod_dtypes in modalities.items():
-            if self.datatype in mod_dtypes.datatypes:
-                return mod_name
+        return datatype_to_modality(self.datatype, self.schema)
 
     @property
     def size(self) -> int:

From eeb692f8728e2d422de5959d0e4af22efffb6f12 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Tue, 9 Sep 2025 14:08:21 +0100
Subject: [PATCH 06/28] add more tests for next stage for Sessions class and
 associated tests for Context class

---
 tests/test_context.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index f8e72db..0f19284 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -59,9 +59,11 @@ def test_context(examples, schema):
     assert file_context.extension == '.nii'
     assert file_context.modality == 'mri'
     assert file_context.size == 352
+    assert isinstance(file_context.subject.sessions, context.Sessions)
+    assert sorted(file_context.subject.sessions.ses_dirs) == ["ses-01", "ses-02"]
+    assert sorted(file_context.subject.sessions.session_id) == ["ses-01", "ses-02"]
 
     ## Tests for:
-    #  subject
     #  sidecar
     #  associations
     #  columns
@@ -70,3 +72,14 @@ def test_context(examples, schema):
     #  nifti_header
     #  ome
     #  tiff
+
+def test_sessions(examples):
+    tree = FileTree.read_from_filesystem(examples / 'synthetic')
+    sub01 = tree / 'sub-01'
+
+    sessions = context.Sessions(sub01)
+
+    assert sorted(sessions.ses_dirs) == ["ses-01", "ses-02"]
+    assert sorted(sessions.session_id) == ["ses-01", "ses-02"]
+    assert sessions.phenotype is None
+

From 7200e9912cbaac913752ebd9a0df2b94276fc2c9 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:06:09 +0100
Subject: [PATCH 07/28] remove sessions.phenotype test

---
 tests/test_context.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index de15ee4..db749f1 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -92,5 +92,3 @@ def test_sessions(examples):
 
     assert sorted(sessions.ses_dirs) == ["ses-01", "ses-02"]
     assert sorted(sessions.session_id) == ["ses-01", "ses-02"]
-    assert sessions.phenotype is None
-

From 729bf51a01f90db2b1b4be28c744edbd829d117a Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:06:48 +0100
Subject: [PATCH 08/28] add sessions class

---
 src/bids_validator/context.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 18afc65..6949933 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -400,3 +400,34 @@ def tiff(self) -> None:
     def sidecar(self) -> None:
         """Sidecar metadata constructed via the inheritance principle."""
         pass
+
+class Sessions:
+    """Collections of sessions in subject."""
+
+    def __init__(self, tree: FileTree):
+        self._tree = tree
+
+    @cached_property
+    def ses_dirs(self) -> list[str]:
+        """Sessions as determined by ses-* directories."""
+        return [
+            child.name
+            for child in self._tree.children.values()
+            if child.is_dir and child.name.startswith('ses-')
+        ]
+
+    @property
+    def session_id(self) -> list[str] | None:
+        """The session_id column of *_sessions.tsv."""
+        for name, value in self._tree.children.items():
+            if name.endswith('_sessions.tsv'):
+                return self._get_session_id(value)
+        else:
+            return None
+
+    @staticmethod
+    def _get_session_id(phenotype_file: FileTree) -> list[str] | None:
+        columns = load_tsv(phenotype_file)
+        if 'session_id' not in columns:
+            return None
+        return list(columns['session_id'])

From 96dd2dcf6413dc14831b7d182e031cf88fa31664 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:08:27 +0100
Subject: [PATCH 09/28] add subject as an input param for Context class

---
 src/bids_validator/context.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 6949933..b7cdb56 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -311,6 +311,7 @@ class Context:
 
     file: FileTree
     dataset: Dataset
+    subject: ctx.Subject
     file_parts: FileParts = attrs.field(init=False)
 
     def __attrs_post_init__(self):
@@ -356,11 +357,6 @@ def size(self) -> int:
         """Length of the current file in bytes."""
         return self.file.direntry.stat().st_size
 
-    @property
-    def subject(self) -> ctx.Subject | None:
-        """Properties and contents of the current subject."""
-        return ctx.Subject()
-
     @property
     def associations(self) -> ctx.Associations:
         """Associated files, indexed by suffix, selected according to the inheritance principle."""

From 1513ff8a093b19ea297cbf1cf015fdc52cc13b73 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:15:50 +0100
Subject: [PATCH 10/28] Update and validate function Include schema as input
 param and instansiate dataset object

---
 src/bids_validator/__main__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index bbea18e..1048907 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -12,6 +12,8 @@
 
 from bids_validator import BIDSValidator
 from bids_validator.types.files import FileTree
+from bids_validator.context import Dataset
+from bidsschematools.types import Namespace
 
 app = typer.Typer()
 
@@ -35,7 +37,7 @@ def walk(tree: FileTree):
             yield child
 
 
-def validate(tree: FileTree):
+def validate(tree: FileTree, schema: Namespace):
     """Check if the file path is BIDS compliant.
 
     Parameters
@@ -45,6 +47,7 @@ def validate(tree: FileTree):
 
     """
     validator = BIDSValidator()
+    dataset = Dataset(tree, schema)
 
     for file in walk(tree):
         # The output of the FileTree.relative_path method always drops the initial for the path

From 685b978b2213fe4b149bbc386711c87a02652d4f Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:17:57 +0100
Subject: [PATCH 11/28] Update walk function now takes dataset as input param,
 generates subject object if required, and yields context object

---
 src/bids_validator/__main__.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index 1048907..9a00a6c 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -12,13 +12,16 @@
 
 from bids_validator import BIDSValidator
 from bids_validator.types.files import FileTree
-from bids_validator.context import Dataset
+from bids_validator.context import Dataset, Sessions, Context
 from bidsschematools.types import Namespace
+from bidsschematools.types.context import Subject
 
 app = typer.Typer()
 
+def is_subject_dir(tree):
+    return tree.name.startswith('sub-')
 
-def walk(tree: FileTree):
+def walk(tree: FileTree, dataset: Dataset, subject = None):
     """Iterate over children of a FileTree and check if they are a directory or file.
 
     If it's a directory then run again recursively, if it's a file file check the file name is
@@ -30,11 +33,14 @@ def walk(tree: FileTree):
         FileTree object to iterate over
 
     """
+    if subject is None and is_subject_dir(tree):
+        subject = Subject(Sessions(tree))
+
     for child in tree.children.values():
         if child.is_dir:
-            yield from walk(child)
+            yield from walk(child, dataset, subject)
         else:
-            yield child
+            yield Context(child, dataset, subject)
 
 
 def validate(tree: FileTree, schema: Namespace):
@@ -49,7 +55,7 @@ def validate(tree: FileTree, schema: Namespace):
     validator = BIDSValidator()
     dataset = Dataset(tree, schema)
 
-    for file in walk(tree):
+    for file in walk(tree, dataset):
         # The output of the FileTree.relative_path method always drops the initial for the path
         # which makes it fail the validator.is_bids check. THis may be a Windows specific thing.
         # This line adds it back.

From d2d9975e2a0bc8748de71acb570ad47a8d64d95c Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:45:08 +0100
Subject: [PATCH 12/28] update tests

---
 tests/test_context.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index db749f1..7ec6dcd 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -1,5 +1,6 @@
 import pytest
 
+from bidsschematools.types.context import Subject
 from bids_validator import context
 from bids_validator.types.files import FileTree
 
@@ -53,13 +54,14 @@ def test_walkback(synthetic_dataset, schema):
     assert len(sidecars) == 1
     assert sidecars[0] is synthetic_dataset / 'task-nback_bold.json'
 
-def test_context(examples, schema):
+def test_context(synthetic_dataset, schema):
 
-    tree = FileTree.read_from_filesystem(examples / 'synthetic')
-    ds = context.Dataset(tree, schema)
-    T1w = tree / 'sub-01' / 'ses-01' / 'anat' / 'sub-01_ses-01_T1w.nii'
-
-    file_context = context.Context(T1w, ds)
+    sub01 = synthetic_dataset / 'sub-01'
+    T1w = sub01 / 'ses-01' / 'anat' / 'sub-01_ses-01_T1w.nii'
+    
+    subject = Subject(context.Sessions(sub01))
+    ds = context.Dataset(synthetic_dataset, schema)
+    file_context = context.Context(T1w, ds, subject)
 
     assert file_context.schema is schema
     assert file_context.dataset is ds
@@ -84,9 +86,8 @@ def test_context(examples, schema):
     #  ome
     #  tiff
 
-def test_sessions(examples):
-    tree = FileTree.read_from_filesystem(examples / 'synthetic')
-    sub01 = tree / 'sub-01'
+def test_sessions(synthetic_dataset):
+    sub01 = synthetic_dataset / 'sub-01'
 
     sessions = context.Sessions(sub01)
 

From 441dd49ab3fe9c2f1e624cb6ba8dadc21a829dfb Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:50:15 +0100
Subject: [PATCH 13/28] tidy for ruff

---
 src/bids_validator/__main__.py | 17 +++++++++++++----
 src/bids_validator/context.py  |  1 +
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index 9a00a6c..9ce4948 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -10,18 +10,21 @@
 import sys
 from typing import Annotated
 
-from bids_validator import BIDSValidator
-from bids_validator.types.files import FileTree
-from bids_validator.context import Dataset, Sessions, Context
 from bidsschematools.types import Namespace
 from bidsschematools.types.context import Subject
 
+from bids_validator import BIDSValidator
+from bids_validator.context import Context, Dataset, Sessions
+from bids_validator.types.files import FileTree
+
 app = typer.Typer()
 
+
 def is_subject_dir(tree):
     return tree.name.startswith('sub-')
 
-def walk(tree: FileTree, dataset: Dataset, subject = None):
+
+def walk(tree: FileTree, dataset: Dataset, subject: Subject = None):
     """Iterate over children of a FileTree and check if they are a directory or file.
 
     If it's a directory then run again recursively, if it's a file file check the file name is
@@ -31,6 +34,10 @@ def walk(tree: FileTree, dataset: Dataset, subject = None):
     ----------
     tree : FileTree
         FileTree object to iterate over
+    dataset: Dataset
+        Object containing properties for entire dataset
+    subject: Subject
+        object containing subject and session info
 
     """
     if subject is None and is_subject_dir(tree):
@@ -50,6 +57,8 @@ def validate(tree: FileTree, schema: Namespace):
     ----------
     tree : FileTree
         Full FileTree object to iterate over and check
+    schema : Namespace
+        Schema object to validate dataset against
 
     """
     validator = BIDSValidator()
diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index b7cdb56..2307dd1 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -397,6 +397,7 @@ def sidecar(self) -> None:
         """Sidecar metadata constructed via the inheritance principle."""
         pass
 
+
 class Sessions:
     """Collections of sessions in subject."""
 

From fa203d1731db459435e370e678edc1fc0638b0c8 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 13:59:52 +0100
Subject: [PATCH 14/28] add schema_path cli option

---
 src/bids_validator/__main__.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index 9ce4948..a62e5f2 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -10,6 +10,7 @@
 import sys
 from typing import Annotated
 
+from bidsschematools.schema import load_schema
 from bidsschematools.types import Namespace
 from bidsschematools.types.context import Subject
 
@@ -103,6 +104,7 @@ def version_callback(value: bool):
 @app.command()
 def main(
     bids_path: str,
+    schema_path: str = None,
     verbose: Annotated[bool, typer.Option('--verbose', '-v', help='Show verbose output')] = False,
     version: Annotated[
         bool,
@@ -119,7 +121,10 @@ def main(
 
     root_path = FileTree.read_from_filesystem(bids_path)
 
-    validate(root_path)
+    if not schema_path:
+        schema = load_schema()
+
+    validate(root_path, schema)
 
 
 if __name__ == '__main__':

From 3aa3fec5aa00a90e018c0919d534b2f54f061231 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 15:12:07 +0100
Subject: [PATCH 15/28] Update validate function walk now returns context
 object which needs to be handled differently

---
 src/bids_validator/__main__.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index a62e5f2..62420cb 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -66,13 +66,8 @@ def validate(tree: FileTree, schema: Namespace):
     dataset = Dataset(tree, schema)
 
     for file in walk(tree, dataset):
-        # The output of the FileTree.relative_path method always drops the initial for the path
-        # which makes it fail the validator.is_bids check. THis may be a Windows specific thing.
-        # This line adds it back.
-        path = f'/{file.relative_path}'
-
-        if not validator.is_bids(path):
-            print(f'{path} is not a valid bids filename')
+        if not validator.is_bids(file.path):
+            print(f'{file.path} is not a valid bids filename')
 
 
 def show_version():

From fbbe129114619a16e14165a6c1ea5d6a2e14dad5 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 15:22:21 +0100
Subject: [PATCH 16/28] feedback changes

---
 src/bids_validator/__main__.py | 3 ++-
 src/bids_validator/context.py  | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index 62420cb..2c2d375 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -8,6 +8,7 @@
     raise SystemExit(1) from None
 
 import sys
+from collections.abc import Iterator
 from typing import Annotated
 
 from bidsschematools.schema import load_schema
@@ -25,7 +26,7 @@ def is_subject_dir(tree):
     return tree.name.startswith('sub-')
 
 
-def walk(tree: FileTree, dataset: Dataset, subject: Subject = None):
+def walk(tree: FileTree, dataset: Dataset, subject: Subject = None) -> Iterator[Context]:
     """Iterate over children of a FileTree and check if they are a directory or file.
 
     If it's a directory then run again recursively, if it's a file file check the file name is
diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 2307dd1..3044ce1 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -311,7 +311,7 @@ class Context:
 
     file: FileTree
     dataset: Dataset
-    subject: ctx.Subject
+    subject: ctx.Subject | None
     file_parts: FileParts = attrs.field(init=False)
 
     def __attrs_post_init__(self):
@@ -350,7 +350,7 @@ def extension(self) -> str | None:
     @property
     def modality(self) -> str | None:
         """Modality of current file, for examples, MRI."""
-        return datatype_to_modality(self.datatype, self.schema)
+        return datatype_to_modality(self.file_parts.datatype, self.schema)
 
     @property
     def size(self) -> int:

From fdd44083be45cfb4dfc786ce6f0f09adcf00464b Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 17:51:21 +0100
Subject: [PATCH 17/28] added tests for sidecar property

---
 tests/test_context.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index 7ec6dcd..029013d 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -75,9 +75,9 @@ def test_context(synthetic_dataset, schema):
     assert isinstance(file_context.subject.sessions, context.Sessions)
     assert sorted(file_context.subject.sessions.ses_dirs) == ["ses-01", "ses-02"]
     assert sorted(file_context.subject.sessions.session_id) == ["ses-01", "ses-02"]
+    assert file_context.sidecar is None
 
     ## Tests for:
-    #  sidecar
     #  associations
     #  columns
     #  json
@@ -86,6 +86,18 @@ def test_context(synthetic_dataset, schema):
     #  ome
     #  tiff
 
+def test_sidecar_inheritance(examples):
+    """Test to ensure inheritance principle is executed correctly"""
+    dataset = FileTree.read_from_filesystem(examples / 'qmri_mp2rage')
+    file = dataset / "sub-1" / "anat"/"sub-1_inv-2_part-mag_MP2RAGE.nii"
+
+    sidecar = context.load_sidecar(file)
+
+    assert sidecar["FlipAngle"] == 7
+    assert sidecar["InversionTime"] == 2.7
+    assert sidecar["RepetitionTimePreparation"] == 5.5
+
+
 def test_sessions(synthetic_dataset):
     sub01 = synthetic_dataset / 'sub-01'
 

From ecc0f37f6749693d305415f12a4e84ae620cb3c9 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 17:52:45 +0100
Subject: [PATCH 18/28] add sidecar method to context class

---
 src/bids_validator/context.py | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 3044ce1..0834314 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -207,6 +207,12 @@ def load_sidecar(file: FileTree) -> dict[str, t.Any]:
     # Uses walk back algorithm
     # https://bids-validator.readthedocs.io/en/latest/validation-model/inheritance-principle.html
     # Accumulates all sidecars
+    metadata = {}
+
+    for json in walk_back(file, inherit=True):
+        metadata = load_json(json) | metadata
+
+    return metadata
 
 
 def walk_back(
@@ -393,9 +399,14 @@ def tiff(self) -> None:
         pass
 
     @property
-    def sidecar(self) -> None:
+    def sidecar(self) -> Namespace | None:
         """Sidecar metadata constructed via the inheritance principle."""
-        pass
+        sidecar = load_sidecar(self.file)
+
+        if sidecar:
+            return Namespace.build(sidecar)
+
+        return None
 
 
 class Sessions:

From 0343be16405bd8ff732ea9c098d961a76443ee4f Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 17:53:25 +0100
Subject: [PATCH 19/28] use orjson over built-in json package

---
 pyproject.toml                | 1 +
 src/bids_validator/context.py | 5 ++---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f45a25c..0ca2857 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,6 +24,7 @@ requires-python = ">=3.9"
 dependencies = [
     "attrs >=24.1",
     "bidsschematools @ git+https://github.com/bids-standard/bids-specification.git@refs/pull/2133/head#subdirectory=tools/schemacode",
+    "orjson>=3.11.3",
     "universal_pathlib >=0.2",
 ]
 
diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 0834314..4a7c8ed 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -3,10 +3,10 @@
 from __future__ import annotations
 
 import itertools
-import json
 from functools import cache
 
 import attrs
+import orjson
 from bidsschematools.types import Namespace
 from bidsschematools.types import context as ctx
 from upath import UPath
@@ -72,8 +72,7 @@ def load_tsv(file: FileTree, *, max_rows=0) -> Namespace:
 @cache
 def load_json(file: FileTree) -> dict[str]:
     """Load JSON file contents."""
-    with open(file) as fobj:
-        return json.load(fobj)
+    return orjson.loads(UPath(file).read_bytes())
 
 
 class Subjects:

From 162a7c9193878ace5943503ee20b1c785d37a55f Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 18:36:03 +0100
Subject: [PATCH 20/28] refine tests for sidecar

---
 tests/test_context.py | 35 ++++++++++++++++++++---------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index 029013d..661c6ca 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -58,24 +58,29 @@ def test_context(synthetic_dataset, schema):
 
     sub01 = synthetic_dataset / 'sub-01'
     T1w = sub01 / 'ses-01' / 'anat' / 'sub-01_ses-01_T1w.nii'
+    bold = sub01 / 'ses-01' / 'func' / 'sub-01_ses-01_task-nback_run-01_bold.nii'
     
     subject = Subject(context.Sessions(sub01))
     ds = context.Dataset(synthetic_dataset, schema)
-    file_context = context.Context(T1w, ds, subject)
-
-    assert file_context.schema is schema
-    assert file_context.dataset is ds
-    assert file_context.entities == {'sub': '01', 'ses': '01'}
-    assert file_context.path == '/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii'
-    assert file_context.datatype == 'anat'
-    assert file_context.suffix == 'T1w'
-    assert file_context.extension == '.nii'
-    assert file_context.modality == 'mri'
-    assert file_context.size == 352
-    assert isinstance(file_context.subject.sessions, context.Sessions)
-    assert sorted(file_context.subject.sessions.ses_dirs) == ["ses-01", "ses-02"]
-    assert sorted(file_context.subject.sessions.session_id) == ["ses-01", "ses-02"]
-    assert file_context.sidecar is None
+    T1w_context = context.Context(T1w, ds, subject)
+
+    assert T1w_context.schema is schema
+    assert T1w_context.dataset is ds
+    assert T1w_context.entities == {'sub': '01', 'ses': '01'}
+    assert T1w_context.path == '/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii'
+    assert T1w_context.datatype == 'anat'
+    assert T1w_context.suffix == 'T1w'
+    assert T1w_context.extension == '.nii'
+    assert T1w_context.modality == 'mri'
+    assert T1w_context.size == 352
+    assert isinstance(T1w_context.subject.sessions, context.Sessions)
+    assert sorted(T1w_context.subject.sessions.ses_dirs) == ["ses-01", "ses-02"]
+    assert sorted(T1w_context.subject.sessions.session_id) == ["ses-01", "ses-02"]
+    assert T1w_context.sidecar is None
+
+    bold_context = context.Context(bold, ds, subject)
+
+    assert bold_context.sidecar.to_dict() == {'TaskName': 'N-Back', 'RepetitionTime': 2.5}
 
     ## Tests for:
     #  associations

From fe42bb714516d58f43149372f28441e89dce0163 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 18:39:31 +0100
Subject: [PATCH 21/28] add test for json property

---
 tests/test_context.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index 661c6ca..2384429 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -59,7 +59,7 @@ def test_context(synthetic_dataset, schema):
     sub01 = synthetic_dataset / 'sub-01'
     T1w = sub01 / 'ses-01' / 'anat' / 'sub-01_ses-01_T1w.nii'
     bold = sub01 / 'ses-01' / 'func' / 'sub-01_ses-01_task-nback_run-01_bold.nii'
-    
+
     subject = Subject(context.Sessions(sub01))
     ds = context.Dataset(synthetic_dataset, schema)
     T1w_context = context.Context(T1w, ds, subject)
@@ -77,10 +77,12 @@ def test_context(synthetic_dataset, schema):
     assert sorted(T1w_context.subject.sessions.ses_dirs) == ["ses-01", "ses-02"]
     assert sorted(T1w_context.subject.sessions.session_id) == ["ses-01", "ses-02"]
     assert T1w_context.sidecar is None
+    assert T1w_context.json is None
 
     bold_context = context.Context(bold, ds, subject)
 
     assert bold_context.sidecar.to_dict() == {'TaskName': 'N-Back', 'RepetitionTime': 2.5}
+    assert bold_context.json is None
 
     ## Tests for:
     #  associations
@@ -91,6 +93,16 @@ def test_context(synthetic_dataset, schema):
     #  ome
     #  tiff
 
+def test_context_json(examples, schema):
+
+    dataset = FileTree.read_from_filesystem(examples / 'qmri_vfa')
+    file = dataset / 'sub-01' / 'anat'/'sub-01_flip-1_VFA.json'
+
+    ds = context.Dataset(dataset, schema)
+    file_context = context.Context(file, ds, subject=None)
+
+    assert file_context.json.to_dict() == {'FlipAngle': 3, 'RepetitionTimeExcitation': 0.0150}
+
 def test_sidecar_inheritance(examples):
     """Test to ensure inheritance principle is executed correctly"""
     dataset = FileTree.read_from_filesystem(examples / 'qmri_mp2rage')

From adb4b754e8cfc19db25e502c7aab30c1b20e31ce Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 18:40:20 +0100
Subject: [PATCH 22/28] ruffed test_context

---
 tests/test_context.py | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index 2384429..6866c59 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -1,6 +1,6 @@
 import pytest
-
 from bidsschematools.types.context import Subject
+
 from bids_validator import context
 from bids_validator.types.files import FileTree
 
@@ -54,8 +54,8 @@ def test_walkback(synthetic_dataset, schema):
     assert len(sidecars) == 1
     assert sidecars[0] is synthetic_dataset / 'task-nback_bold.json'
 
-def test_context(synthetic_dataset, schema):
 
+def test_context(synthetic_dataset, schema):
     sub01 = synthetic_dataset / 'sub-01'
     T1w = sub01 / 'ses-01' / 'anat' / 'sub-01_ses-01_T1w.nii'
     bold = sub01 / 'ses-01' / 'func' / 'sub-01_ses-01_task-nback_run-01_bold.nii'
@@ -74,8 +74,8 @@ def test_context(synthetic_dataset, schema):
     assert T1w_context.modality == 'mri'
     assert T1w_context.size == 352
     assert isinstance(T1w_context.subject.sessions, context.Sessions)
-    assert sorted(T1w_context.subject.sessions.ses_dirs) == ["ses-01", "ses-02"]
-    assert sorted(T1w_context.subject.sessions.session_id) == ["ses-01", "ses-02"]
+    assert sorted(T1w_context.subject.sessions.ses_dirs) == ['ses-01', 'ses-02']
+    assert sorted(T1w_context.subject.sessions.session_id) == ['ses-01', 'ses-02']
     assert T1w_context.sidecar is None
     assert T1w_context.json is None
 
@@ -87,32 +87,32 @@ def test_context(synthetic_dataset, schema):
     ## Tests for:
     #  associations
     #  columns
-    #  json
     #  gzip
     #  nifti_header
     #  ome
     #  tiff
 
-def test_context_json(examples, schema):
 
+def test_context_json(examples, schema):
     dataset = FileTree.read_from_filesystem(examples / 'qmri_vfa')
-    file = dataset / 'sub-01' / 'anat'/'sub-01_flip-1_VFA.json'
+    file = dataset / 'sub-01' / 'anat' / 'sub-01_flip-1_VFA.json'
 
     ds = context.Dataset(dataset, schema)
     file_context = context.Context(file, ds, subject=None)
 
     assert file_context.json.to_dict() == {'FlipAngle': 3, 'RepetitionTimeExcitation': 0.0150}
 
+
 def test_sidecar_inheritance(examples):
     """Test to ensure inheritance principle is executed correctly"""
     dataset = FileTree.read_from_filesystem(examples / 'qmri_mp2rage')
-    file = dataset / "sub-1" / "anat"/"sub-1_inv-2_part-mag_MP2RAGE.nii"
+    file = dataset / 'sub-1' / 'anat' / 'sub-1_inv-2_part-mag_MP2RAGE.nii'
 
     sidecar = context.load_sidecar(file)
 
-    assert sidecar["FlipAngle"] == 7
-    assert sidecar["InversionTime"] == 2.7
-    assert sidecar["RepetitionTimePreparation"] == 5.5
+    assert sidecar['FlipAngle'] == 7
+    assert sidecar['InversionTime'] == 2.7
+    assert sidecar['RepetitionTimePreparation'] == 5.5
 
 
 def test_sessions(synthetic_dataset):
@@ -120,5 +120,5 @@ def test_sessions(synthetic_dataset):
 
     sessions = context.Sessions(sub01)
 
-    assert sorted(sessions.ses_dirs) == ["ses-01", "ses-02"]
-    assert sorted(sessions.session_id) == ["ses-01", "ses-02"]
+    assert sorted(sessions.ses_dirs) == ['ses-01', 'ses-02']
+    assert sorted(sessions.session_id) == ['ses-01', 'ses-02']

From 85f7733d7d9cbc360fa041032a42e5281fc34386 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Wed, 24 Sep 2025 18:41:11 +0100
Subject: [PATCH 23/28] add json property to context class

---
 src/bids_validator/context.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 4a7c8ed..183c029 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -373,9 +373,12 @@ def columns(self) -> None:
         pass
 
     @property
-    def json(self) -> None:
+    def json(self) -> Namespace | None:
         """Contents of the current JSON file."""
-        pass
+        if self.file_parts.extension == '.json':
+            return Namespace.build(load_json(self.file))
+
+        return None
 
     @property
     def gzip(self) -> None:

From 6a90acc23c3bf18eb15258b9641b7bb433db1189 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Mon, 29 Sep 2025 16:56:57 +0100
Subject: [PATCH 24/28] feedback changes

---
 src/bids_validator/__main__.py | 5 ++---
 src/bids_validator/context.py  | 7 ++-----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index 2c2d375..e9ffd88 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -100,7 +100,7 @@ def version_callback(value: bool):
 @app.command()
 def main(
     bids_path: str,
-    schema_path: str = None,
+    schema_path: str | None = None,
     verbose: Annotated[bool, typer.Option('--verbose', '-v', help='Show verbose output')] = False,
     version: Annotated[
         bool,
@@ -117,8 +117,7 @@ def main(
 
     root_path = FileTree.read_from_filesystem(bids_path)
 
-    if not schema_path:
-        schema = load_schema()
+    schema = load_schema(schema_path)
 
     validate(root_path, schema)
 
diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 183c029..3767fad 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -403,12 +403,9 @@ def tiff(self) -> None:
     @property
     def sidecar(self) -> Namespace | None:
         """Sidecar metadata constructed via the inheritance principle."""
-        sidecar = load_sidecar(self.file)
+        sidecar = load_sidecar(self.file) or {}
 
-        if sidecar:
-            return Namespace.build(sidecar)
-
-        return None
+        return Namespace.build(sidecar)
 
 
 class Sessions:

From 37df90aee30c6c7560f614e47eade24329f37f33 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Mon, 29 Sep 2025 17:02:30 +0100
Subject: [PATCH 25/28] update test for context.sidecar

---
 tests/test_context.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_context.py b/tests/test_context.py
index 6866c59..7fdbf75 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -76,7 +76,7 @@ def test_context(synthetic_dataset, schema):
     assert isinstance(T1w_context.subject.sessions, context.Sessions)
     assert sorted(T1w_context.subject.sessions.ses_dirs) == ['ses-01', 'ses-02']
     assert sorted(T1w_context.subject.sessions.session_id) == ['ses-01', 'ses-02']
-    assert T1w_context.sidecar is None
+    assert T1w_context.sidecar == {}
     assert T1w_context.json is None
 
     bold_context = context.Context(bold, ds, subject)

From 1360680623d1a2ead48d0eb6f8b8fd67b70ace54 Mon Sep 17 00:00:00 2001
From: Dan Brady <daniel.brady@sheffield.ac.uk>
Date: Mon, 29 Sep 2025 17:07:01 +0100
Subject: [PATCH 26/28] update typing for main

---
 src/bids_validator/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/bids_validator/__main__.py b/src/bids_validator/__main__.py
index e9ffd88..f2bd949 100644
--- a/src/bids_validator/__main__.py
+++ b/src/bids_validator/__main__.py
@@ -9,7 +9,7 @@
 
 import sys
 from collections.abc import Iterator
-from typing import Annotated
+from typing import Annotated, Optional
 
 from bidsschematools.schema import load_schema
 from bidsschematools.types import Namespace
@@ -100,7 +100,7 @@ def version_callback(value: bool):
 @app.command()
 def main(
     bids_path: str,
-    schema_path: str | None = None,
+    schema_path: Optional[str] = None,
     verbose: Annotated[bool, typer.Option('--verbose', '-v', help='Show verbose output')] = False,
     version: Annotated[
         bool,

From e68bc1d12fe4cd659a4abaa61220ac4c392f33c0 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Mon, 29 Sep 2025 16:50:36 -0400
Subject: [PATCH 27/28] rf: Replace direntry with UPath in FileTree

---
 src/bids_validator/context.py     |   6 +-
 src/bids_validator/types/files.py | 110 ++++++++----------------------
 2 files changed, 30 insertions(+), 86 deletions(-)

diff --git a/src/bids_validator/context.py b/src/bids_validator/context.py
index 3767fad..9baa58f 100644
--- a/src/bids_validator/context.py
+++ b/src/bids_validator/context.py
@@ -61,7 +61,7 @@ def datatype_to_modality(datatype: str, schema: Namespace) -> str:
 @cache
 def load_tsv(file: FileTree, *, max_rows=0) -> Namespace:
     """Load TSV contents into a Namespace."""
-    with open(file) as fobj:
+    with file.path_obj.open() as fobj:
         if max_rows > 0:
             fobj = itertools.islice(fobj, max_rows)
         contents = (line.rstrip('\r\n').split('\t') for line in fobj)
@@ -72,7 +72,7 @@ def load_tsv(file: FileTree, *, max_rows=0) -> Namespace:
 @cache
 def load_json(file: FileTree) -> dict[str]:
     """Load JSON file contents."""
-    return orjson.loads(UPath(file).read_bytes())
+    return orjson.loads(file.path_obj.read_bytes())
 
 
 class Subjects:
@@ -360,7 +360,7 @@ def modality(self) -> str | None:
     @property
     def size(self) -> int:
         """Length of the current file in bytes."""
-        return self.file.direntry.stat().st_size
+        return self.file.path_obj.stat().st_size
 
     @property
     def associations(self) -> ctx.Associations:
diff --git a/src/bids_validator/types/files.py b/src/bids_validator/types/files.py
index a3a6f62..40db627 100644
--- a/src/bids_validator/types/files.py
+++ b/src/bids_validator/types/files.py
@@ -4,103 +4,50 @@
 
 import os
 import posixpath
-import stat
 from functools import cached_property
 from pathlib import Path
 
 import attrs
+from upath import UPath
 
 from . import _typings as t
 
 __all__ = ('FileTree',)
 
 
-@attrs.define
-class UserDirEntry:
-    """Partial reimplementation of :class:`os.DirEntry`.
-
-    :class:`os.DirEntry` can't be instantiated from Python, but this can.
-    """
-
-    path: str = attrs.field(repr=False, converter=os.fspath)
-    name: str = attrs.field(init=False)
-    _stat: os.stat_result = attrs.field(init=False, repr=False, default=None)
-    _lstat: os.stat_result = attrs.field(init=False, repr=False, default=None)
-
-    def __attrs_post_init__(self) -> None:
-        self.name = os.path.basename(self.path)
-
-    def __fspath__(self) -> str:
-        return self.path
-
-    def stat(self, *, follow_symlinks: bool = True) -> os.stat_result:
-        """Return stat_result object for the entry; cached per entry."""
-        if follow_symlinks:
-            if self._stat is None:
-                self._stat = os.stat(self.path, follow_symlinks=True)
-            return self._stat
-        else:
-            if self._lstat is None:
-                self._lstat = os.stat(self.path, follow_symlinks=False)
-            return self._lstat
-
-    def is_dir(self, *, follow_symlinks: bool = True) -> bool:
-        """Return True if the entry is a directory; cached per entry."""
-        _stat = self.stat(follow_symlinks=follow_symlinks)
-        return stat.S_ISDIR(_stat.st_mode)
-
-    def is_file(self, *, follow_symlinks: bool = True) -> bool:
-        """Return True if the entry is a file; cached per entry."""
-        _stat = self.stat(follow_symlinks=follow_symlinks)
-        return stat.S_ISREG(_stat.st_mode)
-
-    def is_symlink(self) -> bool:
-        """Return True if the entry is a symlink; cached per entry."""
-        _stat = self.stat(follow_symlinks=False)
-        return stat.S_ISLNK(_stat.st_mode)
-
-
-def as_direntry(obj: os.PathLike) -> os.DirEntry | UserDirEntry:
-    """Convert PathLike into DirEntry-like object."""
-    if isinstance(obj, os.DirEntry):
-        return obj
-    return UserDirEntry(obj)
-
-
-@attrs.define
+@attrs.define(frozen=True)
 class FileTree:
     """Represent a FileTree with cached metadata."""
 
-    direntry: os.DirEntry | UserDirEntry = attrs.field(repr=False, converter=as_direntry)
-    parent: FileTree | None = attrs.field(repr=False, default=None)
-    is_dir: bool = attrs.field(default=False)
-    children: dict[str, FileTree] = attrs.field(repr=False, factory=dict)
-    name: str = attrs.field(init=False)
+    path_obj: UPath = attrs.field(repr=False, converter=UPath)
+    is_dir: bool = attrs.field(repr=False, default=None)
+    parent: FileTree | None = attrs.field(repr=False, default=None, eq=False)
+    children: dict[str, FileTree] = attrs.field(repr=False, factory=dict, eq=False)
 
     def __attrs_post_init__(self):
-        self.name = self.direntry.name
-        self.children = {
-            name: attrs.evolve(child, parent=self) for name, child in self.children.items()
-        }
+        if self.is_dir is None:
+            object.__setattr__(self, 'is_dir', self.path_obj.is_dir())
+        object.__setattr__(
+            self,
+            'children',
+            {name: attrs.evolve(child, parent=self) for name, child in self.children.items()},
+        )
 
     @classmethod
-    def read_from_filesystem(
-        cls,
-        direntry: os.PathLike,
-        parent: FileTree | None = None,
-    ) -> t.Self:
-        """Read a FileTree from the filesystem.
-
-        Uses :func:`os.scandir` to walk the directory tree.
-        """
-        self = cls(direntry, parent=parent)
-        if self.direntry.is_dir():
-            self.is_dir = True
-            self.children = {
-                entry.name: FileTree.read_from_filesystem(entry, parent=self)
-                for entry in os.scandir(self.direntry)
+    def read_from_filesystem(cls, path_obj: os.PathLike) -> t.Self:
+        """Read a FileTree from the filesystem."""
+        path_obj = UPath(path_obj)
+        children = {}
+        if is_dir := path_obj.is_dir():
+            children = {
+                entry.name: FileTree.read_from_filesystem(entry) for entry in path_obj.iterdir()
             }
-        return self
+        return cls(path_obj, is_dir=is_dir, children=children)
+
+    @property
+    def name(self) -> bool:
+        """The name of the current FileTree node."""
+        return self.path_obj.name
 
     def __contains__(self, relpath: os.PathLike) -> bool:
         parts = Path(relpath).parts
@@ -110,10 +57,7 @@ def __contains__(self, relpath: os.PathLike) -> bool:
         return child and (len(parts) == 1 or posixpath.join(*parts[1:]) in child)
 
     def __fspath__(self):
-        return self.direntry.path
-
-    def __hash__(self):
-        return hash(self.direntry.path)
+        return self.path_obj.__fspath__()
 
     def __truediv__(self, relpath: str | os.PathLike) -> t.Self:
         parts = Path(relpath).parts

From 0d31404e5706b07c8d8c4c8e0952c8524cfa2495 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Mon, 29 Sep 2025 21:14:24 -0400
Subject: [PATCH 28/28] test: Generate dataset in-memory, test sidecar
 overrides

---
 tests/test_context.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/tests/test_context.py b/tests/test_context.py
index 7fdbf75..6dcb040 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -1,3 +1,6 @@
+import json
+
+import fsspec
 import pytest
 from bidsschematools.types.context import Subject
 
@@ -10,6 +13,14 @@ def synthetic_dataset(examples):
     return FileTree.read_from_filesystem(examples / 'synthetic')
 
 
+@pytest.fixture
+def memfs():
+    mem = fsspec.filesystem('memory')
+    mem.store.clear()
+    yield mem
+    mem.store.clear()
+
+
 def test_load(synthetic_dataset, schema):
     ds = context.Dataset(synthetic_dataset, schema)
 
@@ -115,6 +126,33 @@ def test_sidecar_inheritance(examples):
     assert sidecar['RepetitionTimePreparation'] == 5.5
 
 
+def test_sidecar_order(memfs):
+    """Test to ensure inheritance principle is skipped when inherit=False"""
+    root_json = {'rootOverwriteA': 'root', 'rootOverwriteB': 'root', 'rootValue': 'root'}
+    subject_json = {'rootOverwriteA': 'subject', 'subOverwrite': 'subject', 'subValue': 'subject'}
+    anat_json = {'rootOverwriteB': 'anat', 'subOverwrite': 'anat', 'anatValue': 'anat'}
+    memfs.pipe(
+        {
+            '/T1w.json': json.dumps(root_json).encode(),
+            '/sub-01/sub-01_T1w.json': json.dumps(subject_json).encode(),
+            '/sub-01/anat/sub-01_T1w.json': json.dumps(anat_json).encode(),
+            '/sub-01/anat/sub-01_T1w.nii': b'',
+        }
+    )
+
+    dataset = FileTree.read_from_filesystem('memory://')
+    file = dataset / 'sub-01' / 'anat' / 'sub-01_T1w.nii'
+    sidecar = context.load_sidecar(file)
+    assert sidecar == {
+        'rootValue': 'root',
+        'subValue': 'subject',
+        'rootOverwriteA': 'subject',
+        'anatValue': 'anat',
+        'rootOverwriteB': 'anat',
+        'subOverwrite': 'anat',
+    }
+
+
 def test_sessions(synthetic_dataset):
     sub01 = synthetic_dataset / 'sub-01'