Start applying fixes for update

.github/workflows/test.yml

@@ -52,7 +52,7 @@ jobs:
     needs: [ 'quality'  ]
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13.-rc.3']
     steps:
     - uses: khanlab/actions/.github/actions/[email protected]
       id: setup
@@ -68,7 +68,7 @@ jobs:
     needs: [ 'build-cache-env'  ]
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13.-rc.3']
         split: ['1', '2', '3', '4', '5']
       fail-fast: false
     steps:

snakebids/__init__.py

@@ -3,6 +3,7 @@
 
 __submodules__ = ["core", "paths"]
 
+
 from snakebids import _warningformat  # noqa: F401
 
 # isort: split

snakebids/core/_querying.py

@@ -7,8 +7,7 @@
 
 import attrs
 import more_itertools as itx
-from bids.layout import BIDSLayout, Query
-from bids.layout.models import BIDSFile
+from bids.layout import BIDSFile, BIDSLayout, Query
 from typing_extensions import Self, TypeAlias, override
 
 from snakebids.exceptions import ConfigError, PybidsError

snakebids/core/datasets.py

@@ -11,7 +11,7 @@
 
 import attr
 import more_itertools as itx
-from bids import BIDSLayout
+from bids.layout import BIDSLayout
 from pvandyken.deprecated import deprecated
 from typing_extensions import Self, TypedDict
 

snakebids/core/input_generation.py

@@ -17,7 +17,7 @@
 )
 
 import more_itertools as itx
-from bids import BIDSLayout, BIDSLayoutIndexer
+from bids.layout import BIDSLayout, BIDSLayoutIndexer
 
 from snakebids.core._querying import (
     FilterSpecError,

snakebids/resources/bids_tags.json

@@ -183,6 +183,12 @@
         "before": "subset-",
         "match": "[a-zA-Z0-9]+"
     },
+    "nucleus": {
+        "tag": "nucleus",
+        "before": "nuc-",
+        "match": "[a-zA-Z0-9]+"
+
+    },
     "desc": {
         "tag": "desc",
         "before": "desc-",

snakebids/tests/conftest.py

@@ -8,6 +8,7 @@
 import pytest
 from hypothesis import database, settings
 from pyfakefs.fake_filesystem import FakeFilesystem
+from upath import UPath
 
 import snakebids.paths.resources as specs
 from snakebids import resources, set_bids_spec
@@ -51,9 +52,7 @@ def fakefs(
 
 
 @pytest.fixture
-def fakefs_tmpdir(
-    request: pytest.FixtureRequest, fakefs: FakeFilesystem | None
-) -> Path:
+def tmpdir(request: pytest.FixtureRequest, fakefs: FakeFilesystem | None) -> Path:
     """Version of tmpdir compatible with fakefs
 
     If fakefs is disabled, a tmpdir is returned using the builtin tmpdir fixture.

snakebids/tests/test_generate_inputs.py

@@ -27,7 +27,7 @@
 import attrs
 import more_itertools as itx
 import pytest
-from bids import BIDSLayout
+from bids.layout import BIDSLayout
 from hypothesis import HealthCheck, assume, example, given, settings
 from hypothesis import strategies as st
 from pyfakefs.fake_filesystem import FakeFilesystem
@@ -55,6 +55,7 @@
     allow_function_scoped,
     create_dataset,
     create_snakebids_config,
+    debug,
     example_if,
     get_bids_path,
     get_zip_list,
@@ -208,13 +209,13 @@ def test_attribute_errors_from_pybids_qualified_and_raised():
 
 
 class TestFilterBools:
-    @pytest.fixture(autouse=True)
-    def bids_fs(self, bids_fs: FakeFilesystem | None):
-        return bids_fs
+    # @pytest.fixture(autouse=True)
+    # def bids_fs(self, bids_fs: FakeFilesystem | None):
+    #     return bids_fs
 
-    @pytest.fixture
-    def tmpdir(self, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    # @pytest.fixture
+    # def tmpdir(self, tmpdir: Path):
+    #     return tmpdir
 
     def disambiguate_components(self, dataset: BidsDataset):
         assert len(dataset) == 2
@@ -242,7 +243,7 @@ def set_difference(set_: set[str], comp: BidsComponent) -> set[str]:
     )
     @given(dataset=sb_st.datasets())
     def test_ambiguous_paths_with_extra_entities_leads_to_error(
-        self, tmpdir: Path, dataset: BidsDataset
+        self, tmpdir: Path, dataset: BidsDataset, mocker: MockerFixture
     ):
         root = tempfile.mkdtemp(dir=tmpdir)
         create_dataset(root, dataset)
@@ -268,7 +269,7 @@ def test_ambiguous_paths_with_extra_entities_leads_to_error(
     )
     @given(dataset=sb_st.datasets())
     def test_ambiguous_paths_with_missing_entity_leads_to_error(
-        self, tmpdir: Path, dataset: BidsDataset
+        self, tmpdir: Path, dataset: BidsDataset, mocker: MockerFixture
     ):
         root = tempfile.mkdtemp(dir=tmpdir)
         create_dataset(root, dataset)
@@ -519,15 +520,27 @@ def add_entity(component: BidsComponent, entity: str, value: str):
         assert result == BidsDataset({"template": dataset["template"]})
 
 
+@pytest.mark.disable_fakefs(True)
 class TestFilterMethods:
-    @pytest.fixture(autouse=True)
-    def bids_fs(self, bids_fs: FakeFilesystem | None):
-        return bids_fs
+    # @pytest.fixture(autouse=True)
+    # def bids_fs(self, bids_fs: FakeFilesystem | None):
+    #     return bids_fs
 
-    @pytest.fixture
-    def tmpdir(self, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    # @pytest.fixture
+    # def tmpdir(self, fakefs_tmpdir: Path):
+    #     return fakefs_tmpdir
 
+    @debug(
+        component=BidsComponent(
+            name="template",
+            path="sub-{subject}/sub-{subject}_nuc-{nucleus}",
+            zip_lists={
+                "subject": ["0"],
+                "nucleus": ["0"],
+            },
+        ),
+        data=mock_data("0"),
+    )
     @example(
         component=BidsComponent(
             name="template",
@@ -861,10 +874,8 @@ def test_filter_with_invalid_method_raises_error(self, tmpdir: Path, method: str
     max_examples=1,
 )
 @given(dataset=sb_st.datasets_one_comp(unique=True))
-def test_duplicate_wildcards_does_not_create_error(
-    dataset: BidsDataset, bids_fs: Path, fakefs_tmpdir: Path
-):
-    root = tempfile.mkdtemp(dir=fakefs_tmpdir)
+def test_duplicate_wildcards_does_not_create_error(dataset: BidsDataset, tmpdir: Path):
+    root = tempfile.mkdtemp(dir=tmpdir)
     rooted = BidsDataset.from_iterable(
         attrs.evolve(comp, path=os.path.join(root, comp.path))
         for comp in dataset.values()
@@ -1071,8 +1082,8 @@ def get_subset(of: Iterable[T]) -> list[T]:
 
 class TestCustomPaths:
     @pytest.fixture
-    def temp_dir(self, fakefs_tmpdir: Path, bids_fs: Path):
-        return fakefs_tmpdir
+    def temp_dir(self, tmpdir: Path, bids_fs: Path):
+        return tmpdir
 
     def generate_test_directory(
         self, entities: dict[str, list[str]], template: Path, tmpdir: Path
@@ -1596,13 +1607,13 @@ def test_get_lists_from_bids():
 
 
 class TestGenBidsLayout:
-    @pytest.fixture
-    def tmpdir(self, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    # @pytest.fixture
+    # def tmpdir(self, tmpdir: Path):
+    #     return tmpdir
 
-    @pytest.fixture(autouse=True)
-    def bids_fs(self, bids_fs: FakeFilesystem | None):
-        return bids_fs
+    # @pytest.fixture(autouse=True)
+    # def bids_fs(self, bids_fs: FakeFilesystem | None):
+    #     return bids_fs
 
     @settings(
         max_examples=1, suppress_health_check=[HealthCheck.function_scoped_fixture]
@@ -1719,8 +1730,8 @@ def __str__(self):  # __fspath__ calls __str__ by default
     ],
 )
 @given(dataset=sb_st.datasets(unique=True))
-def test_generate_inputs(dataset: BidsDataset, bids_fs: Path, fakefs_tmpdir: Path):
-    root = tempfile.mkdtemp(dir=fakefs_tmpdir)
+def test_generate_inputs(dataset: BidsDataset, tmpdir: Path):
+    root = tempfile.mkdtemp(dir=tmpdir)
     rooted = BidsDataset.from_iterable(
         attrs.evolve(comp, path=os.path.join(root, comp.path))
         for comp in dataset.values()
@@ -1753,8 +1764,8 @@ class TestParticipantFiltering:
     MODE = Literal["include", "exclude"]
 
     @pytest.fixture
-    def tmpdir(self, bids_fs: Path, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    def tmpdir(self, bids_fs: Path, tmpdir: Path):
+        return tmpdir
 
     def get_filter_params(self, mode: MODE, filters: list[str] | str):
         class FiltParams(TypedDict, total=False):
@@ -1932,12 +1943,12 @@ def test_exclude_participant_does_not_make_all_other_filters_regex(
 @settings(max_examples=1, suppress_health_check=[HealthCheck.function_scoped_fixture])
 @given(dataset=sb_st.datasets_one_comp(blacklist_entities=["extension"], unique=True))
 def test_when_all_custom_paths_no_layout_indexed(
-    dataset: BidsDataset, bids_fs: Path, fakefs_tmpdir: Path, mocker: MockerFixture
+    dataset: BidsDataset, bids_fs: Path, tmpdir: Path, mocker: MockerFixture
 ):
     # Need to reset mocker at beginning because hypothesis may call this function
     # multiple times
     mocker.stopall()
-    root = tempfile.mkdtemp(dir=fakefs_tmpdir)
+    root = tempfile.mkdtemp(dir=tmpdir)
     rooted = BidsDataset.from_iterable(
         attrs.evolve(comp, path=os.path.join(root, comp.path))
         for comp in dataset.values()

snakebids/tests/test_plugins/test_snakemake.py

@@ -29,31 +29,31 @@
 class TestFindSnakefileConfig:
     @allow_function_scoped
     @given(snakefile=st.sampled_from(SNAKEFILE_CHOICES))
-    def test_finds_snakefile(self, fakefs_tmpdir: Path, snakefile: str):
-        tmp = Path(tempfile.mkdtemp(dir=fakefs_tmpdir))
+    def test_finds_snakefile(self, tmpdir: Path, snakefile: str):
+        tmp = Path(tempfile.mkdtemp(dir=tmpdir))
         snakefile_path = tmp / snakefile
         snakefile_path.parent.mkdir(parents=True, exist_ok=True)
         snakefile_path.touch()
         app = SnakemakeBidsApp(snakemake_dir=tmp, configfile_path=None)
         assert app.snakefile_path == snakefile_path
 
-    def test_errors_if_no_snakefile_found(self, fakefs_tmpdir: Path):
-        tmp = Path(tempfile.mkdtemp(dir=fakefs_tmpdir))
+    def test_errors_if_no_snakefile_found(self, tmpdir: Path):
+        tmp = Path(tempfile.mkdtemp(dir=tmpdir))
         with pytest.raises(ConfigError, match="Error: no Snakefile"):
             SnakemakeBidsApp(snakemake_dir=tmp, configfile_path=None)
 
     @allow_function_scoped
     @given(configfile=st.sampled_from(CONFIGFILE_CHOICES))
-    def test_finds_config_file(self, fakefs_tmpdir: Path, configfile: str):
-        tmp = Path(tempfile.mkdtemp(dir=fakefs_tmpdir))
+    def test_finds_config_file(self, tmpdir: Path, configfile: str):
+        tmp = Path(tempfile.mkdtemp(dir=tmpdir))
         configfile_path = tmp / configfile
         configfile_path.parent.mkdir(parents=True, exist_ok=True)
         configfile_path.touch()
         app = SnakemakeBidsApp(snakemake_dir=tmp, snakefile_path=Path())
         assert app.configfile_path == configfile_path
 
-    def test_errors_if_no_configfile_found(self, fakefs_tmpdir: Path):
-        tmp = Path(tempfile.mkdtemp(dir=fakefs_tmpdir))
+    def test_errors_if_no_configfile_found(self, tmpdir: Path):
+        tmp = Path(tempfile.mkdtemp(dir=tmpdir))
         with pytest.raises(ConfigError, match="Error: no config file"):
             SnakemakeBidsApp(snakemake_dir=tmp, snakefile_path=Path())