Update updated spec name, declare spec for tests (#369)

* Update updated spec name, declare spec for tests * Show git diff on update-bids failure * Exclude control characters from yaml tests These expose a bug in ruamel round-tripping (not critical for our application)
khanlab · Feb 15, 2024 · 8fce792 · 8fce792
1 parent 8acbd9f
commit 8fce792
Show file tree

Hide file tree

Showing 10 changed files with 46 additions and 45 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -32,7 +32,7 @@ jobs:
         run: |
           poetry run poe update-bids
           git diff --quiet || (
-            git status
+            git diff
             echo 'bids specs out of date, run `poetry run poe update-bids`'
             exit 1
           )

diff --git a/scripts/update_bids.py b/scripts/update_bids.py
@@ -133,7 +133,7 @@ def get_latest(versions: Iterable[BidsPathSpecFile]) -> tuple[str, BidsPathSpecF
 
 def main():
     """update_bids entrypoint."""
-    all_specs = list(get_specs())
+    all_specs = sorted(get_specs(), key=lambda o: o["version"])
     latest_version, latest_spec = get_latest(all_specs)
     generate_stub(
         specs,

diff --git a/snakebids/paths/_config.py b/snakebids/paths/_config.py
@@ -18,7 +18,7 @@
 #       poetry run poe update-bids
 #
 
-VALID_SPECS: TypeAlias = Literal["v0_10_1", "v0_0_0", "latest"]
+VALID_SPECS: TypeAlias = Literal["v0_0_0", "v0_11_0", "latest"]
 # </AUTOUPDATE>
 
 __all__ = ["set_bids_spec"]

diff --git a/snakebids/paths/resources/spec.0.10.1.yaml → snakebids/paths/resources/spec.0.11.0.yaml b/snakebids/paths/resources/spec.0.10.1.yaml → snakebids/paths/resources/spec.0.11.0.yaml
@@ -1,11 +1,11 @@
-version: "v0.10.1"
+version: "v0.11.0"
 description: |
   Spec corresponding to `BIDS v1.9.0`_.
 
   Significantly expanded from the v0.0.0 spec, now including long names for
-  every relevant entity. In addition to the spec, it includes `from` and `to`
-  entities intended for transformations. Unknown entities are placed just before
-  desc, so that the description entity is always last.
+  every relevant entity. In addition to the official spec, it includes `from`
+  and `to` entities intended for transformations. Unknown entities are placed
+  just before desc, so that the description entity is always last.
 
   .. _BIDS v1.9.0: https://bids-specification.readthedocs.io/en/v1.9.0/
 

diff --git a/snakebids/paths/specs.py b/snakebids/paths/specs.py
@@ -15,8 +15,8 @@
 #
 if not TYPE_CHECKING:
     __all__ = [  # noqa:F822
-        "v0_10_1",
         "v0_0_0",
+        "v0_11_0",
         "latest",
         "LATEST",
     ]
@@ -25,8 +25,8 @@ def __dir__():
         return __all__
 
 
-_SPECS = ["v0_10_1", "v0_0_0"]
-# LATEST = "v0_10_1"
+_SPECS = ["v0_0_0", "v0_11_0"]
+# LATEST = "v0_11_0"
 # </AUTOUPDATE>
 
 # To automatically use latest spec as "LATEST", remove this line and uncomment the

diff --git a/snakebids/paths/specs.pyi b/snakebids/paths/specs.pyi
@@ -7,27 +7,21 @@ from ._utils import BidsPathSpec
 
 LATEST: str
 
-def v0_10_1(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
-    """Spec corresponding to `BIDS v1.9.0`_.
-
-    Significantly expanded from the v0.0.0 spec, now including long names for every
-    relevant entity. In addition to the spec, it includes `from` and `to` entities
-    intended for transformations. Unknown entities are placed just before desc, so that
-    the description entity is always last.
+def v0_0_0(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
+    """Get the v0.0.0 BidsPathSpec.
 
-    .. _BIDS v1.9.0: https://bids-specification.readthedocs.io/en/v1.9.0/
+    This spec alone equips :func:`~snakebids.bids` with 2 extra arguments:
+    ``include_subject_dir`` and ``include_session_dir``. These default to ``True``, but
+    if set ``False``, remove the subject and session dirs respectively from the output
+    path. For future specs, this behaviour should be achieved by modifying the spec and
+    generating a new :func:`~snakebids.bids` function
 
     Formatted as::
 
         sub-{subject}/ses-{session}/{datatype}/{prefix}_sub-{subject}_ses-{session}_
-        sample-{sample}_task-{task}_tracksys-{tracksys}_acq-{acquisition}_
-        ce-{ceagent}_stain-{staining}_trc-{tracer}_rec-{reconstruction}_
-        dir-{direction}_run-{run}_mod-{modality}_echo-{echo}_flip-{flip}_
-        inv-{inversion}_mt-{mt}_proc-{processed}_part-{part}_space-{space}_
-        atlas-{atlas}_seg-{segmentation}_hemi-{hemisphere}_res-{resolution}_
-        den-{density}_roi-{roi}_from-{from}_to-{to}_split-{split}_
-        recording-{recording}_chunk-{chunk}_model-{model}_subset-{subset}_
-        label-{label}_..._desc-{description}_{suffix}{extension}
+        task-{task}_acq-{acq}_ce-{ce}_rec-{rec}_dir-{dir}_run-{run}_mod-{mod}_
+        echo-{echo}_hemi-{hemi}_space-{space}_res-{res}_den-{den}_label-{label}_
+        desc-{desc}_..._{suffix}{extension}
 
 
     Parameters
@@ -41,21 +35,27 @@ def v0_10_1(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
     """
     ...
 
-def v0_0_0(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
-    """Get the v0.0.0 BidsPathSpec.
+def v0_11_0(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
+    """Spec corresponding to `BIDS v1.9.0`_.
 
-    This spec alone equips :func:`~snakebids.bids` with 2 extra arguments:
-    ``include_subject_dir`` and ``include_session_dir``. These default to ``True``, but
-    if set ``False``, remove the subject and session dirs respectively from the output
-    path. For future specs, this behaviour should be achieved by modifying the spec and
-    generating a new :func:`~snakebids.bids` function
+    Significantly expanded from the v0.0.0 spec, now including long names for every
+    relevant entity. In addition to the official spec, it includes `from` and `to`
+    entities intended for transformations. Unknown entities are placed just before desc,
+    so that the description entity is always last.
+
+    .. _BIDS v1.9.0: https://bids-specification.readthedocs.io/en/v1.9.0/
 
     Formatted as::
 
         sub-{subject}/ses-{session}/{datatype}/{prefix}_sub-{subject}_ses-{session}_
-        task-{task}_acq-{acq}_ce-{ce}_rec-{rec}_dir-{dir}_run-{run}_mod-{mod}_
-        echo-{echo}_hemi-{hemi}_space-{space}_res-{res}_den-{den}_label-{label}_
-        desc-{desc}_..._{suffix}{extension}
+        sample-{sample}_task-{task}_tracksys-{tracksys}_acq-{acquisition}_
+        ce-{ceagent}_stain-{staining}_trc-{tracer}_rec-{reconstruction}_
+        dir-{direction}_run-{run}_mod-{modality}_echo-{echo}_flip-{flip}_
+        inv-{inversion}_mt-{mt}_proc-{processed}_part-{part}_space-{space}_
+        atlas-{atlas}_seg-{segmentation}_hemi-{hemisphere}_res-{resolution}_
+        den-{density}_roi-{roi}_from-{from}_to-{to}_split-{split}_
+        recording-{recording}_chunk-{chunk}_model-{model}_subset-{subset}_
+        label-{label}_..._desc-{description}_{suffix}{extension}
 
 
     Parameters
@@ -73,9 +73,9 @@ def latest(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
     """Spec corresponding to `BIDS v1.9.0`_.
 
     Significantly expanded from the v0.0.0 spec, now including long names for every
-    relevant entity. In addition to the spec, it includes `from` and `to` entities
-    intended for transformations. Unknown entities are placed just before desc, so that
-    the description entity is always last.
+    relevant entity. In addition to the official spec, it includes `from` and `to`
+    entities intended for transformations. Unknown entities are placed just before desc,
+    so that the description entity is always last.
 
     .. _BIDS v1.9.0: https://bids-specification.readthedocs.io/en/v1.9.0/
 

diff --git a/snakebids/tests/conftest.py b/snakebids/tests/conftest.py
@@ -10,7 +10,7 @@
 from pyfakefs.fake_filesystem import FakeFilesystem
 
 import snakebids.paths.resources as specs
-from snakebids import resources
+from snakebids import resources, set_bids_spec
 
 ## Hypothesis profiles
 
@@ -27,9 +27,10 @@
 
 settings.load_profile(os.getenv("HYPOTHESIS_PROFILE", "dev"))
 
-# Fixtures
+set_bids_spec("v0_0_0")
 
 
+# Fixtures
 @pytest.fixture
 def fakefs(
     request: pytest.FixtureRequest,

diff --git a/snakebids/tests/test_paths/test_bids.py b/snakebids/tests/test_paths/test_bids.py
@@ -302,7 +302,7 @@ def test_missing_essential_entities_gives_error(self, args: dict[str, str]):
 
 TestV0_0_0 = make_bids_testsuite(specs.v0_0_0())
 
-TestV0_10_1 = make_bids_testsuite(specs.v0_10_1())
+TestV0_10_1 = make_bids_testsuite(specs.v0_11_0())
 
 
 def test_benchmark_bids(benchmark: Benchmark):

diff --git a/snakebids/tests/test_paths/test_specs.py b/snakebids/tests/test_paths/test_specs.py
@@ -53,14 +53,14 @@ def test_session_dir_can_be_excluded():
 def test_spec_can_be_set_with_str():
     set_bids_spec("v0_0_0")
     assert bids(acquisition="foo") == "acquisition-foo"
-    set_bids_spec("v0_10_1")
+    set_bids_spec("v0_11_0")
     assert bids(acquisition="foo") == "acq-foo"
 
 
 def test_spec_can_be_set_with_obj():
     set_bids_spec(specs.v0_0_0())
     assert bids(acquisition="foo") == "acquisition-foo"
-    set_bids_spec(specs.v0_10_1())
+    set_bids_spec(specs.v0_11_0())
     assert bids(acquisition="foo") == "acq-foo"
 
 

diff --git a/snakebids/tests/test_yaml.py b/snakebids/tests/test_yaml.py
@@ -16,7 +16,7 @@
 import snakebids.io.yaml as yamlio
 from snakebids.tests.helpers import allow_function_scoped
 
-YAML_SAFE_CHARS = st.characters(blacklist_characters=["\x85"])
+YAML_SAFE_CHARS = st.characters(blacklist_characters=["\\"], blacklist_categories=["C"])
 
 
 @given(path=st.text(YAML_SAFE_CHARS, min_size=1).map(Path))