Eliminate deprecated code

Remove existing references to the deprecated BidsDataset properties.
Some functions, including the tests of these properties, call them by
necessity, so DeprecationWarnings are ignored at these points

snakebids/core/datasets.py

@@ -2,6 +2,7 @@
 
 import itertools as it
 import operator as op
+import warnings
 from collections import UserDict
 from string import Formatter
 from typing import TYPE_CHECKING, Any, Iterable, Optional, Union, cast
@@ -289,9 +290,7 @@ def subjects(self):
         return [
             *{
                 *it.chain.from_iterable(
-                    input_list["subject"]
-                    for input_list in self.entities.values()
-                    if "subject" in input_list
+                    component.entities.get("subject", []) for component in self.values()
                 )
             }
         ]
@@ -302,9 +301,7 @@ def sessions(self):
         return [
             *{
                 *it.chain.from_iterable(
-                    input_list["session"]
-                    for input_list in self.entities.values()
-                    if "session" in input_list
+                    component.entities.get("session", []) for component in self.values()
                 )
             }
         ]
@@ -334,15 +331,17 @@ def as_dict(self):
         -------
         BidsDatasetDict
         """
-        return BidsDatasetDict(
-            input_path=self.input_path,
-            input_lists=self.entities,
-            input_wildcards=self.input_wildcards,
-            input_zip_lists=self.input_zip_lists,
-            subjects=self.subjects,
-            sessions=self.sessions,
-            subj_wildcards=self.subj_wildcards,
-        )
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", category=DeprecationWarning)
+            return BidsDatasetDict(
+                input_path=self.input_path,
+                input_lists=self.entities,
+                input_wildcards=self.input_wildcards,
+                input_zip_lists=self.input_zip_lists,
+                subjects=self.subjects,
+                sessions=self.sessions,
+                subj_wildcards=self.subj_wildcards,
+            )
 
     @classmethod
     def from_iterable(cls, iterable: Iterable[BidsComponent]):

snakebids/project_template/{{cookiecutter.app_name}}/workflow/Snakefile

@@ -26,22 +26,22 @@ wildcard_constraints:  **snakebids.get_wildcard_constraints(config['pybids_input
 
 
 rule smooth:
-    input: inputs.path['bold']
+    input: inputs['bold'].path
     output:
         bids(
             root=config['root'],
             datatype='func',
             desc='smooth{fwhm}mm',
             suffix='bold.nii.gz',
-            **inputs.wildcards['bold']
+            **inputs['bold'].wildcards
         )
     container: config['singularity']['fsl']
     log:
         bids(
             root='logs',
             suffix='smooth.log',
             fwhm='{fwhm}',
-            **inputs.wildcards['bold']
+            **inputs['bold'].wildcards
         )
     params: sigma = lambda wildcards: f'{float(wildcards.fwhm)/2.355:0.2f}'
     shell: 'fslmaths {input} -s {params.sigma} {output}'
@@ -56,6 +56,6 @@ rule all:
                 allow_missing=True,
             ),
             zip,
-            **inputs.zip_lists['bold']
+            **inputs['bold'].zip_lists
         )
     default_target: True

snakebids/tests/test_datasets.py

@@ -1,5 +1,6 @@
 import copy
 import itertools as it
+import warnings
 from typing import Any, Dict, List
 
 import more_itertools as itx
@@ -31,11 +32,13 @@ def test_bids_component_aliases_are_correctly_set(self, component: BidsComponent
 
     @given(sb_st.bids_components())
     def test_bids_dataset_aliases_are_correctly_set(self, component: BidsComponent):
-        dataset = BidsDataset.from_iterable([component])
-        assert dataset.input_path == dataset.path
-        assert dataset.input_zip_lists == dataset.zip_lists
-        assert dataset.input_lists == dataset.input_lists
-        assert dataset.input_wildcards == dataset.wildcards
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", category=DeprecationWarning)
+            dataset = BidsDataset.from_iterable([component])
+            assert dataset.input_path == dataset.path
+            assert dataset.input_zip_lists == dataset.zip_lists
+            assert dataset.input_lists == dataset.input_lists
+            assert dataset.input_wildcards == dataset.wildcards
 
 
 class TestBidsComponentValidation:

snakebids/tests/test_generate_inputs.py

@@ -58,7 +58,6 @@ def tmpdir(self, fakefs_tmpdir: Path):
 
     def disambiguate_components(self, dataset: BidsDataset):
         assert len(dataset) == 2
-        dataset.zip_lists
         comp1, comp2 = dataset.values()
         return sorted([comp1, comp2], key=lambda comp: len(comp.entities.keys()))
 
@@ -271,9 +270,7 @@ def test_missing_filters(self, tmpdir: Path):
             pybids_config=str(Path(__file__).parent / "data" / "custom_config.json"),
             use_bids_inputs=True,
         )
-        template = BidsDataset(
-            {"t1": BidsComponent("t1", config.input_path["t1"], zip_list)}
-        )
+        template = BidsDataset({"t1": BidsComponent("t1", config["t1"].path, zip_list)})
         # Order of the subjects is not deterministic
         assert template == config
         assert config.subj_wildcards == {"subject": "{subject}"}
@@ -297,7 +294,7 @@ def test_missing_wildcards(self, tmpdir: Path):
             pybids_config=str(Path(__file__).parent / "data" / "custom_config.json"),
             use_bids_inputs=True,
         )
-        template = BidsDataset({"t1": BidsComponent("t1", config.input_path["t1"], {})})
+        template = BidsDataset({"t1": BidsComponent("t1", config["t1"].path, {})})
         assert template == config
         assert config.subj_wildcards == {"subject": "{subject}"}
 
@@ -573,7 +570,7 @@ def test_custom_pybids_config(tmpdir: Path):
         }
     )
     assert template == result
-    assert result.input_wildcards == {"t1": {"foo": "{foo}", "subject": "{subject}"}}
+    assert result["t1"].wildcards == {"foo": "{foo}", "subject": "{subject}"}
     # Order of the subjects is not deterministic
     assert result.subj_wildcards == {"subject": "{subject}"}
 
@@ -647,7 +644,7 @@ def test_t1w():
         {
             "t1": BidsComponent(
                 "t1",
-                result.input_path["t1"],
+                result["t1"].path,
                 {"acq": ["mprage", "mprage"], "subject": ["001", "002"]},
             )
         }
@@ -678,14 +675,16 @@ def test_t1w():
         participant_label="001",
         use_bids_inputs=True,
     )
-    assert result.entities == {
-        "scan": {"acq": ["mprage"], "subject": ["001"], "suffix": ["T1w"]}
+    assert result["scan"].entities == {
+        "acq": ["mprage"],
+        "subject": ["001"],
+        "suffix": ["T1w"],
     }
     template = BidsDataset(
         {
             "scan": BidsComponent(
                 "scan",
-                result.input_path["scan"],
+                result["scan"].path,
                 {
                     "acq": [
                         "mprage",
@@ -751,15 +750,13 @@ def test_t1w():
             {
                 "t1": BidsComponent(
                     "t1",
-                    result.input_path["t1"],
+                    result["t1"].path,
                     {
                         "acq": ["mprage", "mprage"],
                         "subject": ["001", "002"],
                     },
                 ),
-                "t2": BidsComponent(
-                    "t2", result.input_path["t2"], {"subject": ["002"]}
-                ),
+                "t2": BidsComponent("t2", result["t2"].path, {"subject": ["002"]}),
             }
         )
         # Order of the subjects is not deterministic