chore: Transition to src/ layout

pyproject.toml

@@ -81,12 +81,12 @@ pybids = "bids.cli:cli"
 [tool.versioneer]
 VCS = "git"
 style = "pep440-pre"
-versionfile_source = "bids/_version.py"
+versionfile_source = "src/bids/_version.py"
 versionfile_build = "bids/_version.py"
 
 [tool.coverage.run]
 branch = true
-source = ["bids/*"]
+source = ["src/bids/*"]
 omit = [
   "*/setup.py",
   "*/external/*",
@@ -95,4 +95,4 @@ omit = [
 ]
 
 [tool.coverage.report]
-include = ["bids/*"]
+include = ["src/bids/*"]

setup.cfg

@@ -1,10 +1,3 @@
-[metadata]
-platforms = OS Independent
-
-[options]
-packages = find:
-include_package_data = True
-
 [codespell]
 skip = ./.git,external,versioneer.py,_version.py
 ignore-words = .github/codespell_ignore_words.txt

bids/conftest.py → src/bids/conftest.py

@@ -41,7 +41,7 @@
 def bids_examples():
     examples_dir = Path(os.getenv(
         "BIDS_EXAMPLES",
-        Path(__file__).absolute().parent.parent / "bids-examples"
+        Path(__file__).absolute().parent.parent.parent / "bids-examples"
     ))
 
     if not Path.is_dir(examples_dir / "ds001"):
@@ -50,3 +50,17 @@
             "Override default location with BIDS_EXAMPLES environment variable."
         )
     return examples_dir
+
+@pytest.fixture(scope='session')
+def tests_dir():
+    test_dir = Path(os.getenv(
+        "PYBIDS_TEST_DATA",
+        Path(__file__).absolute().parent.parent.parent / "tests"
+    ))
+
+    if not Path.is_dir(test_dir / "data"):
+        pytest.skip(
+            f"BIDS examples missing from {test_dir}. "
+            "Override default location with PYBIDS_TEST_DATA environment variable."
+        )
+    return test_dir

src/bids/layout/tests/conftest.py

@@ -0,0 +1,103 @@
+from os.path import join
+
+import pytest
+
+from bids.layout import BIDSLayout
+
+
+# Fixture uses in the rest of the tests
+@pytest.fixture(scope="session")
+def layout_7t_trt(tests_dir):
+    return BIDSLayout(tests_dir / 'data' / '7t_trt')
+
+
+@pytest.fixture(scope="session")
+def layout_7t_trt_relpath(tests_dir):
+    return BIDSLayout(tests_dir / 'data' / '7t_trt', absolute_paths=False)
+
+
+@pytest.fixture(scope="session")
+def layout_ds005(tests_dir):
+    return BIDSLayout(tests_dir / 'data' / 'ds005')
+
+
+@pytest.fixture(scope="session")
+def layout_ds005_no_validate(tests_dir):
+    return BIDSLayout(tests_dir / 'data' / 'ds005', validate=False)
+
+
+@pytest.fixture(scope="session")
+def layout_ds117(tests_dir):
+    return BIDSLayout(tests_dir / 'data' / 'ds000117')
+
+
+@pytest.fixture(scope="session")
+def layout_ds005_derivs(tests_dir):
+    data_dir = tests_dir / 'data' / 'ds005'
+    layout = BIDSLayout(data_dir)
+    deriv_dir = join(data_dir, 'derivatives', 'events')
+    layout.add_derivatives(deriv_dir)
+    return layout
+
+
+@pytest.fixture(scope="session")
+def layout_ds005_deriv_dummy_vxxx(tests_dir):
+    data_dir = tests_dir / 'data' / 'ds005'
+    layout = BIDSLayout(data_dir)
+    deriv_dir = tests_dir / 'data' / 'ds005_derivs' / 'dummy-vx.x.x'
+    layout.add_derivatives(deriv_dir)
+    return layout
+
+
+@pytest.fixture(scope="session")
+def layout_ds005_deriv_both_dummies(tests_dir):
+    data_dir = tests_dir / 'data' / 'ds005'
+    layout = BIDSLayout(data_dir)
+    deriv_dir1 = tests_dir / 'data' / 'ds005_derivs' / 'dummy-vx.x.x'
+    deriv_dir2 = tests_dir / 'data' / 'ds005_derivs' / 'dummy'
+    layout.add_derivatives([deriv_dir1, deriv_dir2])
+    return layout
+
+
+@pytest.fixture(scope="session")
+def db_dir(tmpdir_factory):
+    fn = tmpdir_factory.mktemp("data")
+    return fn
+
+
+@pytest.fixture(scope="session",
+                params=[None, "bidsdb", "bidsdb"])
+def layout_ds005_multi_derivs(tests_dir, request, db_dir):
+    data_dir = tests_dir / 'data' / 'ds005'
+    database_path = str(db_dir / request.param) if request.param else None
+
+    layout = BIDSLayout(data_dir,
+                        database_path=database_path)
+    deriv_dir1 = tests_dir / 'data' / 'ds005_derivs' / 'dummy'
+    deriv_dir2 = join(data_dir, 'derivatives', 'events')
+    layout.add_derivatives([deriv_dir1, deriv_dir2])
+    return layout
+
+@pytest.fixture(scope="session")
+def layout_ds005_deriv_name_collision(tests_dir, request):
+    data_dir = tests_dir / 'data' / 'ds005'
+
+    layout = BIDSLayout(data_dir)
+    deriv_dir1 = tests_dir / 'data' / 'ds005_derivs' / 'dummy'
+    deriv_dir2 = join(data_dir, 'derivatives', 'events')
+    layout.add_derivatives([deriv_dir1, deriv_dir2])
+    return layout
+
+
+@pytest.fixture(
+    scope="session", params=[None, "bidsdb-synth", "bidsdb-synth"])
+def layout_synthetic(tests_dir, request, db_dir):
+    path = tests_dir / 'data' / 'synthetic'
+    database_path = str(db_dir / request.param) if request.param else None
+    return BIDSLayout(path, derivatives=True,
+                      database_path=database_path)
+
+@pytest.fixture(scope="session")
+def layout_synthetic_nodb(tests_dir, request, db_dir):
+    path = tests_dir / 'data' / 'synthetic'
+    return BIDSLayout(path, derivatives=True)