junifer 0.0.3.dev73__tar.gz → 0.0.3.dev75__tar.gz

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.3.dev73
+Version: 0.0.3.dev75
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.3.dev75/docs/changes/newsfragments/227.enh

@@ -0,0 +1 @@
+Adopt ``DataReader`` consistently throughout codebase to match with the documentation by `Synchon Mandal`_

junifer-0.0.3.dev75/docs/changes/newsfragments/228.misc

@@ -0,0 +1 @@
+Consistent docstrings for pytest fixtures used in the test suite by `Synchon Mandal`_

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/docs/understanding/data.rst

@@ -39,7 +39,7 @@ step only contains information about the DataGrabber used.
 
 The :ref:`Data Reader <datareader>` step adds the ``data`` second-level key
 which is the actual data loaded into memory. The ``meta`` key in this step
-adds information about the datareader used to read the data.
+adds information about the DataReader used to read the data.
 
 .. code-block:: python
 

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/docs/understanding/datareader.rst

@@ -14,7 +14,7 @@ files in junifer. It reads the value of the key ``path`` for each
 them into memory. After reading the data into memory, it adds the key ``data``
 to the same level as ``path`` and the value is the actual data in the memory.
 
-Datareaders are meant to be used inside the datagrabber context but you can
+DataReaders are meant to be used inside the datagrabber context but you can
 operate on them outside the context as long as the actual data is in the memory
 and the Python runtime has not garbage-collected it.
 

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/docs/using/codeless.rst

@@ -108,12 +108,12 @@ Data Reader
 ^^^^^^^^^^^
 
 As mentioned before, this section is entirely optional, as junifer only provides
-one data reader (:class:`.DefaultDataReader`), which is the default in case the
+one DataReader (:class:`.DefaultDataReader`), which is the default in case the
 section is not specified.
 
 In any case, the syntax of the section is the same as for the ``datagrabber``
-section, using the ``kind`` key to specify the datareader to use, and additional
-keys to pass parameters to the datareader:
+section, using the ``kind`` key to specify the DataReader to use, and additional
+keys to pass parameters to the DataReader constructor:
 
 .. code-block:: yaml
 

junifer-0.0.3.dev75/junifer/_version.py

@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '0.0.3.dev75'
+__version_tuple__ = version_tuple = (0, 0, 3, 'dev75')

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/api/decorators.py

@@ -39,20 +39,24 @@ def register_datagrabber(klass: Type) -> Type:
 
 
 def register_datareader(klass: Type) -> Type:
-    """Datareader registration decorator.
+    """Register DataReader.
 
-    Registers the datareader so it can be used by name.
+    Registers the DataReader so it can be used by name.
 
     Parameters
     ----------
     klass: class
-        The class of the datareader to register.
+        The class of the DataReader to register.
 
     Returns
     -------
     klass: class
         The unmodified input class.
 
+    Notes
+    -----
+    It should only be used as a decorator.
+
     """
     register(
         step="datareader",

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/api/tests/test_functions.py

@@ -246,9 +246,9 @@ def test_queue_correct_yaml_config(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with monkeypatch.context() as m:
@@ -305,7 +305,7 @@ def test_queue_invalid_job_queue(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
 
     """
     with pytest.raises(ValueError, match="Unknown queue kind"):
@@ -328,7 +328,7 @@ def test_queue_assets_disallow_overwrite(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
 
     """
     with pytest.raises(ValueError, match="Either delete the directory"):
@@ -360,9 +360,9 @@ def test_queue_assets_allow_overwrite(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with monkeypatch.context() as m:
@@ -405,9 +405,9 @@ def test_queue_with_imports(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
     with_ : str or list of str
         The parametrized imports.
 
@@ -456,9 +456,9 @@ def test_queue_with_elements(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
     elements : str of list of str
         The parametrized elements for the queue.
 
@@ -486,9 +486,9 @@ def test_queue_without_elements(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with monkeypatch.context() as m:
@@ -512,7 +512,7 @@ def test_queue_condor_invalid_python_env(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
 
     """
     with pytest.raises(ValueError, match="Unknown env kind"):
@@ -537,9 +537,9 @@ def test_queue_condor_conda_python(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with monkeypatch.context() as m:
@@ -571,9 +571,9 @@ def test_queue_condor_conda_pre_run_python(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with monkeypatch.context() as m:
@@ -613,9 +613,9 @@ def test_queue_condor_venv_python(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with monkeypatch.context() as m:
@@ -677,9 +677,9 @@ def test_queue_condor_assets_generation(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
     elements : str
         The parametrized element names.
     env : dict
@@ -794,7 +794,7 @@ def test_queue_condor_extra_preamble(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
 
     """
     jobname = "condor_extra_preamble_check"
@@ -839,9 +839,9 @@ def test_queue_condor_submission_fail(
     tmp_path : pathlib.Path
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
-        The monkeypatch object.
+        The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
-        The logcapturefixture object.
+        The pytest.LogCaptureFixture object.
 
     """
     with pytest.raises(

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/datareader/default.py

@@ -1,4 +1,4 @@
-"""Provide class for default data reader."""
+"""Provide concrete implementation for default DataReader."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -32,7 +32,7 @@ _readers["TSV"] = {"func": pd.read_csv, "params": {"sep": "\t"}}
 
 @register_datareader
 class DefaultDataReader(PipelineStepMixin, UpdateMetaMixin):
-    """Mixin class for default data reader."""
+    """Concrete implementation for common data reading."""
 
     def validate_input(self, input: List[str]) -> List[str]:
         """Validate input.
@@ -48,6 +48,7 @@ class DefaultDataReader(PipelineStepMixin, UpdateMetaMixin):
         list of str
             The actual elements of the input that will be processed by this
             pipeline step.
+
         """
         # Nothing to validate, any input is fine
         return input

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/datareader/tests/test_default_reader.py

@@ -1,4 +1,4 @@
-"""Provide tests for default data reader."""
+"""Provide tests for DefaultDataReader."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -19,8 +19,8 @@ from junifer.datareader import DefaultDataReader
 @pytest.mark.parametrize(
     "type_", [["T1w", "BOLD", "T2", "dwi"], [], ["whatever"]]
 )
-def test_validation(type_) -> None:
-    """Test validating input/output.
+def test_DefaultDataReader_validation(type_) -> None:
+    """Test DefaultDataReader validating input/output.
 
     Parameters
     ----------
@@ -34,8 +34,8 @@ def test_validation(type_) -> None:
     assert reader.validate(type_) == type_
 
 
-def test_meta() -> None:
-    """Test reader metadata."""
+def test_DefaultDataReader_meta() -> None:
+    """Test DefaultDataReader metadata."""
     reader = DefaultDataReader()
 
     nib_data_path = Path(nib_testing.data_path)
@@ -52,8 +52,8 @@ def test_meta() -> None:
 @pytest.mark.parametrize(
     "fname", ["example4d.nii.gz", "reoriented_anat_moved.nii"]
 )
-def test_read_nifti(fname: str) -> None:
-    """Test reading NIFTI files.
+def test_DefaultDataReader_nifti(fname: str) -> None:
+    """Test DefaultDataReader reading NIfTI files.
 
     Parameters
     ----------
@@ -85,8 +85,8 @@ def test_read_nifti(fname: str) -> None:
     assert output["BOLD"]["path"] == output2["BOLD"]["path"]
 
 
-def test_read_unknown() -> None:
-    """Test (not) reading unknown files."""
+def test_DefaultDataReader_unknown() -> None:
+    """Test DefaultDataReader (not) reading unknown files."""
     reader = DefaultDataReader()
     nib_data_path = Path(nib_testing.data_path)
 
@@ -115,8 +115,8 @@ def test_read_unknown() -> None:
         reader.fit_transform(input)
 
 
-def test_read_csv(tmp_path: Path) -> None:
-    """Test reading CSV files.
+def test_DefaultDataReader_csv(tmp_path: Path) -> None:
+    """Test DefaultDataReader reading CSV files.
 
     Parameters
     ----------

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/markers/collection.py

@@ -25,8 +25,8 @@ class MarkerCollection:
     ----------
     markers : list of marker-like
         The markers to compute.
-    datareader : datareader-like, optional
-        The datareader to use (default None).
+    datareader : DataReader-like object, optional
+        The DataReader to use (default None).
     preprocessing : preprocessing-like, optional
         The preprocessing steps to apply.
     storage : storage-like, optional

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/pipeline/tests/test_registry.py

@@ -42,7 +42,7 @@ def test_register(
     Parameters
     ----------
     caplog : pytest.LogCaptureFixture
-        A pytest fixture to capture logging.
+        The pytest.LogCaptureFixture object.
     step : str
         The parametrized name of the step.
     name : str

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer/utils/tests/test_logging.py

@@ -33,7 +33,7 @@ def test_log_versions(caplog: pytest.LogCaptureFixture) -> None:
     Parameters
     ----------
     caplog : pytest.LogCaptureFixture
-        A pytest fixture to capture logging.
+        The pytest.LogCaptureFixture object.
 
     """
     # Set log capturing at INFO
@@ -161,7 +161,7 @@ def test_log_stdout(caplog: pytest.LogCaptureFixture) -> None:
     Parameters
     ----------
     caplog : pytest.LogCaptureFixture
-        A pytest fixture to capture logging.
+        The pytest.LogCaptureFixture object.
 
     """
     configure_logging()
@@ -197,7 +197,7 @@ def test_raise_error(caplog: pytest.LogCaptureFixture) -> None:
     Parameters
     ----------
     caplog : pytest.LogCaptureFixture
-        A pytest fixture to capture logging.
+        The pytest.LogCaptureFixture object.
 
     """
     with pytest.raises(ValueError, match="test error"):
@@ -212,7 +212,7 @@ def test_warn_with_log(caplog: pytest.LogCaptureFixture) -> None:
     Parameters
     ----------
     caplog : pytest.LogCaptureFixture
-        A pytest fixture to capture logging.
+        The pytest.LogCaptureFixture object.
 
     """
     with pytest.warns(RuntimeWarning, match="test warning"):

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.3.dev73
+Version: 0.0.3.dev75
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.3.dev73 → junifer-0.0.3.dev75}/junifer.egg-info/SOURCES.txt

@@ -60,6 +60,8 @@ docs/changes/newsfragments/222.enh
 docs/changes/newsfragments/223.bugfix
 docs/changes/newsfragments/223.enh
 docs/changes/newsfragments/226.enh
+docs/changes/newsfragments/227.enh
+docs/changes/newsfragments/228.misc
 docs/changes/newsfragments/230.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst

junifer-0.0.3.dev73/junifer/_version.py

@@ -1,4 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-__version__ = version = '0.0.3.dev73'
-__version_tuple__ = version_tuple = (0, 0, 3, 'dev73')