junifer 0.0.3.dev73__py3-none-any.whl → 0.0.3.dev75__py3-none-any.whl

junifer/_version.py

@@ -1,4 +1,4 @@
 # 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')
+__version__ = version = '0.0.3.dev75'
+__version_tuple__ = version_tuple = (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/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/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/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/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/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/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.dist-info → junifer-0.0.3.dev75.dist-info}/METADATA

@@ -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.dist-info → junifer-0.0.3.dev75.dist-info}/RECORD

@@ -1,9 +1,9 @@
 junifer/__init__.py,sha256=rJgTGeR-SOntQoLSGo36zKDTE8IMRBn2-YwC0JSNUpU,377
-junifer/_version.py,sha256=7-PPrI05NryOuKMJEsx3ZEKwZiGZtVKFCqh95qMm3I8,175
+junifer/_version.py,sha256=laYgsBVZiMM-T9aIfloEMTq4U0xz0xKz3Xq41tGUHew,175
 junifer/stats.py,sha256=KUX4jJcLWnlE34coet8EkdFypFd-td4Vtpx5LvlomVs,5879
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=n9jFA68LTdyv3FQrshfwwZJVy3jEWZpf3x6YVyvnIhA,9833
-junifer/api/decorators.py,sha256=_ZvUV3cwrbUSHDRfHLsQxe8fjT8whkf_jS9x_zlsHfE,2530
+junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
 junifer/api/functions.py,sha256=yRxUug8nEdXuZOpbCJGZ-EpvUtTOArcn8_pLcDq6j-Y,22518
 junifer/api/parser.py,sha256=0Eat3oPJFSVlpQA4hJ08QbocjTfLL92cPTItHu_yFKU,3314
 junifer/api/utils.py,sha256=dyjTdPMwX9qeCrn8SQT2Pjshfnu-y1FEyujV7lCzvm0,3333
@@ -15,7 +15,7 @@ junifer/api/res/afni/afni,sha256=6vAE_vVS-TFt-W32AdMs_Y6c7fsq_RSrPf9Jafz4x9Q,41
 junifer/api/res/afni/run_afni_docker.sh,sha256=ABKs-pa-lCGIxdCkqvhUar2pOj4xwQgo4QUg8UXvDho,1106
 junifer/api/tests/test_api_utils.py,sha256=Yls1WwARWA4WEBEUqdnoxobLNGNrrcaKFCXpyR-EUZQ,2321
 junifer/api/tests/test_cli.py,sha256=-V-oyKiEqnIOUOiO_5KHMKuAa71Azmd48Ghy5FcP5H0,2797
-junifer/api/tests/test_functions.py,sha256=h6TvTry9P8_OLO6XdusXJV4p9ftrqQjg1Qi9hNLpUjo,24484
+junifer/api/tests/test_functions.py,sha256=7Jy2TdRzPnMPdfPX8UgdodWKlRRRp8gxowC1A2jwtu8,24652
 junifer/api/tests/test_parser.py,sha256=3GZYamYbpW8bGnx95_RQ1uT783or_H-yqzZ138wQYmE,6107
 junifer/api/tests/data/gmd_mean.yaml,sha256=Ohb_C5cfQMK-59U9O1ZhejXyBtzLc5Y4cv8QyYq2azg,330
 junifer/api/tests/data/gmd_mean_htcondor.yaml,sha256=f7NLv_KIJXTiPNFmOWl2Vw8EfwojhfkGtwbh5prbd6w,417
@@ -86,8 +86,8 @@ junifer/datagrabber/tests/test_multiple.py,sha256=j7_zJ-AyGzmvmoI8fbu6CIcmzMnUO0
 junifer/datagrabber/tests/test_pattern.py,sha256=66TCpCjHVzwTtKsedtw7mZsku4gA3_I9fQt0PUA8DfU,9789
 junifer/datagrabber/tests/test_pattern_datalad.py,sha256=N1RhFi7lkx44chZNpLYH_0zZtb_0Z3rMo5EWxJWC_uU,6103
 junifer/datareader/__init__.py,sha256=WWoiIz6y0EdExWO3WCGiERNw3Y3WUsXyHaWnHilP2kE,263
-junifer/datareader/default.py,sha256=hXKSWj_UFbghOlfJ0ZyeNafVi8FeuJUuUH9YJjkXo8Y,4038
-junifer/datareader/tests/test_default_reader.py,sha256=o2Y4zmSAQonhwaRF5YBcUc9t8YxMBzqdwKlIsgS1E58,5064
+junifer/datareader/default.py,sha256=Ruumq98J2DOjZqgXHjGIO3NCFGcGfx4svJiqi-svTeo,4068
+junifer/datareader/tests/test_default_reader.py,sha256=9dPZSkba1YQjFsA0XwdUbx5sq8DVIEZoy_WfMAcvRus,5220
 junifer/external/__init__.py,sha256=58gL7gNN_PI1GyN6r9CO035TzvJdi8S-zFg5reDt4Xc,116
 junifer/external/h5io/h5io/__init__.py,sha256=LG7ru_Rt3EOE2H4PGYfBhC12Iax3yeTquZkd8TICiKk,469
 junifer/external/h5io/h5io/_h5io.py,sha256=8dWZDYegoPcBkH_fHPdl0eXNWTaRdk9hfIQo8Mcegzo,28748
@@ -99,7 +99,7 @@ junifer/external/nilearn/junifer_nifti_spheres_masker.py,sha256=WVCnsr7_Wj5mqsMp
 junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py,sha256=mQtMgOH7hrtw-Vm09e1ukn5PFN9SpNA3IPtUrAxBF10,10329
 junifer/markers/__init__.py,sha256=exUUmpDsPkoNa9FK6Y7pDusOYv56_zoci8hiOaxyswE,778
 junifer/markers/base.py,sha256=Uuaz8MvdHOfAnRGpUf6ISWgbNWzkmHIMo6f30jlW7zY,6109
-junifer/markers/collection.py,sha256=7Md-Gi8GyOQNvg6R1hoS2VGrPIPr1xEg4c8cCVcOmKM,4585
+junifer/markers/collection.py,sha256=u5DAWdEPsYK1Jmqob1FZgzOK_cm_8JXJ2CpSVxgamBY,4592
 junifer/markers/ets_rss.py,sha256=tmGBjg-aBzMhYRQ3Q8uSvZ2bicNHQgJeDjy7KYnqFSY,4522
 junifer/markers/parcel_aggregation.py,sha256=QXcetgr7O0zhKQiC5gh-4aMs9lwhaqHoZLBlt1fYhPs,8613
 junifer/markers/sphere_aggregation.py,sha256=ipwH6wuYot9-MemhHs8sUSR3p6rFi2AUrDf7OBswe7s,7337
@@ -152,7 +152,7 @@ junifer/pipeline/registry.py,sha256=xHrLxHMymGUGL8kqVhQIWbBhhEoNHZn9C273IyvP9ss,
 junifer/pipeline/update_meta_mixin.py,sha256=4WYnmN0iX0k5kwbhRp_YB0AfphWMBpm58XM4kRR6lD0,1219
 junifer/pipeline/utils.py,sha256=jHgFxFVUH7nNFvt3AvY73gPK6DkiKrRQlopeQLl1jx4,3515
 junifer/pipeline/tests/test_pipeline_step_mixin.py,sha256=7h1sxQhU7aiTm5Jd0Otm-ItAxzz-ud5-5EWuykU3FUo,5085
-junifer/pipeline/tests/test_registry.py,sha256=JgmS1NIdU70EuEWvIC30oGTt7mFpZsQ_Dno3_rcvCjo,4105
+junifer/pipeline/tests/test_registry.py,sha256=rYN0pO3gSueQ6XsasEM9VU5BkLyaNl8WaCZiaO8Rno0,4105
 junifer/pipeline/tests/test_update_meta_mixin.py,sha256=C9cDTZB-9CN4zYLeSHLSo0dpWrB8o1fj0jlWpcP9Wsc,1374
 junifer/preprocess/__init__.py,sha256=GPbiTHFhb9BzUOSgmo_SpgTFNMmkcCJPhQoUA2MQgJI,255
 junifer/preprocess/base.py,sha256=Wu-tQZmMJBWsqcyA8q6lBALfJUHBB_AakTbho3OBUAw,5493
@@ -186,11 +186,11 @@ junifer/utils/__init__.py,sha256=ZDPU9ezSKawAJhb-3T67jDf-16QEyF6e7ONyu-lnBtQ,277
 junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
 junifer/utils/logging.py,sha256=cUB1KPnUzgOWm6FV_gMdnm5y0iMsAEM6MTvwan4dLkU,8957
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
-junifer/utils/tests/test_logging.py,sha256=uTzlwwlOv7bh_7DngitVFxCDbH_OWsqfeXEcNyKvF24,7748
-junifer-0.0.3.dev73.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.3.dev73.dist-info/LICENSE.md,sha256=z5aMVBrc-9kk0pxaOdOAkI62S5YhYMiF6ADsMtZmOZg,34353
-junifer-0.0.3.dev73.dist-info/METADATA,sha256=7Cgv8izSce0uhVL05aVO15NOnHVOR3LUJxwO27FQ9HM,6163
-junifer-0.0.3.dev73.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-junifer-0.0.3.dev73.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.3.dev73.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.3.dev73.dist-info/RECORD,,
+junifer/utils/tests/test_logging.py,sha256=bRdjpbzPoHjFoVUqDmU7ZQ6pj3PNg6ohtceA3nlFnHU,7748
+junifer-0.0.3.dev75.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.3.dev75.dist-info/LICENSE.md,sha256=z5aMVBrc-9kk0pxaOdOAkI62S5YhYMiF6ADsMtZmOZg,34353
+junifer-0.0.3.dev75.dist-info/METADATA,sha256=e-yH7DQXDOSi6qRX4TcLGvv8oo_WgWjzQNTUQ4QWf_o,6163
+junifer-0.0.3.dev75.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+junifer-0.0.3.dev75.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.3.dev75.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.3.dev75.dist-info/RECORD,,