Fixing issues 123. (#177)

* Fixing issues 123.

* Fixing coverage.

* Linting

Author: christian-oreilly

pylossless/conftest.py

@@ -29,8 +29,18 @@ def pipeline_fixture():
     config["find_breaks"]["t_start_after_previous"] = 1
     config["find_breaks"]["t_stop_before_next"] = 0
     config["ica"]["ica_args"]["run1"]["max_iter"] = 5000
+
+    # Testing when passing the config object directly...
+    pipeline = ll.LosslessPipeline("test_config.yaml", config)
+    pipeline = ll.LosslessPipeline(config=config)
     config.save("test_config.yaml")
+
+    # Testing when passing a string...
     pipeline = ll.LosslessPipeline("test_config.yaml")
+
+    # Testing when passing a Path...
+    pipeline = ll.LosslessPipeline(Path("test_config.yaml"))
+
     not_in_1020 = ["EXG1", "EXG2", "EXG3", "EXG4", "EXG5", "EXG6", "EXG7", "EXG8"]
     pipeline.raw = raw.pick("eeg", exclude=not_in_1020).load_data()
     pipeline.run_with_raw(pipeline.raw)

pylossless/pipeline.py

@@ -417,7 +417,7 @@ class LosslessPipeline:
 
     Parameters
     ----------
-    config_fname : pathlib.Path
+    config_path : pathlib.Path
         path to config file specifying the parameters to be used
         in the pipeline.
 
@@ -429,7 +429,7 @@ class LosslessPipeline:
         :class:`~pylossless.flagging.FlaggedChs`,
         :class:`~pylossless.flagging.FlaggedEpochs`, and
         :class:`~pylossless.flagging.FlaggedICs`, respectively.
-    config_fname : pathlib.Path
+    config_path : pathlib.Path
         path to the config file specifying the parameters to be used in the
         in the pipeline.
     config : dict
@@ -445,23 +445,31 @@ class LosslessPipeline:
         during the pipeline.
     """
 
-    def __init__(self, config_fname=None):
+    def __init__(self, config_path=None, config=None):
         """Initialize class.
 
         Parameters
         ----------
-        config_fname : pathlib.Path
-            path to config file specifying the parameters to be used
-            in the pipeline.
+        config_path : pathlib.Path | str | None
+            Path to config file specifying the parameters to be used in the pipeline.
+
+        config : pylossless.config.Config | None
+            :class:`pylossless.config.Config` object for the pipeline.
         """
         self.flags = {
             "ch": FlaggedChs(self),
             "epoch": FlaggedEpochs(self),
             "ic": FlaggedICs(),
         }
-        self.config_fname = config_fname
-        if config_fname:
+        if config:
+            self.config = config
+            if config_path is None:
+                self.config_path = "._tmp_pylossless.yaml"
+        elif config_path:
+            self.config_path = Path(config_path)
             self.load_config()
+        else:
+            self.config_path = None
         self.raw = None
         self.ica1 = None
         self.ica2 = None
@@ -483,13 +491,13 @@ def _repr_html_(self):
         ]
         flagged_times = _sum_flagged_times(self.raw, lossless_flags)
 
-        config_fname = self.config_fname
+        config_path = self.config_path
         raw = self.raw.filenames if self.raw else "Not specified"
 
         html = "<h3>LosslessPipeline</h3>"
         html += "<table>"
         html += f"<tr><td><strong>Raw</strong></td><td>{raw}</td></tr>"
-        html += f"<tr><td><strong>Config</strong></td><td>{config_fname}</td></tr>"
+        html += f"<tr><td><strong>Config</strong></td><td>{config_path}</td></tr>"
         html += "</table>"
 
         # Flagged Channels
@@ -518,9 +526,21 @@ def _repr_html_(self):
 
         return html
 
+    @property
+    def config_fname(self):
+        warn('config_fname is deprecated and will be removed from future versions.',
+             DeprecationWarning)
+        return self.config_path
+
+    @config_fname.setter
+    def config_fname(self, config_path):
+        warn('config_fname is deprecated and will be removed from future versions.',
+             DeprecationWarning)
+        self.config_path = config_path
+
     def load_config(self):
         """Load the config file."""
-        self.config = Config().read(self.config_fname)
+        self.config = Config().read(self.config_path)
 
     def _check_sfreq(self):
         """Make sure sampling frequency is an integer.
@@ -1215,7 +1235,7 @@ def load_ll_derivative(self, derivatives_path):
         )
         self.flags["ic"].load_tsv(iclabels_bidspath.fpath)
 
-        self.config_fname = bpath.update(
+        self.config_path = bpath.update(
             extension=".yaml", suffix="ll_config", check=False
         )
         self.load_config()

pylossless/tests/test_pipeline.py

@@ -44,3 +44,13 @@ def test_find_breaks(logging):
     else:
         pipeline.find_breaks()
     Path(config_fname).unlink()  # delete config file
+
+
+def test_deprecation():
+    """Test the config_name property added for deprecation."""
+    config = ll.config.Config()
+    config.load_default()
+    pipeline = ll.LosslessPipeline(config=config)
+    # with pytest.raises(DeprecationWarning, match=f"config_fname is deprecated"):
+    # DeprecationWarning are currently ignored by pytest given our toml file
+    pipeline.config_fname = pipeline.config_fname

pylossless/tests/test_simulated.py

@@ -26,7 +26,7 @@
 @pytest.mark.parametrize("pipeline", [(pipeline)])
 def test_simulated_raw(pipeline):
     """Test pipeline on simulated EEG."""
-    with pytest.warns(RuntimeWarning, match="sampling frequency"):
+    with pytest.warns(RuntimeWarning, match="The Raw sampling frequency is"):
         pipeline._check_sfreq()
     # This file should have been downsampled
     assert pipeline.raw.info["sfreq"] == 600
@@ -59,5 +59,5 @@ def test_simulated_raw(pipeline):
     assert "EEG 054" in pipeline.flags["ch"]["bridged"]
 
     # Delete temp config file
-    tmp_config_fname = Path(pipeline.config_fname).absolute()
-    tmp_config_fname.unlink()
+    tmp_config_path = Path(pipeline.config_path).absolute()
+    tmp_config_path.unlink()