fix from Raluca's PR for KeyError: mask_attenuation; #160 - fix one e…

…rror; fix one typo; fix FutureWarning for DataArray.dims -> DataArray.sizes; fixed downloading of files over FTP only when those files are missing; fix warning: PytestUnknownMarkWarning.

oceanstream/denoise/apply_masks.py

@@ -57,4 +57,6 @@ def apply_seabed_mask(ds: xr.Dataset, config) -> xr.Dataset:
 
         ds_processed = apply_selected_masks(ds, params)
 
-    return ds_processed
+        return ds_processed
+
+    return ds

oceanstream/denoise/background_noise_remover.py

@@ -7,7 +7,7 @@
 Functions:
 
 - `apply_remove_background_noise`:
-Main function that applies the `remove_noise` function from echopype to an Sv dataset.
+Main function that applies the `remove_noise` function from echopype to a Sv dataset.
 Computes default parameters based on dataset characteristics when not provided.
 The dataset initially passed to the function, processed in the following manner:
 `Sv_corrected` and `Sv_noise` variables are generated by the echopype `remove_noise` function.
@@ -76,7 +76,7 @@ def apply_remove_background_noise(
     # Compute range_sample_num if not provided
     if range_sample_num is None:
         range_sample_nums = []
-        for ch in range(ds_Sv.dims["channel"]):
+        for ch in range(ds_Sv.sizes["channel"]):
             mean_diff = np.nanmean(np.diff(ds_Sv["echo_range"].isel(channel=ch).values[0, :]))
             if np.isnan(mean_diff):
                 raise ValueError(

oceanstream/settings/defaults.config.json

@@ -18,7 +18,11 @@
       "m": null,
       "thr": -5,
       "start": 0,
-      "offset": 0
+      "offset": 0,
+      "dask_chunking": {
+        "ping_time": 100,
+        "range_sample": 100
+      }
     }
   },
   "transient": {

tests/conftest.py

@@ -132,9 +132,15 @@ def denoise_dataset(dataset):
 @pytest.fixture(scope="session")
 def ftp_data():
     test_data_folder = Path(TEST_DATA_FOLDER) / "ek60"
-    # with FTP(FTP_MAIN) as ftp:
-    #     ftp.login()
-    #     download_ftp_directory(ftp, FTP_PARTIAL_PATH, test_data_folder)
+
+    # if there is data in here skip downloading...
+    must_download = not os.path.exists(test_data_folder) or not os.listdir(test_data_folder)
+
+    if must_download:
+        with FTP(FTP_MAIN) as ftp:
+            ftp.login()
+            download_ftp_directory(ftp, FTP_PARTIAL_PATH, test_data_folder)
+
     yield str(test_data_folder)
     # Optional: Cleanup after tests are done
     # shutil.rmtree(TEST_DATA_FOLDER)

tests/pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    ignore: marks a test as ignored.