Merge/add transient fixed conflicts (#109)

.github/workflows/packit.yaml

@@ -20,7 +20,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         python-version: 3.9
 
@@ -52,7 +52,7 @@ jobs:
     needs: build-artifact
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/[email protected].0
+    - uses: actions/[email protected].1
       name: Install Python
       with:
         python-version: 3.9

.github/workflows/pypi.yaml

@@ -24,7 +24,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         python-version: 3.9
 
@@ -56,7 +56,7 @@ jobs:
     needs: build-artifact
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/[email protected].0
+    - uses: actions/[email protected].1
       name: Install Python
       with:
         python-version: 3.9

.github/workflows/windows.yaml

@@ -46,7 +46,7 @@ jobs:
             # Check data endpoint
             curl http://localhost:8080/data/
         - name: Setup Python
-          uses: actions/[email protected].0
+          uses: actions/[email protected].1
           with:
             python-version: ${{ matrix.python-version }}
             architecture: x64

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ exclude: |
   )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -24,7 +24,7 @@ repos:
         args: ["--profile", "black", "--filter-files"]
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.10.1
     hooks:
       - id: black
 
@@ -34,7 +34,7 @@ repos:
       - id: flake8
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         # Checks spelling in `docs/source` and `echopype` dirs ONLY

docs/source/contributing.rst

@@ -37,7 +37,7 @@ This diagram depicts the complete workflow we use in the source GitHub repositor
 - ``doc patch``: Updates to the documentation that refer to the current ``echopype``
   release can be pushed out immediately to the
   `echopype documentation site <https://echopype.readthedocs.io>`_
-  by contibuting patches (PRs) to the ``stable`` branch. See `Documentation development`_
+  by contributing patches (PRs) to the ``stable`` branch. See `Documentation development`_
   below for more details.
 - ``code patch``: Code development is carried out as patches (PRs) to the ``dev``
   branch; changes in the documentation corresponding to changes in the code can be
@@ -231,7 +231,7 @@ To view the HTML files generated by Jupyter Book, open the
 ``docs/_build/html/index.html`` in your browser.
 
 Jupyter Book `configurations <https://jupyterbook.org/en/stable/customize/config.html>`_ can be found in the ``docs/source/_config.yml`` file.
-The `table of contents <https://jupyterbook.org/en/stable/structure/toc.html>`_ arragements for the sidebar can be found in ``docs/source/_toc.yml`` file.
+The `table of contents <https://jupyterbook.org/en/stable/structure/toc.html>`_ arrangements for the sidebar can be found in ``docs/source/_toc.yml`` file.
 
 When ready to commit your changes, please pull request your changes to the `stable` branch. Once the PR is submitted, the `pre-commit` CI will run for basic spelling and formatting check (See the `pre-commit hooks section <contributing.html#pre-commit-hooks>`_ for more details). Any changes from the `pre-commit` check have to be pulled to your branch (via `git pull`) before your push further commits. You will also be able to view the newly built doc in the PR via the "docs/readthedocs.org:echopype" entry shown below.
 

docs/source/data-proc.md

@@ -1,6 +1,6 @@
 # Data processing
 
-Echopype data processing funcionalities are structured into different subpackages with expandability and a series of [data processing levels](processing-levels) in mind. Once the data is converted from the raw instrument data files to standardized [`EchoData` objects](data-format:echodata-object) (or stored in `.zarr` or `.nc` format) and calibrated, the core input and output of most subsequent functions are generic [xarray `Datasets`](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html). This design allows new processing functions be easily added without needing to understand specialized objects, other than functions needing access of data stored only in the raw-converted `EchoData` objects.
+Echopype data processing functionalities are structured into different subpackages with expandability and a series of [data processing levels](processing-levels) in mind. Once the data is converted from the raw instrument data files to standardized [`EchoData` objects](data-format:echodata-object) (or stored in `.zarr` or `.nc` format) and calibrated, the core input and output of most subsequent functions are generic [xarray `Datasets`](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html). This design allows new processing functions be easily added without needing to understand specialized objects, other than functions needing access of data stored only in the raw-converted `EchoData` objects.
 
 The section [**Data processing functionalities**](data-proc:functions) provides information for current processing functions and their usage.
 
@@ -9,6 +9,6 @@ The section [**Additional information for processed data**](data-proc:additional
 (data-proc:format)=
 ## Format of processed data
 
-Once raw data (represented by the `EchoData` objects) are calibrated  (via [`compute_Sv`](echopype.calibrate.compute_Sv)), the calibrated data and the outputs of all subsequent [processing functions](data-process:funcionalities) are generic [xarray Datasets](https://docs.xarray.dev/en/stable/user-guide/data-structures.html#dataset).
+Once raw data (represented by the `EchoData` objects) are calibrated  (via [`compute_Sv`](echopype.calibrate.compute_Sv)), the calibrated data and the outputs of all subsequent [processing functions](data-process:functionalities) are generic [xarray Datasets](https://docs.xarray.dev/en/stable/user-guide/data-structures.html#dataset).
 We currently do not follow any specific conventions for processed data, but we retain provenance information in the dataset, including the [data processing levels](./processing-levels.md).
 However, whether and how data variables used in the processing will be stored remain to be determined.

echopype/clean/api.py

@@ -4,13 +4,21 @@
 import pathlib
 from typing import Union
 
+import xarray as xr
+from pandas import Index
+import pathlib
+from typing import Union
+
 import xarray as xr
 from pandas import Index
 
+from ..utils.io import get_dataset
+from ..utils.misc import frequency_nominal_to_channel
 from ..utils.io import get_dataset
 from ..utils.misc import frequency_nominal_to_channel
 from ..utils.prov import add_processing_level, echopype_prov_attrs, insert_input_processing_level
 from . import impulse_noise, signal_attenuation, transient_noise
+from . import impulse_noise, signal_attenuation, transient_noise
 from .noise_est import NoiseEst
 
 
@@ -92,7 +100,7 @@ def get_transient_noise_mask(
     method: str = "ryan",
 ) -> xr.DataArray:
     """
-    Create a mask based on the identified signal attenuations of Sv values at 38KHz.
+    Create a transient noise mask.
     This method is based on:
     Ryan et al. (2015) ‘Reducing bias due to noise and attenuation in
         open-ocean echo integration data’, ICES Journal of Marine Science,
@@ -166,7 +174,6 @@ def get_impulse_noise_mask(
         Can contain the following:
             thr: Union[Tuple[float, float], int, float]
                 User-defined threshold value (dB) (ryan and ryan iterable)
-                or a 2-element tuple with the range of threshold values (wang).
             m:  Optional[Union[int, float]] = None,
                 Vertical binning length (in number of samples or range)
                 (ryan and ryan iterable).
@@ -175,17 +182,8 @@ def get_impulse_noise_mask(
                 Number of pings either side for comparisons (ryan),
                 or a 2-element tuple specifying the range (ryan iterable).
                 Defaults to None.
-            erode: Optional[List[Tuple[int, int]]] = None,
-                Window size for each erosion cycle (wang).
-                Defaults to None.
-            dilate: Optional[List[Tuple[int, int]]] = None,
-                Window size for each dilation cycle (wang).
-                Defaults to None.
-            median: Optional[List[Tuple[int, int]]] = None,
-                Window size for each median filter cycle (wang).
-                Defaults to None.
     method: str, optional
-        The method (ryan, ryan_iterable or wang) used to mask impulse noise.
+        The method (ryan, ryan_iterable) used to mask impulse noise.
         Defaults to 'ryan'.
 
     Returns
@@ -200,7 +198,7 @@ def get_impulse_noise_mask(
     mask_map = {
         "ryan": impulse_noise._ryan,
         "ryan_iterable": impulse_noise._ryan_iterable,
-        "wang": impulse_noise._wang,
+        # "wang": impulse_noise._wang,
     }
     if method not in mask_map.keys():
         raise ValueError(f"Unsupported method: {method}")
@@ -449,4 +447,3 @@ def get_attenuation_mask_multichannel(
         mask_list.append(mask)
     mask = create_multichannel_mask(mask_list, channel_list)
     return mask
-