Modification of masking using regionmask 3D instead of 2D (#144)

Modification of regions2D masking function using regionmask's 3D mask function instead of it's 2D function, and subsequent modifications to the 2d-to-3d and 3d-to-2d helper API functions. Additionally, modified setup to more closely match that of Echopype. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]> Co-authored-by: Don Setiawan <[email protected]>
OSOceanAcoustics · Oct 2, 2023 · b7d67d0 · b7d67d0
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      # Check for updates once a week
+      interval: 'weekly'
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -0,0 +1,104 @@
+# Publish archives to PyPI and TestPyPI using GitHub Actions
+name: Publish to PyPI
+on: [workflow_dispatch]
+jobs:
+
+  build-artifact:
+
+    name: Build echoregions package
+    runs-on: ubuntu-20.04
+    if: github.repository == 'OSOceanAcoustics/echoregions'
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        # fetch all history so that setuptools-scm works
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/[email protected]
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: python -m pip install setuptools wheel
+
+    # This step is only necessary for testing purposes and for TestPyPI
+    - name: Fix up version string for TestPyPI
+      if: ${{ !startsWith(github.ref, 'refs/tags') }}
+      run: |
+        # Change setuptools-scm local_scheme to "no-local-version" so the
+        # local part of the version isn't included, making the version string
+        # compatible with PyPI.
+        sed --in-place "s/node-and-date/no-local-version/g" pyproject.toml
+
+    - name: Build source and wheel distributions
+      run: |
+        python setup.py sdist bdist_wheel
+        echo ""
+        echo "Generated files:"
+        ls -lh dist/
+    - uses: actions/upload-artifact@v3
+      with:
+        name: releases
+        path: dist
+
+  test-built-dist:
+
+    name: Test echoregions package
+    needs: build-artifact
+    runs-on: ubuntu-20.04
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+    - uses: actions/[email protected]
+      name: Install Python
+      with:
+        python-version: 3.9
+    - uses: actions/download-artifact@v3
+      with:
+        name: releases
+        path: dist
+
+    - name: List contents of built dist
+      run: |
+        ls -ltrh
+        ls -ltrh dist
+
+    - name: Publish to Test PyPI
+      uses: pypa/[email protected]
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true
+        skip-existing: true
+
+    - name: Check pypi packages
+      run: |
+        sleep 3
+        python -m pip install --upgrade pip
+
+        echo "=== Testing wheel file ==="
+        # Install wheel to get dependencies and check import
+        python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre echoregions
+        python -c "import echoregions;"
+        echo "=== Done testing wheel file ==="
+
+        echo "=== Testing source tar file ==="
+        # Install tar gz and check import
+        python -m pip uninstall --yes echoregions
+        python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre --no-binary=:all: echoregions
+        python -c "import echoregions;"
+        echo "=== Done testing source tar file ==="
+
+  publish-pypi:
+    name: Push echoregions to production pypi
+    needs: test-built-dist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        name: releases
+        path: dist
+    - name: Publish to PyPI
+      uses: pypa/[email protected]
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,11 +20,6 @@ repos:
     hooks:
       - id: black
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:

diff --git a/_echoregions_version.py b/_echoregions_version.py
@@ -0,0 +1 @@
+version = "0.1.dev348+ga480450.d20231002"
diff --git a/echoregions/__init__.py b/echoregions/__init__.py
@@ -4,7 +4,9 @@
 that contain the majority of the functionality within echoregions.
 """
 
+from _echoregions_version import version as __version__  # noqa
+
 from .core import read_evl, read_evr
 from .utils.api import convert_mask_2d_to_3d, convert_mask_3d_to_2d
 
-__all__ = ["read_evl", "read_evr", "convert_mask_2d_to_3d", "convert_mask_3d_to_2d"]
+__all__ = ["read_evl", "read_evr", "convert_mask_2d_to_3d", "convert_mask_3d_to_2d"]  # noqa
diff --git a/echoregions/core.py b/echoregions/core.py
@@ -2,18 +2,16 @@
 from .regions2d.regions2d import Regions2D
 
 
-def read_evr(
-    filepath: str, min_depth: float = None, max_depth: float = None
-) -> Regions2D:
+def read_evr(filepath: str, min_depth: float = 0.0, max_depth: float = 1000.0) -> Regions2D:
     """Read an EVR file into a Regions2D object.
 
     Parameters
     ----------
     filepath : str, Path object
         A valid path to an EVR file
-    min_depth : float, default ``None``
+    min_depth : float, default 0
         Depth value in meters to set -9999.99 depth edges to.
-    max_depth : float, default ``None``
+    max_depth : float, default 1000
         Depth value in meters to set 9999.99 depth edges to.
 
     Returns

diff --git a/echoregions/lines/lines.py b/echoregions/lines/lines.py
@@ -23,9 +23,7 @@ def __init__(self, input_file: str, nan_depth_value: float = None):
         self.data = parse_line_file(input_file)
         self.output_file = []
 
-        self._nan_depth_value = (
-            None  # Set to replace -10000.99 depth values with (EVL only)
-        )
+        self._nan_depth_value = None  # Set to replace -10000.99 depth values with (EVL only)
         self._nan_depth_value = nan_depth_value
 
     def __iter__(self) -> Iterable:
@@ -67,9 +65,7 @@ def to_csv(self, save_path: bool = None) -> None:
             path to save the CSV file to
         """
         # Check if the save directory is safe
-        save_path = validate_path(
-            save_path=save_path, input_file=self.input_file, ext=".csv"
-        )
+        save_path = validate_path(save_path=save_path, input_file=self.input_file, ext=".csv")
         # Reorder columns and export to csv
         self.data.to_csv(save_path, index=False)
         self.output_file.append(save_path)
@@ -88,9 +84,7 @@ def to_json(self, save_path: str = None, pretty: bool = True, **kwargs) -> None:
             keyword arguments passed into `parse_file`
         """
         # Check if the save directory is safe
-        save_path = validate_path(
-            save_path=save_path, input_file=self.input_file, ext=".json"
-        )
+        save_path = validate_path(save_path=save_path, input_file=self.input_file, ext=".json")
         indent = 4 if pretty else None
 
         # Save the entire parsed EVR dictionary as a JSON file
@@ -176,8 +170,7 @@ def mask(self, da_Sv: DataArray, method: str = "nearest", limit_area: str = None
 
         if not isinstance(da_Sv, DataArray):
             raise TypeError(
-                "Input da_Sv must be of type DataArray. da_Sv was instead"
-                f" of type {type(da_Sv)}"
+                "Input da_Sv must be of type DataArray. da_Sv was instead" f" of type {type(da_Sv)}"
             )
 
         def filter_bottom(bottom, start_date, end_date):
@@ -264,9 +257,7 @@ def filter_bottom(bottom, start_date, end_date):
                 print(e)
 
             # convert to data array for bottom
-            bottom_da = bottom_interpolated[
-                "depth"
-            ].to_xarray()  # .rename({'index':'ping_time'})
+            bottom_da = bottom_interpolated["depth"].to_xarray()  # .rename({'index':'ping_time'})
             bottom_da = bottom_da.rename({"time": "ping_time"})
 
             # create a data array of depths