Migrate to pyproject.toml and unpin Zarr

.github/workflows/pypi.yaml

@@ -15,7 +15,7 @@ jobs:
   build-artifact:
     name: Build echoshader package
     runs-on: ubuntu-22.04
-    if: github.repository == 'OSOceanAcoustics/echoshader'
+    if: github.repository == 'echostack-org/echoshader'
     steps:
     - name: Checkout
       uses: actions/checkout@v7

.github/workflows/pytest.yaml

@@ -1,5 +1,6 @@
 # .github/workflows/pytest.yml
 name: PyTest
+
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
@@ -9,23 +10,23 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
-        runs-on: [ubuntu-latest]
-        experimental: [false]
+
     steps:
       - name: Check out repository code
         uses: actions/checkout@v7
       - name: Setup Python
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools wheel
-          pip install -r requirements-dev.txt
-          pip install -e .
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -e ".[dev,test]"
+
       - name: Run Coverage Pytest
         run: pytest --cov=./ --cov-report=xml
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v7
         env:

.pre-commit-config.yaml

@@ -4,6 +4,7 @@ exclude: |
     notebooks/|
     docs/source/conf.py
   )
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
@@ -16,34 +17,15 @@ repos:
       - id: pretty-format-json
         args: ["--autofix", "--indent=2", "--no-sort-keys"]
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 9.0.0a3
-    hooks:
-      - id: isort
-        args: ["--profile", "black", "--filter-files"]
-
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.5.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.2
     hooks:
-      - id: black
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.3.0
-    hooks:
-      - id: flake8
+      - id: ruff-check
+        args: ["--fix"]
+      - id: ruff-format
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.49.0
     hooks:
       - id: markdownlint
         args: ["**/**/*.md", "--ignore", "docs/source/gsoc", "--enable", "MD013", "--disable", "MD043", "line_length", "--fix"]
-        # uncomment the below line and comment out the above line to check the lines over 90
-#        args: ["**/**/*.md", "--enable", "MD013", "--disable", "MD043", "--fix"]
-
-  # 09/19/2022 Don.S.: Comment out and not use codespell at the moment
-  # doesn't seem to be ignoring .ipynb when specified...
-  # - repo: https://github.com/codespell-project/codespell
-  #   rev: v2.1.0
-  #   hooks:
-  #     - id: codespell
-  #       args: ["-w", "docs/source", "echoshader"]

.readthedocs.yaml

@@ -8,11 +8,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
-    # You can also specify other tool versions:
-    # nodejs: "20"
-    # rust: "1.70"
-    # golang: "1.20"
+    python: "3.12"
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:

docs/source/version_0.1.0/get_moored_data.ipynb

@@ -248,7 +248,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.11.14"
+      "version": "3.12.13"
     }
   },
   "nbformat": 4,

docs/source/version_0.1.0/get_ship_data.ipynb

@@ -30,12 +30,8 @@
       "outputs": [],
       "source": [
         "from pathlib import Path\n",
-        "import itertools as it\n",
         "import datetime as dt\n",
-        "from dateutil import parser as dtparser\n",
-        "\n",
         "import fsspec\n",
-        "from urllib import request\n",
         "\n",
         "import echopype as ep\n",
         "import xarray as xr"
@@ -215,11 +211,7 @@
         "MVBS_ds[\"longitude\"]=lon\n",
         "MVBS_ds[\"latitude\"]=lat\n",
         "\n",
-        "import datetime\n",
-        "history = (\n",
-        "        f\"{datetime.datetime.utcnow()} +00:00. \"\n",
-        "        \"Interpolated from Platform latitude/longitude.\"\n",
-        "    )\n",
+        "history = f\"{dt.datetime.now(dt.UTC).isoformat()} Interpolated from Platform latitude/longitude.\"\n",
         "MVBS_ds[\"latitude\"] = MVBS_ds[\"latitude\"].assign_attrs({\"history\": history})\n",
         "MVBS_ds[\"longitude\"] = MVBS_ds[\"longitude\"].assign_attrs({\"history\": history})\n",
         "\n",
@@ -253,7 +245,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.11.14"
+      "version": "3.12.13"
     }
   },
   "nbformat": 4,

docs/source/version_0.1.0/hist_examples.ipynb

@@ -26,7 +26,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 1,
+      "execution_count": null,
       "metadata": {},
       "outputs": [
         {
@@ -276,7 +276,6 @@
       "source": [
         "import panel as pn\n",
         "import xarray as xr\n",
-        "import echoshader\n",
         "pn.extension('bokeh', comms='default') "
       ]
     },
@@ -1481,7 +1480,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.11.14"
+      "version": "3.12.13"
     }
   },
   "nbformat": 4,

docs/source/version_0.1.0/track_examples.ipynb

@@ -34,7 +34,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 1,
+      "execution_count": null,
       "metadata": {},
       "outputs": [
         {
@@ -284,7 +284,6 @@
       "source": [
         "import panel as pn\n",
         "import xarray as xr\n",
-        "import echoshader\n",
         "pn.extension('bokeh', comms='default') "
       ]
     },
@@ -1740,7 +1739,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.11.14"
+      "version": "3.12.13"
     }
   },
   "nbformat": 4,

echoshader/core.py

@@ -121,14 +121,11 @@ def _check_input(self):
             else:
                 if actual != expected:
                     raise ValueError(
-                        f"'Sv' dimension at index {i} "
-                        f"must be '{expected}', but got '{actual}'."
+                        f"'Sv' dimension at index {i} must be '{expected}', but got '{actual}'."
                     )
 
     def _init_widget(self):
-        self.colormap = panel.widgets.LiteralInput(
-            name="Colormap", value="jet", type=(str, list)
-        )
+        self.colormap = panel.widgets.LiteralInput(name="Colormap", value="jet", type=(str, list))
 
         self.Sv_range_slider = panel.widgets.EditableRangeSlider(
             name="Sv Range Slider",
@@ -138,9 +135,7 @@ def _init_widget(self):
             step=0.01,
         )
 
-        self.tile_select = panel.widgets.Select(
-            name="Map Tile Select", value="OSM", options=tiles
-        )
+        self.tile_select = panel.widgets.Select(name="Map Tile Select", value="OSM", options=tiles)
 
         self.channel_select = panel.widgets.Select(
             name="Channel Select", options=self.MVBS_ds.channel.values.tolist()
@@ -249,9 +244,7 @@ def echogram(
 
         if rgb_composite is True:
             if channel is None or len(channel) != 3:
-                raise ValueError(
-                    "Must have exactly 3 frequency channels for tricolor echogram."
-                )
+                raise ValueError("Must have exactly 3 frequency channels for tricolor echogram.")
 
             self.tri_channel = channel
 

echoshader/echogram.py

@@ -77,9 +77,7 @@ def single_echogram(
     return echogram
 
 
-def convert_to_color(
-    MVBS_ds: xarray, channel_sel: str, th_bottom: float, th_top: float
-):
+def convert_to_color(MVBS_ds: xarray, channel_sel: str, th_bottom: float, th_top: float):
     """
     Convert backscatter data to a color array based on threshold values.
 
@@ -119,12 +117,8 @@ def convert_to_color(
     )
     """
     da_color = MVBS_ds.sel(channel=channel_sel)
-    da_color = da_color.where(
-        da_color <= th_top, other=th_top
-    )  # set to ceiling at the top
-    da_color = da_color.where(
-        da_color >= th_bottom, other=th_bottom
-    )  # threshold at the bottom
+    da_color = da_color.where(da_color <= th_top, other=th_top)  # set to ceiling at the top
+    da_color = da_color.where(da_color >= th_bottom, other=th_bottom)  # threshold at the bottom
     da_color = da_color.expand_dims("channel")
     da_color = (da_color - th_bottom) / (th_top - th_bottom)
     da_color = numpy.squeeze(da_color.Sv.data).transpose()
@@ -198,9 +192,7 @@ def tricolor_echogram(
     rgb_ch = {"R": None, "G": None, "B": None}
 
     for ch, color in rgb_map.items():
-        rgb_ch[color] = convert_to_color(
-            MVBS_ds, channel_sel=ch, th_bottom=vmin, th_top=vmax
-        )
+        rgb_ch[color] = convert_to_color(MVBS_ds, channel_sel=ch, th_bottom=vmin, th_top=vmax)
 
     rgb = holoviews.RGB(
         (

echoshader/map.py

@@ -50,9 +50,7 @@ def get_track_corners(MVBS_ds: xarray.Dataset):
     return left, bottom, right, top
 
 
-def convert_EPSG(
-    lat: Union[int, float], lon: Union[int, float], mercator_to_coord: bool = True
-):
+def convert_EPSG(lat: Union[int, float], lon: Union[int, float], mercator_to_coord: bool = True):
     """
     Converts coordinates between EPSG coordinate reference systems (CRS).