Merge pull request #99 from ocefpaf/fix_missing_dataset

Fix missing etopo dataset

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest]
       fail-fast: false
 

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
     - id: check-ast
     - id: end-of-file-fixer
@@ -23,23 +23,23 @@ repos:
 #       args: [--config=pyproject.toml]
 
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.8
+  rev: v0.3.9
   hooks:
     - id: blackdoc
 
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.287
+  rev: v0.3.5
   hooks:
     - id: ruff
 
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 24.3.0
   hooks:
   - id: black
     language_version: python3
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
     - id: codespell
       args:
@@ -51,6 +51,6 @@ repos:
     - id: add-trailing-comma
 
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: "1.1.0"
+  rev: "1.7.0"
   hooks:
     - id: pyproject-fmt

oceans/datasets.py

@@ -2,6 +2,7 @@
 import warnings
 
 import numpy as np
+import pooch
 from netCDF4 import Dataset
 
 from oceans.ocfis import get_profile, wrap_lon180
@@ -227,6 +228,16 @@ def woa_subset(
     return ds[[f"{v}_mn"]]  # always return a dataset
 
 
+def _download_etopo2():
+    url = "https://github.com/pyoceans/python-oceans/releases/download"
+    version = "v2024.04"
+
+    return pooch.retrieve(
+        url=f"{url}/{version}/ETOPO2v2c_f4.nc",
+        known_hash="sha256:30159a3f15a06398db3cae4ec75986bedc3317dda8e89d049ddc92ba1c352ff1",
+    )
+
+
 @functools.lru_cache(maxsize=256)
 def etopo_subset(min_lon, max_lon, min_lat, max_lat, tfile=None, smoo=False):
     """
@@ -245,7 +256,7 @@ def etopo_subset(min_lon, max_lon, min_lat, max_lat, tfile=None, smoo=False):
     Based on trondkristiansen contourICEMaps.py
     """
     if tfile is None:
-        tfile = "https://gamone.whoi.edu/thredds/dodsC/usgs/data0/bathy/ETOPO2v2c_f4.nc"
+        tfile = _download_etopo2()
 
     with Dataset(tfile, "r") as etopo:
         lons = etopo.variables["x"][:]
@@ -276,7 +287,7 @@ def get_depth(lon, lat, tfile=None):
     >>> station_lon = [-40, -32]
     >>> station_lat = [-20, -20]
     >>> get_depth(station_lon, station_lat)
-    array([  -32.98816423, -4275.63374601])
+    array([  -32.988163, -4275.634   ], dtype=float32)
 
     """
     lon, lat = list(map(np.atleast_1d, (lon, lat)))

oceans/filters.py

@@ -415,7 +415,10 @@ def medfilt1(x, L=3):
     >>> L = 103
     >>> xout = medfilt1(x=x, L=L)
     >>> ax = plt.subplot(212)
-    >>> (l1, l2,) = ax.plot(
+    >>> (
+    ...     l1,
+    ...     l2,
+    ... ) = ax.plot(
     ...     x
     ... ), ax.plot(xout)
     >>> ax.grid(True)
@@ -608,7 +611,7 @@ def pl33tn(x, dt=1.0, T=33.0, mode="valid", t=None):
     import pandas as pd
     import xarray as xr
 
-    if isinstance(x, (xr.Dataset, pd.DataFrame)):
+    if isinstance(x, xr.Dataset | pd.DataFrame):
         raise TypeError("Input a DataArray not a Dataset, or a Series not a DataFrame.")
 
     if isinstance(x, pd.Series) and not isinstance(

oceans/sw_extras/sw_extras.py

@@ -168,7 +168,7 @@ def cph(bvfr2):
     Returns
     -------
     cph : array_like
-          Brünt-Väisälä Frequency [ cylcles hour :sup:`-1`]
+          Brünt-Väisälä Frequency [ cycles hour :sup:`-1`]
 
     Examples
     --------

pyproject.toml

@@ -16,13 +16,12 @@ maintainers = [
     {name = "Arnaldo Russo"},
     {name = "Filipe Fernandes", email = "[email protected]"},
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
 ]
 dynamic = [
   "dependencies",
@@ -57,7 +56,7 @@ write_to = "oceans/_version.py"
 write_to_template = "__version__ = '{version}'"
 
 [tool.ruff]
-select = [
+lint.select = [
     "A", # flake8-builtins
     "B", # flake8-bugbear
     "C4", # flake8-comprehensions
@@ -68,14 +67,25 @@ select = [
 ]
 target-version = "py311"
 line-length = 79
-ignore = [
+lint.ignore = [
     "B905",  # zip ztrict arg, enable only for py310
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/source/conf.py" = ["E402", "A001"]
 "oceans/plotting.py" = ["T201"]  # `print` found
 
+[tool.check-manifest]
+ignore = [
+    ".coveragerc",
+    "docs",
+    "docs/*",
+    "notebooks",
+    "notebooks/*",
+    "tests",
+    "tests/*",
+]
+
 [tool.pytest.ini_options]
 markers = [
   "web: marks tests require connection (deselect with '-m \"not web\"')"
@@ -93,14 +103,3 @@ exclude = ["docs", "tests"]
 verbose = 1
 quiet = false
 color = true
-
-[tool.check-manifest]
-ignore = [
-    ".coveragerc",
-    "docs",
-    "docs/*",
-    "notebooks",
-    "notebooks/*",
-    "tests",
-    "tests/*",
-]

requirements-dev.txt

@@ -1,10 +1,10 @@
-black
 cartopy
 cf_xarray
 check-manifest
 nbsphinx
 netcdf4
 pandas
+pooch
 pytest
 pytest-cov
 pytest-xdist