Add pandas 3x, legacy xfails, and samples API key (#221)

* Add pandas 3x, legacy xfails, and samples API key

* Ruff fixes

* Remove qwdata example and NADP path fix

* Update ruff CI and config

Author: thodson-usgs

.github/workflows/python-package.yml

@@ -10,30 +10,42 @@ on:
     branches: ['main']
 
 jobs:
-  build:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.14
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+          cache: "pip"
+      - name: Install ruff
+        run: pip install ruff
+      - name: Lint with ruff
+        run: |
+          ruff check . --output-format=github
+          ruff format --check .
+
+  test:
+    needs: lint
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.9, 3.13, 3.14]
+        python-version: ["3.9", "3.13", "3.14"]
 
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .[test,nldi]
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest and report coverage
         run: |
           coverage run -m pytest tests/

.github/workflows/python-publish.yml

@@ -21,20 +21,20 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build
-        pip install setuptools setuptools-scm wheel twine check-manifest
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/sphinx-docs.yml

@@ -11,9 +11,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          cache: "pip"
       - name: Install dataretrieval, dependencies, and Sphinx then build docs
         shell: bash -l {0}
         run: |
@@ -30,7 +35,7 @@ jobs:
           echo ${{ github.ref == 'refs/heads/main' }}
           echo ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
       - name: Deploy to GitHub Pages
-        uses: JamesIves/github-pages-deploy-action@881db5376404c5c8d621010bcbec0310b58d5e29
+        uses: JamesIves/github-pages-deploy-action@v4
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

dataretrieval/__init__.py

@@ -5,11 +5,11 @@
 except PackageNotFoundError:
     __version__ = "version-unknown"
 
-from dataretrieval.nadp import *  # noqa: F403
-from dataretrieval.nwis import *  # noqa: F403
-from dataretrieval.samples import *  # noqa: F403
-from dataretrieval.streamstats import *  # noqa: F403
-from dataretrieval.utils import *  # noqa: F403
-from dataretrieval.waterdata import *  # noqa: F403
-from dataretrieval.waterwatch import *  # noqa: F403
-from dataretrieval.wqp import *  # noqa: F403
+from dataretrieval.nadp import *
+from dataretrieval.nwis import *
+from dataretrieval.samples import *
+from dataretrieval.streamstats import *
+from dataretrieval.utils import *
+from dataretrieval.waterdata import *
+from dataretrieval.waterwatch import *
+from dataretrieval.wqp import *

dataretrieval/codes/__init__.py

@@ -1,2 +1,2 @@
-from .states import *  # noqa: F403
-from .timezones import *  # noqa: F403
+from .states import *
+from .timezones import *

dataretrieval/nadp.py

@@ -30,10 +30,8 @@
 """
 
 import io
-import os
 import re
 import zipfile
-from os.path import basename
 
 import requests
 
@@ -118,7 +116,7 @@ def get_annual_MDN_map(measurement_type, year, path):
     if path:
         z.extractall(path)
 
-    return f"{path}{os.sep}{basename(filename)}"
+    return str(path)
 
 
 def get_annual_NTN_map(measurement_type, measurement=None, year=None, path="."):
@@ -174,7 +172,7 @@ def get_annual_NTN_map(measurement_type, measurement=None, year=None, path="."):
     if path:
         z.extractall(path)
 
-    return f"{path}{os.sep}{basename(filename)}"
+    return str(path)
 
 
 def get_zip(url, filename):

dataretrieval/nldi.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 from json import JSONDecodeError
-from typing import Literal, Optional, Union
+from typing import Literal
 
 from dataretrieval.utils import query
 
@@ -32,13 +34,13 @@ def _query_nldi(url, query_params, error_message):
 def get_flowlines(
     navigation_mode: str,
     distance: int = 5,
-    feature_source: Optional[str] = None,
-    feature_id: Optional[str] = None,
-    comid: Optional[int] = None,
-    stop_comid: Optional[int] = None,
+    feature_source: str | None = None,
+    feature_id: str | None = None,
+    comid: int | None = None,
+    stop_comid: int | None = None,
     trim_start: bool = False,
     as_json: bool = False,
-) -> Union[gpd.GeoDataFrame, dict]:
+) -> gpd.GeoDataFrame | dict:
     """Gets the flowlines for the specified navigation either by comid or feature
     source in WGS84 lat/long coordinates as GeoDataFrame containing a polyline geometry.
 
@@ -116,7 +118,7 @@ def get_basin(
     simplified: bool = True,
     split_catchment: bool = False,
     as_json: bool = False,
-) -> Union[gpd.GeoDataFrame, dict]:
+) -> gpd.GeoDataFrame | dict:
     """Gets the aggregated basin for the specified feature in WGS84 lat/lon
     as GeoDataFrame or as JSON conatining a polygon geometry.
 
@@ -164,17 +166,17 @@ def get_basin(
 
 
 def get_features(
-    data_source: Optional[str] = None,
-    navigation_mode: Optional[str] = None,
+    data_source: str | None = None,
+    navigation_mode: str | None = None,
     distance: int = 50,
-    feature_source: Optional[str] = None,
-    feature_id: Optional[str] = None,
-    comid: Optional[int] = None,
-    lat: Optional[float] = None,
-    long: Optional[float] = None,
-    stop_comid: Optional[int] = None,
+    feature_source: str | None = None,
+    feature_id: str | None = None,
+    comid: int | None = None,
+    lat: float | None = None,
+    long: float | None = None,
+    stop_comid: int | None = None,
     as_json: bool = False,
-) -> Union[gpd.GeoDataFrame, dict]:
+) -> gpd.GeoDataFrame | dict:
     """Gets all features found along the specified navigation either by
     comid or feature source as points in WGS84 lat/long coordinates - a GeoDataFrame
     containing a point geometry.
@@ -247,11 +249,10 @@ def get_features(
             )
 
     if not lat:
-        if comid or data_source:
-            if navigation_mode is None:
-                raise ValueError(
-                    "navigation_mode is required if comid or data_source is provided"
-                )
+        if (comid or data_source) and navigation_mode is None:
+            raise ValueError(
+                "navigation_mode is required if comid or data_source is provided"
+            )
         # validate the feature source and comid
         _validate_feature_source_comid(feature_source, feature_id, comid)
         # validate the data source
@@ -334,14 +335,14 @@ def get_features_by_data_source(data_source: str) -> gpd.GeoDataFrame:
 
 
 def search(
-    feature_source: Optional[str] = None,
-    feature_id: Optional[str] = None,
-    navigation_mode: Optional[str] = None,
-    data_source: Optional[str] = None,
+    feature_source: str | None = None,
+    feature_id: str | None = None,
+    navigation_mode: str | None = None,
+    data_source: str | None = None,
     find: Literal["basin", "flowlines", "features"] = "features",
-    comid: Optional[int] = None,
-    lat: Optional[float] = None,
-    long: Optional[float] = None,
+    comid: int | None = None,
+    lat: float | None = None,
+    long: float | None = None,
     distance: int = 50,
 ) -> dict:
     """Searches for the specified feature in NLDI and returns the results
@@ -489,7 +490,7 @@ def _validate_navigation_mode(navigation_mode: str):
 
 
 def _validate_feature_source_comid(
-    feature_source: Optional[str], feature_id: Optional[str], comid: Optional[int]
+    feature_source: str | None, feature_id: str | None, comid: int | None
 ):
     if feature_source is not None and feature_id is None:
         raise ValueError("feature_id is required if feature_source is provided")