Lint Jupyter notebooks: put *.ipynb in ruff's include

.github/scripts/ruff_check.sh

@@ -22,7 +22,9 @@ if [ $? -ne 0 ]; then
 fi
 
 echo "Running ruff format on staged files..."
-echo "$STAGED_FILES" | xargs ruff format
+# --force-exclude so the [tool.ruff.format] exclude is honored even
+# though paths are passed explicitly (notebooks are linted, not formatted)
+echo "$STAGED_FILES" | xargs ruff format --force-exclude
 if [ $? -ne 0 ]; then
     echo "ruff format failed. Please fix errors before committing."
     exit 1

MAINTENANCE.md

@@ -4,7 +4,6 @@
 - [Maintenance ledger](#maintenance-ledger)
   - [Open](#open)
     - [3.0.1 hotfix release (flopy pin unwind + pyPRMS floor)](#301-hotfix-release-flopy-pin-unwind--pyprms-floor)
-    - [conda-forge feedstock: pyprms floor replaces packaging pin](#conda-forge-feedstock-pyprms-floor-replaces-packaging-pin)
     - [pyPRMS upstream: close PR #64, port its regression test](#pyprms-upstream-close-pr-64-port-its-regression-test)
     - [Reconcile check_version.yaml with release_preflight.sh](#reconcile-check_versionyaml-with-release_preflightsh)
     - [Deliver CI-usage findings to org admins](#deliver-ci-usage-findings-to-org-admins)
@@ -51,16 +50,6 @@ check it), **Action** (what to do once unblocked), and optional
   released flopy until then; flopy imports lazily so this is not an
   import-time problem.
 
-### conda-forge feedstock: pyprms floor replaces packaging pin
-
-- **Blocked on:** feedstock PR #14 (pyprms >=0.10.0 floor, build 1)
-  MERGED 2026-08-19; awaiting the main-branch CI upload. Check:
-  `https://api.anaconda.org/package/conda-forge/pywatershed` shows a
-  3.0.0 build with build number 1.
-- **Action:** verify the new build's run deps carry `pyprms >=0.10.0`
-  and no `packaging <26.3`, then move to Done. This was the last
-  `packaging <26.3` pin anywhere.
-
 ### pyPRMS upstream: close PR #64, port its regression test
 
 - **Blocked on:** nothing — #64 was closed unmerged 2026-08-17; the
@@ -92,6 +81,11 @@ check it), **Action** (what to do once unblocked), and optional
 
 ## Done
 
+- 2026-08-19: conda-forge pywatershed 3.0.0 build 1 published (feedstock
+  PR #14: `pyprms >=0.10.0` replaces `packaging <26.3`; verified on
+  anaconda.org, uploaded 19:35 UTC). The last `packaging <26.3` pin
+  anywhere is gone. Also: PR #407's sagehen ubuntu OOM resolved by
+  serial pytest (`-n=1`) on Linux.
 - 2026-08-19: gh-pages v3.0.0 extended release notes are live upstream
   (`doi-usgs.github.io/pywatershed`, 2026-07-13 post) and all 3.0.0
   release-body links resolve — step 9 done, the 3.0.0 release is

doc/whats-new.rst

@@ -27,11 +27,30 @@ Bug fixes
 
 Internal changes
 ~~~~~~~~~~~~~~~~
+- Lint Jupyter notebooks. ``[tool.ruff] include`` covered only ``*.py``, so
+  ``ruff check .`` and CI never saw notebooks, while the pre-commit hook
+  passed ``*.ipynb`` paths explicitly (which overrides ``include``) and did.
+  Notebook problems were therefore invisible until someone edited a notebook
+  and was met with errors they had not caused. Notebooks are now in
+  ``include``, with ``E501`` and ``I001`` exempted: they are narrative, and
+  several import a module purely for its side effect (``hvplot.xarray``
+  registers a ``.hvplot`` accessor) and must do so after the module they
+  extend, which sorting undoes. Notebooks are linted but not auto-formatted,
+  for the same line-length reason. This surfaced four broken cells that no
+  test covered: two stray ``)``, a string opened with ``"`` and closed with
+  ``'``, and a use of ``pl.Path`` with no ``import pathlib``. Three notebooks
+  needed further cleanup once the syntax errors stopped masking it: unused
+  imports, unused assignments, a semicolon-joined statement, and bare
+  ``except`` clauses narrowed to ``except AssertionError``. Also repairs
+  four malformed ``# noqa`` directives (including a ``# noaq`` typo) that
+  ruff silently ignored, which meant the unused-import fixer would have
+  deleted the ``hvplot`` imports they were meant to protect.
+  (:pull:`412`) By `James McCreight <https://github.com/jmccreight>`_.
 - Add ``MAINTENANCE.md``, a ledger of maintenance todos blocked on external
   events (dependency releases, cross-repo work), each with a mechanically
   checkable unblock condition; the ``/maintenance`` Claude skill checks them
   live and reports what is actionable.
-  (:pull:`XXX`) By `James McCreight <https://github.com/jmccreight>`_.
+  (:pull:`409`) By `James McCreight <https://github.com/jmccreight>`_.
 - Reduce CI footprint with a skeleton/full split: pushes to any branch (in
   this repository or on forks) run a skeleton — installs, linting, domainless
   tests, the docs build, and example notebooks on ubuntu only — while the

evaluation/performance/input_performance.ipynb

@@ -15,7 +15,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pathlib as pl\n",
     "import pywatershed\n",
     "\n",
     "repo_root = pywatershed.constants.__pywatershed_root__.parent"

evaluation/performance/nhm_pynhm_vs_prms_performance.ipynb

@@ -77,7 +77,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pandas\n",
     "import pandas as pd\n",
     "pd.options.plotting.backend = 'holoviews'\n",
     "results_df = pd.DataFrame(results_post).T\n",

evaluation/performance/plot_4_performance_domains.ipynb

@@ -19,6 +19,8 @@
    "source": [
     "%matplotlib inline\n",
     "\n",
+    "import pathlib as pl\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "import geopandas as gpd\n",
     "import contextily as cx"

evaluation/performance/prms_5.2.1_performance.ipynb

@@ -40,7 +40,7 @@
     "    else:\n",
     "        raise FileExistsError(f\"working_dir exists and overwrite=False: {working_dir}\")\n",
     "\n",
-    "    control_dir = data_dir / 'pynhm/performance_runs/PRMS/control_files')\n",
+    "    control_dir = data_dir / 'pynhm/performance_runs/PRMS/control_files'\n",
     "    n_hru_desc = 'multi'\n",
     "    if domain_dir.name == 'hru_1':\n",
     "        n_hru_desc = 'single'\n",
@@ -173,7 +173,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os; os.getcwd()"
+    "os.getcwd()"
    ]
   },
   {

evaluation/prms/panel_errors.ipynb

@@ -17,11 +17,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pathlib as pl\n",
     "import numpy as np\n",
-    "import param\n",
     "import pywatershed\n",
-    "import xarray as xr\n",
     "\n",
     "import panel_errors_helpers"
    ]

examples/01_multi-process_models.ipynb

@@ -28,9 +28,7 @@
    "source": [
     "from copy import deepcopy\n",
     "import pathlib as pl\n",
-    "from platform import processor\n",
     "from pprint import pprint\n",
-    "from sys import platform\n",
     "import yaml\n",
     "\n",
     "import pydoc\n",
@@ -39,7 +37,6 @@
     "import jupyter_black\n",
     "import numpy as np\n",
     "import pywatershed as pws\n",
-    "from pywatershed.utils import gis_files\n",
     "from pywatershed.utils.path import dict_pl_to_str\n",
     "\n",
     "import xarray as xr\n",

examples/02_prms_legacy_models.ipynb

@@ -32,11 +32,7 @@
    "outputs": [],
    "source": [
     "import pathlib as pl\n",
-    "from platform import processor\n",
-    "from pprint import pprint\n",
     "from shutil import rmtree\n",
-    "from sys import platform\n",
-    "import warnings\n",
     "\n",
     "import pydoc\n",
     "\n",

examples/03_compare_pws_prms.ipynb

@@ -45,18 +45,14 @@
    "outputs": [],
    "source": [
     "import pathlib as pl\n",
-    "from platform import processor\n",
-    "from pprint import pprint\n",
     "from shutil import rmtree\n",
     "import subprocess\n",
-    "from sys import platform\n",
     "import warnings\n",
     "\n",
     "import hvplot.pandas  # noqa\n",
     "import hvplot.xarray  # noqa\n",
     "import jupyter_black\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
     "import pywatershed as pws\n",
     "import xarray as xr\n",
     "\n",

examples/04_preprocess_atm.ipynb

@@ -23,13 +23,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from copy import deepcopy\n",
     "import pathlib as pl\n",
-    "from pprint import pprint\n",
     "import shutil\n",
     "\n",
     "import jupyter_black\n",
-    "import numpy as np\n",
     "import pywatershed as pws\n",
     "import xarray as xr\n",
     "\n",
@@ -103,7 +100,7 @@
     "    \"tmin\": dom_dir / \"tmin.cbh\",\n",
     "}\n",
     "\n",
-    "cbh_dir = nb_output_dir / f\"cbh\"\n",
+    "cbh_dir = nb_output_dir / \"cbh\"\n",
     "cbh_dir.mkdir(exist_ok=True)\n",
     "\n",
     "for kk, vv in cbh_files.items():\n",

examples/06_flow_graph_starfit.ipynb

@@ -36,17 +36,19 @@
     "import geopandas as gpd\n",
     "import jupyter_black\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
     "from tqdm.auto import tqdm\n",
     "import xarray as xr\n",
     "\n",
-    "import hvplot.xarray  # noqa, after xr\n",
-    "import hvplot.pandas  # noqa, after pandas\n",
+    "# hvplot.xarray and hvplot.pandas are imported for their side effect:\n",
+    "# each registers a .hvplot accessor, on xarray and pandas objects\n",
+    "# respectively. Neither is referenced by name, so ruff sees them as\n",
+    "# unused. Import them after xarray and pandas.\n",
+    "import hvplot.xarray  # noqa: F401\n",
+    "import hvplot.pandas  # noqa: F401\n",
     "\n",
     "import pyPRMS\n",
     "import pywatershed as pws\n",
     "from pywatershed.plot import DomainPlot\n",
-    "from pywatershed.constants import zero\n",
     "\n",
     "ndays_run = 365 * 2\n",
     "plot_height = 600\n",

examples/07_mmr_to_mf6_chf_dfw.ipynb

@@ -86,14 +86,12 @@
     "import geopandas as gpd\n",
     "import jupyter_black\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
     "import pint\n",
     "import pywatershed as pws\n",
     "import xarray as xr\n",
     "\n",
     "import hvplot.xarray  # noqa\n",
     "\n",
-    "import pywatershed as pws\n",
     "from pywatershed.utils.mmr_to_mf6_dfw import MmrToMf6Dfw\n",
     "\n",
     "jupyter_black.load()\n",

examples/09_model_output.ipynb

@@ -41,7 +41,6 @@
    "source": [
     "import inspect\n",
     "import pathlib as pl\n",
-    "from pprint import pprint\n",
     "\n",
     "import jupyter_black\n",
     "import numpy as np\n",
@@ -682,6 +681,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# some excessive hvplot internal warnings to avoid here\n",
+    "import warnings\n",
+    "\n",
     "plot_data = xr.merge(\n",
     "    [\n",
     "        output2.noi_arrays[\"node_outflows\"]\n",
@@ -699,14 +701,15 @@
     "    }\n",
     ")\n",
     "\n",
-    "# some excessive hvplot internal warnings to avoid here\n",
-    "import warnings\n",
-    "\n",
     "with warnings.catch_warnings():\n",
     "    warnings.simplefilter(\"ignore\")  # Temporarily suppress all warnings\n",
     "    import pandas as pd\n",
-    "    import hvplot.xarray  # noqa, after xr\n",
-    "    import hvplot.pandas  # noaq, after pandas\n",
+    "    # imported for their side effect: each registers a .hvplot\n",
+    "    # accessor, on xarray and pandas objects respectively. Neither is\n",
+    "    # referenced by name, so ruff sees them as unused. Import them\n",
+    "    # after xarray and pandas.\n",
+    "    import hvplot.xarray  # noqa: F401\n",
+    "    import hvplot.pandas  # noqa: F401\n",
     "\n",
     "    display(\n",
     "        plot_data.drop_vars(\n",

examples/developer/01_automated_testing.ipynb

@@ -67,7 +67,6 @@
    "outputs": [],
    "source": [
     "import pywatershed\n",
-    "import os\n",
     "import shutil\n",
     "import subprocess\n",
     "import pathlib as pl\n",

examples/developer/02_process_models.ipynb

@@ -283,7 +283,7 @@
     "    pywatershed.analysis.ModelGraph(\n",
     "        multi_proc_model, process_colors=palette, hide_variables=False\n",
     "    ).SVG(verbose=True)\n",
-    "except:\n",
+    "except Exception:\n",
     "    print(\"Sorry, this fails for no good reason on Mac ARM architecture\")"
    ]
   },
@@ -412,7 +412,7 @@
     "    pywatershed.analysis.ModelGraph(\n",
     "        nhm, process_colors=palette, hide_variables=False\n",
     "    ).SVG(verbose=True)\n",
-    "except:\n",
+    "except Exception:\n",
     "    print(\"Sorry, this fails for no good reason on Mac ARM architecture\")"
    ]
   },

examples/model_loop_custom_output.ipynb

@@ -30,14 +30,12 @@
    "outputs": [],
    "source": [
     "from itertools import product\n",
-    "import math\n",
     "import pathlib as pl\n",
     "import shutil\n",
     "import time\n",
     "\n",
     "import numpy as np\n",
     "import pywatershed as pws\n",
-    "from tqdm import tqdm\n",
     "import xarray as xr"
    ]
   },

examples/runoff_errors.ipynb

@@ -29,8 +29,7 @@
    "outputs": [],
    "source": [
     "import pathlib as pl\n",
-    "from pprint import pprint\n",
-    "from shutil import rmtree, copy2\n",
+    "from shutil import copy2\n",
     "\n",
     "import hvplot.xarray  # noqa\n",
     "from IPython.display import display\n",
@@ -99,11 +98,9 @@
    "outputs": [],
    "source": [
     "def run_prms(binary: pl.Path, run_dir: pl.Path, skip_if_exists=False):\n",
-    "    import shlex\n",
     "    import subprocess\n",
     "\n",
-    "    from pywatershed import CsvFile, Soltab\n",
-    "    from pywatershed.parameters import PrmsParameters\n",
+    "    from pywatershed import CsvFile\n",
     "\n",
     "    if skip_if_exists and run_dir.exists():\n",
     "        print(\n",
@@ -127,7 +124,7 @@
     "    output_dir.mkdir()\n",
     "\n",
     "    exe_command = f\"time ./{binary.name} nhm.control -MAXDATALNLEN 60000 2>&1 | tee run.log\"\n",
-    "    result = subprocess.run(\n",
+    "    subprocess.run(\n",
     "        exe_command,\n",
     "        shell=True,\n",
     "        # stdout = subprocess.PIPE,\n",
@@ -373,7 +370,7 @@
     "    assert (output_dir / f\"{vv}.nc\").exists()\n",
     "    try:\n",
     "        assert (input_dir_cp / f\"{vv}.nc\").exists()\n",
-    "    except:\n",
+    "    except AssertionError:\n",
     "        print(f\"********** {vv} not in input_dir_cp\")"
    ]
   },