Fix notebooks for new RavenPy (#524)

### What kind of change does this PR introduce?

* Updates the notebooks and re-runs all of them to ensure they are
working with latest libraries
* Adds a few missing testing data files to the pooch registry
* Unpin `scipy` version (related dependency issues addressed)
* Adjusts a few triggers and allowed connections for CI workflows

### Does this PR introduce a breaking change?

Yes. Testing data was added to the `registry.txt` so a new version of
`RavenPy` is needed on PAVICS.

### Other information:

We don't currently run the notebooks here in CI, as a few of them take
far too long to compute. Perhaps we need to add a build for this
regardless.

Changes here required for:
Ouranosinc/PAVICS-e2e-workflow-tests#150

Author: Zeitsperre

.github/workflows/bump-version.yml

@@ -19,15 +19,15 @@ on:
       - .zenodo.json
       - AUTHORS.rst
       - CHANGELOG.rst
-      - CI/**/*.in
-      - CI/**/*.py
-      - CI/**/*.txt
+      - CI/**.in
+      - CI/**.txt
       - CODE_OF_CONDUCT.md
       - CONTRIBUTING.rst
       - Makefile
       - .readthedocs.yml
       - docs/*.py
-      - docs/*.rst
+      - docs/**.rst
+      - docs/notebooks/**.ipynb
       - environment-docs.yml
       - environment-dev.yml
       - pyproject.toml

.github/workflows/cache-cleaner.yml

@@ -19,7 +19,12 @@ jobs:
         uses: step-security/harden-runner@6c439dc8bdf85cadbbce9ed30d1c7b959517bc49 # v2.12.2
         with:
           disable-sudo: true
-          egress-policy: audit
+          egress-policy: block
+          allowed-endpoints: >
+            api.github.com:443
+            github.com:443
+            objects.githubusercontent.com:443
+            release-assets.githubusercontent.com:443
 
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2

CHANGELOG.rst

@@ -2,6 +2,19 @@
 Changelog
 =========
 
+v0.19.1 (unreleased)
+--------------------
+
+Breaking changes
+^^^^^^^^^^^^^^^^
+* `scipy` is no longer pinned below v1.16.0, as newer `statsmodels` is now compatible with modern `scipy` versions. (PR #524)
+
+Internal changes
+^^^^^^^^^^^^^^^^
+* Updates the notebooks and re-runs all of them to ensure they are working with latest libraries. (PR #524)
+* Adds a few missing testing data files to the `pooch` ``registry.txt`` file that are necessary for running the notebooks. (PR #524)
+* Slightly adjusted CI workflows for security and behaviour improvements. (PR #524)
+
 v0.19.0 (2025-07-16)
 --------------------
 

docs/notebooks/05_Advanced_RavenPy_configuration.ipynb

@@ -26,6 +26,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "# Utility that simplifies fetching and caching data hosted on GitHub\n",
     "from ravenpy.testing.utils import get_file"
    ]
@@ -80,9 +82,9 @@
     "from ravenpy import OutputReader, ravenpy\n",
     "\n",
     "run_name = \"raven-gr4j-salmon\"  # As can be seen in the config above, this is the name of the .rvX files.\n",
-    "configdir = config[\n",
-    "    0\n",
-    "].parent  # We can get the path to the folder containing the .rvX files this way\n",
+    "configdir = Path(\n",
+    "    config[0]\n",
+    ").parent  # We can get the path to the folder containing the .rvX files this way\n",
     "\n",
     "# Run the model and get the path to outputs\n",
     "outputs_path = ravenpy.run(modelname=run_name, configdir=configdir, overwrite=True)\n",
@@ -216,7 +218,7 @@
     "\n",
     "# Observed weather data for the Salmon river. We extracted this using Tutorial Notebook 03 and the\n",
     "# salmon_river.geojson file as the contour.\n",
-    "ts = yangtze.fetch(\"notebook_inputs/ERA5_weather_data_Salmon.nc\")\n",
+    "ts = get_file(\"notebook_inputs/ERA5_weather_data_Salmon.nc\")\n",
     "\n",
     "# Set alternate variable names in the timeseries data file\n",
     "alt_names = {\n",
@@ -573,7 +575,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

docs/notebooks/09_Hydrological_impacts_of_climate_change.ipynb

@@ -206,7 +206,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

docs/notebooks/12_Performing_hindcasting_experiments.ipynb

@@ -23,11 +23,15 @@
     "# This entire section is cookiecutter template to import required packages and prepare the temporary writing space.\n",
     "import datetime as dt\n",
     "import tempfile\n",
+    "import warnings\n",
     "from pathlib import Path\n",
     "\n",
     "import xarray as xr\n",
     "from clisops.core import subset\n",
     "\n",
+    "# ignore warnings from xsdba\n",
+    "warnings.simplefilter(\"ignore\", category=UserWarning)\n",
+    "\n",
     "from ravenpy import Emulator\n",
     "from ravenpy.config import commands as rc\n",
     "from ravenpy.config.emulators import GR4JCN\n",
@@ -69,9 +73,8 @@
     "    ts_subset = subset.subset_shape(ts_hindcast, basin_contour).mean(\n",
     "        dim=(\"rlat\", \"rlon\")\n",
     "    )\n",
-    "ts_subset = ts_subset.resample(time=\"6H\").nearest(\n",
-    "    tolerance=\"1H\"\n",
-    ")  # To make the timesteps identical across the entire duration"
+    "# To make the timesteps identical across the entire duration\n",
+    "ts_subset = ts_subset.resample(time=\"6h\").nearest(tolerance=\"1h\")"
    ]
   },
   {
@@ -312,7 +315,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

docs/notebooks/Assess_probabilistic_flood_risk.ipynb

@@ -148,7 +148,7 @@
     "    params=[0.529, -3.396, 407.29, 1.072, 16.9, 0.947],\n",
     "    Gauge=[\n",
     "        rc.Gauge.from_nc(\n",
-    "            yangtze.fetch(file),\n",
+    "            get_file(file),\n",
     "            data_type=data_type,\n",
     "            alt_names=alt_names,\n",
     "            data_kwds=data_kwds,\n",
@@ -257,7 +257,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

docs/notebooks/Comparing_hindcasts_and_ESP_forecasts.ipynb

@@ -22,11 +22,15 @@
     "%matplotlib inline\n",
     "\n",
     "import datetime as dt\n",
+    "import warnings\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",
     "from clisops.core import subset\n",
     "\n",
+    "# ignore warnings from xsdba\n",
+    "warnings.simplefilter(\"ignore\", category=UserWarning)\n",
+    "\n",
     "from ravenpy import Emulator\n",
     "from ravenpy.config import commands as rc\n",
     "from ravenpy.config.emulators import GR4JCN\n",
@@ -337,9 +341,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

docs/notebooks/Hydrological_realtime_forecasting.ipynb

@@ -17,14 +17,18 @@
    "source": [
     "%matplotlib inline\n",
     "\n",
-    "# Import the required packages\n",
-    "\n",
     "import datetime as dt\n",
     "\n",
+    "# Import the required packages\n",
+    "import warnings\n",
+    "\n",
     "import fiona\n",
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",
     "\n",
+    "# ignore warnings from xsdba\n",
+    "warnings.simplefilter(\"ignore\", category=UserWarning)\n",
+    "\n",
     "from ravenpy import Emulator\n",
     "from ravenpy.config import commands as rc\n",
     "from ravenpy.config import emulators\n",
@@ -160,8 +164,11 @@
     "    },\n",
     "}\n",
     "\n",
+    "# Handle CFTime encoding\n",
+    "time_coder = xr.coders.CFDatetimeCoder(use_cftime=True)\n",
+    "\n",
     "# ECCC forecast time format is a bit complex to work with, so we will use cftime to make it more manageable.\n",
-    "fcst_tmp = xr.open_dataset(fname, use_cftime=True)\n",
+    "fcst_tmp = xr.open_dataset(fname, decode_times=time_coder)\n",
     "\n",
     "# Get the first timestep that will be used for the model simulation\n",
     "start_date = fcst_tmp.time.data[0] + dt.timedelta(days=1)\n",
@@ -243,9 +250,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

docs/notebooks/Running_HMETS_with_CANOPEX_dataset.ipynb

@@ -358,7 +358,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,