Merge pull request #337 from CSHS-CWRA/deps-update

Update dependencies
CSHS-CWRA · Feb 9, 2024 · 4cce1ef · 4cce1ef
2 parents 89c356c + fac0978
commit 4cce1ef
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -117,7 +117,7 @@ jobs:
       - name: Patch Environment File
         if: matrix.os == 'windows-latest'
         run: |
-          sed -i 's/climpred >=2.2.0/xesmf/' environment.yml
+          sed -i 's/climpred >=2.4.0/xesmf/' environment.yml
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@v1
         with:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -32,12 +32,12 @@ repos:
     hooks:
       - id: toml-sort-fix
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.12.1
+    rev: 24.1.1
     hooks:
       - id: black
         exclude: ^docs/
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [ '--config=setup.cfg' ]
@@ -52,11 +52,11 @@ repos:
         args: [ '--py38-plus' ]
         additional_dependencies: [ 'pyupgrade==3.15.0' ]
       - id: nbqa-black
-        additional_dependencies: [ 'black==23.12.1' ]
+        additional_dependencies: [ 'black==24.1.1' ]
       - id: nbqa-isort
         additional_dependencies: [ 'isort==5.13.2' ]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         files: ".ipynb"
@@ -70,14 +70,14 @@ repos:
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==23.12.1' ]
+        additional_dependencies: [ 'black==24.1.1' ]
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.34.0
     hooks:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.27.3
+    rev: 0.28.0
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

diff --git a/docs/conf.py b/docs/conf.py
@@ -46,13 +46,13 @@
     "sphinx_click",
     "sphinx_codeautolink",
     "sphinx_copybutton",
-    # "sphinxcontrib.autodoc_pydantic",
+    # "sphinxcontrib.autodoc_pydantic",  # FIXME: Does not seem to be compatible with RavenPy codebase.
 ]
 
 linkcheck_ignore = [
     r"https://www.ouranos.ca",  # bad ssl certificate
     # Added on 2023-03-06: Wiley does not allow linkcheck requests (error 403)
-    r"https://doi.org/10.1029/2020WR029229"
+    r"https://doi.org/10.1029/2020WR029229",
 ]
 
 nbsphinx_custom_formats = {
@@ -68,7 +68,7 @@
 nb_execution_excludepatterns = [
     "configuration.md",
     "notebooks/*.ipynb",
-    "notebooks/paper/*.ipynb"
+    "notebooks/paper/*.ipynb",
 ]
 
 # nbsphinx_execute = "auto"
@@ -94,6 +94,7 @@
     "clisops",
     "fiona",
     "gdal",
+    "h5netcdf",
     "netCDF4",
     "osgeo",
     "geopandas",
@@ -150,8 +151,15 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".jupyter_cache", "jupyter_execute", "notebooks/paper",
-                    "notebooks/HydroShare_integration.ipynb", ]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    ".jupyter_cache",
+    "jupyter_execute",
+    "notebooks/paper",
+    "notebooks/HydroShare_integration.ipynb",
+]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
@@ -160,10 +168,7 @@
 todo_include_todos = False
 
 # Suppress "WARNING: unknown mimetype for ..." when building EPUB.
-suppress_warnings = [
-    "epub.unknown_project_files",
-    "mystnb.unknown_mime_type"
-]
+suppress_warnings = ["epub.unknown_project_files", "mystnb.unknown_mime_type"]
 
 # -- Options for HTML output -------------------------------------------
 

diff --git a/docs/notebooks/06_Raven_calibration.ipynb b/docs/notebooks/06_Raven_calibration.ipynb
@@ -2,15 +2,15 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "4a5f03fb",
+   "id": "0",
    "metadata": {},
    "source": [
     "# 06 - Calibration of a Raven hydrological model"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "d1ce69fb",
+   "id": "1",
    "metadata": {},
    "source": [
     "## Calibration of a Raven model\n",
@@ -23,7 +23,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "565a7b6c",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "cbfe7818",
+   "id": "3",
    "metadata": {},
    "source": [
     "## Preparing the model to be calibrated on a given watershed\n",
@@ -48,7 +48,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bf6a2500",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -65,7 +65,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e5611922",
+   "id": "5",
    "metadata": {},
    "source": [
     "The process is very similar to setting up a hydrological model. We first need to create the model with its configuration. We must provide the same information as before, except for the model parameters since those need to be calibrated."
@@ -74,7 +74,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2105f6ea",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -129,7 +129,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "40c8371c",
+   "id": "7",
    "metadata": {},
    "source": [
     "## Spotpy Calibration\n",
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c089720",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +160,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2b6351b2",
+   "id": "9",
    "metadata": {},
    "source": [
     "Now that the model is setup and configured and that `SpotSetup` object exists, we need to create a sampler from `spotpy` module  which will optimize the hydrological model paramaters. You can see that we are using the DDS algorithm to optimize the parameters:\n",
@@ -175,7 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "77d168a1",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -197,7 +197,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f789c674",
+   "id": "11",
    "metadata": {},
    "source": [
     "## Analysing the calibration results\n",
@@ -207,7 +207,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ae1fc2c4",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -234,7 +234,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d22ea8c6-173d-44e9-82c2-cf87a0227180",
+   "id": "13",
    "metadata": {},
    "source": [
     "## Next steps\n",
@@ -244,7 +244,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c4655f07",
+   "id": "14",
    "metadata": {},
    "source": [
     "## List of Model-Boundaries\n",

diff --git a/docs/notebooks/Assess_probabilistic_flood_risk.ipynb b/docs/notebooks/Assess_probabilistic_flood_risk.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "chinese-dealer",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Probabilistic flood risk assessment\n",
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "79d923bd-4ce5-41f1-a441-f439b23fc388",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "descending-bedroom",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "genuine-dodge",
+   "id": "3",
    "metadata": {},
    "source": [
     "Perform the time series analysis on observed data for the catchment using the frequency analysis WPS capabilities."
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "quiet-queens",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +71,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "appointed-toner",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -96,7 +96,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "explicit-accent",
+   "id": "6",
    "metadata": {},
    "source": [
     "## Probabilistic forecast\n",
@@ -107,7 +107,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "excessive-apparatus",
+   "id": "7",
    "metadata": {
     "pycharm": {
      "is_executing": true
@@ -172,7 +172,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8308cde3",
+   "id": "8",
    "metadata": {},
    "source": [
     "Now that the configuration is ready, launch the ESP forecasting tool to generate an ensemble hydrological forecast:"
@@ -181,7 +181,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c0b126a",
+   "id": "9",
    "metadata": {
     "pycharm": {
      "is_executing": true
@@ -201,7 +201,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "embedded-patrol",
+   "id": "10",
    "metadata": {
     "pycharm": {
      "is_executing": true
@@ -220,7 +220,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "british-bunch",
+   "id": "11",
    "metadata": {
     "pycharm": {
      "is_executing": true
@@ -247,7 +247,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "surface-constitutional",
+   "id": "12",
    "metadata": {},
    "source": [
     "### Results analysis\n",