Update ensemble notebook to use latest xclim (#98)

Fixes 1/2 of
Ouranosinc/pavics-jupyter-env-issues#11

For new Jupyter env in
Ouranosinc/PAVICS-e2e-workflow-tests#137

### Changes

* Updates the ensemble analysis tools to use the latest xclim
conventions
* Updates the pre-commit configuration
* Uses `https` for external links where possible
* Fixes a small typo in the ReadMe file

.gitignore

@@ -0,0 +1,2 @@
+# PyCharm
+.idea/

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     rev: v3.17.0
     hooks:
       - id: pyupgrade
-        args: [ '--py37-plus' ]
+        args: [ '--py310-plus' ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -23,7 +23,7 @@ repos:
     rev: 24.10.0
     hooks:
       - id: black
-        args: [ '--target-version=py37' ]
+        args: [ '--target-version=py310' ]
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
@@ -33,11 +33,11 @@ repos:
     rev: 1.8.7
     hooks:
       - id: nbqa-pyupgrade
-        args: [ '--py37-plus' ]
-        additional_dependencies: [ 'pyupgrade==v3.16.0' ]
+        args: [ '--py310-plus' ]
+        additional_dependencies: [ 'pyupgrade==v3.17.0' ]
       - id: nbqa-black
-        args: [ '--target-version=py37' ]
-        additional_dependencies: [ 'black==24.4.2' ]
+        args: [ '--target-version=py310' ]
+        additional_dependencies: [ 'black==24.10.0' ]
       - id: nbqa-isort
         args: [ '--profile=black' ]
         additional_dependencies: [ 'isort==5.13.2' ]

README.md

@@ -17,5 +17,5 @@ For testing, you can run `npx http-server src -c-1` to view the site locally, or
 
 # Python environment.yml
 
-To ensure notebooks and exemples will run on the platform correctly it is advised to use the most recent PAVICS environment.yml
+To ensure notebooks and examples will run on the platform correctly it is advised to use the most recent PAVICS environment.yml
 https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/master/docker/environment.yml

content/homepage/hydro-intro_en.md

@@ -1,4 +1,4 @@
-PAVICS offers a suite of tools to streamline the analysis of climate change's impacts on hydrology. It relies on [Raven](http://raven.uwaterloo.ca/), an hydrological modeling framework that lets hydrologists define custom hydrological models or emulate existing ones. These models are minimally driven by daily time series of temperature and precipitation, and return series of flow and state variables such as snow pack and soil water.
+PAVICS offers a suite of tools to streamline the analysis of climate change's impacts on hydrology. It relies on [Raven](https://raven.uwaterloo.ca/), an hydrological modeling framework that lets hydrologists define custom hydrological models or emulate existing ones. These models are minimally driven by daily time series of temperature and precipitation, and return series of flow and state variables such as snow pack and soil water.
 
 The platform can, among other functionalities
   * simulate stream flow using one of four global models: HMETS, GR4J-CemaNeige, HBV-EC and MOHYSE;

content/homepage/hydro-intro_fr.md

@@ -1,4 +1,4 @@
-PAVICS offre une gamme d'outils pour faciliter l'analyse des impacts des changements climatiques sur l'hydrologie. Elle s'appuie pour cela sur [Raven](http://raven.uwaterloo.ca/), un cadre de modélisation hydrologique qui permet d'assembler différents processus hydrologiques pour créer des modèles sur mesure ou émuler des modèles existant. Ces modèles doivent minimalement être forcés par des séries journalières de température et précipitation, et retournent des séries de débits en rivière et les variables d'état du modèle, comme la neige ou l'eau dans le sol.
+PAVICS offre une gamme d'outils pour faciliter l'analyse des impacts des changements climatiques sur l'hydrologie. Elle s'appuie pour cela sur [Raven](https://raven.uwaterloo.ca/), un cadre de modélisation hydrologique qui permet d'assembler différents processus hydrologiques pour créer des modèles sur mesure ou émuler des modèles existant. Ces modèles doivent minimalement être forcés par des séries journalières de température et précipitation, et retournent des séries de débits en rivière et les variables d'état du modèle, comme la neige ou l'eau dans le sol.
 
 La plateforme permet entre autres de
 * simuler les débits en rivière par quatre modèles globaux: HMETS, GR4J-CemaNeige, HBV-EC et MOHYSE;

content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.html

@@ -7331,12 +7331,11 @@
     if (!diagrams.length) {
       return;
     }
-    const mermaid = (await import("https://cdnjs.cloudflare.com/ajax/libs/mermaid/10.7.0/mermaid.esm.min.mjs")).default;
+    const mermaid = (await import("https://cdnjs.cloudflare.com/ajax/libs/mermaid/10.6.0/mermaid.esm.min.mjs")).default;
     const parser = new DOMParser();
 
     mermaid.initialize({
       maxTextSize: 100000,
-      maxEdges: 100000,
       startOnLoad: false,
       fontFamily: window
         .getComputedStyle(document.body)
@@ -7407,8 +7406,7 @@
       let results = null;
       let output = null;
       try {
-        let { svg } = await mermaid.render(id, raw, el);
-        svg = cleanMermaidSvg(svg);
+        const { svg } = await mermaid.render(id, raw, el);
         results = makeMermaidImage(svg);
         output = document.createElement("figure");
         results.map(output.appendChild, output);
@@ -7423,38 +7421,6 @@
       parent.appendChild(output);
     }
 
-
-    /**
-     * Post-process to ensure mermaid diagrams contain only valid SVG and XHTML.
-     */
-    function cleanMermaidSvg(svg) {
-      return svg.replace(RE_VOID_ELEMENT, replaceVoidElement);
-    }
-
-
-    /**
-     * A regular expression for all void elements, which may include attributes and
-     * a slash.
-     *
-     * @see https://developer.mozilla.org/en-US/docs/Glossary/Void_element
-     *
-     * Of these, only `<br>` is generated by Mermaid in place of `\n`,
-     * but _any_ "malformed" tag will break the SVG rendering entirely.
-     */
-    const RE_VOID_ELEMENT =
-      /<\s*(area|base|br|col|embed|hr|img|input|link|meta|param|source|track|wbr)\s*([^>]*?)\s*>/gi;
-
-    /**
-     * Ensure a void element is closed with a slash, preserving any attributes.
-     */
-    function replaceVoidElement(match, tag, rest) {
-      rest = rest.trim();
-      if (!rest.endsWith('/')) {
-        rest = `${rest} /`;
-      }
-      return `<${tag} ${rest}>`;
-    }
-
     void Promise.all([...diagrams].map(renderOneMarmaid));
   });
 </script>
@@ -7528,7 +7494,7 @@
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p>PAVICS climate <a href="/datasets.html" target="_blank">datasets<a></a> are hosted on a <a href="https://www.unidata.ucar.edu/software/tds/current/" target="_blank">THREDDS data server</a> at <a href="https://pavics.ouranos.ca/thredds" target="_blank">https://pavics.ouranos.ca/thredds</a>. Although THREDDS provides a user-interface for browsing datasets, it is often more practical to  navigate the catalogue programatically.  The tutorial introduces the <a href="https://unidata.github.io/siphon/latest/index.html" target="_blank">siphon</a> library to browse the THREDDS catalog, and <a href="http://xarray.pydata.org/en/stable/index.html" target="_blank">xarray</a> to open a streaming connection to the remote data.</a></p>
+<p>PAVICS climate <a href="/datasets.html" target="_blank">datasets<a></a> are hosted on a <a href="https://www.unidata.ucar.edu/software/tds/current/" target="_blank">THREDDS data server</a> at <a href="https://pavics.ouranos.ca/thredds" target="_blank">https://pavics.ouranos.ca/thredds</a>. Although THREDDS provides a user-interface for browsing datasets, it is often more practical to  navigate the catalogue programatically.  The tutorial introduces the <a href="https://unidata.github.io/siphon/latest/index.html" target="_blank">siphon</a> library to browse the THREDDS catalog, and <a href="https://docs.xarray.dev/en/stable/index.html" target="_blank">xarray</a> to open a streaming connection to the remote data.</a></p>
 <p>More specifically, the tutorial demonstrates how to access an ensemble of climate simulations, namely Ouranos' Ensemble of Bias-adjusted Simulations - Global models CMIP6 - RDRS v2.1 <a href="https://www.nature.com/articles/s41597-023-02855-z" target="_blank"><strong>(ESPO-G6-R2 v1.0)</strong></a>, using python commands. The ensemble contains <a href="https://pavics.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/simulations/bias_adjusted/cmip6/ouranos/ESPO-G/ESPO-G6-R2v1.0.0/catalog.html" target="_blank">76 </a> bias-adjusted CMIP6 climate simulations based on a high-resolution North American reanalysis  , each with three variables (tasmin, tasmax, pr). The server can provide multiple <a href="https://www.unidata.ucar.edu/software/tds/current/reference/Services.html#dataAccessServices" target="_blank"> data access</a> and <a href="https://www.unidata.ucar.edu/software/tds/current/reference/Services.html#metadataServices" target="_blank"> metadata services</a> but in the following steps the tutorial will focus on the <em>OPeNDAP</em> service, where instead of downloading huge volumes of data locally, only the relevant portion is accessed using a standard called Data Access Protocol (DAP).</p>
 <ul>
 <li>For general information on selecting climate models and emission scenarios for climate change adaptation projects you can consult Ouranos' <a href="https://www.ouranos.ca/en/scientific-guidelines" target="_blank">Guidance Document</a></li>
@@ -9207,7 +9173,7 @@ <h3 id="Advanced-example">Advanced example<a class="anchor-link" href="#Advanced
     <span class="s2">"NorESM2-LM"</span><span class="p">,</span>
     <span class="s2">"KACE-1-0-G"</span><span class="p">,</span>
     <span class="s2">"GFDL-ESM4"</span><span class="p">,</span>
-    <span class="s2">"MIROC-ES2L"</span>
+    <span class="s2">"MIROC-ES2L"</span><span class="p">,</span>
 <span class="p">]</span>