Merge branch 'master' into fix-lazy-indexing

.github/workflows/actions-versions-updater.yml

@@ -11,9 +11,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
         with:
           token: ${{ secrets.WORKFLOW_TOKEN }}
+          persist-credentials: false
       - name: Run GitHub Actions Version Updater
         uses: saadmk11/[email protected]
         with:

.github/workflows/bump-version.yml

@@ -29,7 +29,7 @@ jobs:
     name: Bumpversion Patch
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
         with:
           persist-credentials: false
       - uses: actions/[email protected]

.github/workflows/cache-cleaner.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out code
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4.1.0
 
       - name: Cleanup
         run: |

.github/workflows/codeql-analysis.yml

@@ -35,7 +35,7 @@ jobs:
           - 'python'
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4.1.0
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
         uses: github/codeql-action/init@codeql-bundle-20230524

.github/workflows/dependency-review.yml

@@ -16,6 +16,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout Repository'
-        uses: actions/checkout@v3.6.0
+        uses: actions/checkout@v4.1.0
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@v3.0.8
+        uses: actions/dependency-review-action@v3.1.0

.github/workflows/label_on_approval.yml

@@ -37,22 +37,23 @@ jobs:
   comment_approved:
     name: Comment Concerning Approved Tag
     if: |
-      (github.event_name == 'pull_request_target') ||
+      (github.event_name == 'pull_request_target') &&
       (github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name)
     runs-on: ubuntu-latest
     steps:
       - name: Find comment
-        uses: peter-evans/find-comment@v2
+        uses: peter-evans/find-comment@v2.4.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
           comment-author: 'github-actions[bot]'
           body-includes: This Pull Request is coming from a fork and must be manually tagged `approved` in order to perform additional testing
       - name: Create comment
         if: |
-          (steps.fc.outputs.comment-id == '') ||
-          (!contains(github.event.pull_request.labels.*.name, 'approved'))
-        uses: peter-evans/create-or-update-comment@v3
+          (steps.fc.outputs.comment-id == '') &&
+          (!contains(github.event.pull_request.labels.*.name, 'approved')) &&
+          (github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name)
+        uses: peter-evans/[email protected]
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
@@ -63,12 +64,13 @@ jobs:
       - name: Update comment
         if: |
           contains(github.event.pull_request.labels.*.name, 'approved')
-        uses: peter-evans/create-or-update-comment@v3
+        uses: peter-evans/create-or-update-comment@v3.0.2
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
           body: |
-            Pull Request is approved!
+            > **Note**
+            > This Pull Request is approved!
           reactions: |
             hooray
           edit-mode: append

.github/workflows/main.yml

@@ -22,6 +22,11 @@ on:
 env:
   XCLIM_TESTDATA_BRANCH: v2023.9.12
 
+concurrency:
+  # For a given workflow, if we push to the same branch, cancel all previous builds on that branch except on master.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
+
 jobs:
   lint:
     name: Black (Python${{ matrix.python-version }})
@@ -35,11 +40,7 @@ jobs:
         python-version:
           - "3.8"
     steps:
-      - name: Cancel previous runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
-      - uses: actions/[email protected]
+      - uses: actions/[email protected]
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/[email protected]
         with:
@@ -63,7 +64,7 @@ jobs:
           - tox-env: "py39"
             python-version: "3.9"
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/[email protected]
         with:
@@ -103,7 +104,7 @@ jobs:
             python-version: "3.11"
             markers: -m 'not slow and not requires_internet'
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
       - name: Install Eigen3
         if: contains(matrix.tox-env, 'sbck')
         run: |
@@ -140,9 +141,9 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           cache-downloads: true
           cache-environment: true

.github/workflows/publish-mastodon.template.md

@@ -1,4 +1,4 @@
-New #xclim release: v{{ .version }} 🎉
+New #xclim release: {{ .version }} 🎉
 
 Latest source code available at: https://github.com/Ouranosinc/xclim/releases/tag/{{ .version }}
 Check out the docs for more information: https://xclim.readthedocs.io/en/stable/

.github/workflows/publish-mastodon.yml

@@ -16,13 +16,13 @@ on:
         type: boolean
 
 jobs:
-  build:
+  toot:
     runs-on: ubuntu-latest
     environment: production
     steps:
 
     - name: Checkout
-      uses: actions/checkout@v3.6.0
+      uses: actions/checkout@v4.1.0
 
     - name: Current Version
       if: ${{ !github.event.inputs.version-tag }}

.github/workflows/publish-pypi.yml

@@ -14,7 +14,7 @@ jobs:
       id-token: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
       - name: Set up Python3
         uses: actions/[email protected]
         with:

.github/workflows/tag-testpypi.yml

@@ -14,7 +14,7 @@ jobs:
       id-token: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
       - name: Set up Python3
         uses: actions/[email protected]
         with:

.github/workflows/testdata_version.yml

@@ -14,7 +14,7 @@ jobs:
     name: Check Latest xclim-testdata Tag
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
       - name: Find xclim-testdata Tag and CI Testing Branch
         run: |
           XCLIM_TESTDATA_TAG="$( \

.github/workflows/upstream.yml

@@ -34,11 +34,11 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3.6.0
+      - uses: actions/checkout@v4.1.0
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           cache-downloads: true
           cache-environment: true

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.10.1
+  rev: v3.14.0
   hooks:
   - id: pyupgrade
     args: ['--py38-plus']
@@ -33,7 +33,7 @@ repos:
   - id: yamllint
     args: ['--config-file=.yamllint.yaml']
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 23.9.1
   hooks:
   - id: black
 - repo: https://github.com/pycqa/flake8
@@ -71,9 +71,9 @@ repos:
   hooks:
   - id: blackdoc
     exclude: '(xclim/indices/__init__.py|docs/installation.rst)'
-    additional_dependencies: ['black==23.7.0']
+    additional_dependencies: ['black==23.9.1']
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.26.3
+  rev: 0.27.0
   hooks:
   - id: check-github-workflows
   - id: check-readthedocs

CHANGES.rst

@@ -12,12 +12,14 @@ New features and enhancements
 * `xclim` now has a dedicated console command for prefetching testing data from `xclim-testdata` with branch options (e.g.: `$ xclim prefetch_testing_data --branch some_development_branch`). This command can be used to download the testing data to a local cache, which can then be used to run the testing suite without internet access or in "offline" mode. For more information, see the contributing documentation section for `Updating Testing Data`. (:issue:`1468`, :pull:`1473`).
 * The testing suite now offers a means of running tests in "offline" mode (using `pytest-socket <https://github.com/miketheman/pytest-socket>`_ to block external connections). This requires a local copy of `xclim-testdata` to be present in the user's home cache directory and for certain `pytest` options and markers to be set when invoked. For more information, see the contributing documentation section for `Running Tests in Offline Mode`. (:issue:`1468`, :pull:`1473`).
 * The `SKIP_NOTEBOOKS` flag to speed up docs builds is now documented. See the contributing documentation section `Get Started!` for details. (:issue:`1470`, :pull:`1476`).
+* Refactored the indicators page with the addition of a search bar.
 
 Bug fixes
 ^^^^^^^^^
 * Fixed an error in the `pytest` configuration that prevented copying of testing data to thread-safe caches of workers under certain conditions (this should always occur). (:pull:`1473`).
   * Coincidentally, this also fixes an error that caused `pytest` to error-out when invoked without an active internet connection. Running `pytest` without network access is now supported (requires cached testing data). (:issue:`1468`).
 * Calling a ``sdba.map_blocks``-wrapped function with data chunked along the reduced dimensions will raise an error. This forbids chunking the trained dataset along the distribution dimensions, for example. (:issue:`1481`, :pull:`1482`).
+* Optimization of indicators ``huglin_index`` and ``biologically_effective_degree_days`` when used with dask and flox. As a side effect, the indice functions (i.e. under ``xc.indices``) no longer mask incomplete periods. The indicators' output is unchanged under the default "check_missing" setting (:issue:`1494`, :pull:`1495`).
 * Fixed ``xclim.indices.run_length.lazy_indexing`` which would sometimes trigger the loading of auxiliary coordinates. (:issue:`1483`, :pull:`1484`).
 
 Breaking changes
@@ -36,6 +38,8 @@ Internal changes
 * Changes to the ``.zenodo.json`` file no longer are marked as CI-related changes. (:pull:`1479`).
 * GitHub deployment workflows now employs use of deployment environments for workflow security and uses the `Trusted Publisher <https://docs.pypi.org/trusted-publishers/using-a-publisher/>`_ feature to sign and publish the `xclim` wheel and source distributions. (:pull:`1469`).
 * Mastodon publishing now uses `chuhlomin/render-template <https://github.com/chuhlomin/render-template>`_ and a standard formatting markdown document to format Mastodon toots. (:pull:`1469`).
+* GitHub testing workflows now use `Concurrency` instead of the styfle/cancel-workflow-action to cancel redundant workflows. (:pull:`1487`).
+* The `pkg_resources` library has been replaced for the `packaging` library when version comparisons have been performed, and a few warning messages have been silenced in the testing suite. (:issue:`1489`, :pull:`1490`).
 * New ``xclim.testing.helpers.assert_lazy`` context manager to assert the laziness of code blocks. (:pull:`1484`).
 
 v0.45.0 (2023-09-05)

Makefile

@@ -5,7 +5,7 @@ define BROWSER_PYSCRIPT
 import os, webbrowser, sys
 from urllib.request import pathname2url
 
-webbrowser.open(f"file://{pathname2url(os.path.abspath(sys.argv[1]))}")
+webbrowser.open(sys.argv[1])
 endef
 export BROWSER_PYSCRIPT
 
@@ -93,7 +93,11 @@ linkcheck: autodoc-custom-index ## run checks over all external links found thro
 docs: autodoc-custom-index ## generate Sphinx HTML documentation, including API docs, but without indexes for for indices and indicators
 	$(MAKE) -C docs html
 ifndef READTHEDOCS
-	$(BROWSER) docs/_build/html/index.html
+	## Start http server and show in browser.
+	## We want to have the cli command run in the foreground, so it's easy to kill.
+	## And we wait 2 sec for the server to start before opening the browser.
+	\{ sleep 2; $(BROWSER) http://localhost:54345 \} &
+	python -m http.server 54345 --directory docs/_build/html/
 endif
 
 servedocs: docs ## compile the docs watching for changes

docs/_static/indsearch.js

@@ -0,0 +1,95 @@
+/* Array of indicator objects */
+let indicators = [];
+
+/* MiniSearch object defining search mechanism */
+let miniSearch = new MiniSearch({
+  fields: ['title', 'abstract', 'variables', 'keywords'], // fields to index for full-text search
+  storeFields: ['title', 'abstract', 'vars', 'realm', 'module', 'name', 'keywords'], // fields to return with search results
+  searchOptions: {
+    boost: {'title': 3, 'variables': 2},
+    fuzzy: 0.1,
+    prefix: true,
+  },
+  extractField: (doc, field) => {
+    if (field === 'variables') {
+      return Object.keys(doc['vars']).join(' ');
+    }
+    return MiniSearch.getDefault('extractField')(doc, field);
+  }
+});
+
+// Populate search object with complete list of indicators
+fetch('indicators.json')
+  .then(data => data.json())
+  .then(data => {
+    indicators = Object.entries(data).map(([k, v]) => {
+      return {id: k.toLowerCase(), ...v}
+    });
+    miniSearch.addAll(indicators);
+    indFilter();
+  });
+
+
+// Populate list of variables
+//function getVariables() {
+//    fetch('variables.json')
+//        .then((res) => {
+//            return res.json();
+//        })
+//}
+//const variables = getVariables();
+
+
+function makeKeywordLabel(ind) {
+    /* Print list of keywords only if there is at least one. */
+    if (ind.keywords[0].length > 0) {
+        const keywords = ind.keywords.map(v => `<code class="keywordlabel">${v.trim()}</code>`).join('');
+        return `<div class="keywords">Keywords: ${keywords}</div>`;
+        }
+    else {
+        return "";
+        }
+}
+
+
+function makeVariableList(ind) {
+    /* Print list of variables and include mouse-hover tooltip with variable description. */
+    return Object.entries(ind.vars).map((kv) => {
+        const tooltip = `<button class="indVarname" title="${kv[1]}" alt="${kv[1]}">${kv[0]}</button>`;
+        return tooltip
+    }).join('');
+}
+
+function indTemplate(ind) {
+  // const varlist = Object.entries(ind.vars).map((kv) => `<code class="indVarname">${kv[0]}</code>`).join('');
+  const varlist = makeVariableList(ind);
+  return `
+    <div class="indElem" id="${ind.id}">
+      <div class="indHeader">
+        <b class="indTitle">${ind.title}</b>
+        <a class="reference_internal indName" href="api.html#xclim.indicators.${ind.module}.${ind.name}" title="${ind.name}">
+          <code>${ind.module}.${ind.name}</code>
+        </a>
+      </div>
+      <div class="indVars">Uses: ${varlist}</div>
+      <div class="indDesc"><p>${ind.abstract}</p></div>
+      ${makeKeywordLabel(ind)}
+      <div class="indID">Yaml ID: <code>${ind.id}</code></div>
+    </div>
+  `;
+}
+
+function indFilter() {
+  const input = document.getElementById("queryInput").value;
+  let inds = [];
+  if (input === "") {
+    inds = indicators;
+  } else {
+    inds = miniSearch.search(input);
+  }
+
+  const newTable = inds.map(indTemplate).join('');
+  const tableElem = document.getElementById("indTable");
+  tableElem.innerHTML = newTable;
+  return newTable;
+}