Merge branch 'main' into deprecate-sdba

.github/workflows/add-to-project.yml

@@ -16,7 +16,7 @@ jobs:
       repository-projects: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block
@@ -25,7 +25,7 @@ jobs:
 
       - name: Generate App Token
         id: token_generator
-        uses: actions/create-github-app-token@67e27a7eb7db372a1c61a7f9bdab8699e9ee57f7 # v1.11.3
+        uses: actions/create-github-app-token@0d564482f06ca65fa9e77e2510873638c82206f2 # v1.11.5
         with:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}

.github/workflows/bump-version.yml

@@ -37,7 +37,7 @@ jobs:
       actions: read
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block
@@ -48,7 +48,7 @@ jobs:
             pypi.org:443
       - name: Generate App Token
         id: token_generator
-        uses: actions/create-github-app-token@67e27a7eb7db372a1c61a7f9bdab8699e9ee57f7 # v1.11.3
+        uses: actions/create-github-app-token@0d564482f06ca65fa9e77e2510873638c82206f2 # v1.11.5
         with:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}

.github/workflows/cache-cleaner.yml

@@ -15,7 +15,7 @@ jobs:
       actions: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/codeql.yml

@@ -40,7 +40,7 @@ jobs:
           - 'python'
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/dependency-review.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/first-pull-request.yml

@@ -16,7 +16,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/label-on-approval.yml

@@ -24,7 +24,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block
@@ -51,7 +51,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/label.yml

@@ -27,7 +27,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/main.yml

@@ -40,7 +40,7 @@ jobs:
       (github.event_name == 'push')
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block
@@ -115,7 +115,7 @@ jobs:
         testdata-cache: [ '~/.cache/xclim-testdata' ]
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block
@@ -246,7 +246,7 @@ jobs:
             tox-env: doctests
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           egress-policy: block
           allowed-endpoints: >
@@ -353,7 +353,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block
@@ -443,7 +443,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/publish-mastodon.yml

@@ -15,7 +15,7 @@ jobs:
     environment: production
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/publish-pypi.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/scorecard.yml

@@ -32,7 +32,7 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           egress-policy: audit
 

.github/workflows/tag-testpypi.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/testdata-version.yml

@@ -22,7 +22,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/upstream.yml

@@ -39,7 +39,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/workflow-warning.yml

@@ -26,7 +26,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        uses: step-security/harden-runner@4d991eb9b905ef189e4c376166672c3f2f230481 # v2.11.0
         with:
           disable-sudo: true
           egress-policy: block

.zenodo.json

@@ -153,6 +153,11 @@
       "name": "Lehner, Sebastian",
       "affiliation": "GeoSphere Austria, Vienna, Austria",
       "orcid": "0000-0002-7562-8172"
+    },
+    {
+      "name": "Hamon, Baptiste",
+      "affiliation": "University of Canterbury, Christchurch, New Zealand",
+      "orcid": "0009-0007-4530-9772"
     }
   ],
   "keywords": [

AUTHORS.rst

@@ -48,3 +48,4 @@ Contributors
 * Adrien Lamarche `@LamAdr <https://github.com/LamAdr>`_
 * Faisal Mahmood <[email protected]> <[email protected]> `@faimahsho <https://github.com/faimahsho>`_
 * Sebastian Lehner <[email protected]> `@seblehner <https://github.com/seblehner>`_
+* Baptiste Hamon <[email protected]> `@baptistehamon <https://github.com/baptistehamon>`_

CHANGELOG.rst

@@ -4,7 +4,7 @@ Changelog
 
 v0.55.0 (unreleased)
 --------------------
-Contributors to this version: Juliette Lavoie (:user:`juliettelavoie`), Trevor James Smith (:user:`Zeitsperre`), Sascha Hofmann (:user:`saschahofmann`), Pascal Bourgault (:user:`aulemahal`), Éric Dupuis (:user:`coxipi`).
+Contributors to this version: Juliette Lavoie (:user:`juliettelavoie`), Trevor James Smith (:user:`Zeitsperre`), Sascha Hofmann (:user:`saschahofmann`), Pascal Bourgault (:user:`aulemahal`), Éric Dupuis (:user:`coxipi`), Baptiste Hamon (:user:`baptistehamon`).
 
 Breaking changes
 ^^^^^^^^^^^^^^^^
@@ -30,16 +30,18 @@ New features and enhancements
 * ``xclim.testing.helpers.test_timeseries`` now accepts a `calendar` argument that is forwarded to ``xr.cftime_range``. (:pull:`2019`).
 * New ``xclim.indices.fao_allen98``, exporting the FAO-56 Penman-Monteith equation for potential evapotranspiration (:issue:`2004`, :pull:`2067`).
 * Missing values method "pct" and "at_least_n" now accept a new "subfreq" option that allows to compute the missing mask in two steps. When given, the algorithm is applied at this "subfreq" resampling frequency first and then the result is resampled at the target indicator frequency. In the output, a period is invalid if any of its subgroup where flagged as invalid by the chosen method. (:pull:`2058`, :issue:`1820`).
-* `rv_continuous` functions can now be given directly as the `dist` argument in ``standardized_precipitation_index`` and ``standardized_precipitation_evapotranspiration_index`` indicators. This includes `lmoments3` distribution when specifying `method="PWM"`. (:issue:`2043`, :pull:`2045`).
+* ``rv_continuous`` functions can now be given directly as the ``dist`` argument in ``standardized_precipitation_index`` and ``standardized_precipitation_evapotranspiration_index`` indicators. This includes `lmoments3` distribution when specifying ``method="PWM"``. (:issue:`2043`, :pull:`2045`).
+* Time selection in ``xclim.core.calendar.select_time`` and the ``**indexer`` argument of indicators now supports day-of-year bounds given as DataArrays with spatial and/or temporal dimensions. (:issue:`1987`, :pull:`2055`).
 
 Internal changes
 ^^^^^^^^^^^^^^^^
 * `sphinx-codeautolink` and `pygments` have been temporarily pinned due to breaking API changes. (:pull:`2030`).
 * Adjusted the ``TestOfficialYaml`` test to use a dynamic method for finding the installed location of `xclim`. (:pull:`2028`).
 * Adjusted two tests for better handling when running in Windows environments. (:pull:`2057`).
-* Refactor of the ``xclim.core.missing`` module, usage of the ``Missing`` objects has been broken. (:pull:`2058`, :issue:`1820`, :issue:`2000`).
+* Refactor of the ``xclim.core.missing`` module, usage of the ``Missing`` objects has been broken. (:pull:`2058`, :pull:`2055`, :pull:`2076`, :issue:`1820`, :issue:`2000`).
     - Objects are initialized with their options and then called with the data, input frequency, target frequency and indexer.
     - Subclasses receive non-resampled DataArray in their ``is_missing`` methods.
+    - Subclasses receive the array of valid timesteps ``valid`` instead of ``null``, the invalid ones.
     - ``MissingWMO`` now uses ``xclim.indices.helpers.resample_map`` which should greatly improve performance in a dask context.
 * There is now a warning stating that `fitkwargs` are not employed when using the `lmoments3` distribution. One exception is the use of `'floc'` which is allowed with the gamma distribution. `'floc'` is used to shift the distribution before computing fitting parameters with the `lmoments3` distribution since ``loc=0`` is always assumed in the library. (:issue:`2043`, :pull:`2045`).
 * `xclim.sdba` now emits a `FutureWarning` on import to inform users that the submodule is being deprecated. (:pull:`2073`).

docs/notebooks/customize.ipynb

@@ -157,7 +157,7 @@
     "\n",
     "Finally, it is possible for advanced users to register their own methods. Xclim's missing methods are in fact class-based. To create a custom missing class, one should implement a subclass of `xclim.core.checks.MissingBase` and override at least the `is_missing` method. This method should take the following arguments:\n",
     "\n",
-    "- `null`, a `DataArray` of the mask of invalid values in the input data array (with the same time coordinate as the raw data).\n",
+    "- `valid`, a `DataArray` of the mask of valid values in the input data array (with the same time coordinate as the raw data).\n",
     "- `count`, `DataArray` of the number of days in each resampled periods\n",
     "- `freq`, the resampling frequency.\n",
     "\n",
@@ -185,8 +185,9 @@
     "    def __init__(self, max_n: int = 5):\n",
     "        super().__init__(max_n=max_n)\n",
     "\n",
-    "    def is_missing(self, null, count, freq):\n",
+    "    def is_missing(self, valid, count, freq):\n",
     "        \"\"\"Return a boolean mask where True values are for elements that are considered missing and masked on the output.\"\"\"\n",
+    "        null = ~valid\n",
     "        return (\n",
     "            null.resample(time=freq).map(longest_run, dim=\"time\")\n",
     "            >= self.options[\"max_n\"]\n",

pyproject.toml

@@ -137,7 +137,7 @@ target-version = [
 ]
 
 [tool.bumpversion]
-current_version = "0.54.1-dev.13"
+current_version = "0.54.1-dev.14"
 commit = true
 commit_args = "--no-verify --signoff"
 tag = false

src/xclim/__init__.py

@@ -13,7 +13,7 @@
 
 __author__ = """Travis Logan"""
 __email__ = "[email protected]"
-__version__ = "0.54.1-dev.13"
+__version__ = "0.54.1-dev.14"
 
 
 with _resources.as_file(_resources.files("xclim.data")) as _module_data: