Merge branch 'master' into security-policy

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

@@ -63,7 +63,7 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
       - name: Find comment
-        uses: peter-evans/find-comment@a54c31d7fa095754bfef525c0c8e5e5674c4b4b1 # v2.4.0
+        uses: peter-evans/find-comment@d5fe37641ad8451bdd80312415672ba26c86575e # v3.0.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -74,7 +74,7 @@ jobs:
           (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/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3.1.0
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
@@ -85,7 +85,7 @@ jobs:
       - name: Update comment
         if: |
           contains(github.event.pull_request.labels.*.name, 'approved')
-        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3.1.0
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}

.github/workflows/main.yml

@@ -117,10 +117,10 @@ jobs:
     strategy:
       matrix:
         include:
-          - tox-env: py38-coverage-eofs
+          - tox-env: py38-coverage
             python-version: "3.8"
             markers: -m 'not slow'
-          - tox-env: py39-coverage-sbck-eofs
+          - tox-env: py39-coverage-sbck
             python-version: "3.9"
             markers: -m 'not slow'
           - tox-env: py310-coverage  # No markers -- includes slow tests

.github/workflows/testdata-version.yml

@@ -46,7 +46,7 @@ jobs:
           echo "Latest xclim-testdata tag: ${{ env.XCLIM_TESTDATA_TAG }}"
           echo "Tag for xclim-testdata in CI: ${{ env.XCLIM_TESTDATA_BRANCH }}"
       - name: Find Comment
-        uses: peter-evans/find-comment@a54c31d7fa095754bfef525c0c8e5e5674c4b4b1 # v2.4.0
+        uses: peter-evans/find-comment@d5fe37641ad8451bdd80312415672ba26c86575e # v3.0.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -60,7 +60,7 @@ jobs:
             core.setFailed('Configured `xclim-testdata` tag is not `latest`.')
       - name: Update Failure Comment
         if: ${{ failure() }}
-        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3.1.0
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
@@ -76,7 +76,7 @@ jobs:
           edit-mode: replace
       - name: Update Success Comment
         if: ${{ success() }}
-        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3.1.0
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}

.github/workflows/workflow-warning.yml

@@ -33,7 +33,7 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
       - name: Find comment
-        uses: peter-evans/find-comment@a54c31d7fa095754bfef525c0c8e5e5674c4b4b1 # v2.4.0
+        uses: peter-evans/find-comment@d5fe37641ad8451bdd80312415672ba26c86575e # v3.0.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -45,7 +45,7 @@ jobs:
           (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/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3.1.0
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
@@ -57,7 +57,7 @@ jobs:
       - name: Update comment
         if: |
           contains(github.event.pull_request.labels.*.name, 'approved')
-        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3.1.0
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}

CHANGES.rst

@@ -16,7 +16,7 @@ Announcements
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 * Added uncertainty partitioning method `lafferty_sriver` from Lafferty and Sriver (2023), which can partition uncertainty related to the downscaling method. (:issue:`1497`, :pull:`1529`).
-* Validate YAML indicators description before trying to build module. (:issue:`1523`, :pull:`1560`).
+* Validate YAML indicators description before trying to build module. (:issue:`1523`, :issue:`1595`, :pull:`1560`, :pull:`1596`, :pull:`1600`).
 * Support ``indexer`` keyword in YAML indicator description. (:issue:`1522`, :pull:`1561`).
 * New ``xclim.core.calendar.stack_periods`` and ``unstack_periods`` for performing ``rolling(time=...).construct(..., stride=...)`` but with non-uniform temporal periods like years or months. They replace ``xclim.sdba.processing.construct_moving_yearly_window`` and ``unpack_moving_yearly_window`` which are deprecated and will be removed in a future release.
 
@@ -25,6 +25,7 @@ Breaking changes
 * `bump2version` has been replaced with `bump-my-version` to bump the version number using configurations set in the `pyproject.toml` file. (:issue:`1557`, :pull:`1569`).
 * `xclim`'s units registry and units formatting are now extended from `cf-xarray`. The exponent sign "^" is now never added in the ``units`` attribute. For example, square meters are given as "m2" instead of "m^2" by xclim, both are still accepted as input. (:issue:`1010`, :pull:`1590`).
 * `yamale` is now listed as a core dependency (was previously listed in the `dev` installation recipe). (:issue:`1595`, :pull:`1596`).
+* Due to a licensing limitation, the calculation of empirical orthogonal function  based on `eofs` (``xclim.sdba.properties.first_eof``) has been removed from `xclim`. (:issue:`1620`, :pull:`1621`).
 
 Bug fixes
 ^^^^^^^^^

docs/installation.rst

@@ -11,7 +11,7 @@ To install `xclim` via `pip`, run this command in your terminal:
 
 .. code-block:: shell
 
-    $ pip install xclim
+    $ python -m pip install xclim
 
 If you don't have `pip`_ installed, this `Python installation guide`_ can guide you through the process.
 
@@ -55,7 +55,7 @@ Both of these libraries are available on PyPI and conda-forge:
 
 .. code-block:: shell
 
-    $ pip install flox clisops
+    $ python -m pip install flox clisops
     # Or, alternatively:
     $ conda install -c conda-forge flox clisops
 
@@ -70,7 +70,7 @@ For convenience, these libraries can be installed alongside `xclim` using the fo
 
 .. code-block:: shell
 
-    $ pip install -r requirements_upstream.txt
+    $ python -m pip install -r requirements_upstream.txt
 
 Or, alternatively:
 
@@ -105,17 +105,8 @@ Afterwards, `SBCK` can be installed from PyPI using `pip`:
 
 .. code-block:: shell
 
-    $ pip install SBCK
+    $ python -m pip install pybind11 sbck
 
-Another experimental function :py:indicator:`xclim.sdba.property.first_eof` makes use of the `eofs`_ library, which is available on both PyPI and conda-forge:
-
-.. code-block:: shell
-
-    $ pip install eofs
-    # or alternatively,
-    $ conda install -c conda-forge eofs
-
-.. _eofs: https://ajdawson.github.io/eofs/
 .. _SBCK: https://github.com/yrobink/SBCK
 .. _Eigen3: https://eigen.tuxfamily.org/index.php
 
@@ -145,7 +136,7 @@ Once you have extracted a copy of the source, you can install it with pip:
 
 .. code-block:: shell
 
-    $ pip install -e ".[dev]"
+    $ python -m pip install -e ".[dev]"
 
 Alternatively, you can also install a local development copy via `flit`_:
 
@@ -160,10 +151,10 @@ Alternatively, you can also install a local development copy via `flit`_:
 Creating a Conda environment
 ----------------------------
 
-To create a conda environment including `xclim`'s dependencies and several optional libraries (notably: `clisops`, `eigen`, `eofs`, and `flox`) and development dependencies, run the following command from within your cloned repo:
+To create a conda environment including `xclim`'s dependencies and several optional libraries (notably: `clisops`, `eigen`, `sbck`, and `flox`) and development dependencies, run the following command from within your cloned repo:
 
 .. code-block:: console
 
     $ conda env create -n my_xclim_env python=3.8 --file=environment.yml
     $ conda activate my_xclim_env
-    (my_xclim_env) $ pip install -e .
+    (my_xclim_env) $ python -m pip install -e .

docs/references.bib

@@ -1835,26 +1835,6 @@ @article{roy_extremeprecip_2023
 	year = {2023},
 }
 
-@article{dawson_eofs_2016,
-	title = {eofs: {A} {Library} for {EOF} {Analysis} of {Meteorological}, {Oceanographic}, and {Climate} {Data}},
-	volume = {4},
-	issn = {2049-9647},
-	shorttitle = {eofs},
-	url = {https://openresearchsoftware.metajnl.com/article/10.5334/jors.122/},
-	doi = {10.5334/jors.122},
-	abstract = {Article: eofs: A Library for EOF Analysis of Meteorological, Oceanographic, and Climate Data},
-	language = {eng},
-	number = {1},
-	urldate = {2022-11-11},
-	journal = {Journal of Open Research Software},
-	author = {Dawson, Andrew},
-	month = apr,
-	year = {2016},
-	note = {Number: 1
-Publisher: Ubiquity Press},
-	pages = {e14},
-}
-
 @article{francois_multivariate_2020,
 	title = {Multivariate bias corrections of climate simulations: which benefits for which losses?},
 	volume = {11},

environment.yml

@@ -27,7 +27,6 @@ dependencies:
   - xarray >=2022.06.0,<2023.11.0
   - yamale
   # Extras
-  - eofs
   - flox
   # Testing and development dependencies
   - black >=22.12

pyproject.toml

@@ -124,7 +124,7 @@ target-version = [
 ]
 
 [tool.bumpversion]
-current_version = "0.47.5-dev.8"
+current_version = "0.47.5-dev.9"
 commit = true
 commit_args = "--no-verify"
 tag = false

tests/test_sdba/test_properties.py

@@ -515,19 +515,3 @@ def test_get_measure(self, open_dataset):
 
         meas = sdba.properties.var.get_measure()(sim_var, ref_var)
         np.testing.assert_allclose(meas, [0.408327], rtol=1e-3)
-
-
-class TestEOF:
-    def test_first_eof(self, open_dataset):
-        pytest.importorskip("eofs")
-        sim = (
-            open_dataset("NRCANdaily/nrcan_canada_daily_tasmax_1990.nc")
-            .tasmax.isel(lon=slice(0, 10), lat=slice(50, 60))
-            .load()
-        )
-
-        out = sdba.properties.first_eof(sim)
-        np.testing.assert_allclose(
-            [out.mean(), out.max()], [0.099976, 0.103867], rtol=1e-5
-        )
-        assert (out.isnull() == sim.isnull().any("time")).all()

tox.ini

@@ -5,7 +5,6 @@ env_list =
     docs
     notebooks_doctests
     offline-prefetch
-;    opt-slow
     py38
     py39-upstream-doctest
     py310
@@ -58,8 +57,10 @@ allowlist_externals =
 # Requires tox-conda compatible with [email protected]
 ;[testenv:conda]
 ;description = Run tests with pytest under {basepython} (Anaconda distribution)
+;commands_pre =
 ;conda_channels = conda-forge
 ;conda_env = environment-dev.yml
+;deps =
 ;extras =
 
 [testenv:notebooks_doctests{-coverage,}]
@@ -68,15 +69,6 @@ commands =
     pytest --no-cov --nbval --dist=loadscope --rootdir=tests/ --ignore=docs/notebooks/example.ipynb docs/notebooks
     pytest --rootdir=tests/ --xdoctest xclim
 
-# Requires tox-conda compatible with [email protected]
-;[testenv:opt-{slow,not_slow}]
-;description = Run tests with optional requirements (SBCK (experimental), eofs) and pytest under {basepython} (Anaconda distribution)
-;conda_env = environment-dev.yml
-;commands =
-;    pip check
-;    !slow: pytest xclim -m "not slow" --durations=10
-;    slow: pytest xclim --durations=10
-
 [testenv:offline{-prefetch,}{-coverage,}]
 description = Run tests with pytest under {basepython}, preventing socket connections (except for unix sockets for async support)
 commands:
@@ -112,7 +104,6 @@ deps =
     numba: llvmlite==0.42.0rc1
     coverage: coveralls
     upstream: -rrequirements_upstream.txt
-    eofs: eofs
     sbck: pybind11
 install_command = python -m pip install --no-user {opts} {packages}
 download = True

xclim/__init__.py

@@ -15,7 +15,7 @@
 
 __author__ = """Travis Logan"""
 __email__ = "[email protected]"
-__version__ = "0.47.5-dev.8"
+__version__ = "0.47.5-dev.9"
 
 
 _module_data = _files("xclim.data")

xclim/core/indicator.py

@@ -78,6 +78,8 @@
             units: <param units>  # Only valid if "compute" points to a generic function
             default : <param default>
             description: <param description>
+            kind: <param kind> # Override the parameter kind.
+                             # This is mostly useful for transforming an optional variable into a required one by passing ``kind: 0``.
         ...
       ...  # and so on.
 

xclim/data/schema.yml

@@ -10,7 +10,7 @@ variables: map(include('variable'), key=regex(r'^[\w]+$'), required=False)
 indicator:
   abstract: str(required=False)
   allowed_periods: list(enum('A', 'Q', 'M', 'W'), required=False)
-  src_freq: list(str(), required=False)
+  src_freq: any(str(), list(str()), required=False)
   base: str(required=False)
   compute: str(required=False)
   input: map(str(), key=str(), required=False)
@@ -32,6 +32,7 @@ parameter:
   default: any(str(), num(), bool(), null(), include('indexer'), required=False)
   choices: list(str(), required=False)
   units: str(required=False)
+  kind: int(required=False)
 
 indexer:
   drop: bool(required=False)