merge mast

.cruft.json

@@ -11,7 +11,7 @@
       "project_slug": "xscen",
       "project_short_description": "A climate change scenario-building analysis framework, built with xclim/xarray.",
       "pypi_username": "RondeauG",
-      "version": "0.6.19-beta",
+      "version": "0.7.2-beta",
       "use_pytest": "y",
       "use_black": "y",
       "add_pyup_badge": "n",

.github/labeler.yml

@@ -0,0 +1,26 @@
+# label rules used by .github/workflows/label.yml
+
+# label 'ci' all automation-related steps and files
+#   Since this repository is in itself an automation process to deploy a server instance,
+#   we refer here to CI as the 'meta' configuration files for managing the code and integrations with the repository,
+#   not configurations related to the deployment process itself.
+
+CI:
+  - .*  # all '.<something>' files
+  - .github/workflows/*
+  - docs/Makefile
+  - tox.ini
+  - Makefile
+
+docs:
+  - .readthedocs.yml
+  - docs/**/*
+  - AUTHORS.rst
+  - CONTRIBUTING.rst
+  - ISSUE_TEMPLATE/**/*
+  - ISSUE_TEMPLATE.md
+  - PULL_REQUEST_TEMPLATE.md
+  - README.rst
+
+xclim:
+  - xscen/xclim_modules/**/*

.github/workflows/label.yml

@@ -0,0 +1,25 @@
+# This workflow will triage pull requests and apply a label based on the
+# paths that are modified in the pull request.
+#
+# To use this workflow, you will need to set up a .github/labeler.yml
+# file with configuration.  For more information, see:
+# https://github.com/actions/labeler/blob/master/README.md
+
+name: Labeler
+on: [pull_request_target]
+  # Note: potential security risk from this action using pull_request_target.
+  # Do not add actions in here which need a checkout of the repo, and do not use any caching in here.
+  # See: https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#pull_request_target
+
+permissions:
+  checks: write
+  contents: read
+  pull-requests: write
+
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/labeler@v4
+      with:
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/main.yml

@@ -29,13 +29,13 @@ jobs:
           python-version: "3.9"
       - name: Install tox
         run: |
-          pip install tox~=3.0
+          pip install tox
       - name: Run linting suite
         run: |
           tox -e black
 
   testing:
-    name: Smoke Test with Python${{ matrix.python-version }}
+    name: Test with Python${{ matrix.python-version }}
     needs: black
     runs-on: ubuntu-latest
     strategy:

.github/workflows/remove-obsolete-cache.yml

@@ -0,0 +1,32 @@
+# Example taken from https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows#managing-caches
+name: Cleanup Caches on PR Merge
+
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+          REPO=${{ github.repository }}
+          BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 )
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

HISTORY.rst

@@ -2,13 +2,24 @@
 History
 =======
 
-v0.7.0 (unreleased)
+v0.7.1 (2023-08-23)
+-------------------
+* Update dependencies by removing ``pygeos``, pinning ``shapely>=2`` and ``intake-esm>=2023.07.07`` as well as other small fixes to the environment files. (:pull:`243`).
+* Fix ``xs.aggregate.spatial_mean`` with method ``cos-lat`` when the data is on a rectilinear grid. (:pull:`243`).
+
+Internal changes
+^^^^^^^^^^^^^^^^
+* Added a workflow that removes obsolete GitHub Workflow caches from merged pull requests. (:pull:`250`).
+* Added a workflow to perform automated labeling of pull requests, dependent on the files changed. (:pull:`250`).
+
+v0.7.0 (2023-08-22)
 -------------------
 Contributors to this version: Gabriel Rondeau-Genesse (:user:`RondeauG`), Pascal Bourgault (:user:`aulemahal`), Trevor James Smith (:user:`Zeitsperre`), Juliette Lavoie (:user:`juliettelavoie`), Marco Braun (:user:`vindelico`).
 
 Announcements
 ^^^^^^^^^^^^^
 * Dropped support for Python 3.8, added support for 3.11. (:pull:`199`, :pull:`222`).
+* `xscen` is now available on `conda-forge <https://anaconda.org/conda-forge/xscen>`_, and can be installed with ``conda install -c conda-forge xscen``. (:pull:`241`)
 
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -23,7 +34,9 @@ New features and enhancements
 * Add more comments in the template. (:pull:`233`, :issue:`232`).
 * ``generate_weights`` now allows to split weights between experiments, and make them vary along the time/horizon axis. (:issue:`108`, :pull:`231`).
 * New independence_level, `institution`, added to ``generate_weights``. (:pull:`231`).
-* Updated ``produce_horizon`` so it can accept multiple periods or warming levels. (:pull:`231`).
+* Updated ``produce_horizon`` so it can accept multiple periods or warming levels. (:pull:`231`, :pull:`240`).
+* Add more comments in the template. (:pull:`233`, :pull:`235`, :issue:`232`).
+* New function ``diagnostics.health_checks`` that can perform multiple checkups on a dataset. (:pull:`238`).
 
 Breaking changes
 ^^^^^^^^^^^^^^^^
@@ -38,6 +51,7 @@ Breaking changes
 * Legacy support for `stats_kwargs` in ``ensemble_stats`` was dropped. (:pull:`231`).
 * `period` in ``produce_horizon`` has been deprecated and replaced with `periods`. (:pull:`231`).
 * Some automated `to_level` were updated to reflect more recent changes. (:pull:`231`).
+* Removed ``diagnostics.fix_unphysical_values``. (:pull:`238`).
 
 Bug fixes
 ^^^^^^^^^

MANIFEST.in

@@ -13,6 +13,7 @@ recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 recursive-exclude docs notebooks *.rst conf.py Makefile make.bat *.jpg *.png *.gif *.ipynb *.csv *.json *.yml *.md
 recursive-exclude docs notebooks samples *.csv *.json
+recursive-exclude conda *.yml
 recursive-exclude templates *.csv *.json *.py *.yml
 
 exclude .cruft.json

README.rst

@@ -2,7 +2,7 @@
 xscen |logo|
 ============
 
-|pypi| |status| |build| |coverage| |docs| |black| |pre-commit| |versions|
+|pypi| |conda| |status| |build| |coverage| |docs| |black| |pre-commit| |versions|
 
 A climate change scenario-building analysis framework, built with Intake-esm catalogs and xarray-based packages such as xclim and xESMF.
 
@@ -11,11 +11,11 @@ For documentation concerning `xscen`, see: https://xscen.readthedocs.io/en/lates
 Features
 --------
 * Supports workflows with YAML configuration files for better transparency, reproducibility, and long-term backups.
-* Intake_esm-based catalog to find and manage climate data.
+* `Intake-esm`_-based catalog to find and manage climate data.
 * Climate dataset extraction, subsetting, and temporal aggregation.
-* Calculate missing variables through Intake-esm's DerivedVariableRegistry.
-* Regridding with xESMF.
-* Bias adjustment with xclim.
+* Calculate missing variables through intake-esm's `DerivedVariableRegistry`_.
+* Regridding powered by `xESMF`_.
+* Bias adjustment tools provided by `xclim`_.
 
 Installation
 ------------
@@ -29,6 +29,10 @@ This package was created with Cookiecutter_ and the `Ouranosinc/cookiecutter-pyp
 .. _Cookiecutter: https://github.com/cookiecutter/cookiecutter
 .. _Ouranosinc/cookiecutter-pypackage: https://github.com/Ouranosinc/cookiecutter-pypackage
 .. _installation docs: https://xscen.readthedocs.io/en/latest/installation.html
+.. _Intake-esm: https://intake-esm.readthedocs.io/
+.. _DerivedVariableRegistry: https://intake-esm.readthedocs.io/en/latest/how-to/define-and-use-derived-variable-registry.html
+.. _xclim: https://xclim.readthedocs.io/
+.. _xESMF: https://xesmf.readthedocs.io/
 
 .. |logo| image:: https://raw.githubusercontent.com/Ouranosinc/xscen/main/docs/_static/_images/xscen-logo-small.png
         :target: https://github.com/Ouranosinc/xscen
@@ -46,6 +50,10 @@ This package was created with Cookiecutter_ and the `Ouranosinc/cookiecutter-pyp
         :target: https://pypi.python.org/pypi/xscen
         :alt: Python Package Index Build
 
+.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/xscen.svg
+        :target: https://anaconda.org/conda-forge/xscen
+        :alt: Conda Build
+
 .. |docs| image:: https://readthedocs.org/projects/xscen/badge/?version=latest
         :target: https://xscen.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status

conda/xscen/meta.yaml

@@ -18,34 +18,37 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - pip
   run:
-    - python >=3.8
     - cartopy
     - cftime
     - cf_xarray >=0.7.6
-    - clisops >=0.9.5
+    - clisops >=0.10
     - dask-core
     - flox
     - fsspec
     - geopandas
     - h5netcdf
-    - intake
-    - intake-esm >=2022.9.18
-    - matplotlib-base
-    - pyarrow  # Used when opening catalogs.
-    - pygeos
-    - netcdf4
+    - h5py
+    - intake-esm >=2023.07.07
+    - matplotlib
+    - netCDF4
     - numpy
-    - pandas
+    - pandas >= 2
+    - parse
     - pyyaml
     - rechunker
-    - shapely
-    - xarray <2023.3.0
-    - xclim >=0.37
+    - shapely >= 2
+    - sparse
+    - toolz
+    - xarray
+    - xclim >=0.43.0
     - xesmf >=0.7
     - zarr
+    # Opt
+    - nc-time-axis >=1.3.1
+    - pyarrow >=1.0.0
 
 test:
   imports:

conda/xscen/recipe.yaml

@@ -19,34 +19,37 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - pip
   run:
-    - python >=3.8
     - cartopy
     - cftime
     - cf_xarray >=0.7.6
-    - clisops
+    - clisops >=0.10
     - dask-core
     - flox
     - fsspec
     - geopandas
     - h5netcdf
-    - intake
-    - intake-esm >=2022.9.18
-    - matplotlib-base
-    - pyarrow  # Used when opening catalogs.
-    - pygeos
-    - netcdf4
+    - h5py
+    - intake-esm >=2023.07.07
+    - matplotlib
+    - netCDF4
     - numpy
-    - pandas
+    - pandas >= 2
+    - parse
     - pyyaml
     - rechunker
-    - shapely
+    - shapely >= 2
+    - sparse
+    - toolz
     - xarray
-    - xclim >=0.37
+    - xclim >=0.43.0
     - xesmf >=0.7
     - zarr
+    # Opt
+    - nc-time-axis >=1.3.1
+    - pyarrow >=1.0.0
 
 test:
   imports:

docs/index.rst

@@ -26,7 +26,6 @@ Features
 
     readme
     installation
-    templates
     goodtoknow
     notebooks/1_catalog
     notebooks/2_getting_started
@@ -35,6 +34,7 @@ Features
     notebooks/5_warminglevels
     notebooks/6_config
     columns
+    templates
     api
     contributing
     authors

docs/installation.rst

@@ -5,14 +5,13 @@ Installation
 Official Sources
 ----------------
 
-Because of some packages being absent from PyPI (such as `xESMF`), we strongly recommend installing
-`xscen` in an Anaconda environment.
+Because of some packages being absent from PyPI (such as `xESMF`), we strongly recommend installing `xscen` in an Anaconda environment.
 
-`xscen` can be installed directly from Anaconda.org:
+`xscen` can be installed directly from conda-forge:
 
 .. code-block:: console
 
-    $ conda install -c ouranosinc xscen
+    $ conda install -c conda-forge xscen
 
 .. note::
 
@@ -24,8 +23,8 @@ If for some reason you wish to install the `PyPI` version of `xscen` into an exi
 
     $ pip install xscen
 
-Development Installation (conda + pip)
---------------------------------------
+Development Installation (Anaconda + pip)
+-----------------------------------------
 
 For development purposes, we provide the means for generating a conda environment with the latest dependencies in an `environment.yml` file at the top-level of the `Github repo`_.