Squashed commit of the following:

commit 48fe12a
Author: Carsten Ehbrecht <[email protected]>
Date:   Mon Nov 27 06:36:11 2023 +0100

    update conda env with clisops

commit f08309d
Author: Carsten Ehbrecht <[email protected]>
Date:   Fri Nov 24 19:43:51 2023 +0100

    update requirements for clisops

commit f2a2edf
Author: Carsten Ehbrecht <[email protected]>
Date:   Mon Nov 20 11:31:29 2023 +0100

    added roocs-grids conda package

commit 68fd5fa
Merge: b1deb93 a9a8ff9
Author: Pingu Carsti <[email protected]>
Date:   Fri Nov 17 15:47:04 2023 +0100

    Merge branch 'regrid-main' into regrid-main-ce

commit b1deb93
Author: Pingu Carsti <[email protected]>
Date:   Thu Nov 16 15:19:37 2023 +0100

    added dev requirements to workflow

commit b98da60
Author: Pingu Carsti <[email protected]>
Date:   Thu Nov 16 15:09:01 2023 +0100

    fix workflow

commit 962b60b
Author: Pingu Carsti <[email protected]>
Date:   Thu Nov 16 15:07:26 2023 +0100

    test with conda on github

commit 5167449
Author: Pingu Carsti <[email protected]>
Date:   Thu Nov 16 14:07:24 2023 +0100

    update regrid test

commit 733772f
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 19:54:53 2023 +0100

    skip xfail

commit 814cf37
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 18:25:10 2023 +0100

    added xesmf

commit c0d0d8d
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 15:58:14 2023 +0100

    use regrid branch of clisops

commit f06e440
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 15:37:17 2023 +0100

    xfail regrid

commit b36a0ef
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 15:37:04 2023 +0100

    revert to main

commit 9b4d64d
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 15:25:38 2023 +0100

    xfail all regrid tests

commit 14f7b3b
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 15:18:21 2023 +0100

    xfail regrid test

commit 08e78a3
Merge: 469427f 4b94991
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 15:13:11 2023 +0100

    Merge branch 'prepare-release-0.8.2' into regrid-main-ce

commit 4b94991
Author: Pingu Carsti <[email protected]>
Date:   Wed Nov 15 14:37:05 2023 +0100

    fix errors in docs build

commit 4095532
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 17:25:32 2023 +0100

    update rtd config

commit 81816f1
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 17:21:29 2023 +0100

    updated history

commit 2672d73
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 17:15:32 2023 +0100

    pep8

commit 5674f9b
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 17:12:14 2023 +0100

    enabled lint

commit b7d07ec
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 16:56:12 2023 +0100

    test also on python 3.10 and 3.11

commit 9e651a5
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 16:55:53 2023 +0100

    update dependency to clisops >=0.10

commit 105eb12
Merge: babe443 d662261
Author: Pingu Carsti <[email protected]>
Date:   Tue Nov 14 16:50:31 2023 +0100

    Merge branch 'master' into prepare-release-0.8.2

commit babe443
Author: Carsten Ehbrecht <[email protected]>
Date:   Wed Feb 1 16:42:41 2023 +0100

    updete dev requirements

commit 209b17f
Author: Carsten Ehbrecht <[email protected]>
Date:   Wed Feb 1 15:16:29 2023 +0100

    update history

commit 78107f5
Author: Carsten Ehbrecht <[email protected]>
Date:   Wed Feb 1 15:11:35 2023 +0100

    update pre-commit

commit 39d6d3c
Author: Carsten Ehbrecht <[email protected]>
Date:   Wed Feb 1 14:51:45 2023 +0100

    update reqs

.github/workflows/main.yml

@@ -5,37 +5,46 @@ on: [ push, pull_request ]
 jobs:
   build:
 
+    name: Conda Build with Python${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install packages
       run: |
         sudo apt-get -y install pandoc
-      if: matrix.python-version == 3.8
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      if: matrix.python-version == 3.9
+    - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python-version }}
+        cache-downloads: true
+        cache-environment: true
+        environment-file: environment.yml
+        create-args: >-
+          conda
+          python=${{ matrix.python-version }}
+    - name: Conda and Mamba versions
+      run: |
+        conda --version
+        echo "micromamba: $(micromamba --version)"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        # pip install flake8 black pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install --no-user --editable "."
         if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
-        # pip install the package, command-line unit tests work 
-        pip install --no-deps -e .
     - name: Lint with flake8
       run: make lint
-      if: matrix.python-version == 3.8
+      if: matrix.python-version == 3.9
 #    - name: Check formatting with black
-#      run: black --check --target-version py38 daops tests
-#      if: matrix.python-version == 3.8
+#      run: black --check --target-version py39 daops tests
+#      if: matrix.python-version == 3.9
     - name: Test with pytest
       run: |
         python -m pytest -v tests
     - name: Build docs 🏗️
       run: make docs
-      if: matrix.python-version == 3.8
+      if: matrix.python-version == 3.9

daops/ops/average.py

@@ -40,7 +40,7 @@ def average_over_dims(
     apply_fixes=True,
 ):
     """
-    Average input dataset over indicated dimensions.
+    Average input dataset according over indicated dimensions.
     Can be averaged over multiple dimensions.
 
     Parameters

environment.yml

@@ -5,15 +5,17 @@ channels:
   - defaults
 dependencies:
   - pip
-  - numpy>=1.16
-  - xarray>=0.15
+  - numpy >=1.16
+  - xarray >=0.21,<2023.3.0 # https://github.com/pydata/xarray/issues/7794
   - dask
   - netcdf4
-  - clisops>=0.10.0
+  - clisops >=0.12.0
+  - roocs-grids >=0.1.2
+  - xesmf >=0.8.2
   - elasticsearch>=7.9.1
   - roocs-utils>=0.6.2
   # logging
-  - loguru>=0.5.3
+  - loguru >=0.5.3
   # catalog
   - intake
   - fsspec

requirements.txt

@@ -1,11 +1,14 @@
 numpy>=1.16
-xarray>=0.19
+xarray>=0.21
+xesmf>=0.8.2
 dask[complete]
 cftime
 netcdf4
 elasticsearch>=8.0.1
-clisops>=0.10.0
-roocs-utils>=0.6.2
+clisops>=0.12.0
+## clisops @ git+https://github.com/roocs/clisops.git@master#egg=clisops
+roocs-utils>=0.6.4
+roocs_grids>=0.1.2
 # logging
 loguru>=0.5.3
 # catalog

tests/conftest.py

@@ -40,4 +40,3 @@ def load_esgf_test_data():
         repo = Repo(target)
         repo.git.checkout(branch)
         repo.remotes[0].pull()
-

tests/test_operations/test_average.py

@@ -36,7 +36,7 @@ def test_average_dims_time(tmpdir):
 
 
 @pytest.mark.online
-def test_average_time_lat(tmpdir, load_esgf_test_data):
+def test_average_time_lat(tmpdir):
     result = average_over_dims(
         CMIP5_IDS[1],
         dims=["latitude", "time"],
@@ -51,7 +51,7 @@ def test_average_time_lat(tmpdir, load_esgf_test_data):
 
 
 @pytest.mark.online
-def test_average_time_lon(tmpdir, load_esgf_test_data):
+def test_average_time_lon(tmpdir):
     result = average_over_dims(
         CMIP5_IDS[1],
         dims=["time", "longitude"],
@@ -66,7 +66,7 @@ def test_average_time_lon(tmpdir, load_esgf_test_data):
 
 
 @pytest.mark.online
-def test_average_none(tmpdir, load_esgf_test_data):
+def test_average_none(tmpdir):
     with pytest.raises(InvalidParameterValue) as exc:
         average_over_dims(
             CMIP5_IDS[1],
@@ -79,7 +79,7 @@ def test_average_none(tmpdir, load_esgf_test_data):
 
 
 @pytest.mark.online
-def test_average_level(tmpdir, load_esgf_test_data):
+def test_average_level(tmpdir):
     with pytest.raises(InvalidParameterValue) as exc:
         average_over_dims(
             CMIP5_IDS[1],

tests/test_operations/test_regrid.py

@@ -2,17 +2,14 @@
 
 import pytest
 import xarray as xr
-from roocs_utils.exceptions import InvalidParameterValue
 
-from daops import CONFIG
-from daops.ops.regrid import regrid
 
-CMIP5_IDS = [
-    "cmip5.output1.INM.inmcm4.rcp45.mon.ocean.Omon.r1i1p1.latest.zostoga",
-    "cmip5.output1.MOHC.HadGEM2-ES.rcp85.mon.atmos.Amon.r1i1p1.latest.tas",
-    "cmip5.output1.MOHC.HadGEM2-ES.historical.mon.land.Lmon.r1i1p1.latest.rh",
-]
-CMIP5_MRSOS_ID = "cmip5.output1.MOHC.HadGEM2-ES.rcp85.day.land.day.r1i1p1.latest.mrsos"
+# from daops.ops.regrid import regrid
+
+# TODO: remove when upgraded to new clisops version
+# pytestmark = pytest.mark.xfail(reason="needs clisops>=0.12 with regrid operator")
+
+CMIP6_IDS = ["CMIP6.CMIP.MPI-M.MPI-ESM1-2-HR.historical.r1i1p1f1.Omon.tos.gn.v20190710"]
 
 
 def _check_output_nc(result, fname="output_001.nc"):
@@ -21,8 +18,10 @@ def _check_output_nc(result, fname="output_001.nc"):
 
 @pytest.mark.online
 def test_regrid(tmpdir, load_esgf_test_data):
+    from daops.ops.regrid import regrid
+
     result = regrid(
-        CMIP5_MRSOS_ID,
+        CMIP6_IDS[0],
         method="conservative",
         adaptive_masking_threshold=0.5,
         grid="1deg",
@@ -33,4 +32,5 @@ def test_regrid(tmpdir, load_esgf_test_data):
 
     _check_output_nc(result)
     ds = xr.open_dataset(result.file_uris[0], use_cftime=True)
-
+    assert "time" in ds.dims
+    assert "tos" in ds