Update umamba gha

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# See https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    labels:
+      - "Bot"

.github/workflows/deploy-docs.yml

@@ -1,4 +1,4 @@
-name: Build and Deploy docs
+name: Documentation
 
 on:
   pull_request:
@@ -19,23 +19,26 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Setup Mamba
-      uses: mamba-org/provision-with-micromamba@v13
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file requirements-dev.txt
+          --channel conda-forge
 
-    - name: Build environment
+    - name: Install ciso
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=3 --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        micromamba activate TEST
         python -m pip install -e . --no-deps --force-reinstall
 
     - name: Build documentation
       shell: bash -l {0}
       run: |
         set -e
-        micromamba activate TEST
         jupyter nbconvert --to notebook --execute notebooks/ciso_unstructure.ipynb --output=ciso_unstructure-output.ipynb
         jupyter nbconvert --to notebook --execute notebooks/ciso_c_grid.ipynb --output=ciso_c_grid-output.ipynb
         mv notebooks/*output.ipynb docs/source/
@@ -44,7 +47,7 @@ jobs:
         popd
 
     - name: Deploy
-      if: github.event_name == 'release' || github.event_name == 'push'
+      if: success() && github.event_name == 'release'
       uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yml

@@ -10,27 +10,30 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [windows-latest, ubuntu-latest, macos-latest]
       fail-fast: false
 
     steps:
     - uses: actions/checkout@v3
 
-    - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v13
+    - name: Setup Micromamba ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip
+          --file requirements.txt
+          --file requirements-dev.txt
+          --channel conda-forge
 
-    - name: Python ${{ matrix.python-version }}
+    - name: Install ciso
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=${{ matrix.python-version }} --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        micromamba activate TEST
         python -m pip install -e . --no-deps --force-reinstall
 
     - name: Tests
       shell: bash -l {0}
       run: |
-        micromamba activate TEST
         python -m pytest -rxs ciso/tests

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.4.0
   hooks:
     - id: trailing-whitespace
     - id: check-ast
@@ -13,32 +13,32 @@ repos:
       files: requirements-dev.txt
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 5.0.4
+  rev: 6.0.0
   hooks:
     - id: flake8
       exclude: docs/source/conf.py
       args: [--max-line-length=105]
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
     - id: isort
       additional_dependencies: [toml]
       args: ["--profile", "black", "--filter-files"]
 
 - repo: https://github.com/psf/black
-  rev: 22.10.0
+  rev: 23.3.0
   hooks:
   - id: black
     language_version: python3
 
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.7
+  rev: v0.3.8
   hooks:
     - id: blackdoc
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.4
   hooks:
     - id: codespell
       exclude: >
@@ -49,24 +49,24 @@ repos:
         - --quiet-level=2
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.1.0
+  rev: v3.4.0
   hooks:
     - id: pyupgrade
       args:
         - --py36-plus
 
 - repo: https://github.com/dosisod/refurb
-  rev: v1.4.0
+  rev: v1.16.0
   hooks:
     - id: refurb
 
 - repo: https://github.com/asottile/add-trailing-comma
-  rev: v2.3.0
+  rev: v2.4.0
   hooks:
     - id: add-trailing-comma
 
 - repo: https://github.com/pycqa/pydocstyle
-  rev: 6.1.1
+  rev: 6.3.0
   hooks:
     - id: pydocstyle
       exclude: ^(docs|setup.py|ciso/tests)

notebooks/ciso_c_grid.ipynb

@@ -14,15 +14,14 @@
    "outputs": [],
    "source": [
     "import warnings\n",
-    "\n",
     "import iris\n",
     "\n",
-    "url = \"https://tds.marine.rutgers.edu/thredds/dodsC/roms/doppio/2017_da/avg/Averages_Best\"\n",
     "\n",
+    "url = \"https://tds.marine.rutgers.edu/thredds/dodsC/roms/doppio/2017_da/avg/Averages_Best\"\n",
     "\n",
     "with warnings.catch_warnings():\n",
     "    warnings.simplefilter(\"ignore\")\n",
-    "    cubes = iris.load(url)"
+    "    cubes = iris.load_raw(url)"
    ]
   },
   {
@@ -119,7 +118,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.11.3"
   }
  },
  "nbformat": 4,

notebooks/ciso_unstructure.ipynb

@@ -16,15 +16,14 @@
    "outputs": [],
    "source": [
     "import warnings\n",
-    "\n",
     "import iris\n",
     "\n",
-    "url = \"http://www.smast.umassd.edu:8080/thredds/dodsC/FVCOM/NECOFS/Forecasts/NECOFS_GOM3_FORECAST.nc\"\n",
     "\n",
+    "url = \"http://www.smast.umassd.edu:8080/thredds/dodsC/FVCOM/NECOFS/Forecasts/NECOFS_GOM3_FORECAST.nc\"\n",
     "\n",
     "with warnings.catch_warnings():\n",
     "    warnings.simplefilter(\"ignore\")\n",
-    "    cubes = iris.load(url)"
+    "    cubes = iris.load_raw(url)"
    ]
   },
   {
@@ -58,8 +57,8 @@
     "import numpy as np\n",
     "from ciso import zslice\n",
     "\n",
-    "p0 = -25\n",
     "\n",
+    "p0 = -25\n",
     "isoslice = zslice(q, p, -50)"
    ]
   },
@@ -71,6 +70,7 @@
    "source": [
     "import numpy.ma as ma\n",
     "\n",
+    "\n",
     "# Cannot tricontourf with NaNs.\n",
     "isoslice = ma.masked_invalid(isoslice)\n",
     "vmin, vmax = isoslice.min(), isoslice.max()\n",
@@ -107,6 +107,7 @@
    "source": [
     "import gridgeo\n",
     "\n",
+    "\n",
     "grid = gridgeo.GridGeo(url, standard_name=\"sea_water_salinity\")"
    ]
   },
@@ -146,7 +147,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.11.3"
   }
  },
  "nbformat": 4,