provision-with-micromamba is deprecated

.github/workflows/deploy-docs.yml

@@ -20,32 +20,31 @@ jobs:
         fetch-depth: 0
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
-
-    - name: Build environment
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file docs/requirements.txt
+          --channel conda-forge
+
+    - name: Install ioos_qc
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=3 --file requirements.txt --file docs/requirements.txt --channel conda-forge
-        micromamba activate TEST
         python -m pip install -e . --no-deps --force-reinstall
 
-    - name: Get the version
-      id: get_version
-      run: echo ::set-output name=VERSION::$(python setup.py --version)
-
     - name: Build documentation
       shell: bash -l {0}
-      run: |
+      run: >
         set -e
-        micromamba activate TEST
         pushd docs
         make clean html linkcheck
         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/pypi.yml

@@ -26,7 +26,7 @@ jobs:
 
     - name: Install build tools
       run: |
-        python -m pip install --upgrade pip wheel setuptools setuptools_scm build twine
+        python -m pip install --upgrade pip build twine
       shell: bash
 
     - name: Build binary wheel

.github/workflows/tests.yml

@@ -10,43 +10,38 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
         os: [ubuntu-latest]
         numba: [true, false]
       fail-fast: false
 
     steps:
     - uses: actions/checkout@v3
 
-    - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@main
+    - name: Setup Micromamba ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
-
-    - name: Python ${{ matrix.python-version }}
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip
+          --file requirements.txt
+          --file requirements-dev.txt
+          --channel conda-forge
+
+    - name: Install ioos_qc
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=${{ matrix.python-version }} --file requirements.txt --file tests/requirements.txt --channel conda-forge
-        micromamba activate TEST
-        pip install -e . --no-deps --force-reinstall
+        python -m pip install -e . --no-deps --force-reinstall
 
     - name: numba
       # numba is listed in requirements.txt so we need to remove it below.
       if: ${{ ! matrix.numba }}
       shell: bash -l {0}
       run: |
-        micromamba activate TEST
         micromamba remove numba
 
-    - name: Debug conda
-      shell: bash -l {0}
-      run: |
-        micromamba activate TEST
-        micromamba info --all
-        micromamba list
-
     - name: Tests
       shell: bash -l {0}
       run: |
-        micromamba activate TEST
-        python -m  pytest --disable-warnings
+        python -m pytest --disable-warnings

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.5.0
   hooks:
     - id: trailing-whitespace
     - id: check-ast
@@ -10,12 +10,12 @@ repos:
     - id: file-contents-sorter
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 3.9.2
+  rev: 7.0.0
   hooks:
     - id: flake8
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.1
+  rev: v2.2.6
   hooks:
     - id: codespell
       exclude: >

docs/source/examples/usage/storms_qc_test_1054.ipynb

@@ -1007,7 +1007,7 @@
     "xs = XarrayStream(data_xr, time=\"time\", lat=\"latitude\", lon=\"longitude\")\n",
     "qc_results = xs.run(c)\n",
     "\n",
-    "# Since we may want to re-use the results in multiple\n",
+    "# Since we may want to reuse the results in multiple\n",
     "# stores we want to evaluate the checks now so it isn't\n",
     "# a generator. This is going to run all of the checks!\n",
     "qc_results = list(qc_results)\n",
@@ -1756,7 +1756,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1770,7 +1770,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

docs/source/examples/usage/storms_qc_test_1055.ipynb

@@ -968,7 +968,7 @@
     "xs = XarrayStream(data_xr, time=\"time\", lat=\"latitude\", lon=\"longitude\")\n",
     "qc_results = xs.run(c)\n",
     "\n",
-    "# Since we may want to re-use the results in multiple\n",
+    "# Since we may want to reuse the results in multiple\n",
     "# stores we want to evaluate the checks now so it isn't\n",
     "# a generator. This is going to run all of the checks!\n",
     "qc_results = list(qc_results)"
@@ -1716,7 +1716,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1730,7 +1730,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

docs/source/examples/usage/storms_qc_test_ncCF_error.ipynb

@@ -1003,7 +1003,7 @@
     "xs = XarrayStream(data_xr, time=\"time\", lat=\"latitude\", lon=\"longitude\")\n",
     "qc_results = xs.run(c)\n",
     "\n",
-    "# Since we may want to re-use the results in multiple\n",
+    "# Since we may want to reuse the results in multiple\n",
     "# stores we want to evaluate the checks now so it isn't\n",
     "# a generator. This is going to run all of the checks!\n",
     "qc_results = list(qc_results)\n",
@@ -1717,7 +1717,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1731,7 +1731,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

tests/requirements.txt → requirements-dev.txt

@@ -1,6 +1,9 @@
+bokeh
 dask
 erddapy
 flake8
 isort
+nco
+numba<0.57
 pytest
 pytest-flake8>=1.0.4  # https://github.com/tholo/pytest-flake8/pull/59

requirements.txt

@@ -1,9 +1,7 @@
-bokeh
 geographiclib
 geojson
 h5netcdf
 jsonschema
-numba
 numpy>=1.14
 pandas
 pyparsing

tests/test_config.py

@@ -112,8 +112,8 @@ def setUp(self):
         config_str = """
             region: something
             window:
-                starting: 2020-01-01T00:00:00Z
-                ending: 2020-04-01T00:00:00Z
+                starting: 2020-01-01T00:00:00
+                ending: 2020-04-01T00:00:00
             streams:
                 variable1:
                     qartod:
@@ -171,8 +171,8 @@ def setUp(self):
                             type: Point
                             coordinates: [-72, 34]
                     window:
-                        starting: 2020-01-01T00:00:00Z
-                        ending: 2020-04-01T00:00:00Z
+                        starting: 2020-01-01T00:00:00
+                        ending: 2020-04-01T00:00:00
                     streams:
                         variable1:
                             qartod:
@@ -188,8 +188,8 @@ def setUp(self):
                             type: Point
                             coordinates: [-80,40]
                     window:
-                        starting: 2020-01-01T00:00:00Z
-                        ending: 2020-04-01T00:00:00Z
+                        starting: 2020-01-01T00:00:00
+                        ending: 2020-04-01T00:00:00
                     streams:
                         variable1:
                             qartod:

tests/test_streams.py

@@ -28,8 +28,8 @@ def setUp(self):
         config = """
             region: something
             window:
-                starting: 2020-01-01T00:00:00Z
-                ending: 2020-04-01T00:00:00Z
+                starting: 2020-01-01T00:00:00
+                ending: 2020-04-01T00:00:00
             streams:
                 variable1:
                     qartod:
@@ -146,8 +146,8 @@ def setUp(self):
         config = """
             region: something
             window:
-                starting: 2020-01-01T00:00:00Z
-                ending: 2020-04-01T00:00:00Z
+                starting: 2020-01-01T00:00:00
+                ending: 2020-04-01T00:00:00
             streams:
                 variable1:
                     qartod:
@@ -206,8 +206,8 @@ def setUp(self):
         config = """
             region: something
             window:
-                starting: 2020-01-01T00:00:00Z
-                ending: 2020-04-01T00:00:00Z
+                starting: 2020-01-01T00:00:00
+                ending: 2020-04-01T00:00:00
             streams:
                 variable1:
                     qartod:
@@ -271,8 +271,8 @@ def setUp(self):
         config = """
             region: something
             window:
-                starting: 2020-01-01T00:00:00Z
-                ending: 2020-04-01T00:00:00Z
+                starting: 2020-01-01T00:00:00
+                ending: 2020-04-01T00:00:00
             streams:
                 variable1:
                     qartod:
@@ -336,8 +336,8 @@ def setUp(self):
             contexts:
                 -   region: something
                     window:
-                        starting: 2020-01-01T00:00:00Z
-                        ending: 2020-02-01T00:00:00Z
+                        starting: 2020-01-01T00:00:00
+                        ending: 2020-02-01T00:00:00
                     streams:
                         variable1:
                             qartod:
@@ -351,8 +351,8 @@ def setUp(self):
                                     fail_span: [22, 25]
                 -   region: something else
                     window:
-                        starting: 2020-02-01T00:00:00Z
-                        ending: 2020-03-01T00:00:00Z
+                        starting: 2020-02-01T00:00:00
+                        ending: 2020-03-01T00:00:00
                     streams:
                         variable1:
                             qartod:
@@ -423,8 +423,8 @@ def setUp(self):
             contexts:
                 -   region: something
                     window:
-                        starting: 2020-01-01T00:00:00Z
-                        ending: 2020-02-01T00:00:00Z
+                        starting: 2020-01-01T00:00:00
+                        ending: 2020-02-01T00:00:00
                     streams:
                         variable1:
                             qartod:
@@ -438,8 +438,8 @@ def setUp(self):
                                     fail_span: [22, 25]
                 -   region: something else
                     window:
-                        starting: 2020-02-01T00:00:00Z
-                        ending: 2020-03-01T00:00:00Z
+                        starting: 2020-02-01T00:00:00
+                        ending: 2020-03-01T00:00:00
                     streams:
                         variable1:
                             qartod: