adding SCCOOS HABS R notebook

.binder/environment-python_and_r.yml

@@ -2,12 +2,13 @@ name: IOOS
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   - bagit
   - bokeh
   - cartopy
   - cc-plugin-glider
   - cc-plugin-ncei
+  - cf_xarray
   - cftime
   - compliance-checker
   - cython
@@ -22,24 +23,23 @@ dependencies:
   - geopandas
   - gridgeo
   - hvplot
-  - ioos-tools
   - ioos_qc
   - ipyleaflet
   - joblib
   - jupyter
-  - jupyter-book >=0.11.3
-  - jupyter_contrib_nbextensions
-  - jupyter_nbextensions_configurator
+  - jupyter-book >=0.12.1
   - matplotlib-base
   - nbdime
   - nbval
   - nc-time-axis
   - nco
   - oceans
   - oct2py
+  - odvc
   - palettable
   - phantomjs
   - pocean-core
+  - pre-commit
   - pyoos
   - pyresample
   - pysgrid
@@ -50,6 +50,7 @@ dependencies:
   - seaborn
   - selenium
   - sensorml2iso
+  - simplekml
   - siphon
   - sympy
   - thredds_crawler

.binder/environment.yml

@@ -2,15 +2,15 @@ name: IOOS
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   - bagit
   - bokeh
   - cartopy
   - cc-plugin-glider
   - cc-plugin-ncei
+  - cf_xarray
   - cftime
   - compliance-checker
-  - cython
   - descartes
   - easyargs
   - erddapy
@@ -22,24 +22,23 @@ dependencies:
   - geopandas
   - gridgeo
   - hvplot
-  - ioos-tools
   - ioos_qc
   - ipyleaflet
   - joblib
   - jupyter
-  - jupyter-book >=0.11.3
-  - jupyter_contrib_nbextensions
-  - jupyter_nbextensions_configurator
+  - jupyter-book >=0.12.1
   - matplotlib-base
   - nbdime
   - nbval
   - nc-time-axis
   - nco
   - oceans
   - oct2py
+  - odvc
   - palettable
   - phantomjs
   - pocean-core
+  - pre-commit
   - pyoos
   - pyresample
   - pysgrid
@@ -50,6 +49,7 @@ dependencies:
   - seaborn
   - selenium
   - sensorml2iso
+  - simplekml
   - siphon
   - sympy
   - thredds_crawler

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,5 @@
+Thank you for send a Pull Request to our code gallery! When adding or updating a notebook please check if:
+
+- [ ] The notebook has all the dependencies required to run in the IOOS env, if not please update the environment file.
+- [ ] You added a title, description, and a line with `Created: YYYY-MM-DD` in the first cell.
+- [ ] If you are updating a notebook add a line with `Updated: YYYY-MM-DD` below the created date.

.github/workflows/deploy-docs.yml

@@ -1,37 +1,38 @@
 name: Build and Deploy docs
 
 on:
+  pull_request:
   push:
-    branches: [master]
+    branches: [main]
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-    - name: Setup Conda
-      uses: s-weigand/setup-conda@v1
-      with:
-        activate-conda: false
-        conda-channels: conda-forge
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: false
 
-    - name: Build environment
-      shell: bash -l {0}
-      run: |
-         conda create --name IOOS --file .binder/conda-linux-64.lock
-         source activate IOOS
+      - name: Build environment
+        shell: bash -l {0}
+        run: |
+          micromamba create --name IOOS --file .binder/conda-lock.yml
+          micromamba activate IOOS
 
-    - name: Build documentation
-      shell: bash -l {0}
-      run: |
-        set -e
-        source activate IOOS
-        jupyter-book build jupyterbook
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          set -e
+          micromamba activate IOOS
+          jupyter-book build jupyterbook
 
-    - name: GitHub Pages action
-      uses: peaceiris/[email protected]
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: jupyterbook/_build/html
+      - name: GitHub Pages action
+        if: github.ref == 'refs/heads/main'
+        uses: peaceiris/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: jupyterbook/_build/html

.github/workflows/test-env.yml

@@ -0,0 +1,25 @@
+name: Test Environment
+
+on:
+  pull_request:
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: false
+      - name: Build environment
+        shell: bash -l {0}
+        run: |
+          micromamba create --name IOOS --file .binder/conda-lock.yml
+          micromamba activate IOOS
+          python -c 'import osgeo.gdal; print(dir(osgeo.gdal))'

.github/workflows/test_data_access_notebooks.yml

@@ -0,0 +1,28 @@
+name: Test Data Access Notebook
+
+on:
+  pull_request:
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: false
+
+      - name: Build environment
+        shell: bash -l {0}
+        run: |
+          micromamba create --name IOOS --file .binder/conda-lock.yml
+          micromamba activate IOOS
+
+      - name: Notebook tests
+        shell: bash -l {0}
+        run: |
+          micromamba activate IOOS
+          pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_access_notebooks/

.github/workflows/test_data_analysis_and_visualization_notebooks.yml

@@ -0,0 +1,28 @@
+name: Test Data Analysis And Visualization Notebooks
+
+on:
+  pull_request:
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: false
+
+      - name: Build environment
+        shell: bash -l {0}
+        run: |
+          micromamba create --name IOOS --file .binder/conda-lock.yml
+          micromamba activate IOOS
+
+      - name: Notebook tests
+        shell: bash -l {0}
+        run: |
+          micromamba activate IOOS
+          pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/

.github/workflows/test_data_management_notebooks.yml

@@ -0,0 +1,28 @@
+name: Test Data Management Notebooks
+
+on:
+  pull_request:
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: false
+
+      - name: Build environment
+        shell: bash -l {0}
+        run: |
+          micromamba create --name IOOS --file .binder/conda-lock.yml
+          micromamba activate IOOS
+
+      - name: Notebook tests
+        shell: bash -l {0}
+        run: |
+          micromamba activate IOOS
+          pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_management_notebooks/