Merge pull request #247 from ocefpaf/py313

Upgrade the IOOS environment to Python 3.13
ioos · Dec 16, 2024 · 83c9019 · 83c9019
2 parents e81bbed + 01b7d08
commit 83c9019
Show file tree

Hide file tree

Showing 14 changed files with 14,595 additions and 30,317 deletions.
diff --git a/.binder/conda-lock.yml b/.binder/conda-lock.yml
diff --git a/.binder/environment-python_and_r.yml b/.binder/environment-python_and_r.yml
@@ -2,103 +2,59 @@ name: IOOS
 channels:
   - conda-forge
 dependencies:
-  - python=3.12
-  - bagit
+  - python=3.13
   - bokeh
   - cartopy
-  - cc-plugin-glider
-  - cc-plugin-ncei
   - cf_xarray
-  - cftime
+  - cf-units
   - ckanapi
   - compliance-checker
-  - dask
-  - descartes
-  - easyargs
   - erddapy
-  - flake8
   - folium
-  - geodatasets
-  - geojson
-  - geojsonio
-  - geolinks
+  - gdal
   - geopandas
   - geoplot
-  - gliderpy
   - gridgeo
   - humanize
-  - hvplot
-  - intake
   - ioos_qc
+  - ioos_tools
   - ioos-metrics
   - ipyleaflet
-  - joblib
+  - ipywidgets
   - jupyter
-  - jupyter-book >=0.12.1
-  - jupyterlab
+  - lxml
   - matplotlib-base
   - nbclassic
-  - nbdime
-  - nbval
-  - nc-time-axis
-  - nco
+  - netcdf4
+  - numpy
   - oceans
-  - oct2py
   - odvc
-  - openpyxl
+  - owslib
   - palettable
-  - phantomjs
-  - pocean-core >=3.1
-  - pre-commit
-  - pyarrow
+  - pandas
+  - pocean-core
   - pyobis
   - pyoos
-  - pyresample
   - pysgrid
-  - pytest
   - pyugrid
   - pyworms
-  - rasterio
-  - seaborn
-  - selenium
-  - sensorml2iso
-  - simplekml
-  - siphon
-  - sympy
-  - tabulate
-  - thredds_crawler
+  - requests
+  - retrying
+  - seawater
+  - shapely
   - tqdm
-  - utide
-  - windrose
   - xarray
-  - xmltodict
   - zarr
   # R packages.
-  - rpy2
   - r-base=4
+  - r-irkernel
   - r-dplyr
-  - r-dt
-  - r-finch
-  - r-ggfortify
-  - r-ggplot2
-  - r-gsw
   - r-htmlwidgets
-  - r-httr
-  - r-irkernel
-  - r-lubridate
-  - r-mapdata
-  - r-ncdf4
-  - r-obistools
-  - r-oce
-  - r-rcolorbrewer
+  - r-maps
   - r-readr
-  - r-rerddap
-  - r-reshape2
-  - r-robis>=2.3.9
-  - r-sp
-  - r-xtractomatic
-  - r-xts
+  - r-robis  # hoding osx-arm64
 platforms:
   - linux-64
   - osx-64
+  # - osx-arm64
   - win-64
diff --git a/.binder/environment.yml b/.binder/environment.yml
@@ -3,6 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python=3.13
+  - bokeh
   - cartopy
   - cf_xarray
   - cf-units

diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -10,25 +10,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 #v1
+      - name: Set up Python
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
-          environment-name: IOOS
-          init-shell: bash
-          create-args: >-
-            --file .binder/conda-lock.yml
+          python-version: "3.x"
+
 
       - name: Build documentation
-        shell: bash -l {0}
         run: >
           set -e
+          && pip install jupyter-book
           && jupyter-book build jupyterbook
 
       - name: GitHub Pages action
         if: github.ref == 'refs/heads/main'
-        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e #v4
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: jupyterbook/_build/html
diff --git a/.github/workflows/docs-linkchecker.yml b/.github/workflows/docs-linkchecker.yml
@@ -0,0 +1,32 @@
+name: Check linkrot
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+
+      - name: Set up Python
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        with:
+          python-version: "3.x"
+
+
+      - name: Linkcheck
+        run: >
+          set -e
+          && pip install jupyter-book
+          && jupyter-book build jupyterbook --builder linkcheck
+
+      - name: GitHub Pages action
+        if: github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: jupyterbook/_build/html
diff --git a/.github/workflows/test-env.yml b/.github/workflows/test-env.yml
@@ -1,4 +1,4 @@
-name: Test Environment and link rot
+name: Test Environment
 
 on:
   pull_request:
@@ -8,17 +8,18 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ macos-latest, ubuntu-latest, windows-latest ]
+        # macos-latest is osx-arm64 and the env is not building there yet b/c of robis.
+        os: [ macos-13, ubuntu-latest, windows-latest ]
       fail-fast: false
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 #v1
+        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 # v2.0.3
         with:
           environment-name: IOOS
           init-shell: bash
@@ -28,8 +29,3 @@ jobs:
       - name: Test environment
         run: >
           python -c 'import osgeo.gdal; print(dir(osgeo.gdal))'
-
-      - name: Test links
-        if: startsWith(matrix.os, 'ubuntu')
-        run: >
-          jupyter-book build jupyterbook --builder linkcheck
diff --git a/.github/workflows/test_data_access_notebooks.yml b/.github/workflows/test_data_access_notebooks.yml
@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 #v1
+        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 # v2.0.3
         with:
           environment-name: IOOS
           init-shell: bash
@@ -20,5 +20,6 @@ jobs:
 
       - name: Notebook tests
         shell: bash -l {0}
-        run: |
-          python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_access_notebooks/
+        run: >
+          micromamba install nbval
+          && python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_access_notebooks/
diff --git a/.github/workflows/test_data_analysis_and_visualization_notebooks.yml b/.github/workflows/test_data_analysis_and_visualization_notebooks.yml
@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 #v1
+        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 # v2.0.3
         with:
           environment-name: IOOS
           init-shell: bash
@@ -20,5 +20,6 @@ jobs:
 
       - name: Notebook tests
         shell: bash -l {0}
-        run: |
-          python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/
+        run: >
+          micromamba install nbval
+          && python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/
diff --git a/.github/workflows/test_data_management_notebooks.yml b/.github/workflows/test_data_management_notebooks.yml
@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 #v1
+        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 # v2.0.3
         with:
           environment-name: IOOS
           init-shell: bash
@@ -20,5 +20,6 @@ jobs:
 
       - name: Notebook tests
         shell: bash -l {0}
-        run: |
-          python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_management_notebooks/
+        run: >
+          micromamba install nbval
+          && python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_management_notebooks/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -34,7 +34,7 @@ repos:
       - id: add-trailing-comma
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.3
     hooks:
       - id: ruff
 

diff --git a/jupyterbook/_config.yml b/jupyterbook/_config.yml
@@ -90,6 +90,8 @@ sphinx:
       "./data_management_notebooks/.*",
       "./data_analysis_and_visualization_notebooks/.*",
       "https://www.ncei.noaa.gov/archive/accession/0282699",  # slow
+      "https://gcoos4.tamu.edu/erddap/info/fk_CREMP_yearly_revisited_DATA_v3_1996/index.html", # data is gone
+      "https://gcoos4.tamu.edu/erddap/tabledap/fk_CREMP_yearly_revisited_DATA_v3_1996.html", # data is gone
       ]
     linkcheck_anchors_ignore: ["aboutPanel", "searchPanel", "!forum/ioos_tech"]
     html_show_copyright: false

diff --git a/...allery/data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.ipynb b/...allery/data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.ipynb
@@ -106,7 +106,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To demonstrate the Matlab/Octave notebook we will use a well known toolbox for tidal analysis [`t_tide`](https://www.eoas.ubc.ca/~rich/).\n",
+    "To demonstrate the Matlab/Octave notebook we will use a well known toolbox for tidal analysis [`t_tide`](https://www-old.eoas.ubc.ca/~rich/).\n",
     "First we need to add it to the path."
    ]
   },

diff --git a/...content/code_gallery/data_analysis_and_visualization_notebooks/2024-09-13-OBIS_EOVs.ipynb b/...content/code_gallery/data_analysis_and_visualization_notebooks/2024-09-13-OBIS_EOVs.ipynb
diff --git a/pytest.ini b/pytest.ini
@@ -10,14 +10,18 @@ addopts =
     --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2018-03-15-ssh-skillscore.archived.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2018-03-30-wave_height_assessment.archived.ipynb"
     # Missing library/rely on versions that are too old
-    --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-09-09-hurricane_irma.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2019-05-27-hurricane_gis_part02.ipynb"
+    --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.ipynb"
+    --ignore="jupyterbook/content/code_gallery/data_management_notebooks/2017-11-01-Creating-Archives-Using-Bagit.ipynb"
     # Take too long to run
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2019-03-08-grids-temperature.ipynb"
+    --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2024-09-17-CKAN_API_Query.ipynb"
     # Skipping all the notbooks with the R kernel
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-08-01-xtractoR.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-11-30-rerddap.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2018-02-20-obis.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2017-01-23-R-notebook.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2024-05-16-white_shark_water_temp.ipynb"
+    # ERDDAP 403
+    --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2021-10-25-ERDDAP-interpolate.ipynb"