Catching up with main

Merge branch 'main' into surf_trip

.binder/environment-python_and_r.yml

@@ -21,13 +21,17 @@ dependencies:
   - geojsonio
   - geolinks
   - geopandas
+  - geoplot
   - gridgeo
+  - humanize
   - hvplot
   - ioos_qc
   - ipyleaflet
   - joblib
   - jupyter
+  - jupyter_server <2.0.0
   - jupyter-book >=0.12.1
+  - jupyterlab
   - matplotlib-base
   - nbdime
   - nbval
@@ -38,8 +42,9 @@ dependencies:
   - odvc
   - palettable
   - phantomjs
-  - pocean-core
+  - pocean-core >=3.1
   - pre-commit
+  - pyobis
   - pyoos
   - pyresample
   - pysgrid
@@ -53,13 +58,15 @@ dependencies:
   - simplekml
   - siphon
   - sympy
+  - tabulate
   - thredds_crawler
   - tqdm
   - utide
   - windrose
   - xarray
   - xlrd
   - xmltodict
+  - zarr
   # R packages.
   - rpy2
   - r-base=4

.binder/environment.yml

@@ -20,13 +20,17 @@ dependencies:
   - geojsonio
   - geolinks
   - geopandas
+  - geoplot
   - gridgeo
+  - humanize
   - hvplot
   - ioos_qc
   - ipyleaflet
   - joblib
   - jupyter
+  - jupyter_server <2.0.0
   - jupyter-book >=0.12.1
+  - jupyterlab
   - matplotlib-base
   - nbdime
   - nbval
@@ -37,8 +41,9 @@ dependencies:
   - odvc
   - palettable
   - phantomjs
-  - pocean-core
+  - pocean-core >=3.1
   - pre-commit
+  - pyobis
   - pyoos
   - pyresample
   - pysgrid
@@ -52,10 +57,12 @@ dependencies:
   - simplekml
   - siphon
   - sympy
+  - tabulate
   - thredds_crawler
   - tqdm
   - utide
   - windrose
   - xarray
   - xlrd
   - xmltodict
+  - zarr

.github/ISSUE_TEMPLATE/NEW_NOTEBOOK.yml

@@ -0,0 +1,36 @@
+name: New Notebook
+description: Request to add a new notebook
+title: "[New Notebook]: "
+labels: ["Notebook idea"]
+assignees:
+  - mathewbiddle
+  - ocefpaf
+body:
+  - type: markdown
+    attributes:
+      value: |
+      If you want to suggest a notebook for the [IOOS CodeLab](https://ioos.github.io/ioos_code_lab/content/intro.html#) please answer these questions:
+  - type: input
+    id: language
+    attributes:
+      label: Programming Language
+      description: What programming language(s) will be used in the example?
+      placeholder: Python
+  - type: input
+    id: tool
+    attributes:
+      label: Module/Software/IOOS data service?
+      description: Is it focused on a particular module/software or an IOOS data service?
+      placeholder: ERDDAP
+  - type: input
+    id: example
+    attributes:
+      label: Module/Software/IOOS data service?
+      description: Can you provide a minimum example of the expected code and results in a notebook?
+      placeholder: ""
+  - type: input
+    id: description
+    attributes:
+      label: Provide a description.
+      description: Please provide a detailed description of the suggested example below.
+      placeholder: ""

.github/PULL_REQUEST_TEMPLATE/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/dependabot.yml

@@ -0,0 +1,10 @@
+# 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

@@ -13,26 +13,22 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Setup Micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: false
-
-      - name: Build environment
-        shell: bash -l {0}
-        run: |
-          micromamba create --name IOOS --file .binder/conda-lock.yml
-          micromamba activate IOOS
+          environment-name: IOOS
+          init-shell: bash
+          create-args: >-
+            --file .binder/conda-lock.yml
 
       - name: Build documentation
         shell: bash -l {0}
         run: |
           set -e
-          micromamba activate IOOS
           jupyter-book build jupyterbook
 
       - name: GitHub Pages action
         if: github.ref == 'refs/heads/main'
-        uses: peaceiris/actions-gh-pages@v3.8.0
+        uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: jupyterbook/_build/html

.github/workflows/test-env.yml

@@ -13,13 +13,16 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+
       - 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: IOOS
+          init-shell: bash
+          create-args: >-
+            --file .binder/conda-lock.yml
+
+      - name: Test 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

@@ -11,18 +11,14 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Setup Micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: false
-
-      - name: Build environment
-        shell: bash -l {0}
-        run: |
-          micromamba create --name IOOS --file .binder/conda-lock.yml
-          micromamba activate IOOS
+          environment-name: IOOS
+          init-shell: bash
+          create-args: >-
+            --file .binder/conda-lock.yml
 
       - name: Notebook tests
         shell: bash -l {0}
         run: |
-          micromamba activate IOOS
-          pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_access_notebooks/
+          python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_access_notebooks/

.github/workflows/test_data_analysis_and_visualization_notebooks.yml

@@ -11,18 +11,14 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Setup Micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: false
-
-      - name: Build environment
-        shell: bash -l {0}
-        run: |
-          micromamba create --name IOOS --file .binder/conda-lock.yml
-          micromamba activate IOOS
+          environment-name: IOOS
+          init-shell: bash
+          create-args: >-
+            --file .binder/conda-lock.yml
 
       - name: Notebook tests
         shell: bash -l {0}
         run: |
-          micromamba activate IOOS
-          pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/
+          python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/

.github/workflows/test_data_management_notebooks.yml

@@ -11,18 +11,14 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Setup Micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: false
-
-      - name: Build environment
-        shell: bash -l {0}
-        run: |
-          micromamba create --name IOOS --file .binder/conda-lock.yml
-          micromamba activate IOOS
+          environment-name: IOOS
+          init-shell: bash
+          create-args: >-
+            --file .binder/conda-lock.yml
 
       - name: Notebook tests
         shell: bash -l {0}
         run: |
-          micromamba activate IOOS
-          pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_management_notebooks/
+          python -m pytest --nbval --nbval-lax jupyterbook/content/code_gallery/data_management_notebooks/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: ".binder/conda-lock.yml"
 
 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
@@ -17,25 +17,53 @@ repos:
       - id: double-quote-string-fixer
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+    rev: v3.0.0
     hooks:
       - id: prettier
+        types_or: [html]
         exclude: "_templates/layout.html"
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
-    hooks:
-      - id: flake8
-        exclude: docs/source/conf.py
-        args: [--max-line-length=105]
-
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: v2.3.0
+    rev: v3.0.1
     hooks:
       - id: add-trailing-comma
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.281
+    hooks:
+      - id: ruff
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      # mdformat works on the CLI but not as pre-commit yet.
+      # Use `nbqa mdformat jupyterbook --nbqa-md` to run it locally.
+      # - id: mdformat
+      - id: nbqa-check-ast
+      - id: nbqa-black
+      - id: nbqa-ruff
+        args: [--fix, --extend-ignore=E402]
+        # Skipping b/c These notebooks mix R and Python and
+        # will return false positive for "F821 Undefined name.""
+        exclude: 2017-11-30-rerddap\.ipynb$|2018-02-20-obis.ipynb$
+
+  - repo: https://github.com/bdice/nb-strip-paths
+    rev: 'v0.1.0'
+    hooks:
+      - id: nb-strip-paths
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+    for more information, see https://pre-commit.ci
+  autofix_prs: false
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: []
+  submodules: false

CONTRIBUTING.md

@@ -42,10 +42,10 @@ If you would like to work on a notebook that has been proposed, follow these ste
    1. Notebooks are kept in the [jupyterbook/content/code_gallery](https://github.com/ioos/ioos_code_lab/tree/main/jupyterbook/content/code_gallery) directory of this repository.
       1. There are three directories where notebooks can be placed:
          1. `data_access_notebooks` -
-         2. `data_analysis_and_visualization_notebooks` -
-         3. `data_management_notebooks` -
-   2. Typically, it's best to copy an existing (working) notebook to a new file. If you are creating a python notebook, copy one of the python notebooks. If you are creating an R notebook, copy one of the R notebooks, etc
-   3. Name the notebook following the convention `[date]-[short name].ipynb`. Where, `[date]` is the date (YYYY-MM-DD) you started the new notebook and `[short name]` is an abbreviation for what the notebook will cover. Look at the existing notebook filenames to get a sense of the short names used.
+         1. `data_analysis_and_visualization_notebooks` -
+         1. `data_management_notebooks` -
+   1. Typically, it's best to copy an existing (working) notebook to a new file. If you are creating a python notebook, copy one of the python notebooks. If you are creating an R notebook, copy one of the R notebooks, etc
+   1. Name the notebook following the convention `[date]-[short name].ipynb`. Where, `[date]` is the date (YYYY-MM-DD) you started the new notebook and `[short name]` is an abbreviation for what the notebook will cover. Look at the existing notebook filenames to get a sense of the short names used.
 1. Edit the notebook following the [Jupyter Notebook documentation](https://jupyter-notebook.readthedocs.io/en/stable/notebook.html). The notebook should include the following information:
    1. Descriptive title for what the notebook is doing.
    1. A short summary providing context and expanding on the title.

README.md

@@ -13,7 +13,7 @@ To suggest a notebook or ask questions please open an issue at: https://github.c
 
 [![DOI](https://zenodo.org/badge/399546690.svg)](https://zenodo.org/badge/latestdoi/399546690)
 
----
+______________________________________________________________________
 
 ## Build the JupyterBook locally
 
@@ -24,7 +24,7 @@ To suggest a notebook or ask questions please open an issue at: https://github.c
 ### Requirements:
 
 - Git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
-- Jupyter{Book}: https://jupyterbook.org/intro.html
+- Jupyter\{Book}: https://jupyterbook.org/intro.html
 - Web Browser
 
 ### Installation