Merge pull request #128 from ocefpaf/use_ruff

use ruff linter

.github/ISSUE_TEMPLATE.md

@@ -1,8 +1,8 @@
 If you are opening an issue regarding an existing notebook/code or the webpage just ignore the instructions below.
 If you want to suggest a notebook for the code gallery please answer these questions:
 
-- [ ] What is language(s) for used in the example?
-- [ ] Is it focused on a particular module/software or an IOOS data service?
-- [ ] Can you provide a minimum example of the expected code and results in a notebook?
+- \[ \] What is language(s) for used in the example?
+- \[ \] Is it focused on a particular module/software or an IOOS data service?
+- \[ \] Can you provide a minimum example of the expected code and results in a notebook?
 
 Please provide a detailed description of the suggested example below:

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +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.
+- \[ \] 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.

.pre-commit-config.yaml

@@ -20,15 +20,9 @@ repos:
     rev: v3.0.0-alpha.6
     hooks:
       - id: prettier
+        types_or: [html]
         exclude: "_templates/layout.html"
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        exclude: docs/source/conf.py
-        args: [--max-line-length=105]
-
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
@@ -40,6 +34,25 @@ repos:
     hooks:
       - id: add-trailing-comma
 
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.254
+    hooks:
+      - id: ruff
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.6.3
+    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$|2018-02-20-obis.ipynb$
+
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit.com hooks

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

jupyterbook/content/Video_Demo_Markdown/glos.md

@@ -1,9 +1,11 @@
 # GLOS Links
 
 ```{image} ../../images/GLOS.png
-:alt: IOOS
-:width: 150px
-:align: center
+---
+alt: IOOS
+width: 150px
+align: center
+---
 ```
 
 - [How to use the GLOS data portal](https://www.youtube.com/playlist?list=PLEK-mxRrHSZ5LkSSUyYHEy4lEXnEdNJJc)

jupyterbook/content/Video_Demo_Markdown/ioos.md

@@ -1,9 +1,11 @@
 # IOOS
 
 ```{image} ../../images/placeholder.png
-:alt: IOOS
-:width: 150px
-:align: center
+---
+alt: IOOS
+width: 150px
+align: center
+---
 ```
 
 - [COMT Tutorial](https://www.youtube.com/watch?v=Dqc1C1HeemQ)

jupyterbook/content/Video_Demo_Markdown/nanoos.md

@@ -1,9 +1,11 @@
 # NANOOS
 
 ```{image} ../../images/NANOOS.png
-:alt: IOOS
-:width: 150px
-:align: center
+---
+alt: IOOS
+width: 150px
+align: center
+---
 ```
 
 - [NANOOS Visualization System](https://www.youtube.com/watch?v=MEVz0jOsqmI)

jupyterbook/content/Video_Demo_Markdown/ooi.md

@@ -1,9 +1,11 @@
 # OOI Demonstration Videos
 
 ```{image} ../../images/OOI_Logo.png
-:alt: IOOS
-:width: 150px
-:align: center
+---
+alt: IOOS
+width: 150px
+align: center
+---
 ```
 
 - [Demo of OOI ERDDAP endpoint](https://www.youtube.com/watch?v=tj4M9hodTG0)

jupyterbook/content/Video_Demo_Markdown/python_dem.md

@@ -1,9 +1,11 @@
 # Python Demonstration Videos
 
 ```{image} ../../images/python.png
-:alt: IOOS
-:width: 150px
-:align: center
+---
+alt: IOOS
+width: 150px
+align: center
+---
 ```
 
 - [Catalog Driven Reproducible Workflows for Ocean-science](https://www.youtube.com/watch?v=05ax0lkQFrg)

jupyterbook/content/code_gallery/data_access.md

@@ -12,12 +12,10 @@ Matlab, R, etc).
 
 For more information on accessing IOOS data, see <https://ioos.noaa.gov/data/access-ioos-data/>.
 
----
+______________________________________________________________________
 
 ## Chapter table of contents
 
 ```{tableofcontents}
 
 ```
-
----

jupyterbook/content/code_gallery/data_access_notebooks/2016-10-12-fetching_data.ipynb

@@ -28,7 +28,6 @@
    "source": [
     "from erddapy import ERDDAP\n",
     "\n",
-    "\n",
     "e = ERDDAP(\n",
     "    server=\"https://opendap.co-ops.nos.noaa.gov/erddap\",\n",
     "    protocol=\"tabledap\",\n",
@@ -39,7 +38,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The geographical bounding box includes all the states in the [SECOORA](http://secoora.org/) region: Florida, Georgia, South and North Carolina. "
+    "The geographical bounding box includes all the states in the [SECOORA](http://secoora.org/) region: Florida, Georgia, South and North Carolina."
    ]
   },
   {
@@ -142,14 +141,15 @@
    "source": [
     "import folium\n",
     "\n",
-    "\n",
     "lon = (min_lon + max_lon) / 2\n",
     "lat = (min_lat + max_lat) / 2\n",
     "\n",
     "m = folium.Map(location=[lat, lon], tiles=\"OpenStreetMap\", zoom_start=5)\n",
     "\n",
-    "folium.Polygon([(min_lat,min_lon), (max_lat,min_lon), (max_lat,max_lon), (min_lat,max_lon)],\n",
-    "              fill=True).add_to(m)\n",
+    "folium.Polygon(\n",
+    "    [(min_lat, min_lon), (max_lat, min_lon), (max_lat, max_lon), (min_lat, max_lon)],\n",
+    "    fill=True,\n",
+    ").add_to(m)\n",
     "\n",
     "m"
    ]
@@ -158,7 +158,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Unfortunately, as you'll notice below, adding the bounding box as a constraint won't help because this ERDDAP server requires the `STATION_ID` number as a mandatory argument for the request. "
+    "Unfortunately, as you'll notice below, adding the bounding box as a constraint won't help because this ERDDAP server requires the `STATION_ID` number as a mandatory argument for the request."
    ]
   },
   {
@@ -225,7 +225,6 @@
    "source": [
     "import pandas as pd\n",
     "\n",
-    "\n",
     "df = pd.read_csv(e.get_search_url(response=\"csv\"))\n",
     "df[\"Dataset ID\"]"
    ]
@@ -258,9 +257,7 @@
     "\n",
     "e.dataset_id = dataset_id\n",
     "\n",
-    "variables = e.get_var_by_attr(\n",
-    "    standard_name=std_name\n",
-    ")\n",
+    "variables = e.get_var_by_attr(standard_name=std_name)\n",
     "\n",
     "print(f\"Found {','.join(variables)} variable(s) in the dataset.\")\n",
     "\n",
@@ -399,7 +396,11 @@
     }
    ],
    "source": [
-    "print(station_id_info.loc[station_id_info[\"Attribute Name\"] == \"comment\"][\"Value\"].squeeze())"
+    "print(\n",
+    "    station_id_info.loc[station_id_info[\"Attribute Name\"] == \"comment\"][\n",
+    "        \"Value\"\n",
+    "    ].squeeze()\n",
+    ")"
    ]
   },
   {
@@ -425,10 +426,7 @@
     ")[[\"name\", \"ID\"]]\n",
     "\n",
     "\n",
-    "locations = pd.read_xml(\n",
-    "    url,\n",
-    "    xpath=\"//*[contains(name(),\\\"location\\\")]\"\n",
-    ")\n",
+    "locations = pd.read_xml(url, xpath='//*[contains(name(),\"location\")]')\n",
     "\n",
     "df = pd.concat([names, locations], axis=1)"
    ]
@@ -455,15 +453,17 @@
    ],
    "source": [
     "mask = (\n",
-    "    (df[\"lat\"] >= min_lat) &\n",
-    "    (df[\"lat\"] <= max_lat) &\n",
-    "    (df[\"long\"] >= min_lon) &\n",
-    "    (df[\"long\"] <= max_lon)\n",
+    "    (df[\"lat\"] >= min_lat)\n",
+    "    & (df[\"lat\"] <= max_lat)\n",
+    "    & (df[\"long\"] >= min_lon)\n",
+    "    & (df[\"long\"] <= max_lon)\n",
     ")\n",
     "\n",
     "df = df[mask]\n",
     "\n",
-    "print(f\"We filtered out all stations but those from {', '.join(filter(None, set(df['state'])))} states.\")"
+    "print(\n",
+    "    f\"We filtered out all stations but those from {', '.join(filter(None, set(df['state'])))} states.\"\n",
+    ")"
    ]
   },
   {
@@ -640,11 +640,12 @@
     "import matplotlib\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "\n",
     "station_ids = df.loc[df[\"state\"] == \"NC\"][\"ID\"]\n",
     "\n",
     "with matplotlib.style.context([\"seaborn-notebook\", \"seaborn-darkgrid\"]):\n",
-    "    fix, axes = plt.subplots(nrows=len(station_ids), sharex=True, sharey=True, figsize=(11, 2.25 * 5))\n",
+    "    fix, axes = plt.subplots(\n",
+    "        nrows=len(station_ids), sharex=True, sharey=True, figsize=(11, 2.25 * 5)\n",
+    "    )\n",
     "\n",
     "    for k, station_id in enumerate(station_ids):\n",
     "        series = water_level[station_id]\n",

jupyterbook/content/code_gallery/data_access_notebooks/2016-11-15-glider_data_example.ipynb

@@ -33,9 +33,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import xarray as xr\n",
     "import cf_xarray\n",
     "\n",
+    "print(cf_xarray.__version__)\n",
+    "import xarray as xr\n",
     "\n",
     "xr.set_options(keep_attrs=True)\n",
     "ds = xr.open_dataset(url)"
@@ -619,7 +620,6 @@
    "source": [
     "import folium\n",
     "\n",
-    "\n",
     "tiles = (\n",
     "    \"http://services.arcgisonline.com/arcgis/rest/services/\"\n",
     "    \"World_Topo_Map/MapServer/MapServer/tile/{z}/{y}/{x}\"\n",
@@ -657,7 +657,6 @@
     "import numpy as np\n",
     "import numpy.ma as ma\n",
     "\n",
-    "\n",
     "# Find the deepest profile.\n",
     "idx = np.nonzero(~ma.masked_invalid(temp[:, -1]).mask)[0][0]\n",
     "\n",
@@ -691,7 +690,6 @@
    "source": [
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "\n",
     "ncols = 3\n",
     "fig, (ax0, ax1, ax2) = plt.subplots(\n",
     "    sharey=True, sharex=False, ncols=ncols, figsize=(3.25 * ncols, 5)\n",
@@ -749,9 +747,7 @@
     "    return np.r_[0, np.cumsum(dist)]\n",
     "\n",
     "\n",
-    "def plot_glider(\n",
-    "    x, y, z, t, data, cmap=plt.cm.viridis, figsize=(11, 3.75)):\n",
-    "\n",
+    "def plot_glider(x, y, z, t, data, cmap=plt.cm.viridis, figsize=(11, 3.75)):\n",
     "    fig, ax = plt.subplots(figsize=figsize)\n",
     "    dist = distance(x, y, units=\"km\")\n",
     "    z = np.abs(z)\n",
@@ -818,7 +814,6 @@
    "source": [
     "from palettable import cmocean\n",
     "\n",
-    "\n",
     "haline = cmocean.sequential.Haline_20.mpl_colormap\n",
     "thermal = cmocean.sequential.Thermal_20.mpl_colormap\n",
     "dense = cmocean.sequential.Dense_20.mpl_colormap\n",
@@ -871,7 +866,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.11.0"
   }
  },
  "nbformat": 4,