Merge pull request #54 from ProjectPythia/main

jukent · web-flow · commit 326ae19d5d21 · 2025-02-10T11:58:25.000-07:00
[pull] main from ProjectPythia:main
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -4,8 +4,8 @@ updates:
   #   directory: "/"
   #   schedule:
   #     interval: daily
-  - package-ecosystem: 'github-actions'
-    directory: '/'
+  - package-ecosystem: "github-actions"
+    directory: "/"
     schedule:
       # Check for updates once a week
-      interval: 'weekly'
+      interval: "weekly"
diff --git a/.github/workflows/nightly-build.yaml b/.github/workflows/nightly-build.yaml
@@ -3,7 +3,7 @@ name: nightly-build
 on:
   workflow_dispatch:
   schedule:
-    - cron: '0 0 * * *' # Daily “At 00:00”
+    - cron: "0 0 * * *" # Daily “At 00:00”
 
 jobs:
   build:
diff --git a/.github/workflows/publish-book.yaml b/.github/workflows/publish-book.yaml
@@ -16,5 +16,3 @@ jobs:
   deploy:
     needs: build
     uses: ProjectPythia/cookbook-actions/.github/workflows/deploy-book.yaml@main
-    with:
-      cname: foundations.projectpythia.org
diff --git a/.github/workflows/trigger-preview.yaml b/.github/workflows/trigger-preview.yaml
@@ -17,8 +17,7 @@ jobs:
     with:
       artifact_name: book-zip-${{ needs.find-pull-request.outputs.number }}
       destination_dir: _preview/${{ needs.find-pull-request.outputs.number }} # deploy to subdirectory labeled with PR number
-      is_preview: 'true'
-      cname: foundations.projectpythia.org
+      is_preview: "true"
 
   preview-comment:
     needs: find-pull-request
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -10,7 +10,7 @@ repos:
       - id: double-quote-string-fixer
 
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 25.1.0
     hooks:
       - id: black
 
@@ -20,7 +20,7 @@ repos:
       - id: blackdoc
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
 
@@ -29,17 +29,12 @@ repos:
     hooks:
       - id: seed-isort-config
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
       - id: isort
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.1.0
-    hooks:
-      - id: prettier
-
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.1
+    rev: 1.9.1
     hooks:
       - id: nbqa-black
         additional_dependencies: [black]
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,5 +1,5 @@
 cff-version: 1.2.0
-message: 'If you use this resource, please cite it as below.'
+message: "If you use this resource, please cite it as below."
 authors:
   - family-names: Rose
     given-names: Brian E. J.
@@ -69,6 +69,6 @@ authors:
     orcid: https://orcid.org/0000-0002-2666-8493
     website: https://github.com/anissa111
     affiliation: UCAR/NCAR
-title: 'Pythia Foundations'
+title: "Pythia Foundations"
 version: v2023.05.01
 doi: 10.5281/zenodo.7884571
diff --git a/_config.yml b/_config.yml
@@ -5,7 +5,7 @@ title: Pythia Foundations
 author: the <a href="https://projectpythia.org/">Project Pythia</a> Community
 logo: images/logos/pythia_logo-white-rtext.svg
 email: projectpythia@ucar.edu
-copyright: '2024'
+copyright: "2024"
 
 exclude_patterns:
   - README.md
@@ -91,15 +91,15 @@ sphinx:
   config:
     nb_execution_raise_on_error: true # raise exception in build if there are notebook errors (this flag is ignored if building on binder)
     linkcheck_request_headers:
-      'https://docs.github.com/':
+      "https://docs.github.com/":
         User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:24.0) Gecko/20100101 Firefox/24.0
     html_favicon: images/icons/favicon.ico
-    html_last_updated_fmt: '%-d %B %Y'
+    html_last_updated_fmt: "%-d %B %Y"
     html_theme: sphinx_pythia_theme
     html_permalinks_icon: '<i class="fas fa-link"></i>'
     html_theme_options:
       analytics:
-        google_analytics_id: 'G-G57FLM9M46'
+        google_analytics_id: "G-G57FLM9M46"
       home_page_in_toc: true
       repository_url: https://github.com/ProjectPythia/pythia-foundations # Online location of your book
       repository_branch: main # Which branch of the repository should be used when creating links (optional)
diff --git a/core/data-formats/netcdf-cf.ipynb b/core/data-formats/netcdf-cf.ipynb
@@ -983,7 +983,6 @@
     "\n",
     "- [CF Conventions doc (1.7)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html)\n",
     "- [Jonathan Gregory's old CF presentation](http://cfconventions.org/Data/cf-documents/overview/viewgraphs.pdf)\n",
-    "- [NASA ESDS \"Dataset Interoperability Recommendations for Earth Science\"](https://earthdata.nasa.gov/user-resources/standards-and-references/dataset-interoperability-recommendations-for-earth-science)\n",
     "- [CF Data Model (cfdm) python package tutorial](https://ncas-cms.github.io/cfdm/tutorial.html)\n",
     "- [Tim Whiteaker's cfgeom python package (GitHub repo)](https://github.com/twhiteaker/CFGeom) and [(tutorial)]( https://twhiteaker.github.io/CFGeom/tutorial.html)\n",
     "- [netCDF4 Documentation](https://unidata.github.io/netcdf4-python/)"
@@ -1013,7 +1012,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/core/datetime/datetime.ipynb b/core/datetime/datetime.ipynb
@@ -351,7 +351,7 @@
     "\n",
     "In these examples, we will look at current data pertaining to coastal tides during a [tropical cyclone storm surge](http://www.nhc.noaa.gov/surge/).\n",
     "\n",
-    "The [lunar day](http://oceanservice.noaa.gov/education/kits/tides/media/supp_tide05.html) is 24 hours and 50 minutes; there are two low tides and two high tides in that time duration. If we know the time of the current high tide, we can easily calculate the occurrence of the next low and high tides by using the [timedelta class](https://docs.python.org/3/library/datetime.html#timedelta-objects). (In reality, the *exact time* of tides is influenced by local coastal effects, in addition to the laws of celestial mechanics, but we will ignore that fact for this exercise.)\n",
+    "The [lunar day](https://tidesandcurrents.noaa.gov/glossary.html#lunarday) is 24 hours and 50 minutes; there are two low tides and two high tides in that time duration. If we know the time of the current high tide, we can easily calculate the occurrence of the next low and high tides by using the [timedelta class](https://docs.python.org/3/library/datetime.html#timedelta-objects). (In reality, the *exact time* of tides is influenced by local coastal effects, in addition to the laws of celestial mechanics, but we will ignore that fact for this exercise.)\n",
     "\n",
     "The `timedelta` class is initialized by supplying time duration, usually supplied with [keyword arguments](https://docs.python.org/3/glossary.html#term-argument), to clearly express the length of time. The `timedelta` class allows you to perform arithmetic with dates and times using standard operators (i.e., `+`, `-`, `*`, `/`).  You can use these operators with a `timedelta` object, and either another `timedelta` object, a datetime object, or a numeric literal, to obtain objects representing new dates and times.\n",
     "\n",
@@ -554,7 +554,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/core/overview.md b/core/overview.md
@@ -98,8 +98,8 @@ Increasingly, these individuals and groups
 are formally packaging and releasing their code for use within their community.
 For instance, Andrew Dawson (an atmospheric scientist at Oxford)
 does a lot of EOF analysis and manipulation of wind data,
-so he has released his [eofs](https://ajdawson.github.io/eofs/latest/)
-and [windspharm](https://ajdawson.github.io/windspharm/latest/) libraries
+so he has released his [eofs](https://ajdawson.github.io/eofs/)
+and [windspharm](https://ajdawson.github.io/windspharm/) libraries
 (which are able to handle data arrays from NumPy or Xarray).
 Similarly, a group at the Atmospheric Radiation Measurement (ARM) Climate Research Facility
 have released their Python ARM Radar Toolkit ([Py-ART](http://arm-doe.github.io/pyart/))
diff --git a/core/xarray.md b/core/xarray.md
@@ -1,4 +1,4 @@
-![xarray Logo](https://docs.xarray.dev/en/stable/_static/Xarray_Logo_RGB_Final.svg 'xarray Logo')
+![xarray Logo](https://docs.xarray.dev/en/stable/_static/Xarray_Logo_RGB_Final.svg "xarray Logo")
 
 # Xarray
 
diff --git a/environment.yml b/environment.yml
@@ -13,11 +13,11 @@ dependencies:
   - dask
   - pyproj
   - pythia-datasets
-  - python
+  - python<3.12 # Waiting on https://github.com/jupyter/jupyter_events/issues/99
   - scipy
   - ffmpeg
   - xarray
   - python-graphviz
   - graphviz
-  - setuptools>=69.0.3
+  - setuptools
   - sphinx-pythia-theme
diff --git a/foundations/conda.md b/foundations/conda.md
@@ -31,16 +31,17 @@ Package management is useful because you may want to update a package for one of
 
 ## Installing Conda
 
-We recommend you install Miniconda. You can do that by following the [instructions for your machine](https://docs.conda.io/en/latest/miniconda.html).
+We recommend you install Miniforge. You can do that by following the [instructions for your machine](https://github.com/conda-forge/miniforge).
 
-Miniconda only comes with the `conda` package management system; it is a pared-down version of the full Anaconda Python distribution.
+Miniforge uses the `conda` package management system and is based on Miniconda, which is a pared-down version of the full Anaconda Python distribution.
 
 [Installing Anaconda](https://docs.anaconda.com/anaconda/install/) takes longer and uses up more disk space, but provides you with more functionality, including Spyder (a Python-specific integrated development environment or IDE) and Jupyter, in addition to other immediately installed packages. Also, the interface of Anaconda is great if you are uncomfortable with the terminal.
 
-We recommend Miniconda for two reasons:
+We recommend Miniforge for these reasons:
 
 1. It's quicker and takes up less disk space.
 2. It encourages you to install only the packages you need in reproducible isolated environments for specific projects. This is generally a more robust way to work with open source tools.
+3. It uses `conda-forge` as the default channel for packages, which is our recommended way to get up-to-date, interoperable packages..
 
 Once you have `conda` via the Miniconda installer, the next step is to create an environment and install packages.
 
diff --git a/foundations/jupyter.md b/foundations/jupyter.md
@@ -24,7 +24,7 @@ You'd like to learn to run Python in a Jupyter session. Here we will cover:
 
 To run a Jupyter session, you will need to install some necessary packages into your Conda environment.
 
-Install `miniconda` by following the [instructions for your machine](https://docs.conda.io/en/latest/miniconda.html).
+Install `miniforge` by following the [instructions for your machine](https://github.com/conda-forge/miniforge).
 
 [Learn more about Conda here](conda.md)
 
@@ -41,11 +41,7 @@ $ conda activate pythia_foundations_env
 $ jupyter lab
 ```
 
-Or you can install the full [Anaconda](https://www.anaconda.com/products/distribution), and select **LAUNCH** under the Jupyter panel in the GUI.
-
-![Anaconda Navigator](../images/Anaconda.png)
-
-In both methods, a new window should open automatically in your default browser. You can change the browser when launching from the terminal with (for example):
+A new window should open automatically in your default browser. You can change the browser when launching from the terminal with (for example):
 
 ```
 jupyter lab —browser=chrome
@@ -81,6 +77,15 @@ jupyter lab —browser=chrome
 
 **Congratulations!** You have just set up your first Python environment and run your first Python code in a Jupyter notebook.
 
+<div class="admonition alert alert-info">
+    <p class="admonition-title" style="font-weight:bold">Info</p>
+    There are a few code-syntax differences between running Python in a Jupyter notebook and a script:
+    <ul>
+        <li>In a Python script, to print a variable to the terminal, you need to call <code>print([THING YOU WANT TO PRINT])</code>, whereas in Jupyter, you can simply have the last line of a code cell be <code>[THING YOU WANT TO PRINT]</code>.</li>
+        <li>Similarly with plots, in Python, you have to call <code>plt.show()</code> to display your plot, but plots are shown automatically in Jupyter.</li>
+    </ul>
+</div>
+
 ## Saving your notebook and exiting
 
 When you are done with your work, it is time to save and exit.
@@ -112,4 +117,5 @@ Jupyter notebooks are a free, open-source, interactive tool running inside a web
 
 ## Resources and References
 
-- [Anaconda](https://www.anaconda.com/products/distribution)
+- [conda-forge](https://conda-forge.org)
+- [Miniforge Releases](https://conda-forge.org/miniforge/)
diff --git a/foundations/terminal.md b/foundations/terminal.md
@@ -21,7 +21,7 @@ You'd like to learn to run Python in the terminal. Here we will cover:
 
 ## Installing Python in the Terminal
 
-If you are running Python in the terminal, it is best to install Miniconda. You can do that by following the [instructions for your machine](https://docs.conda.io/en/latest/miniconda.html).
+If you are running Python in the terminal, it is best to install Miniforge. You can do that by following the [instructions for your machine](https://github.com/conda-forge/miniforge).
 
 [Learn more about Conda here](conda.md)
 
diff --git a/preamble/how-to-use.md b/preamble/how-to-use.md
@@ -96,7 +96,7 @@ can be done with two commands from the terminal, one to create the
 environment and one to activate it:
 
 ```
-conda env create --force -f https://raw.githubusercontent.com/ProjectPythia/pythia-foundations/main/environment.yml
+conda env create --yes -f https://raw.githubusercontent.com/ProjectPythia/pythia-foundations/main/environment.yml
 conda activate pythia-book-dev
 ```
 
