diff --git a/.github/workflows/publish-site.yaml b/.github/workflows/publish-site.yaml index b2bcec23..adcc7e9b 100644 --- a/.github/workflows/publish-site.yaml +++ b/.github/workflows/publish-site.yaml @@ -30,6 +30,7 @@ jobs: with: name: repo-zip path: . + include-hidden-files: 'true' build: needs: automate-metrics @@ -47,5 +48,4 @@ jobs: needs: build uses: ProjectPythia/cookbook-actions/.github/workflows/deploy-book.yaml@main with: - cname: projectpythia.org publish_dir: 'portal/_build/html' diff --git a/.github/workflows/sphinx-link-checker.yaml b/.github/workflows/sphinx-link-checker.yaml index d0331783..96ce4326 100644 --- a/.github/workflows/sphinx-link-checker.yaml +++ b/.github/workflows/sphinx-link-checker.yaml @@ -33,14 +33,12 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Setup Mambaforge + - name: Setup Miniforge uses: conda-incubator/setup-miniconda@v2 with: - miniforge-variant: Mambaforge miniforge-version: latest python-version: "3.10" # binderbot is failing with python 3.11 activate-environment: ${{ inputs.environment_name }} - use-mamba: true - name: Set cache date if: inputs.use_cached_environment == 'true' @@ -60,8 +58,8 @@ jobs: (inputs.use_cached_environment != 'true' || steps.cache.outputs.cache-hit != 'true') run: | - mamba env update -n ${{ inputs.environment_name }} -f ${{ inputs.environment_file }} - mamba install -c conda-forge sphinxcontrib-applehelp=1.0.4 sphinxcontrib-devhelp=1.0.2 sphinxcontrib-htmlhelp=2.0.1 sphinxcontrib-qthelp=1.0.3 sphinxcontrib-serializinghtml=1.1.5 + conda env update -n ${{ inputs.environment_name }} -f ${{ inputs.environment_file }} + conda install -c conda-forge sphinxcontrib-applehelp=1.0.4 sphinxcontrib-devhelp=1.0.2 sphinxcontrib-htmlhelp=2.0.1 sphinxcontrib-qthelp=1.0.3 sphinxcontrib-serializinghtml=1.1.5 - name: Check external links run: | diff --git a/.github/workflows/trigger-preview.yaml b/.github/workflows/trigger-preview.yaml index f914d8b2..c3aea861 100644 --- a/.github/workflows/trigger-preview.yaml +++ b/.github/workflows/trigger-preview.yaml @@ -19,7 +19,6 @@ jobs: artifact_name: book-zip-${{ 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: projectpythia.org publish_dir: 'portal/_build/html' preview-comment: diff --git a/.github/workflows/update-resource-gallery.yaml b/.github/workflows/update-resource-gallery.yaml index ab1e9371..650e85cc 100644 --- a/.github/workflows/update-resource-gallery.yaml +++ b/.github/workflows/update-resource-gallery.yaml @@ -95,10 +95,15 @@ jobs: resource_gallery_file = 'portal/resource_gallery.yaml' with open(submission_file, 'r') as file: - data = json.load(file) + new_data = json.load(file) + + with open(resource_gallery_file, 'r') as yaml_file: + existing_data = yaml.load(yaml_file, Loader=yaml.SafeLoader) or [] + + existing_data.append(new_data) with open(resource_gallery_file, 'w') as yaml_file: - yaml.dump(data, yaml_file) + yaml.dump(existing_data, yaml_file, default_flow_style=False) - name: Run pre-commit hooks run: | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cc2bbd21..adffb9d0 100644 --- 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: v4.6.0 + 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: 24.8.0 + rev: 25.1.0 hooks: - id: black @@ -25,12 +25,12 @@ repos: - id: flake8 - repo: https://github.com/PyCQA/isort - rev: 5.13.2 + rev: 6.0.0 hooks: - id: isort - repo: https://github.com/nbQA-dev/nbQA - rev: 1.8.7 + rev: 1.9.1 hooks: - id: nbqa-black - id: nbqa-pyupgrade diff --git a/CODEOFCONDUCT.md b/CODEOFCONDUCT.md index ec9da685..7ce2932b 100644 --- a/CODEOFCONDUCT.md +++ b/CODEOFCONDUCT.md @@ -43,7 +43,11 @@ Project administrators are responsible for clarifying the standards of acceptabl ## Reporting -Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as outlined in the Consequences section below. +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the @ProjectPythia/core GitHub handle and/or projectpythia@ucar.edu as the community leaders in charge of these can view and manage the reported content, and hence are responsible for enforcement as outlined in the Consequences section below. + +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the reporter of any incident. ## Consequences diff --git a/portal/_static/custom.css b/portal/_static/custom.css index bb94f5ab..ec39ae44 100644 --- a/portal/_static/custom.css +++ b/portal/_static/custom.css @@ -3,10 +3,13 @@ } .bd-main .bd-content .bd-article-container { - max-width: 100%; /* default is 60em */ + max-width: 100%; + /* default is 60em */ } + .bd-page-width { - max-width: 100%; /* default is 88rem */ + max-width: 100%; + /* default is 88rem */ } .sd-card-footer { @@ -20,7 +23,8 @@ main.banner-main #project-pythia { } main.banner-main #project-pythia p { - font-size: 1.4rem; /* default: 1.25rem * / + font-size: 1.4rem; + /* default: 1.25rem * / /* font-weight: 700; default: 300 */ } @@ -163,7 +167,7 @@ details.sd-dropdown { box-shadow: none !important; } -details.sd-dropdown summary.sd-card-header + div.sd-summary-content { +details.sd-dropdown summary.sd-card-header+div.sd-summary-content { background-color: white !important; border: 0.2rem solid var(--pst-sd-dropdown-color) !important; border-radius: calc(.25rem - 1px); @@ -195,18 +199,33 @@ p { margin-bottom: 1rem; } -html[data-theme="dark"] h1.display-1 { - color: white; +/* Set a light color for text throughout in dark mode */ +html[data-theme="dark"] body { + color: #e0e0e0; + /* Light gray */ } -html[data-them="dark"] h4.display-4.p-0 { - color: black !important; +/* Ensure links are visible */ +html[data-theme="dark"] a { + color: #b0c4de; + /* Light blue */ } +/* Target specific elements that need adjustment */ html[data-theme="dark"] .sd-card-body.docutils { - background-color: white; -} - -html[data-theme="dark"] .container p { - color: black !important; + background-color: #202020; + /* Darker gray background for cards */ + color: #e0e0e0; + /* Light gray text in cards */ +} + +/* Adjust headings if necessary */ +html[data-theme="dark"] h1, +html[data-theme="dark"] h2, +html[data-theme="dark"] h3, +html[data-theme="dark"] h4, +html[data-theme="dark"] h5, +html[data-theme="dark"] h6 { + color: #f5f5f5; + /* Almost white for headings */ } diff --git a/portal/_static/images/posts/IMG_5686.jpeg b/portal/_static/images/posts/IMG_5686.jpeg new file mode 100644 index 00000000..a8c7acb3 Binary files /dev/null and b/portal/_static/images/posts/IMG_5686.jpeg differ diff --git a/portal/_static/images/posts/IMG_5854.jpeg b/portal/_static/images/posts/IMG_5854.jpeg new file mode 100644 index 00000000..d0c4c467 Binary files /dev/null and b/portal/_static/images/posts/IMG_5854.jpeg differ diff --git a/portal/_static/images/posts/IMG_6055.jpeg b/portal/_static/images/posts/IMG_6055.jpeg new file mode 100644 index 00000000..7ffa5909 Binary files /dev/null and b/portal/_static/images/posts/IMG_6055.jpeg differ diff --git a/portal/_static/images/posts/IMG_6546.jpg b/portal/_static/images/posts/IMG_6546.jpg new file mode 100644 index 00000000..531ef18a Binary files /dev/null and b/portal/_static/images/posts/IMG_6546.jpg differ diff --git a/portal/about.md b/portal/about.md index 1f05ea97..d0db6c0e 100644 --- a/portal/about.md +++ b/portal/about.md @@ -63,6 +63,7 @@ To learn more about Project Pythia and its history, see this list of presentatio | Forum | Date | Presenter | Format | Title (with link) | | --- | --- | --- | --- | --- | +| Pangeo Showcase | 2024-10 | Brian Rose | slides | [Project Pythia Cookbooks: Challenges and progress in breaking down barriers to Open Science](https://docs.google.com/presentation/d/1-RS9DviJnOzwlRMNv1786UMYJ8PmQU-ohu0vo51NM0Q/edit?usp=sharing) | | Ocean Sciences | 2024-02 | Brian Rose | slides | [The Project Pythia Cookbook Initiative](https://docs.google.com/presentation/d/1tvABElX-0CgiuzMfY7XFY-gsXzGUXqWV6k2qJeTw5bk/edit?usp=sharing) | | AMS | 2024-01 | Drew Camron | slides | [Project Pythia: Three Years of Community Building Through Open Source Technology and Education](https://drive.google.com/file/d/1nZfWWozBKQzVCYpKUqWPX51MEgSAhgfM/view?usp=sharing) | | AMS | 2024-01 | Kevin Tyle | slides | [Cooking up a Storm with Project Pythia](https://docs.google.com/presentation/d/1zMsoCg1RMHGZDuLLV0QsZB6NwKE7CKo5_8iFAGDGj6o/edit?usp=drive_link) | diff --git a/portal/index.md b/portal/index.md index 6b1cd91a..0962ca87 100644 --- a/portal/index.md +++ b/portal/index.md @@ -9,9 +9,17 @@ An education and training hub for the geoscientific Python community +

+ + + Round-up of new Cookbooks from our 2024 Cook-off hackathon! + +
+ Donate to support Project Pythia! +
[Project Pythia](about) is the education working group for [Pangeo](https://pangeo.io) and is an educational resource for the entire geoscience community. diff --git a/portal/posts/binderhub_status.md b/portal/posts/binderhub_status.md new file mode 100644 index 00000000..0bdc87ba --- /dev/null +++ b/portal/posts/binderhub_status.md @@ -0,0 +1,12 @@ +--- +blogpost: true +date: Jan 20, 2025 +author: Kevin Tyle +tags: ["binderhub", "maintenance"] +--- + +# binder.projectpythia.org Maintenance + +Our [BinderHub](https://binder.projectpythia.org) will be offline from **1400 UTC 20 Jan 2025** through **1500 UTC 20 Jan 2025**. + +Our [alternate BinderHub](https://binder.pythia.2i2c.cloud) will be available as normal during that time. diff --git a/portal/posts/new-cookbooks.md b/portal/posts/new-cookbooks.md new file mode 100644 index 00000000..b78a418e --- /dev/null +++ b/portal/posts/new-cookbooks.md @@ -0,0 +1,191 @@ +--- +blogpost: true +date: Jan 10, 2025 +author: Brian Rose +tags: cook-off +--- + +# Hello world, new Cookbooks! + +The Project Pythia team is excited to announce the publication of new community-contributed Cookbooks from our successful [2024 Pythia Cook-Off hackathon](https://projectpythia.org/pythia-cookoff-2024/), which was held June 11 - 14 2024, at the NSF NCAR's Mesa Lab in Boulder, Colorado and online. + +[Cookbooks](https://cookbooks.projectpythia.org) are geoscience-flavored collections of tutorials, recipes, and reproducible example workflows for Python-based data analysis and visualization. Cookbooks are supported by a rich computational infrastructure enabling collaborative authoring, automated health-checking, and interactive use. Cookbooks undergo a review process, are citable by DOI, and are tested and maintained by the Project Pythia community. + +It's time to celebrate the Cook-off projects that have made it across the finish line. *[Watch this space!](https://cookbooks.projectpythia.org)* There are several more exciting Cookbooks still in development. + +## Cookbook round-up + +Here you can find brief descriptions and links to the new (and significantly updated) books on the [Pythia Cookbook Gallery](https://cookbooks.projectpythia.org). Try also filtering the [gallery](https://cookbooks.projectpythia.org) with the new "events" dropdown menu! + + +### [EOFs Cookbook](https://projectpythia.org/eofs-cookbook/) + +EOF cookbook thumbnail + +**Authors:** [Robert Ford](https://github.com/r-ford) + +[![DOI](https://zenodo.org/badge/656765685.svg)](https://zenodo.org/badge/latestdoi/656765685) + +This Cookbook covers Empirical Orthogonal Function (EOF) analysis and its application to climate data. EOF analysis is an essential tool for studying the variability of the atmosphere-ocean system. Meteorological and oceanographic data is noisy and multidimensional, but an EOF analysis allows us to pull out patterns from the data that might otherwise be difficult to find. The goal of this cookbook is to provide background and context to the analysis alongside practical examples of carrying out the analysis using Python packages. + +**Contributors:** + + + + + +### [Ocean Biogeochemistry Cookbook](https://projectpythia.org/ocean-bgc-cookbook/) + + + +**Authors:** [Lev Romashkov](https://github.com/rmshkv) and [Kristen Krumhardt](https://github.com/kristenkrumhardt) + +DOI + +This Cookbook covers working with various sources of ocean biogeochemistry data, including Community Earth System Model (CESM) output and observational data. It provides a brief introduction to some metrics important to ocean biogeochemistry, from physical quantities like temperature to biological quantities like plankton biomass. It also demonstrates some of the data science techniques used to work with this information, and provides an introduction to the relationship between modeled and observational estimates. + +**Contributors:** + + + + + +### [Investigating interhemispheric precipitation changes over the past millennium](https://projectpythia.org/paleoPCA-cookbook/) + +LinkedEarth Logo + +**Authors:** [Deborah Khider](https://github.com/khider), [Hari Sundar](https://github.com/sriharisundar), and [Varun Ratnakar](https://github.com/varunratnakar) + +[![DOI](https://zenodo.org/badge/813352705.svg)](https://zenodo.org/badge/latestdoi/813352705) + +This Cookbook covers paleoclimate model-data comparison using spatio-temporal pattern obtained using Principal Component Analysis (PCA). + +Paleoclimate observations obtained from tree rings or the geochemical composition of speleothems, ice and sediments provide an out-of-sample validation of climate models. However, comparing the output of climate models directly with the paleoclimate observations is difficult: (1) they are often expressed in different quantities (i.e., temperature vs ring width), (2) paleoclimate observations have large time uncertainties, (3) paleoclimate observations often incorporate more than one environmental signal (i.e., temperature AND moisture). + +Recently, [Steinman et al. (2022)](https://doi.org/10.1073/pnas.2120015119) used PCA analysis to compare model and data output. Here, we use a similar approach with the [CESM Last Millennium simulation](https://www2.cesm.ucar.edu/models/cesm1.2/) and proxy records stored on the [LiPDverse](https://lipdverse.org). This repository contains paleoclimate datasets that have been curated by the community and are archived in a standard format, facilitating analysis. + + +**Contributors:** + + + + + +### [ESGF Cookbook](https://projectpythia.org/esgf-cookbook/) + +thumbnail + +**Authors:** [Max Grover](@mgrover1), [Nathan Collier](@nocollier), [Carsten Ehbrecht](@cehbrecht), [Jacqueline Nugent](@jacnugent), and [Gerardo Rivera Tello](@griverat) + +[![DOI](https://zenodo.org/badge/721319801.svg)](https://doi.org/10.5281/zenodo.11663067) + +This Cookbook covers how to access and analyze datasets that can be accessed from Earth System Grid Federation (ESGF) cyberinfrastructure. + +This cookbook focuses on highlighting analysis recipes, as well as data acccess methods, all accesible within the Python programming language. This cookbook also spans beyond the scope of a single Climate Model Intercomparison Project (ex. CMIP6), expanding to other experiments/datasets such as CMIP5 and obs4MIPs. + +**Contributors:** + + + + +### [Radar Cookbook](https://projectpythia.org/radar-cookbook/) + +radar thumbnail + +**Authors:** [Max Grover](https://github.com/mgrover1), [Zachary Sherman](https://github.com/zssherman), [Milind Sharma](https://github.com/gewitterblitz), [Alfonso Ladino](https://github.com/aladinor), [Crystal Camron](https://github.com/crystalclearwx), and [Takashi Unuma](https://github.com/TakashiUNUMA) + +[![DOI](https://zenodo.org/badge/479066261.svg)](https://zenodo.org/badge/latestdoi/479066261) + +Pythia's very first cookbook continues to grow! + +This cookbook provides the essential materials to learning how to work with weather radar data using Python. Most of the curriculum is focused around the Python ARM Toolkit. Once you go through this material, you will have the skills to read in radar data, apply data corrections, and visualize your data, building off of the core foundational Python material covered in the Foundations Book + +The Example Workflows section contains a growing collection of real-world case studies. + +**Contributors:** + + + + + +### [ARCO ERA-5 Interactive Visualization Cookbook](https://projectpythia.org/ERA5_interactive-cookbook/) + +ERA5 thumbnail + +**Authors:** [Kevin Tyle](https://github.com/ktyle), [Michael Barletta](https://github.com/Michael-Barletta), [Negin Sobhani](https://github.com/negin513), [Nicholas Cote](https://github.com/ncote) , [Harsha Hampapura](https://github.com/hrhampapura) , and [Philip Chmielowiec](https://github.com/philip2c) + +[![DOI](https://zenodo.org/badge/657280462.svg)](https://zenodo.org/badge/latestdoi/657280462) + +This Cookbook covers accessing, regridding, and visualizing the [ECMWF Reanalysis version 5](https://www.ecmwf.int/en/forecasts/dataset/ecmwf-reanalysis-v5) (aka **ERA-5**) dataset in a [Analysis Ready, Cloud Optimized](https://www.frontiersin.org/articles/10.3389/fclim.2021.782909/full) (aka **ARCO**) format. + +The ERA-5 represents the current state-of-the-art meteorological reanalysis, extending from well back into the 20th century to the present. While the data is freely-available for download by archival centers such as [Copernicus](https://www.copernicus.eu/en) and [RDA](https://rda.ucar.edu/), the data format and directory structure are typically not well-suited for interactive exploration. Specifically, parameters of interest are stored in individual files, for a limited period of time. + +A team at Google Cloud and Research has made interactive exploration much more tenable by representing the data in [Zarr](https://zarr.readthedocs.io/en/stable/) format. + +This Cookbook demonstrates how to do the following: + +1. Access parameters of interest from the Zarr store on Google Cloud +2. Regrid from model native (Gaussian) to lat-lon (Cartesian) coordinates +3. Plot a map at a specific time using Matplotlib and Cartopy +4. Create interactive visualizations, leveraging the [Holoviz](https://holoviz.org) ecosystem + + +**Contributors:** + + + + +### [Wavelet Cookbook](https://projectpythia.org/wavelet-cookbook/) + +Wavelet thumbnail + +**Authors:** [Cora Schneck](https://github.com/cyschneck) + +[![DOI](https://zenodo.org/badge/815311051.svg)](https://zenodo.org/badge/latestdoi/815311051) + +This Cookbook covers how to work with wavelets in Python. Wavelets are a powerful tool to analyze time-series data. When data frequencies vary over time, wavelets can be applied to analysis trends and overcome the time/frequency limitations of Fourier Transforms + +**Contributors:** + + + + + +## The 2024 Cook-off + +### In pictures + +2024 Cookoff group photo +
+Breakout group +Cookoff attendees at Mesa Lab +Virtual presentation + +### By the numbers + +- Number of attendees: 92 (49 in-person, 43 remote) +- Number of attendees receiving travel support from Project Pythia: 16 +- Career stage: + - 14% undergrad + - 29% graduate + - 14% postdoc + - 43% faculty or staff +- Gender of attendees: + - 59% men + - 30% women + - 11% other +- Number of individual project breakout groups: 9 +- New cookbooks published to the [Pythia Gallery](https://cookbooks.projectpythia.org): 5 _(as of this writing)_ +- Heavily revised cookbooks: 2 + +## Want to get involved? + + + SAVE THE DATE! Project Pythia is hosting our next Cookbook Cook-off hackathon event at the NSF NCAR's Mesa Lab, August 5-8 2025. + + +Do you have some feedback or ideaa for a new Cookbook project? Unsure how to get started? We'd love to hear from you at any of our [open meetings](https://projectpythia.org/#monthly-pythia-meetings), through the [Pangeo Discourse](https://discourse.pangeo.io/c/education/project-pythia/), or via any of our social media. Join us at our next Cook-off 2025! + +Take a look at our [guide for Cookbook contributors](https://projectpythia.org/cookbook-guide.html). diff --git a/portal/resource_gallery.yaml b/portal/resource_gallery.yaml index 65dc3a41..70fefa7f 100644 --- a/portal/resource_gallery.yaml +++ b/portal/resource_gallery.yaml @@ -1496,7 +1496,8 @@ - matplotlib - numpy - pandas - formats: code + formats: + - code domains: - Earth System Science - Chemical Oceanography @@ -1505,7 +1506,7 @@ url: https://podaac.github.io/tutorials/ description: | A place to find NASA ocean, climate, and surface water data recipes and tutorials for the Physical Oceanography Distributed Active Archive Center (PO.DAAC) datasets, tools & services! - thumbnail: https://github.com/podaac/tutorials/blob/master/images/podaac_cookbook_thumbnail.png + thumbnail: https://raw.githubusercontent.com/podaac/tutorials/master/images/podaac_cookbook_thumbnail.png authors: - name: PO.DAAC Team affiliation: Jet Propulsion Laboratory, California Institute of Technology @@ -1531,58 +1532,14 @@ description: Xarray extension for unstructured climate and global weather data thumbnail: https://raw.githubusercontent.com/UXARRAY/uxarray/921dd8f42f661692f0cec170ee5c7dbedb294237/docs/_static/images/logos/uxarray_logo_v_dark.svg authors: - - name: Aaron Zedwick - affiliation: Liberty University - affiliation_url: https://www.liberty.edu/ - - name: Amber Chen - - name: Anissa Zacharias - affiliation: NSF National Center for Atmospheric Research - affiliation_url: https://ncar.ucar.edu/ - - name: Brian Medeiros - affiliation: NSF National Center for Atmospheric Research - affiliation_url: https://ncar.ucar.edu/ - - name: Colin Zarzycki - affiliation: The Pennsylvania State University - affiliation_url: https://www.psu.edu/ - - name: Hongyu Chen - affiliation: University of California, Davis - affiliation_url: https://www.ucdavis.edu/ - - name: Ian Franda - affiliation: University of Wisconsin-Madison - affiliation_url: https://www.wisc.edu/ - - name: John Clyne - affiliation: NSF National Center for Atmospheric Research - affiliation_url: https://ncar.ucar.edu/ - - name: Michaela Sizemore - affiliation: National Renewable Energy Laboratory - affiliation_url: https://www.nrel.gov/ - - name: Orhan Eroglu - affiliation: NSF National Center for Atmospheric Research - affiliation_url: https://ncar.ucar.edu/ - email: oero@ucar.edu - - name: Paul Ullrich - affiliation: University of California, Davis - affiliation_url: https://www.ucdavis.edu/ - - name: Philip Chmielowiec - affiliation: NSF National Center for Atmospheric Research - affiliation_url: https://ncar.ucar.edu/ - - name: Rachel Tam - affiliation: University of Illinois Urbana-Champaign - affiliation_url: https://illinois.edu/ - - name: Rajeev Jain - affiliation: Argonne National Laboratory - affiliation_url: https://www.anl.gov/ - - name: Robert Jacob - affiliation: Argonne National Laboratory - affiliation_url: https://www.anl.gov/ + - name: The UXarray Developers + affiliation: NSF NCAR & Department of Energy tags: packages: - xarray - dask - numba - numpy - - spatialpandas - - datashader - holoviews - matplotlib formats: