diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index dd95f62a..f4f1032a 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -31,7 +31,7 @@ jobs: - name: Build documentation run: > set -e - && pip install "jupyter-book<2" + && pip install "jupyter-book>=2" && jupyter-book build jupyterbook - name: GitHub Pages action diff --git a/.github/workflows/docs-linkchecker.yml b/.github/workflows/docs-linkchecker.yml index 8970d888..b2622f58 100644 --- a/.github/workflows/docs-linkchecker.yml +++ b/.github/workflows/docs-linkchecker.yml @@ -26,5 +26,5 @@ jobs: - name: Linkcheck run: > set -e - && pip install "jupyter-book<2" + && pip install "jupyter-book>=2" && jupyter-book build jupyterbook --builder linkcheck diff --git a/.gitignore b/.gitignore index dcc3b77b..cd1717b8 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,6 @@ *.swp .ipynb_checkpoints/ index.html + +# MyST build outputs +_build diff --git a/jupyterbook/_config.yml b/jupyterbook/_config.yml deleted file mode 100644 index 1ee27138..00000000 --- a/jupyterbook/_config.yml +++ /dev/null @@ -1,110 +0,0 @@ -# Book settings -title: The U.S. Integrated Ocean Observing System (IOOS) # The title of the book. Will be placed in the left navbar. -author: IOOS # The author of the book -logo: images/IOOS_logo.png # A path to the book logo - -# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb") -exclude_patterns: [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints", "**.archived.ipynb"] -# Auto-exclude files not in the toc -only_build_toc_files: true - -####################################################################################### -# Execution settings -execute: - execute_notebooks: off # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off") - cache: "" # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/` - exclude_patterns: [] # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time) - timeout: 30 # The maximum time (in seconds) each notebook cell is allowed to run. - run_in_temp: false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),otherwise the notebook's parent directory will be the cwd. - allow_errors: false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run. - stderr_output: show # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe' - -####################################################################################### -# Parse and render settings -parse: - myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html - - amsmath - - colon_fence - - deflist - - dollarmath - - html_admonition - - html_image - - linkify - - replacements - - smartquotes - - substitution - - myst_url_schemes: [mailto, http, https] # URI schemes that will be recognized as external URLs in Markdown links - myst_dmath_double_inline: true # Allow display math ($$) within an inline context - -####################################################################################### -# HTML-specific settings -html: - favicon: "images/IOOS_logo.png" # A path to a favicon image - use_edit_page_button: false # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in - use_repository_button: true # Whether to add a link to your repository button - use_issues_button: true # Whether to add an "open an issue" button - extra_navbar: IOOS # Will be displayed underneath the left navbar. - extra_footer: ioos.noaa.gov   - Facebook   - Twitter   - Contact Us
- U.S. Integrated Ocean Observing System Program
- 1315 East-West Highway
- SSMC3, 2nd Floor
- Silver Spring, MD 20910
- (240) 533-9444 - google_analytics_id: "G-546J258RCJ" - home_page_in_navbar: false # Whether to include your home page in the left Navigation Bar - baseurl: "https://ioos.github.io/ioos_code_lab/" # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/ - comments: - hypothesis: false - utterances: false - ####################################################################################### -# LaTeX-specific settings -latex: - latex_engine: pdflatex # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex' - use_jupyterbook_latex: true # use jupyterbook-latex for pdf builds as default - -####################################################################################### -# Launch button settings -launch_buttons: - notebook_interface: jupyterlab # The interface interactive links will activate ["classic", "jupyterlab"] - binderhub_url: https://mybinder.org # The URL of the BinderHub (e.g., https://mybinder.org) - jupyterhub_url: "" # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu) - thebe: false # Add a thebe button to pages (requires the repository to run on Binder) - colab_url: "https://colab.research.google.com" # The URL of Google Colab (https://colab.research.google.com) - -repository: - url: https://github.com/ioos/ioos_code_lab # The URL to your book's repository - path_to_book: "jupyterbook" # A path to your book's folder, relative to the repository root. - branch: main # Which branch of the repository should be used when creating links - -####################################################################################### -# Advanced and power-user settings -sphinx: - config: - linkcheck_ignore: [ - "./data_access_notebooks/.*", - "./data_analysis_and_visualization_notebooks/.*", - "./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 - myst_heading_anchors: 3 - nb_mime_priority_overrides: [ - ["html", "application/vnd.jupyter.widget-view+json", 10], - ["html", "application/javascript", 20], - ["html", "text/html", 30], - ["html", "image/svg+xml", 40], - ["html", "image/png", 50], - ["html", "image/gif", 60], - ["html", "image/jpeg", 70], - ["html", "text/markdown", 80], - ["html", "text/latex", 90], - ["html", "text/plain", 100] - ] diff --git a/jupyterbook/_toc.yml b/jupyterbook/_toc.yml deleted file mode 100644 index 1836ac38..00000000 --- a/jupyterbook/_toc.yml +++ /dev/null @@ -1,40 +0,0 @@ -format: jb-book -root: content/intro.md -title: The IOOS Data Demo Center -parts: - - - caption: Getting Started - chapters: - - file: content/ioos_installation_conda.md - title: Installing the IOOS Conda Environment - - - caption: Code Gallery - chapters: - - file: content/code_gallery/gallery.md - title: Notebooks gallery - - file: content/code_gallery/data_access.md - sections: - - glob: content/code_gallery/data_access_notebooks/* - - - file: content/code_gallery/data_analysis_and_visualization.md - sections: - - glob: content/code_gallery/data_analysis_and_visualization_notebooks/* - - - file: content/code_gallery/data_management.md - sections: - - glob: content/code_gallery/data_management_notebooks/* - - - caption: Video Tutorials - chapters: - - glob: content/Video_Demo_Markdown/* - - - caption: Other Resources - chapters: - - url: https://help.aodn.org.au/aodn-data-tools/user-code-library/ - title: Opening netCDF files - hints from AODN - - url: http://unidata.github.io/notebook-gallery/ - title: Unidata Jupyter Notebook Gallery - - url: http://iobis.org/tutorial/ - title: Extracting and Enriching OBIS data with R - - url: https://github.com/USGS-R - title: USGS-R Examples diff --git a/jupyterbook/myst.yml b/jupyterbook/myst.yml new file mode 100644 index 00000000..0edb1975 --- /dev/null +++ b/jupyterbook/myst.yml @@ -0,0 +1,54 @@ +version: 1 +project: + exclude: + - _build + - Thumbs.db + - .DS_Store + - '*.ipynb_checkpoints' + - '*.archived.ipynb' + github: ioos/ioos_code_lab + thebe: + binder: + repo: ioos/ioos_code_lab + provider: github + url: https://mybinder.org + ref: main + toc: + - file: content/intro.md + - title: Getting Started + children: + - file: content/ioos_installation_conda.md + title: Installing the IOOS Conda Environment + - title: Code Gallery + children: + - file: content/code_gallery/gallery.md + title: Notebooks gallery + - file: content/code_gallery/data_access.md + children: + - pattern: content/code_gallery/data_access_notebooks/* + - file: content/code_gallery/data_analysis_and_visualization.md + children: + - pattern: content/code_gallery/data_analysis_and_visualization_notebooks/* + - file: content/code_gallery/data_management.md + children: + - pattern: content/code_gallery/data_management_notebooks/* + - title: Video Tutorials + children: + - pattern: content/Video_Demo_Markdown/* + - title: Other Resources + children: + - url: https://help.aodn.org.au/aodn-data-tools/user-code-library/ + title: Opening netCDF files - hints from AODN + - url: http://unidata.github.io/notebook-gallery/ + title: Unidata Jupyter Notebook Gallery + - url: http://iobis.org/tutorial/ + title: Extracting and Enriching OBIS data with R + - url: https://github.com/USGS-R + title: USGS-R Examples +site: + options: + logo: images/IOOS_logo.png + favicon: images/IOOS_logo.png + analytics_google: G-546J258RCJ + folders: true + template: book-theme