Merge branch 'main' into add-linkcheck

napari · Nov 7, 2024 · b48a621 · b48a621
2 parents e0cbb0a + 7cb63ef
commit b48a621
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diff --git a/.github/workflows/build_and_deploy.yml b/.github/workflows/build_and_deploy.yml
@@ -17,6 +17,11 @@ on:
     branches:
       - main
   workflow_dispatch:
+    inputs:
+      target_directory:
+        description: 'The directory to deploy the docs to'
+        required: true
+        default: 'dev'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -104,23 +109,6 @@ jobs:
           # Downloads to '/home/runner/work/docs/docs/html'
           path: html
 
-      - name: get directory name
-        # if this is a tag, use the tag name as the directory name else dev
-        env:
-          REF: ${{ github.ref }}
-        run: |
-          TAG="${GITHUB_REF/refs\/tags\/v/}"
-          VER="${TAG/a*/}"  # remove alpha identifier
-          VER="${VER/b*/}"  # remove beta identifier
-          VER="${VER/rc*/}"  # remove rc identifier
-          VER="${VER/post*/}"  # remove post identifier
-
-          if [[ "$REF" == "refs/tags/v"* ]]; then
-            echo "branch_name=$VER" >> "$GITHUB_ENV"
-          else
-            echo "branch_name=dev" >> "$GITHUB_ENV"
-          fi
-
       - name: Deploy Docs
         if: (github.event_name == 'push' || github.event_name == 'workflow_dispatch') && (startsWith(github.ref, 'refs/tags/v') || startsWith(github.ref, 'refs/heads/main'))
         uses: peaceiris/actions-gh-pages@v4
@@ -129,5 +117,5 @@ jobs:
           external_repository: napari/napari.github.io
           publish_dir: ./html
           publish_branch: gh-pages
-          destination_dir: ${{ env.branch_name }}
+          destination_dir: ${{ github.event.inputs.target_directory || 'dev' }}
           cname: napari.org
diff --git a/EULA.md b/EULA.md
@@ -7,7 +7,7 @@ https://napari.org.
 
 <!-- Links -->
 
-[napari_installers]: https://napari.org/stable/index.html#installation
+[napari_installers]: https://napari.org/stable/tutorials/fundamentals/installation.html
 
 <!-- List of EULAs starts here -->
 <!--

diff --git a/docs/_scripts/update_preference_docs.py b/docs/_scripts/update_preference_docs.py
@@ -6,7 +6,7 @@
 from qtpy.QtWidgets import QMessageBox
 
 from napari._qt.dialogs.preferences_dialog import PreferencesDialog
-from napari._qt.qt_event_loop import get_app
+from napari._qt.qt_event_loop import get_qapp
 from napari._qt.qt_resources import get_stylesheet
 from napari.settings import NapariSettings
 
@@ -99,7 +99,7 @@ def generate_images():
     section of the docs.
     """
 
-    app = get_app()
+    app = get_qapp()
     pref = PreferencesDialog()
     pref.setStyleSheet(get_stylesheet("dark"))
     pref.show()

diff --git a/docs/images/2D-button.png → docs/_static/images/2D-button.png b/docs/images/2D-button.png → docs/_static/images/2D-button.png
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diff --git a/docs/images/3D_paths.png → docs/_static/images/3D_paths.png b/docs/images/3D_paths.png → docs/_static/images/3D_paths.png
diff --git a/docs/guides/images/3d_interaction.ai → docs/_static/images/3d_interaction.ai b/docs/guides/images/3d_interaction.ai → docs/_static/images/3d_interaction.ai
diff --git a/...ides/images/3d_interaction_click_line.png → ...atic/images/3d_interaction_click_line.png b/...ides/images/3d_interaction_click_line.png → ...atic/images/3d_interaction_click_line.png
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diff --git a/...mages/3d_interaction_ray_intersection.png → ...mages/3d_interaction_ray_intersection.png b/...mages/3d_interaction_ray_intersection.png → ...mages/3d_interaction_ray_intersection.png
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diff --git a/docs/guides/images/blending.png → docs/_static/images/blending.png b/docs/guides/images/blending.png → docs/_static/images/blending.png
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diff --git a/docs/tutorials/assets/tutorials/console.png → docs/_static/images/console.png b/docs/tutorials/assets/tutorials/console.png → docs/_static/images/console.png
diff --git a/docs/guides/images/context_type_hint.png → docs/_static/images/context_type_hint.png b/docs/guides/images/context_type_hint.png → docs/_static/images/context_type_hint.png
diff --git a/docs/images/coverage_report.png → docs/_static/images/coverage_report.png b/docs/images/coverage_report.png → docs/_static/images/coverage_report.png
diff --git a/.../tutorials/assets/tutorials/dask_repr.png → docs/_static/images/dask_repr.png b/.../tutorials/assets/tutorials/dask_repr.png → docs/_static/images/dask_repr.png
diff --git a/...ssets/tutorials/dims_roll_lock_widget.png → .../_static/images/dims_roll_lock_widget.png b/...ssets/tutorials/dims_roll_lock_widget.png → .../_static/images/dims_roll_lock_widget.png
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diff --git a/...ibuting/documentation/images/doc-ci-2.png → docs/_static/images/doc-ci-2.png b/...ibuting/documentation/images/doc-ci-2.png → docs/_static/images/doc-ci-2.png
diff --git a/...ibuting/documentation/images/doc-ci-3.png → docs/_static/images/doc-ci-3.png b/...ibuting/documentation/images/doc-ci-3.png → docs/_static/images/doc-ci-3.png
diff --git a/docs/images/edit_token_permissions.png → ..._static/images/edit_token_permissions.png b/docs/images/edit_token_permissions.png → ..._static/images/edit_token_permissions.png
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diff --git a/...als/assets/tutorials/launch_cli_empty.png → docs/_static/images/launch_cli_empty.png b/...als/assets/tutorials/launch_cli_empty.png → docs/_static/images/launch_cli_empty.png
diff --git a/...als/assets/tutorials/launch_cli_image.png → docs/_static/images/launch_cli_image.png b/...als/assets/tutorials/launch_cli_image.png → docs/_static/images/launch_cli_image.png
diff --git a/...rials/assets/tutorials/launch_ipython.png → docs/_static/images/launch_ipython.png b/...rials/assets/tutorials/launch_ipython.png → docs/_static/images/launch_ipython.png
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diff --git a/...ages/lines_not_run_highlighted_in_red.png → ...ages/lines_not_run_highlighted_in_red.png b/...ages/lines_not_run_highlighted_in_red.png → ...ages/lines_not_run_highlighted_in_red.png
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diff --git a/...s/main-menu-file-sub-menu-preferences.png → ...s/main-menu-file-sub-menu-preferences.png b/...s/main-menu-file-sub-menu-preferences.png → ...s/main-menu-file-sub-menu-preferences.png
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diff --git a/...rials/assets/tutorials/main-menu-view.png → docs/_static/images/main-menu-view.png b/...rials/assets/tutorials/main-menu-view.png → docs/_static/images/main-menu-view.png
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diff --git a/docs/images/napari-logo-3-with-guides.png → ...atic/images/napari-logo-3-with-guides.png b/docs/images/napari-logo-3-with-guides.png → ...atic/images/napari-logo-3-with-guides.png
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diff --git a/docs/images/token_permission_form.png → .../_static/images/token_permission_form.png b/docs/images/token_permission_form.png → .../_static/images/token_permission_form.png
diff --git a/docs/images/token_permission_selection.png → ...tic/images/token_permission_selection.png b/docs/images/token_permission_selection.png → ...tic/images/token_permission_selection.png
diff --git a/...orials/assets/tutorials/tracks_btrack.png → docs/_static/images/tracks_btrack.png b/...orials/assets/tutorials/tracks_btrack.png → docs/_static/images/tracks_btrack.png
diff --git a/docs/images/transform-icon.svg → docs/_static/images/transform-icon.svg b/docs/images/transform-icon.svg → docs/_static/images/transform-icon.svg
diff --git a/docs/images/transform-tool.png → docs/_static/images/transform-tool.png b/docs/images/transform-tool.png → docs/_static/images/transform-tool.png
diff --git a/docs/images/update_token_permissions.png → ...tatic/images/update_token_permissions.png b/docs/images/update_token_permissions.png → ...tatic/images/update_token_permissions.png
diff --git a/...rials/assets/tutorials/viewer-buttons.png → docs/_static/images/viewer-buttons.png b/...rials/assets/tutorials/viewer-buttons.png → docs/_static/images/viewer-buttons.png
diff --git a/...orials/assets/tutorials/viewer_layout.jpg → docs/_static/images/viewer_layout.jpg b/...orials/assets/tutorials/viewer_layout.jpg → docs/_static/images/viewer_layout.jpg
diff --git a/docs/images/vs_code_debug.png → docs/_static/images/vs_code_debug.png b/docs/images/vs_code_debug.png → docs/_static/images/vs_code_debug.png
diff --git a/...ation/windows_bundle_command_terminal.png → ...mages/windows_bundle_command_terminal.png b/...ation/windows_bundle_command_terminal.png → ...mages/windows_bundle_command_terminal.png
diff --git a/...ation/windows_bundle_installer_finish.png → ...mages/windows_bundle_installer_finish.png b/...ation/windows_bundle_installer_finish.png → ...mages/windows_bundle_installer_finish.png
diff --git a/...ion/windows_bundle_installer_progress.png → ...ges/windows_bundle_installer_progress.png b/...ion/windows_bundle_installer_progress.png → ...ges/windows_bundle_installer_progress.png
diff --git a/...lation/windows_bundle_installer_start.png → ...images/windows_bundle_installer_start.png b/...lation/windows_bundle_installer_start.png → ...images/windows_bundle_installer_start.png
diff --git a/...ls/installation/windows_launch_napari.png → .../_static/images/windows_launch_napari.png b/...ls/installation/windows_launch_napari.png → .../_static/images/windows_launch_napari.png
diff --git a/docs/_static/version_switcher.json b/docs/_static/version_switcher.json
@@ -5,11 +5,26 @@
 		"url": "https://napari.org/dev/"
 	},
 	{
-		"name": "stable (0.5.1)",
-		"version": "0.5.1",
+		"name": "stable (0.5.4)",
+		"version": "0.5.4",
 		"preferred": true,
 		"url": "https://napari.org/stable/"
 	},
+	{
+		"name": "0.5.3",
+		"version": "0.5.3",
+		"url": "https://napari.org/0.5.3/"
+	},
+	{
+		"name": "0.5.2",
+		"version": "0.5.2",
+		"url": "https://napari.org/0.5.2/"
+	},
+	{
+		"name": "0.5.1",
+		"version": "0.5.1",
+		"url": "https://napari.org/0.5.1/"
+	},
 	{
 		"name": "0.5.0",
 		"version": "0.5.0",

diff --git a/docs/_templates/calendar-template.html b/docs/_templates/calendar-template.html
@@ -0,0 +1,9 @@
+<nav class="bd-docs-nav bd-links">
+    <div class="bd-toc-item navbar-nav">
+        <ul class="nav bd-sidenav">
+            <li class="toctree-l1">
+                <a class="reference internal" href="community/meeting_schedule.html">Community calendar</a>
+            </li>
+        </ul>
+    </div>
+</nav>
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -75,6 +75,58 @@ subtrees:
       - file: further-resources/napari-workshops
       - file: further-resources/sample_data
       - file: gallery
+      - file: release/index
+        subtrees:
+        - entries:
+          - file: release/release_0_5_4
+          - file: release/release_0_5_3
+          - file: release/release_0_5_2
+          - file: release/release_0_5_1
+          - file: release/release_0_5_0
+          - file: release/release_0_4_19
+          - file: release/release_0_4_18
+          - file: release/release_0_4_17
+          - file: release/release_0_4_16
+          - file: release/release_0_4_15
+          - file: release/release_0_4_14
+          - file: release/release_0_4_13
+          - file: release/release_0_4_12
+          - file: release/release_0_4_11
+          - file: release/release_0_4_10
+          - file: release/release_0_4_9
+          - file: release/release_0_4_8
+          - file: release/release_0_4_7
+          - file: release/release_0_4_6
+          - file: release/release_0_4_5
+          - file: release/release_0_4_4
+          - file: release/release_0_4_3
+          - file: release/release_0_4_2
+          - file: release/release_0_4_1
+          - file: release/release_0_4_0
+          - file: release/release_0_3_8
+          - file: release/release_0_3_7
+          - file: release/release_0_3_6
+          - file: release/release_0_3_5
+          - file: release/release_0_3_4
+          - file: release/release_0_3_3
+          - file: release/release_0_3_2
+          - file: release/release_0_3_1
+          - file: release/release_0_3_0
+          - file: release/release_0_2_12
+          - file: release/release_0_2_11
+          - file: release/release_0_2_10
+          - file: release/release_0_2_9
+          - file: release/release_0_2_8
+          - file: release/release_0_2_7
+          - file: release/release_0_2_6
+          - file: release/release_0_2_5
+          - file: release/release_0_2_4
+          - file: release/release_0_2_3
+          - file: release/release_0_2_1
+          - file: release/release_0_2_0
+          - file: release/release_0_1_5
+          - file: release/release_0_1_3
+          - file: release/release_0_1_0
   - file: plugins/index
     subtrees:
     - entries:
@@ -178,55 +230,6 @@ subtrees:
           - file: naps/7-key-binding-dispatch
           - file: naps/8-telemetry
           - file: naps/9-multiple-canvases
-      - file: release/index
-        subtrees:
-        - entries:
-          - file: release/release_0_5_1
-          - file: release/release_0_5_0
-          - file: release/release_0_4_19
-          - file: release/release_0_4_18
-          - file: release/release_0_4_17
-          - file: release/release_0_4_16
-          - file: release/release_0_4_15
-          - file: release/release_0_4_14
-          - file: release/release_0_4_13
-          - file: release/release_0_4_12
-          - file: release/release_0_4_11
-          - file: release/release_0_4_10
-          - file: release/release_0_4_9
-          - file: release/release_0_4_8
-          - file: release/release_0_4_7
-          - file: release/release_0_4_6
-          - file: release/release_0_4_5
-          - file: release/release_0_4_4
-          - file: release/release_0_4_3
-          - file: release/release_0_4_2
-          - file: release/release_0_4_1
-          - file: release/release_0_4_0
-          - file: release/release_0_3_8
-          - file: release/release_0_3_7
-          - file: release/release_0_3_6
-          - file: release/release_0_3_5
-          - file: release/release_0_3_4
-          - file: release/release_0_3_3
-          - file: release/release_0_3_2
-          - file: release/release_0_3_1
-          - file: release/release_0_3_0
-          - file: release/release_0_2_12
-          - file: release/release_0_2_11
-          - file: release/release_0_2_10
-          - file: release/release_0_2_9
-          - file: release/release_0_2_8
-          - file: release/release_0_2_7
-          - file: release/release_0_2_6
-          - file: release/release_0_2_5
-          - file: release/release_0_2_4
-          - file: release/release_0_2_3
-          - file: release/release_0_2_1
-          - file: release/release_0_2_0
-          - file: release/release_0_1_5
-          - file: release/release_0_1_3
-          - file: release/release_0_1_0
       - file: roadmaps/index
         subtrees:
         - entries:

diff --git a/docs/community/governance.md b/docs/community/governance.md
@@ -74,7 +74,7 @@ developer community (including the SC members) fails to reach such a consensus
 in a reasonable timeframe, the SC is the entity that resolves the issue.
 
 Members of the SC also have the "owner" role within the [napari GitHub organization](https://github.com/napari)
-and are ultimately responsible for managing the napari GitHub account, the [@napari_imaging](https://twitter.com/napari_imaging)
+and are ultimately responsible for managing the napari GitHub account, the [@napari_imaging](https://x.com/napari_imaging)
 twitter account, the [napari website](https://napari.org), and other similar napari owned resources.
 
 The SC will be no less than three members and no more than five members,

diff --git a/docs/community/index.md b/docs/community/index.md
@@ -5,13 +5,32 @@ There are several different ways to be a part of the napari community. From
 being a code or documentation contributor, to creating educational content or
 examples, you are welcome to help develop and improve napari.
 
+## Questions
+
 To ask questions and interact with the team, you can join our
 [zulip chat](https://napari.zulipchat.com/login/) or participate in our
 [meetings](meeting-schedule).
 
+To ask general questions about napari usage to the community, including plugins,
+you can visit ![forum image.sc logo](../images/image_sc_logo.png) [forum.image.sc/tag/napari](https://forum.image.sc/tag/napari)
+
+## News and updates
+
+To trace latest news from napari you may follow us on:
+ * ![twitter logo](../images/twitter_logo.svg) twitter/X [napari_imaging](https://x.com/napari_imaging/) 
+ * ![mastodon logo](../images/mastodon_logo.svg) mastodon [fosstodon.org/@napari](https://fosstodon.org/@napari)    
+
+
+## Contributing and Bug reporting
+
+The napari development happens in the napari GitHub repository [github.com/napari/napari](https://github.com/napari/napari). 
+If you spot a bug, please check our [issues list](https://github.com/napari/napari/issues) . If you 
+do not find a matching report, please open a new issue. 
+
 If you are interested in contributing, check out our
-[contributing guide](contributing).
+[contributing guide](napari-contributing).
 
+## Blog
 To read announcements, learn more about who is using napari and see what our
 community has to say, check out our blog, the
 [Island Dispatch](https://napari.org/island-dispatch).
diff --git a/docs/community/mission_and_values.md b/docs/community/mission_and_values.md
@@ -76,4 +76,4 @@ As noted above, we'll be beginning to actively work on the plugin infrastructure
 
 ## Acknowledgements
 
-We share a lot of our mission and values with the `scikit-image` project with whom we share founding members, and acknowledge the influence of their [mission and values statement](https://scikit-image.org/docs/dev/values.html) on this document.
+We share a lot of our mission and values with the `scikit-image` project with whom we share founding members, and acknowledge the influence of their [mission and values statement](https://scikit-image.org/docs/stable/about/values.html) on this document.
diff --git a/docs/community/team.md b/docs/community/team.md
@@ -47,7 +47,7 @@ You can read a full history of the project’s founding and early development in
 
 Over time, napari has grown to over 80 direct contributors. Talley Lambert, from Harvard Medical School, began contributing around the time of Juan's blog post, and has been a critical driver of napari's development ever since. We have core developers located in three continents and three biweekly community calls spread across the day to try to accommodate users and contributors in any time zone.
 
-Read more about napari’s [mission and values](https://napari.org/community/mission_and_values.html), how to get started as a [contributor](https://napari.org/developers/contributing.html) or join us in our [zulip chat](https://napari.zulipchat.com/login/) for a more synchronous conversation. You can also follow us on [twitter](https://twitter.com/napari_imaging).
+Read more about napari’s [mission and values](https://napari.org/stable/community/mission_and_values.html), how to get started as a [contributor](https://napari.org/stable/developers/contributing.html) or join us in our [zulip chat](https://napari.zulipchat.com/login/) for a more synchronous conversation. You can also follow us on [twitter](https://x.com/napari_imaging).
 
 ## Institutional and funding Partners
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -130,6 +130,11 @@
     "footer_end": ["napari-copyright"],
 }
 
+html_sidebars = {
+    "**": ["search-field.html", "sidebar-nav-bs"],
+    "index": ["search-field.html" , "calendar-template"],
+}
+
 html_context = {
    # use Light theme only, don't auto switch (default)
    "default_mode": "light"
@@ -139,7 +144,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
-html_logo = "images/logo.png"
+html_logo = "_static/images/logo.png"
 html_sourcelink_suffix = ''
 html_title = 'napari'
 
@@ -276,7 +281,7 @@ def napari_scraper(block, block_vars, gallery_conf):
     """
     imgpath_iter = block_vars['image_path_iterator']
 
-    if app := napari.qt.get_app():
+    if app := napari.qt.get_qapp():
         app.processEvents()
     else:
         return ""
@@ -294,14 +299,37 @@ def napari_scraper(block, block_vars, gallery_conf):
 
     return scrapers.figure_rst(img_paths, gallery_conf['src_dir'])
 
+from sphinx_gallery import gen_rst
+
+gen_rst.EXAMPLE_HEADER = """
+.. DO NOT EDIT.
+.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
+.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
+.. "{0}"
+.. LINE NUMBERS ARE GIVEN BELOW.
+
+.. only:: html
+
+    .. note::
+        :class: sphx-glr-download-link-note
+
+        :ref:`Go to the end <sphx_glr_download_{1}>`
+        to download the full example as a Python script or as a
+        Jupyter notebook.{2}
+
+.. rst-class:: sphx-glr-example-title
+
+.. _sphx_glr_{1}:
+
+"""
 
 sphinx_gallery_conf = {
     # path to your example scripts (this value is set in the Makefile)
     # 'examples_dirs': '../../napari/examples',
     'gallery_dirs': 'gallery',  # path to where to save gallery generated output
     'filename_pattern': '/*.py',
     'ignore_pattern': 'README.rst|/*_.py',
-    'default_thumb_file': Path(__file__).parent / 'images' / 'logo.png',
+    'default_thumb_file': Path(__file__).parent / '_static' / 'images' / 'logo.png',
     'plot_gallery': "'True'",  # https://github.com/sphinx-gallery/sphinx-gallery/pull/304/files
     'download_all_examples': False,
     'min_reported_time': 10,
@@ -410,12 +438,23 @@ def get_attributes(item, obj, modulename):
 autosummary_ignore_module_all = False
 
 linkcheck_anchors_ignore = [r'^!', r'L\d+-L\d+', r'r\d+', r'issuecomment-\d+']
-
 linkcheck_ignore = [
-    'https://napari.zulipchat.com/',
-    '../_tags',
-    'https://en.wikipedia.org/wiki/Napari#/media/File:Tabuaeran_Kiribati.jpg',
+    "https://napari.zulipchat.com/",
+    "../_tags",
+    "https://en.wikipedia.org/wiki/Napari#/media/File:Tabuaeran_Kiribati.jpg",
+    "http://localhost:8000",
+    "https://datadryad.org/stash/downloads/file_stream/182482",
+    "https://github.com/napari/docs/issues/new/choose",
+    "https://github.com/napari/napari/issues/new/choose",
+    "https://github.com/napari/napari/issues/new",
+    "https://napari-hub.org",
+    "https://github.com/napari/napari/releases/latest",
+    "https://onlinelibrary.wiley.com/doi/10.1002/col.20327",
 ]
+linkcheck_allowed_redirects = {
+    r"https://youtu\.be/.*": r"https://www\.youtube\.com/.*",
+    r"https://github\.com/napari/napari/releases/download/.*": r"https://objects\.githubusercontent\.com/.*",
+}
 
 
 def rewrite_github_anchor(app, uri: str):
Original file line number	Diff line number	Diff line change
Expand Up		@@ -76,4 +76,4 @@ As noted above, we'll be beginning to actively work on the plugin infrastructure

		## Acknowledgements

		We share a lot of our mission and values with the `scikit-image` project with whom we share founding members, and acknowledge the influence of their [mission and values statement](https://scikit-image.org/docs/dev/values.html) on this document.
		We share a lot of our mission and values with the `scikit-image` project with whom we share founding members, and acknowledge the influence of their [mission and values statement](https://scikit-image.org/docs/stable/about/values.html) on this document.