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Add autodoc_default_options to inherit docstrings - #830

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quentinblampey:fix_inheritence_docs
Jan 15, 2025
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Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom
quentinblampey:fix_inheritence_docs

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@quentinblampeyquentinblampey commented Jan 15, 2025

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Closes#828

I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.

autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.72%. Comparing base (f209018) to head (743535b).
Report is 36 commits behind head on main.

Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@LucaMarconato
LucaMarconato merged commit 4630fa1 into scverse:mainJan 15, 2025
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, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
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setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
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addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
Skip to content
Add autodoc_default_options to inherit docstrings - #830
Merged
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Conversation
@quentinblampey
@quentinblampeyquentinblampey
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Jan 15, 2025

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Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
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Jan 15, 2025•

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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 4630fa1
into
scverse:mainJan 15, 2025
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Image2DModel and Image3DModel docs rendered without text


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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
Skip to content
Add autodoc_default_options to inherit docstrings - #830
Merged
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Conversation
@quentinblampey
@quentinblampeyquentinblampey
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Jan 15, 2025

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Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
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Jan 15, 2025•

edited

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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 4630fa1
into
scverse:mainJan 15, 2025
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
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var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
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document.head.appendChild(style);
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if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
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node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
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observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
Skip to content
Add autodoc_default_options to inherit docstrings - #830
Merged
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Conversation
@quentinblampey
@quentinblampeyquentinblampey
commented
Jan 15, 2025

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Contributor
Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
@codecov
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Jan 15, 2025•

edited

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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 4630fa1
into
scverse:mainJan 15, 2025
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Image2DModel and Image3DModel docs rendered without text


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@quentinblampey@LucaMarconato

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
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var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
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});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
Skip to content
Add autodoc_default_options to inherit docstrings - #830
Merged
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Conversation
@quentinblampey
@quentinblampeyquentinblampey
commented
Jan 15, 2025

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Contributor
Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
@codecov
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Jan 15, 2025•

edited

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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 4630fa1
into
scverse:mainJan 15, 2025
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Image2DModel and Image3DModel docs rendered without text


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@quentinblampey@LucaMarconato

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
Skip to content
Add autodoc_default_options to inherit docstrings - #830
Merged
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Conversation
@quentinblampey
@quentinblampeyquentinblampey
commented
Jan 15, 2025

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Contributor
Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 4630fa1
into
scverse:mainJan 15, 2025
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Image2DModel and Image3DModel docs rendered without text


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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
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unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
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} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
Skip to content
Add autodoc_default_options to inherit docstrings - #830
Merged
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Conversation
@quentinblampey
@quentinblampeyquentinblampey
commented
Jan 15, 2025

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Contributor
Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
@codecov
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Jan 15, 2025•

edited

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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 4630fa1
into
scverse:mainJan 15, 2025
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Image2DModel and Image3DModel docs rendered without text


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@quentinblampey@LucaMarconato

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
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/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Add autodoc_default_options to inherit docstrings by quentinblampey · Pull Request #830 · scverse/spatialdata · GitHub
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Add autodoc_default_options to inherit docstrings - #830
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LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
Jan 15, 2025
Merged
Add autodoc_default_options to inherit docstrings#830
LucaMarconato merged 2 commits into
scverse:mainfrom 
quentinblampey:fix_inheritence_docs
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@quentinblampey
@quentinblampeyquentinblampey
commented
Jan 15, 2025

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Closes#828
I set the following defaults for the autodoc. The first interesting thing is that 'inherited-members': Truefixes#828 because it will now show the inherited docstrings. The second thing is that 'members': True significantly cleans up the docs because I can remove it everywhere else.
autodoc_default_options = {
'members': True,
'inherited-members': True,
'show-inheritance': True,
}

Note that I also removed :undoc-members:, because I don't think we should show methods that are not documented (it adds a lot of unreadable sections). But feel free to add it in the defaults if you prefer to have it @LucaMarconato
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Jan 15, 2025•

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Codecov Report
All modified and coverable lines are covered by tests ✅
Project coverage is 91.72%. Comparing base (f209018) to head (743535b).

Report is 36 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #830 +/- ##
=======================================
Coverage 91.72% 91.72% =======================================
Files 46 46 Lines 7166 7166 =======================================
Hits 6573 6573 Misses 593 593 
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@LucaMarconato
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merged commit 4630fa1
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scverse:mainJan 15, 2025
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Image2DModel and Image3DModel docs rendered without text


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