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Fix adata layers None after anndata X unification#1122

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Merged
LucaMarconato merged 1 commit into from
May 8, 2026
+5 −1
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Fix adata layers None after anndata X unification #1122

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4 changes: 4 additions & 0 deletions src/spatialdata/_core/validation.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
exc_type=ValueError,
) as collect_error:
for key in keys:
if key is None:
continue
normalized_key = key.lower()
with collect_error(location=location + (key,)):
check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
with collect_error(location=attr_path):
check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
for key in getattr(data, attr):
if key is None:
continue
key_path = attr_path + (key,)
with collect_error(location=key_path):
if attr in ("obs", "var"):
Expand Down
2 changes: 1 addition & 1 deletion tests/io/test_multi_table.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
n_obs = full_sdata["table"].n_obs
full_sdata["table"].obs["instance_id"] = range(n_obs)
# introduce null values
full_sdata["table"].obs.loc[0, "instance_id"] = None
full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
with pytest.raises(ValueError, match="must not contain null values, but it does."):
full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
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try {
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var __re = new RegExp('^' + "github\\.com" + '
Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
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 Merged

LucaMarconato
merged 1 commit into

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May 8, 2026

+5

−1

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Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
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color-scheme: dark light;
}
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})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
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 Merged

LucaMarconato
merged 1 commit into

from

May 8, 2026

+5

−1

 Merged


Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
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Array.from(node.childNodes).forEach(highlight);
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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('^' + ".*" + '
Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
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Fix adata layers None after anndata X unification#1122

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 Merged

LucaMarconato
merged 1 commit into

from

May 8, 2026

+5

−1

 Merged


Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
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var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
Skip to content
Fix adata layers None after anndata X unification#1122

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 Merged

LucaMarconato
merged 1 commit into

from

May 8, 2026

+5

−1

 Merged


Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
Loading

, '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();
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lastUrl = location.href;
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
Skip to content
Fix adata layers None after anndata X unification#1122

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 Merged

LucaMarconato
merged 1 commit into

from

May 8, 2026

+5

−1

 Merged


Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
Loading

, '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) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
Skip to content
Fix adata layers None after anndata X unification#1122

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 Merged

LucaMarconato
merged 1 commit into

from

May 8, 2026

+5

−1

 Merged


Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
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style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
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background: #1a1a2e !important;
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filter: invert(1) hue-rotate(180deg) !important;
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pre code, pre code * {
filter: none !important;
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filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
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Fix adata layers None after anndata X unification by LucaMarconato · Pull Request #1122 · scverse/spatialdata · GitHub
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Fix adata layers None after anndata X unification#1122

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LucaMarconato
merged 1 commit into

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May 8, 2026

+5

−1

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Fix adata layers None after anndata X unification
#1122
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4 changes: 4 additions & 0 deletions
src/spatialdata/_core/validation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -150,6 +150,8 @@ def check_all_keys_case_insensitively_unique(keys: Collection[str], location: tu
 exc_type=ValueError,
 ) as collect_error:
 for key in keys:
 if key is None:
 continue
 normalized_key = key.lower()
 with collect_error(location=location + (key,)):
 check_key_is_case_insensitively_unique(key, seen)
Expand DownExpand Up@@ -247,6 +249,8 @@ def validate_table_attr_keys(data: AnnData, location: tuple[str, ...] = ()) -> N
 with collect_error(location=attr_path):
 check_all_keys_case_insensitively_unique(getattr(data, attr).keys(), location=attr_path)
 for key in getattr(data, attr):
 if key is None:
 continue
 key_path = attr_path + (key,)
 with collect_error(location=key_path):
 if attr in ("obs", "var"):
Expand Down

2 changes: 1 addition & 1 deletion
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -47,7 +47,7 @@ def test_null_values_in_instance_key_column(self, full_sdata: SpatialData):
 n_obs = full_sdata["table"].n_obs
 full_sdata["table"].obs["instance_id"] = range(n_obs)
 # introduce null values
 full_sdata["table"].obs.loc[0, "instance_id"] = None
 full_sdata["table"].obs.at[full_sdata["table"].obs_names[0], "instance_id"] = None
 with pytest.raises(ValueError, match="must not contain null values, but it does."):
 full_sdata.validate_table_in_spatialdata(table=full_sdata["table"])

Expand Down
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