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Fix _search_for_backing_files_recursively() to support multifile parquet#1127

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Merged
LucaMarconato merged 1 commit into from
May 13, 2026
+40 −11
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Fix _search_for_backing_files_recursively() to support multifile parquet #1127

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51 changes: 40 additions & 11 deletions src/spatialdata/_io/_utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
# This occurs when for example points and images are mixed, the main task still starts with
# read_parquet, but the execution happens through a subgraph which we iterate over to get the
# actual read_parquet task.
for task in v.args[0].values():
# Recursively go through tasks, this is required because differences between dask versions.
piece_dict = _find_piece_dict(task)
if isinstance(piece_dict, dict) and "piece" in piece_dict:
parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
raise ValueError(
f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
f"report this bug."
)
files.append(os.path.realpath(parquet_file))
#
# v.args[0] has two known shapes:
# dict – keys are task keys, values are Task objects (classic subgraph case)
# list – list of piece dicts produced when aggregate_files=True aggregates multiple
# parquet files into one partition; check0/check1 are row-group selectors
# ([0], []) rather than None, so only the file extension is validated.
args0 = v.args[0]
if isinstance(args0, dict):
for task in args0.values():
# Recursively go through tasks, this is required because differences between dask
# versions.
piece_dict = _find_piece_dict(task)
if isinstance(piece_dict, dict) and "piece" in piece_dict:
parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
if (
not parquet_file.endswith(".parquet")
or check0 is not None
or check1 is not None
):
raise ValueError(
f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
f"Please report this bug."
)
files.append(os.path.realpath(parquet_file))
elif isinstance(args0, list):
for item in args0:
if isinstance(item, dict) and "piece" in item:
parquet_file = item["piece"][0]
if not parquet_file.endswith(".parquet"):
raise ValueError(
f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
f"Please report this bug."
)
files.append(os.path.realpath(parquet_file))
else:
logger.warning(
f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
f"Backing files may not be detected correctly. Please report this as a bug."
)


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
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" + '
Fix _search_for_backing_files_recursively() to support multifile parquet by LucaMarconato · Pull Request #1127 · scverse/spatialdata · GitHub
Skip to content
Fix _search_for_backing_files_recursively() to support multifile parquet#1127

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 Merged

LucaMarconato
merged 1 commit into

from

May 13, 2026

+40

−11

 Merged


Fix _search_for_backing_files_recursively() to support multifile parquet
#1127
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51 changes: 40 additions & 11 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
 # This occurs when for example points and images are mixed, the main task still starts with
 # read_parquet, but the execution happens through a subgraph which we iterate over to get the
 # actual read_parquet task.
 for task in v.args[0].values():
 # Recursively go through tasks, this is required because differences between dask versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
 f"report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 #
 # v.args[0] has two known shapes:
 # dict – keys are task keys, values are Task objects (classic subgraph case)
 # list – list of piece dicts produced when aggregate_files=True aggregates multiple
 # parquet files into one partition; check0/check1 are row-group selectors
 # ([0], []) rather than None, so only the file extension is validated.
 args0 = v.args[0]
 if isinstance(args0, dict):
 for task in args0.values():
 # Recursively go through tasks, this is required because differences between dask
 # versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if (
 not parquet_file.endswith(".parquet")
 or check0 is not None
 or check1 is not None
 ):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 elif isinstance(args0, list):
 for item in args0:
 if isinstance(item, dict) and "piece" in item:
 parquet_file = item["piece"][0]
 if not parquet_file.endswith(".parquet"):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 else:
 logger.warning(
 f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
 f"Backing files may not be detected correctly. Please report this as a bug."
 )


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
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 = '
.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('^' + ".*" + '
Fix _search_for_backing_files_recursively() to support multifile parquet by LucaMarconato · Pull Request #1127 · scverse/spatialdata · GitHub
Skip to content
Fix _search_for_backing_files_recursively() to support multifile parquet#1127

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 Merged

LucaMarconato
merged 1 commit into

from

May 13, 2026

+40

−11

 Merged


Fix _search_for_backing_files_recursively() to support multifile parquet
#1127
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51 changes: 40 additions & 11 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
 # This occurs when for example points and images are mixed, the main task still starts with
 # read_parquet, but the execution happens through a subgraph which we iterate over to get the
 # actual read_parquet task.
 for task in v.args[0].values():
 # Recursively go through tasks, this is required because differences between dask versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
 f"report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 #
 # v.args[0] has two known shapes:
 # dict – keys are task keys, values are Task objects (classic subgraph case)
 # list – list of piece dicts produced when aggregate_files=True aggregates multiple
 # parquet files into one partition; check0/check1 are row-group selectors
 # ([0], []) rather than None, so only the file extension is validated.
 args0 = v.args[0]
 if isinstance(args0, dict):
 for task in args0.values():
 # Recursively go through tasks, this is required because differences between dask
 # versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if (
 not parquet_file.endswith(".parquet")
 or check0 is not None
 or check1 is not None
 ):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 elif isinstance(args0, list):
 for item in args0:
 if isinstance(item, dict) and "piece" in item:
 parquet_file = item["piece"][0]
 if not parquet_file.endswith(".parquet"):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 else:
 logger.warning(
 f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
 f"Backing files may not be detected correctly. Please report this as a bug."
 )


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
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')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
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);
}
});
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);
});
});
});
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 _search_for_backing_files_recursively() to support multifile parquet by LucaMarconato · Pull Request #1127 · scverse/spatialdata · GitHub
Skip to content
Fix _search_for_backing_files_recursively() to support multifile parquet#1127

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

LucaMarconato
merged 1 commit into

from

May 13, 2026

+40

−11

 Merged


Fix _search_for_backing_files_recursively() to support multifile parquet
#1127
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51 changes: 40 additions & 11 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
 # This occurs when for example points and images are mixed, the main task still starts with
 # read_parquet, but the execution happens through a subgraph which we iterate over to get the
 # actual read_parquet task.
 for task in v.args[0].values():
 # Recursively go through tasks, this is required because differences between dask versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
 f"report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 #
 # v.args[0] has two known shapes:
 # dict – keys are task keys, values are Task objects (classic subgraph case)
 # list – list of piece dicts produced when aggregate_files=True aggregates multiple
 # parquet files into one partition; check0/check1 are row-group selectors
 # ([0], []) rather than None, so only the file extension is validated.
 args0 = v.args[0]
 if isinstance(args0, dict):
 for task in args0.values():
 # Recursively go through tasks, this is required because differences between dask
 # versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if (
 not parquet_file.endswith(".parquet")
 or check0 is not None
 or check1 is not None
 ):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 elif isinstance(args0, list):
 for item in args0:
 if isinstance(item, dict) and "piece" in item:
 parquet_file = item["piece"][0]
 if not parquet_file.endswith(".parquet"):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 else:
 logger.warning(
 f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
 f"Backing files may not be detected correctly. Please report this as a bug."
 )


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
Expand Down
Loading

, '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) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
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" + '
Fix _search_for_backing_files_recursively() to support multifile parquet by LucaMarconato · Pull Request #1127 · scverse/spatialdata · GitHub
Skip to content
Fix _search_for_backing_files_recursively() to support multifile parquet#1127

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

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 Merged

LucaMarconato
merged 1 commit into

from

May 13, 2026

+40

−11

 Merged


Fix _search_for_backing_files_recursively() to support multifile parquet
#1127
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51 changes: 40 additions & 11 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
 # This occurs when for example points and images are mixed, the main task still starts with
 # read_parquet, but the execution happens through a subgraph which we iterate over to get the
 # actual read_parquet task.
 for task in v.args[0].values():
 # Recursively go through tasks, this is required because differences between dask versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
 f"report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 #
 # v.args[0] has two known shapes:
 # dict – keys are task keys, values are Task objects (classic subgraph case)
 # list – list of piece dicts produced when aggregate_files=True aggregates multiple
 # parquet files into one partition; check0/check1 are row-group selectors
 # ([0], []) rather than None, so only the file extension is validated.
 args0 = v.args[0]
 if isinstance(args0, dict):
 for task in args0.values():
 # Recursively go through tasks, this is required because differences between dask
 # versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if (
 not parquet_file.endswith(".parquet")
 or check0 is not None
 or check1 is not None
 ):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 elif isinstance(args0, list):
 for item in args0:
 if isinstance(item, dict) and "piece" in item:
 parquet_file = item["piece"][0]
 if not parquet_file.endswith(".parquet"):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 else:
 logger.warning(
 f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
 f"Backing files may not be detected correctly. Please report this as a bug."
 )


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
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();
}
}
// 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('^' + ".*" + '
Fix _search_for_backing_files_recursively() to support multifile parquet by LucaMarconato · Pull Request #1127 · scverse/spatialdata · GitHub
Skip to content
Fix _search_for_backing_files_recursively() to support multifile parquet#1127

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 Merged

LucaMarconato
merged 1 commit into

from

May 13, 2026

+40

−11

 Merged


Fix _search_for_backing_files_recursively() to support multifile parquet
#1127
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51 changes: 40 additions & 11 deletions
src/spatialdata/_io/_utils.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
 # This occurs when for example points and images are mixed, the main task still starts with
 # read_parquet, but the execution happens through a subgraph which we iterate over to get the
 # actual read_parquet task.
 for task in v.args[0].values():
 # Recursively go through tasks, this is required because differences between dask versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
 f"report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 #
 # v.args[0] has two known shapes:
 # dict – keys are task keys, values are Task objects (classic subgraph case)
 # list – list of piece dicts produced when aggregate_files=True aggregates multiple
 # parquet files into one partition; check0/check1 are row-group selectors
 # ([0], []) rather than None, so only the file extension is validated.
 args0 = v.args[0]
 if isinstance(args0, dict):
 for task in args0.values():
 # Recursively go through tasks, this is required because differences between dask
 # versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if (
 not parquet_file.endswith(".parquet")
 or check0 is not None
 or check1 is not None
 ):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 elif isinstance(args0, list):
 for item in args0:
 if isinstance(item, dict) and "piece" in item:
 parquet_file = item["piece"][0]
 if not parquet_file.endswith(".parquet"):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 else:
 logger.warning(
 f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
 f"Backing files may not be detected correctly. Please report this as a bug."
 )


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
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) {
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';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
})();
Fix _search_for_backing_files_recursively() to support multifile parquet by LucaMarconato · Pull Request #1127 · scverse/spatialdata · GitHub
Skip to content
Fix _search_for_backing_files_recursively() to support multifile parquet#1127

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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 Merged

LucaMarconato
merged 1 commit into

from

May 13, 2026

+40

−11

 Merged


Fix _search_for_backing_files_recursively() to support multifile parquet
#1127
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


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51 changes: 40 additions & 11 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
 # This occurs when for example points and images are mixed, the main task still starts with
 # read_parquet, but the execution happens through a subgraph which we iterate over to get the
 # actual read_parquet task.
 for task in v.args[0].values():
 # Recursively go through tasks, this is required because differences between dask versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
 f"report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 #
 # v.args[0] has two known shapes:
 # dict – keys are task keys, values are Task objects (classic subgraph case)
 # list – list of piece dicts produced when aggregate_files=True aggregates multiple
 # parquet files into one partition; check0/check1 are row-group selectors
 # ([0], []) rather than None, so only the file extension is validated.
 args0 = v.args[0]
 if isinstance(args0, dict):
 for task in args0.values():
 # Recursively go through tasks, this is required because differences between dask
 # versions.
 piece_dict = _find_piece_dict(task)
 if isinstance(piece_dict, dict) and "piece" in piece_dict:
 parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
 if (
 not parquet_file.endswith(".parquet")
 or check0 is not None
 or check1 is not None
 ):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 elif isinstance(args0, list):
 for item in args0:
 if isinstance(item, dict) and "piece" in item:
 parquet_file = item["piece"][0]
 if not parquet_file.endswith(".parquet"):
 raise ValueError(
 f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
 f"Please report this bug."
 )
 files.append(os.path.realpath(parquet_file))
 else:
 logger.warning(
 f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
 f"Backing files may not be detected correctly. Please report this as a bug."
 )


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
Expand Down
Loading