From ca3ffb53a51f6d2a76e37cc2a6d92452e8aba158 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 10 Dec 2025 11:25:50 +0000 Subject: [PATCH 1/2] Increase file size limit from 5GB to 50GB Bump the log_filesize_limit to 50GB to handle larger Xenium files. Updated code, log messages, and documentation. --- CLAUDE.md | 2 +- README.md | 2 +- multiqc_xenium_extra/xenium_extra.py | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index 43faa76..7bcc25d 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -32,7 +32,7 @@ multiqc /path/to/xenium/data The plugin uses MultiQC's hook system (v1) to extend functionality: -- **`xenium_extra_execution_start`**: Called at startup to register search patterns for `transcripts.parquet`, `cells.parquet`, and `cell_feature_matrix.h5` files, and increase file size limit to 5GB. +- **`xenium_extra_execution_start`**: Called at startup to register search patterns for `transcripts.parquet`, `cells.parquet`, and `cell_feature_matrix.h5` files, and increase file size limit to 50GB. - **`extend_xenium_module`**: Called after the core Xenium module runs, receives the module instance and adds extra sections/data. diff --git a/README.md b/README.md index 76542f2..f8e32c5 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ pip install multiqc-xenium-extra The plugin automatically adjusts the file size limit to handle large Xenium files: ```yaml -log_filesize_limit: 5000000000 # 5GB +log_filesize_limit: 50000000000 # 50GB ``` ## Usage diff --git a/multiqc_xenium_extra/xenium_extra.py b/multiqc_xenium_extra/xenium_extra.py index aab40ef..2a72ed9 100644 --- a/multiqc_xenium_extra/xenium_extra.py +++ b/multiqc_xenium_extra/xenium_extra.py @@ -76,9 +76,9 @@ def xenium_extra_execution_start(): # Increase file size limit to handle large Xenium files (if not already set by user) # Default is 50MB, Xenium files can be several GB - if config.log_filesize_limit < 5000000000: # 5GB - log.debug("Increasing log_filesize_limit to 5GB for Xenium parquet files") - config.log_filesize_limit = 5000000000 + if config.log_filesize_limit < 50000000000: # 50GB + log.debug("Increasing log_filesize_limit to 50GB for Xenium parquet files") + config.log_filesize_limit = 50000000000 # Extension function and helper functions below From eb63c7fd5c3f85df61a32deba6e10329e2f0b608 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 10 Dec 2025 12:07:21 +0000 Subject: [PATCH 2/2] Bump version to 1.0.2 for release Update changelog with file size limit increase. --- CHANGELOG.md | 4 ++++ pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 212fea0..e6d6d4c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # multiqc-xenium-extra changelog +## v1.0.2 [2025-12-10] + +Increase file size limit from 5GB to 50GB to handle larger Xenium files. + ## v1.0.1 [2025-10-25] Move over some additional code from core MultiQC that diff --git a/pyproject.toml b/pyproject.toml index d7671c3..8eb0e30 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "multiqc_xenium_extra" -version = "1.0.1" +version = "1.0.2" authors = [ {name = "Phil Ewels", email = "phil.ewels@seqera.io"}, ]