Merge pull request #20 from openpipelines-bio/enable-deflate64-compression

enable deflate64 compression

Author: dorien-er

CHANGELOG.md

@@ -12,7 +12,7 @@
 
 ## NEW FUNCTIONALITY
 
-* `convert`: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19).
+* `convert`: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19, PR #20).
 
 # openpipeline_spatial 0.1.0
 

src/convert/from_cells2stats_to_h5mu/config.vsh.yaml

@@ -114,10 +114,15 @@ engines:
       - type: apt
         packages: 
           - procps
+          - build-essential
+          - zlib1g-dev
+          - git
       - type: python
         __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - pyarrow
+        packages: [ pyarrow ]
+        # Windows explorer uses DEFLATE64 compression for large ZIP files,
+        # which is not supported by most standard library zipfile module
+        git: [ https://codeberg.org/miurahr/[email protected] ]
     test_setup:
       - type: apt
         packages:

src/convert/from_cells2stats_to_h5mu/script.py

@@ -6,7 +6,7 @@
 import anndata as ad
 import re
 import json
-import zipfile
+import zipfile_inflate64 as zipfile
 import os
 
 ## VIASH START

src/convert/from_cosmx_to_h5mu/config.vsh.yaml

@@ -54,8 +54,15 @@ engines:
       - type: apt
         packages: 
           - procps
+          - build-essential
+          - zlib1g-dev
+          - git
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/squidpy.yaml]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/squidpy.yaml, .]
+        packages: [ pyarrow ]
+        # Windows explorer uses DEFLATE64 compression for large ZIP files,
+        # which is not supported by most standard library zipfile module
+        git: [ https://codeberg.org/miurahr/[email protected] ]
     test_setup:
       - type: apt
         packages:

src/convert/from_cosmx_to_h5mu/script.py

@@ -2,7 +2,7 @@
 import os
 import squidpy as sq
 import mudata as mu
-import zipfile
+import zipfile_inflate64 as zipfile
 from pathlib import Path
 
 ## VIASH START

src/convert/from_cosmx_to_spatialexperiment/test.R

@@ -75,8 +75,9 @@ spe <- paste0(meta[["resources_dir"]], "/Lung5_Rep2_tiny")
 out_rds <- "output.rds"
 
 create_folder_archive <- function(
-    folder_path,
-    archive = "Lung5_Rep2_tiny.zip") {
+  folder_path,
+  archive = "Lung5_Rep2_tiny.zip"
+) {
   old_wd <- getwd()
   on.exit(setwd(old_wd))
   setwd(meta$resources_dir)

src/convert/from_xenium_to_h5mu/config.vsh.yaml

@@ -56,10 +56,15 @@ engines:
       - type: apt
         packages: 
           - procps
+          - build-essential
+          - zlib1g-dev
+          - git
       - type: python
         __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
-        packages:
-          - pyarrow
+        packages: [ pyarrow ]
+        # Windows explorer uses DEFLATE64 compression for large ZIP files,
+        # which is not supported by most standard library zipfile module
+        git: [ https://codeberg.org/miurahr/[email protected] ]
     test_setup:
       - type: apt
         packages:

src/convert/from_xenium_to_h5mu/script.py

@@ -3,7 +3,7 @@
 import scanpy as sc
 import pandas as pd
 import mudata as mu
-import zipfile
+import zipfile_inflate64 as zipfile
 import json
 import os
 

src/convert/from_xenium_to_spatialdata/config.vsh.yaml

@@ -91,8 +91,14 @@ engines:
       - type: apt
         packages: 
           - procps
+          - build-essential
+          - zlib1g-dev
+          - git
       - type: python
-        __merge__: [ /src/base/requirements/spatialdata-io.yaml ]
+        # Windows explorer uses DEFLATE64 compression for large ZIP files,
+        # which is not supported by most standard library zipfile module
+        git: [ https://codeberg.org/miurahr/[email protected] ]
+        __merge__: [ /src/base/requirements/spatialdata-io.yaml, . ]
     test_setup:
       - type: apt
         packages:

src/convert/from_xenium_to_spatialdata/script.py

@@ -1,6 +1,6 @@
 import sys
 from spatialdata_io import xenium
-import zipfile
+import zipfile_inflate64 as zipfile
 from pathlib import Path
 
 ## VIASH START