update dependencies

CHANGELOG.MD

@@ -1,3 +1,19 @@
+# openpipeline_qc 0.3.0
+
+## MAJOR CHANGES
+
+* Bump OpenPipeline dependency to v4.1.0, relevant updates include major changes to memory consumption and runtimes for and support for MuData encoded in Zarr format for `calculate_qc_metrics` (PR #24). 
+
+* Bump CraftBox dependency to v0.3.2, relevant updates include support for symbolic link preservation for `move_files_to_directory` (PR #24).
+
+* Bump Viash to 0.9.7 (PR #24).
+
+* Bump anndata to 0.12.16 (PR #24).
+
+* Bump mudata to 0.3.8 (PR #24).
+
+* Testing: bump viashpy to 0.10.0 (PR #24).
+
 # openpipeline_qc 0.2.2
 
 ## BUG FIX

_viash.yaml

@@ -1,4 +1,4 @@
-viash_version: 0.9.4
+viash_version: 0.9.7
 
 source: src
 target: target
@@ -14,11 +14,11 @@ repositories:
   - name: openpipeline
     repo: openpipeline
     type: vsh
-    tag: v4.0.0
+    tag: v4.1.0
   - name: craftbox
     repo: craftbox
     type: vsh
-    tag: v0.2.0 
+    tag: v0.3.2 
 
 info:
   test_resources:

src/base/requirements/anndata.yaml

@@ -1,2 +1,4 @@
 packages:
-  - anndata~=0.11.1
+  - anndata~=0.12.16
+  - awkward
+  - scipy~=1.17.1 # Exclude scipy 1.17.0 because https://github.com/scverse/anndata/issues/339

src/base/requirements/anndata_mudata.yaml

@@ -1,9 +1,5 @@
 __merge__: [/src/base/requirements/anndata.yaml, .]
 packages:
-  - mudata~=0.3.1
-# Make sure that awkward is not installed. Currently, support of awkward arrays
-# in anndata is experimental, and it is enabled based on whether or not the package
-# is available. By making sure that awkward is not installed, the functionality is
-# not enabled.
+  - mudata~=0.3.8
 script: |
-  exec("try:\n  import awkward\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  exit(1)")
+    exec("try:\n  import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  assert int(version(\"zarr\").partition(\".\")[0]) > 2")

src/base/requirements/viashpy.yaml

@@ -1,2 +1,2 @@
 packages:
-  - viashpy==0.8.0
+  - viashpy==0.10.0