Update scanpy to 1.9.5 (#594)

* Update scanpy to 1.9.5

* Add CHANGELOG entry

CHANGELOG.md

@@ -27,6 +27,8 @@ Implementing this changes involved breaking some existing functionality:
 
 ## MINOR CHANGES
 
+* Several components: bump scanpy to 1.9.5 (PR #594).
+
 * Refactored `prot_multisample` and `prot_singlesample` pipelines to use `fromState` and `toState` functionality (PR #585).
 
 # openpipelines 0.11.0

src/annotate/popv/config.vsh.yaml

@@ -137,8 +137,8 @@ platforms:
           - build-essential
           - wget
       - type: python
+        __merge__: [ /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.4
           - scvi-tools~=1.0.3
           - popv~=0.3.2
           - jax==0.4.10

src/base/requirements/scanpy.yaml

@@ -0,0 +1,3 @@
+
+packages:
+  - scanpy~=1.9.5

src/cluster/leiden/config.vsh.yaml

@@ -85,9 +85,8 @@ platforms:
           - cmake
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.2
           - leidenalg~=0.8.9
   - type: nextflow
     directives:

src/convert/from_10xh5_to_h5mu/config.vsh.yaml

@@ -64,9 +64,7 @@ platforms:
         packages:
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
   - type: nextflow
     directives:
       label: [lowmem, singlecpu]

src/convert/from_10xmtx_to_h5mu/config.vsh.yaml

@@ -41,9 +41,7 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
   - type: nextflow
     directives:
       label: [lowmem, singlecpu]

src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml

@@ -60,9 +60,8 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.2
           - scirpy~=0.11.1
           - pandas~=2.0.0
     test_setup:

src/convert/from_h5mu_to_seurat/config.vsh.yaml

@@ -51,8 +51,8 @@ platforms:
           - python3-pip
           - python-is-python3
       - type: python
+        __merge__: [/src/base/requirements/scanpy.yaml, .]
         packages: 
-          - scanpy~=1.9.2
           - anndata~=0.9.1
       - type: r
         cran: [ anndata, hdf5r, testthat ]

src/correction/cellbender_remove_background/config.vsh.yaml

@@ -301,7 +301,6 @@ platforms:
       - type: python
         packages: 
           - muon
-          - scanpy
   - type: nextflow
     directives:
       label: [singlecpu, lowmem, gpu]

src/correction/cellbender_remove_background/script.py

@@ -166,9 +166,6 @@ def setup_logger():
     out = subprocess.check_output(cmd_pars).decode("utf-8")
 
     logger.info("Reading CellBender 10xh5 output file: '%s'", output_file)
-    # have to use custom read_10x_h5 function for now
-    # will be fixed when https://github.com/scverse/scanpy/pull/2344 is merged
-    # adata_out = sc.read_10x_h5(output_file, gex_only=False)
     adata_out = anndata_from_h5(output_file, analyzed_barcodes_only=False)
 
     logger.info("CellBender output format:", adata_out)

src/correction/cellbender_remove_background/test.py

@@ -33,7 +33,6 @@
 # check if file exists
 assert path.exists("output.h5mu"), "No output was created."
 
-# read it with scanpy
 data = mu.read_h5mu("output.h5mu")
 
 # check whether gex was found

src/correction/cellbender_remove_background_v0_2/config.vsh.yaml

@@ -184,7 +184,6 @@ platforms:
       - type: python
         packages: 
           - muon~=0.1.4
-          - scanpy~=1.9.2
   - type: nextflow
     directives:
       label: [gpu]

src/dimred/pca/config.vsh.yaml

@@ -87,9 +87,7 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/dimred/umap/config.vsh.yaml

@@ -111,9 +111,7 @@ platforms:
         packages:
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/filter/filter_with_hvg/config.vsh.yaml

@@ -125,9 +125,8 @@ platforms:
     image: python:3.9
     setup: 
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.2
           - scikit-misc
     test_setup:
       - type: python

src/filter/filter_with_scrublet/config.vsh.yaml

@@ -124,9 +124,8 @@ platforms:
           - procps
           - build-essential
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.2
           - scrublet
           - annoy==1.16.3
     test_setup:

src/integrate/harmonypy/config.vsh.yaml

@@ -67,10 +67,9 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
           - harmonypy~=0.0.6
-          - scanpy~=1.9.2
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/integrate/scanorama/config.vsh.yaml

@@ -80,9 +80,8 @@ platforms:
           - procps
           - build-essential
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.2
           - scanorama
     test_setup:
       - type: python

src/integrate/scvi/config.vsh.yaml

@@ -236,9 +236,7 @@ platforms:
         run: |
           pip install "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
       - type: python
         upgrade: false
         packages:

src/labels_transfer/knn/config.vsh.yaml

@@ -42,11 +42,11 @@ platforms:
           - liblapack-dev
           - gfortran
       - type: python
+        __merge__: [/src/base/requirements/scanpy.yaml, .]
         packages:
           - pynndescent~=0.5.8
           - numba~=0.56.4
           - numpy~=1.23.5
-          - scanpy~=1.9.1
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/labels_transfer/xgboost/config.vsh.yaml

@@ -130,11 +130,11 @@ platforms:
           - liblapack-dev
           - gfortran
       - type: python
+        __merge__: [/src/base/requirements/scanpy.yaml, .]
         packages:
           - xgboost~=1.7.1
           - scikit-learn~=1.1.1
           - numpy~=1.23.5
-          - scanpy~=1.9.1
           - pandas~=1.4.4
     test_setup:
       - type: python

src/neighbors/bbknn/config.vsh.yaml

@@ -88,9 +88,8 @@ platforms:
           - procps
           - build-essential
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
-          - scanpy~=1.9.2 # Will result in NameError: name 'logg' is not defined otherwise
           - bbknn
           - scikit-learn~=1.2.2
     test_setup:

src/neighbors/find_neighbors/config.vsh.yaml

@@ -93,9 +93,7 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/process_10xh5/filter_10xh5/config.vsh.yaml

@@ -53,9 +53,7 @@ platforms:
       - type: apt
         packages: libhdf5-dev python3-pip python3-dev
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages: 
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
       - type: r
         cran: [ testthat, anndata, hdf5r ]
   - type: nextflow

src/qc/calculate_qc_metrics/config.vsh.yaml

@@ -96,9 +96,7 @@ platforms:
           - scikit-learn~=1.2.0
     test_setup:
       - type: python
-        __merge__: [ /src/base/requirements/viashpy.yaml, .]
-        packages: 
-          - scanpy~=1.9.2
+        __merge__: [ /src/base/requirements/viashpy.yaml, /src/base/requirements/scanpy.yaml, .]
   - type: nextflow
     directives:
       label: [singlecpu, midmem]

src/transform/clr/config.vsh.yaml

@@ -50,10 +50,9 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages:
           - muon~=0.1.5
-          - scanpy~=1.9.2
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/transform/log1p/config.vsh.yaml

@@ -69,9 +69,7 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/transform/normalize_total/config.vsh.yaml

@@ -78,9 +78,7 @@ platforms:
           - libhdf5-dev
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/transform/regress_out/config.vsh.yaml

@@ -53,9 +53,7 @@ platforms:
         packages: 
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/transform/scaling/config.vsh.yaml

@@ -60,9 +60,7 @@ platforms:
           - libhdf5-dev
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
-        packages:
-          - scanpy~=1.9.2
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
     test_setup:
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]

src/velocity/velocyto_to_h5mu/config.vsh.yaml

@@ -69,9 +69,8 @@ platforms:
         packages:
           - procps
       - type: python
-        __merge__: [/src/base/requirements/anndata_mudata.yaml, .]
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
         packages: 
-          - scanpy~=1.9.2
           - loompy
   - type: nextflow
     directives: