update base images

openproblems-bio · Oct 11, 2024 · bf55247 · bf55247
1 parent d32a41c
commit bf55247
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Showing 15 changed files with 21 additions and 23 deletions.
diff --git a/src/control_methods/random_proportions/config.vsh.yaml b/src/control_methods/random_proportions/config.vsh.yaml
@@ -1,11 +1,11 @@
 __merge__: ../../api/comp_control_method.yaml
 
 name: random_proportions
+label: Random Proportions
+summary: "Negative control method that randomly assigns celltype proportions from a Dirichlet distribution."
+description: |
+  A negative control method with random assignment of predicted celltype proportions from a Dirichlet distribution.
 info:
-  label: Random Proportions
-  summary: "Negative control method that randomly assigns celltype proportions from a Dirichlet distribution."
-  description: |
-    A negative control method with random assignment of predicted celltype proportions from a Dirichlet distribution.
   preferred_normalization: counts
 
 resources:
@@ -14,7 +14,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: numpy

diff --git a/src/control_methods/true_proportions/config.vsh.yaml b/src/control_methods/true_proportions/config.vsh.yaml
@@ -14,7 +14,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
 
 runners:
   - type: executable

diff --git a/src/methods/cell2location/config.vsh.yaml b/src/methods/cell2location/config.vsh.yaml
@@ -70,7 +70,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: 

diff --git a/src/methods/destvi/config.vsh.yaml b/src/methods/destvi/config.vsh.yaml
@@ -27,7 +27,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
+    image: openproblems/base_pytorch_nvidia:1.0.0
     setup:
       - type: python
         packages: 

diff --git a/src/methods/nmfreg/config.vsh.yaml b/src/methods/nmfreg/config.vsh.yaml
@@ -23,7 +23,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: 

diff --git a/src/methods/nnls/config.vsh.yaml b/src/methods/nnls/config.vsh.yaml
@@ -17,7 +17,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: 

diff --git a/src/methods/rctd/config.vsh.yaml b/src/methods/rctd/config.vsh.yaml
@@ -27,7 +27,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.4
+    image: openproblems/base_r:1.0.0
     setup:
       - type: r
         cran: [ Matrix, pak ]

diff --git a/src/methods/seurat/config.vsh.yaml b/src/methods/seurat/config.vsh.yaml
@@ -27,7 +27,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.4
+    image: openproblems/base_r:1.0.0
     setup:
       - type: r
         cran: [Matrix, Seurat]

diff --git a/src/methods/stereoscope/config.vsh.yaml b/src/methods/stereoscope/config.vsh.yaml
@@ -28,7 +28,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
+    image: openproblems/base_pytorch_nvidia:1.0.0
     setup:
       - type: python
         packages: 

diff --git a/src/methods/tangram/config.vsh.yaml b/src/methods/tangram/config.vsh.yaml
@@ -27,7 +27,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: tangram-sc

diff --git a/src/methods/vanillanmf/config.vsh.yaml b/src/methods/vanillanmf/config.vsh.yaml
@@ -23,7 +23,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: 

diff --git a/src/metrics/jsd/config.vsh.yaml b/src/metrics/jsd/config.vsh.yaml
@@ -21,7 +21,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_images/python:1.1.0
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: [numpy, scipy]

diff --git a/src/metrics/r2/config.vsh.yaml b/src/metrics/r2/config.vsh.yaml
@@ -21,7 +21,7 @@ resources:
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: openproblems/base_python:1.0.0
     setup:
       - type: python
         packages: scikit-learn

diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
@@ -1,5 +1,5 @@
-namespace: "workflows"
-name: "process_datasets"
+namespace: workflows
+name: process_datasets
 argument_groups:
   - name: Inputs
     arguments:

diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
@@ -1,5 +1,5 @@
-name: "run_benchmark"
-namespace: "workflows"
+name: run_benchmark
+namespace: workflows
 argument_groups:
   - name: Inputs
     arguments:
@@ -47,8 +47,6 @@ resources:
   - type: nextflow_script
     path: main.nf
     entrypoint: run_wf
-  - type: file
-    path: "../../api/task_info.yaml"
 dependencies:
   - name: common/check_dataset_schema
     repository: openproblems_v2