bump base images to base_*:1.0.2 (#263)

openproblems-bio · Oct 12, 2023 · 2077e79 · 2077e79
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commit 2077e79
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Showing 87 changed files with 88 additions and 88 deletions.
diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml
@@ -48,7 +48,7 @@ functionality:
       path: test.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     test_setup:
       - type: python
         packages: viashpy

diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml
@@ -18,7 +18,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py
@@ -141,11 +141,11 @@ def generate_resources(par, script_path) -> str:
 def generate_docker_platform(par) -> str:
   """Set up the docker platform for Python."""
   if par["language"] == "python":
-    image_str = "ghcr.io/openproblems-bio/base_python:1.0.1"
+    image_str = "ghcr.io/openproblems-bio/base_python:1.0.2"
     setup_type = "python"
     package_example = "scib==1.1.3"
   elif par["language"] == "r":
-    image_str = "ghcr.io/openproblems-bio/base_r:1.0.1"
+    image_str = "ghcr.io/openproblems-bio/base_r:1.0.2"
     setup_type = "r"
     package_example = "tidyverse"
   return strip_margin(f'''\

diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml
@@ -33,7 +33,7 @@ functionality:
       dest: openproblems-v2/_viash.yaml
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64]

diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml
@@ -26,7 +26,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: [ tidyverse ]

diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml
@@ -8,7 +8,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: [ purrr, dplyr, yaml, rlang, processx ]

diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml
@@ -8,7 +8,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: [ purrr, dplyr, yaml, rlang, processx ]

diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml
@@ -8,7 +8,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: [ purrr, dplyr, yaml, rlang, processx ]

diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml
@@ -23,7 +23,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: [ tidyverse ]

diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml
@@ -8,6 +8,6 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
   - type: native
diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml
@@ -60,7 +60,7 @@ functionality:
       path: test.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: apt
         packages: git

diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml
@@ -68,7 +68,7 @@ functionality:
       path: test.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: apt
         packages: git

diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml
@@ -16,7 +16,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         packages:

diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml
@@ -12,7 +12,7 @@ functionality:
       description: "Number of counts per cell"
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
     directives: 
       label: [ "midtime", lowmem, lowcpu ]
diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml
@@ -7,7 +7,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: [ Matrix, rlang, bit64, scran, BiocParallel ]

diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml
@@ -12,7 +12,7 @@ functionality:
       description: "Number of counts per cell"
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
     directives: 
       label: [ "midtime", lowmem, lowcpu ]
diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml
@@ -7,5 +7,5 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml
@@ -7,5 +7,5 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml
@@ -11,5 +11,5 @@ functionality:
   #   - path: "../../../resources_test/common/pancreas"
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml
@@ -41,7 +41,7 @@ functionality:
     - path: /resources_test/common/pancreas
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     test_setup:
       - type: python
         packages:

diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml
@@ -7,7 +7,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi: [scikit-learn]

diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml
@@ -25,6 +25,6 @@ functionality:
       path: test.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
   - type: nextflow
   - type: native
diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml
@@ -32,7 +32,7 @@ functionality:
       path: test.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     test_setup:
       - type: docker
         run: "git clone https://github.com/openproblems-bio/openproblems-v2.git"

diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml
@@ -19,7 +19,7 @@ functionality:
       path: test.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi: git+https://github.com/sciunto-org/python-bibtexparser@main
diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml
@@ -15,7 +15,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.0
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml
@@ -15,7 +15,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.0
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml
@@ -19,7 +19,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.0
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml
@@ -15,7 +15,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.0
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml
@@ -26,7 +26,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml
@@ -29,7 +29,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi: 

diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml
@@ -19,7 +19,7 @@ functionality:
       path: script.R
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_r:1.0.1
+    image: ghcr.io/openproblems-bio/base_r:1.0.2
     setup:
       - type: r
         cran: rliger

diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml
@@ -23,7 +23,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml
@@ -24,7 +24,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml
@@ -24,7 +24,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml
@@ -33,7 +33,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml
@@ -21,7 +21,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml
@@ -38,7 +38,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml
@@ -26,7 +26,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml
@@ -35,7 +35,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml
@@ -49,7 +49,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml
@@ -35,7 +35,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml
@@ -34,7 +34,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml
@@ -28,7 +28,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi:

diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml
@@ -40,7 +40,7 @@ functionality:
       path: script.py
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.1
+    image: ghcr.io/openproblems-bio/base_python:1.0.2
     setup:
       - type: python
         pypi: