move common submodules out of scr

openproblems-bio · Jun 7, 2024 · e5a5845 · e5a5845
1 parent 2aefb0d
commit e5a5845
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Showing 16 changed files with 13 additions and 11 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,6 @@
 [submodule "src/common"]
 	path = src/common
 	url = https://github.com/openproblems-bio/common-resources.git
+[submodule "common"]
+	path = common
+	url = https://github.com/openproblems-bio/common-resources.git
diff --git a/src/api/comp_control_method.yaml b/src/api/comp_control_method.yaml
@@ -30,9 +30,9 @@ functionality:
       required: true
   test_resources:
     - type: python_script
-      path: /src/common/component_tests/check_method_config.py
+      path: /common/component_tests/check_method_config.py
     - type: python_script
-      path: /src/common/component_tests/run_and_check_output.py
+      path: /common/component_tests/run_and_check_output.py
     - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas
       dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas
     - path: /common/library.bib
diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml
@@ -21,9 +21,9 @@ functionality:
       required: true
   test_resources:
     - type: python_script
-      path: /src/common/component_tests/check_method_config.py
+      path: /common/component_tests/check_method_config.py
     - type: python_script
-      path: /src/common/component_tests/run_and_check_output.py
+      path: /common/component_tests/run_and_check_output.py
     - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas
       dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas
     - path: /common/library.bib
diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
@@ -22,9 +22,9 @@ functionality:
       required: true
   test_resources:
     - type: python_script
-      path: /src/common/component_tests/check_metric_config.py
+      path: /common/component_tests/check_metric_config.py
     - type: python_script
-      path: /src/common/component_tests/run_and_check_output.py
+      path: /common/component_tests/run_and_check_output.py
     - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas
       dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas
     - path: /common/library.bib

diff --git a/src/api/comp_process_dataset.yaml b/src/api/comp_process_dataset.yaml
@@ -26,7 +26,7 @@ functionality:
       required: true
   test_resources:
     - type: python_script
-      path: /src/common/component_tests/run_and_check_output.py
+      path: /common/component_tests/run_and_check_output.py
     # - path: /resources_test/common/cxg_mouse_pancreas_atlas
     #   dest: resources_test/common/cxg_mouse_pancreas_atlas
     - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas

diff --git a/src/common b/src/common
diff --git a/src/dataset_simulator/config.vsh.yaml b/src/dataset_simulator/config.vsh.yaml
@@ -185,7 +185,7 @@ functionality:
       path: script.py
   test_resources:
     - type: python_script
-      path: /src/common/component_tests/run_and_check_output.py
+      path: /common/component_tests/run_and_check_output.py
     - path: /resources_test/common/cxg_mouse_pancreas_atlas
       dest: resources_test/common/cxg_mouse_pancreas_atlas
 platforms:

diff --git a/src/process_dataset/split_dataset/config.vsh.yaml b/src/process_dataset/split_dataset/config.vsh.yaml
@@ -4,7 +4,7 @@ functionality:
   resources:
     - type: python_script
       path: script.py
-    - path: /src/common/helper_functions/subset_anndata.py
+    - path: /common/helper_functions/subset_anndata.py
 platforms:
   - type: docker
     image: ghcr.io/openproblems-bio/base_python:1.0.4

diff --git a/scripts/add_component.sh → src/scripts/add_component.sh b/scripts/add_component.sh → src/scripts/add_component.sh
diff --git a/scripts/build_components.sh → src/scripts/build_components.sh b/scripts/build_components.sh → src/scripts/build_components.sh
diff --git a/scripts/download_resources.sh → src/scripts/download_resources.sh b/scripts/download_resources.sh → src/scripts/download_resources.sh
diff --git a/scripts/render_readme.sh → src/scripts/render_readme.sh b/scripts/render_readme.sh → src/scripts/render_readme.sh
diff --git a/scripts/run_benchmark.sh → src/scripts/run_benchmark.sh b/scripts/run_benchmark.sh → src/scripts/run_benchmark.sh
diff --git a/scripts/run_benchmark_tw.sh → src/scripts/run_benchmark_tw.sh b/scripts/run_benchmark_tw.sh → src/scripts/run_benchmark_tw.sh
diff --git a/scripts/test_components.sh → src/scripts/test_components.sh b/scripts/test_components.sh → src/scripts/test_components.sh
diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
@@ -34,7 +34,7 @@ functionality:
     - type: nextflow_script
       path: main.nf
       entrypoint: run_wf
-    - path: /src/common/nextflow_helpers/helper.nf
+    - path: /common/nextflow_helpers/helper.nf
   dependencies:
     - name: common/check_dataset_schema
       repository: openproblems_v2