diff --git a/.gitmodules b/.gitmodules index 58e5fdb..97b3552 100644 --- 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 index cfdc001..dde7893 100644 --- 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 index 558dbbb..dfc13d1 100644 --- 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 \ No newline at end of file diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml index e0c364f..d333524 100644 --- 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 index 35125b2..a72684c 100644 --- 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 deleted file mode 160000 index 81d4268..0000000 --- a/src/common +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 81d42682169dcf3990f26a9865d658baf67e6335 diff --git a/src/dataset_simulator/config.vsh.yaml b/src/dataset_simulator/config.vsh.yaml index 1ad5b88..af9b429 100644 --- 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 index 51a8565..c430b01 100644 --- 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 b/src/scripts/add_component.sh similarity index 100% rename from scripts/add_component.sh rename to src/scripts/add_component.sh diff --git a/scripts/build_components.sh b/src/scripts/build_components.sh similarity index 100% rename from scripts/build_components.sh rename to src/scripts/build_components.sh diff --git a/scripts/download_resources.sh b/src/scripts/download_resources.sh similarity index 100% rename from scripts/download_resources.sh rename to src/scripts/download_resources.sh diff --git a/scripts/render_readme.sh b/src/scripts/render_readme.sh similarity index 100% rename from scripts/render_readme.sh rename to src/scripts/render_readme.sh diff --git a/scripts/run_benchmark.sh b/src/scripts/run_benchmark.sh similarity index 100% rename from scripts/run_benchmark.sh rename to src/scripts/run_benchmark.sh diff --git a/scripts/run_benchmark_tw.sh b/src/scripts/run_benchmark_tw.sh similarity index 100% rename from scripts/run_benchmark_tw.sh rename to src/scripts/run_benchmark_tw.sh diff --git a/scripts/test_components.sh b/src/scripts/test_components.sh similarity index 100% rename from scripts/test_components.sh rename to src/scripts/test_components.sh diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml index 70ddd37..47f3332 100644 --- 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