move scripts into bfabric_scripts namespace package

fgcz · Oct 3, 2024 · 6479df1 · 6479df1
1 parent 0656797
commit 6479df1
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Showing 34 changed files with 25 additions and 25 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -53,31 +53,31 @@ Homepage = "https://github.com/fgcz/bfabricPy"
 Repository = "https://github.com/fgcz/bfabricPy"
 
 [project.scripts]
-"bfabric_flask.py"="bfabric.scripts.bfabric_flask:main"
-#bfabric_feeder_resource_autoQC="bfabric.scripts.bfabric_feeder_resource_autoQC:main"
-"bfabric_list_not_existing_storage_directories.py"="bfabric.scripts.bfabric_list_not_existing_storage_directories:main"
-"bfabric_list_not_available_proteomics_workunits.py"="bfabric.scripts.bfabric_list_not_available_proteomics_workunits:main"
-"bfabric_list_workunit_parameters.py"="bfabric.scripts.bfabric_list_workunit_parameters:main"
-"bfabric_upload_resource.py"="bfabric.scripts.bfabric_upload_resource:main"
-"bfabric_logthis.py"="bfabric.scripts.bfabric_logthis:main"
-"bfabric_setResourceStatus_available.py"="bfabric.scripts.bfabric_setResourceStatus_available:main"
-"bfabric_setExternalJobStatus_done.py"="bfabric.scripts.bfabric_setExternalJobStatus_done:main"
-"bfabric_setWorkunitStatus_available.py"="bfabric.scripts.bfabric_setWorkunitStatus:main_available"
-"bfabric_setWorkunitStatus_processing.py"="bfabric.scripts.bfabric_setWorkunitStatus:main_processing"
-"bfabric_setWorkunitStatus_failed.py"="bfabric.scripts.bfabric_setWorkunitStatus:main_failed"
-"bfabric_delete.py"="bfabric.scripts.bfabric_delete:main"
-"bfabric_read.py"="bfabric.scripts.bfabric_read:main"
-"bfabric_read_samples_of_workunit.py"="bfabric.scripts.bfabric_read_samples_of_workunit:main"
-"bfabric_read_samples_from_dataset.py"="bfabric.scripts.bfabric_read_samples_from_dataset:main"
-"bfabric_save_csv2dataset.py"="bfabric.scripts.bfabric_save_csv2dataset:main"
-"bfabric_save_dataset2csv.py"="bfabric.scripts.bfabric_save_dataset2csv:main"
-"bfabric_save_fasta.py"="bfabric.scripts.bfabric_save_fasta:main"
-"bfabric_save_importresource_sample.py"="bfabric.scripts.bfabric_save_importresource_sample:main"
-"bfabric_save_link_to_workunit.py"="bfabric.scripts.bfabric_save_link_to_workunit:main"
-#bfabric_save_resource="bfabric.scripts.bfabric_save_resource:main"
-"bfabric_save_workunit_attribute.py"="bfabric.scripts.bfabric_save_workunit_attribute:main"
-"bfabric_save_workflowstep.py"="bfabric.scripts.bfabric_save_workflowstep:main"
-"bfabric_slurm_queue_status.py"="bfabric.scripts.bfabric_slurm_queue_status:main"
+"bfabric_flask.py"="bfabric_scripts.bfabric_flask:main"
+#bfabric_feeder_resource_autoQC="bfabric_scripts.bfabric_feeder_resource_autoQC:main"
+"bfabric_list_not_existing_storage_directories.py"="bfabric_scripts.bfabric_list_not_existing_storage_directories:main"
+"bfabric_list_not_available_proteomics_workunits.py"="bfabric_scripts.bfabric_list_not_available_proteomics_workunits:main"
+"bfabric_list_workunit_parameters.py"="bfabric_scripts.bfabric_list_workunit_parameters:main"
+"bfabric_upload_resource.py"="bfabric_scripts.bfabric_upload_resource:main"
+"bfabric_logthis.py"="bfabric_scripts.bfabric_logthis:main"
+"bfabric_setResourceStatus_available.py"="bfabric_scripts.bfabric_setResourceStatus_available:main"
+"bfabric_setExternalJobStatus_done.py"="bfabric_scripts.bfabric_setExternalJobStatus_done:main"
+"bfabric_setWorkunitStatus_available.py"="bfabric_scripts.bfabric_setWorkunitStatus:main_available"
+"bfabric_setWorkunitStatus_processing.py"="bfabric_scripts.bfabric_setWorkunitStatus:main_processing"
+"bfabric_setWorkunitStatus_failed.py"="bfabric_scripts.bfabric_setWorkunitStatus:main_failed"
+"bfabric_delete.py"="bfabric_scripts.bfabric_delete:main"
+"bfabric_read.py"="bfabric_scripts.bfabric_read:main"
+"bfabric_read_samples_of_workunit.py"="bfabric_scripts.bfabric_read_samples_of_workunit:main"
+"bfabric_read_samples_from_dataset.py"="bfabric_scripts.bfabric_read_samples_from_dataset:main"
+"bfabric_save_csv2dataset.py"="bfabric_scripts.bfabric_save_csv2dataset:main"
+"bfabric_save_dataset2csv.py"="bfabric_scripts.bfabric_save_dataset2csv:main"
+"bfabric_save_fasta.py"="bfabric_scripts.bfabric_save_fasta:main"
+"bfabric_save_importresource_sample.py"="bfabric_scripts.bfabric_save_importresource_sample:main"
+"bfabric_save_link_to_workunit.py"="bfabric_scripts.bfabric_save_link_to_workunit:main"
+#bfabric_save_resource="bfabric_scripts.bfabric_save_resource:main"
+"bfabric_save_workunit_attribute.py"="bfabric_scripts.bfabric_save_workunit_attribute:main"
+"bfabric_save_workflowstep.py"="bfabric_scripts.bfabric_save_workflowstep:main"
+"bfabric_slurm_queue_status.py"="bfabric_scripts.bfabric_slurm_queue_status:main"
 
 [tool.black]
 line-length = 120

diff --git a/src/bfabric/scripts/__init__.py → src/bfabric_scripts/__init__.py b/src/bfabric/scripts/__init__.py → src/bfabric_scripts/__init__.py
diff --git a/src/bfabric/scripts/bfabric_delete.py → src/bfabric_scripts/bfabric_delete.py b/src/bfabric/scripts/bfabric_delete.py → src/bfabric_scripts/bfabric_delete.py
diff --git a/...ic_executable_submitter_functionalTest.py → ...ic_executable_submitter_functionalTest.py b/...ic_executable_submitter_functionalTest.py → ...ic_executable_submitter_functionalTest.py
diff --git a/...fabric_executable_submitter_gridengine.py → ...fabric_executable_submitter_gridengine.py b/...fabric_executable_submitter_gridengine.py → ...fabric_executable_submitter_gridengine.py
diff --git a/...pts/bfabric_executable_submitter_slurm.py → ...pts/bfabric_executable_submitter_slurm.py b/...pts/bfabric_executable_submitter_slurm.py → ...pts/bfabric_executable_submitter_slurm.py
diff --git a/...ipts/bfabric_executable_wrappercreator.py → ...ipts/bfabric_executable_wrappercreator.py b/...ipts/bfabric_executable_wrappercreator.py → ...ipts/bfabric_executable_wrappercreator.py
diff --git a/src/bfabric/scripts/bfabric_feeder_mascot.py → src/bfabric_scripts/bfabric_feeder_mascot.py b/src/bfabric/scripts/bfabric_feeder_mascot.py → src/bfabric_scripts/bfabric_feeder_mascot.py
diff --git a/...scripts/bfabric_feeder_resource_autoQC.py → ...scripts/bfabric_feeder_resource_autoQC.py b/...scripts/bfabric_feeder_resource_autoQC.py → ...scripts/bfabric_feeder_resource_autoQC.py
diff --git a/src/bfabric/scripts/bfabric_flask.py → src/bfabric_scripts/bfabric_flask.py b/src/bfabric/scripts/bfabric_flask.py → src/bfabric_scripts/bfabric_flask.py
diff --git a/...ist_not_available_proteomics_workunits.py → ...ist_not_available_proteomics_workunits.py b/...ist_not_available_proteomics_workunits.py → ...ist_not_available_proteomics_workunits.py
diff --git a/..._list_not_existing_storage_directories.py → ..._list_not_existing_storage_directories.py b/..._list_not_existing_storage_directories.py → ..._list_not_existing_storage_directories.py
diff --git a/...ripts/bfabric_list_workunit_parameters.py → ...ripts/bfabric_list_workunit_parameters.py b/...ripts/bfabric_list_workunit_parameters.py → ...ripts/bfabric_list_workunit_parameters.py
diff --git a/src/bfabric/scripts/bfabric_logthis.py → src/bfabric_scripts/bfabric_logthis.py b/src/bfabric/scripts/bfabric_logthis.py → src/bfabric_scripts/bfabric_logthis.py
diff --git a/src/bfabric/scripts/bfabric_read.py → src/bfabric_scripts/bfabric_read.py b/src/bfabric/scripts/bfabric_read.py → src/bfabric_scripts/bfabric_read.py
diff --git a/...ipts/bfabric_read_samples_from_dataset.py → ...ipts/bfabric_read_samples_from_dataset.py b/...ipts/bfabric_read_samples_from_dataset.py → ...ipts/bfabric_read_samples_from_dataset.py
diff --git a/...ripts/bfabric_read_samples_of_workunit.py → ...ripts/bfabric_read_samples_of_workunit.py b/...ripts/bfabric_read_samples_of_workunit.py → ...ripts/bfabric_read_samples_of_workunit.py
diff --git a/...abric/scripts/bfabric_save_csv2dataset.py → ...abric_scripts/bfabric_save_csv2dataset.py b/...abric/scripts/bfabric_save_csv2dataset.py → ...abric_scripts/bfabric_save_csv2dataset.py
diff --git a/...abric/scripts/bfabric_save_dataset2csv.py → ...abric_scripts/bfabric_save_dataset2csv.py b/...abric/scripts/bfabric_save_dataset2csv.py → ...abric_scripts/bfabric_save_dataset2csv.py
diff --git a/src/bfabric/scripts/bfabric_save_fasta.py → src/bfabric_scripts/bfabric_save_fasta.py b/src/bfabric/scripts/bfabric_save_fasta.py → src/bfabric_scripts/bfabric_save_fasta.py
diff --git a/...pts/bfabric_save_importresource_sample.py → ...pts/bfabric_save_importresource_sample.py b/...pts/bfabric_save_importresource_sample.py → ...pts/bfabric_save_importresource_sample.py
diff --git a/.../scripts/bfabric_save_link_to_workunit.py → ..._scripts/bfabric_save_link_to_workunit.py b/.../scripts/bfabric_save_link_to_workunit.py → ..._scripts/bfabric_save_link_to_workunit.py
diff --git a/...bric/scripts/bfabric_save_workflowstep.py → ...bric_scripts/bfabric_save_workflowstep.py b/...bric/scripts/bfabric_save_workflowstep.py → ...bric_scripts/bfabric_save_workflowstep.py
diff --git a/...cripts/bfabric_save_workunit_attribute.py → ...cripts/bfabric_save_workunit_attribute.py b/...cripts/bfabric_save_workunit_attribute.py → ...cripts/bfabric_save_workunit_attribute.py
diff --git a/...ipts/bfabric_setExternalJobStatus_done.py → ...ipts/bfabric_setExternalJobStatus_done.py b/...ipts/bfabric_setExternalJobStatus_done.py → ...ipts/bfabric_setExternalJobStatus_done.py
diff --git a/...ts/bfabric_setResourceStatus_available.py → ...ts/bfabric_setResourceStatus_available.py b/...ts/bfabric_setResourceStatus_available.py → ...ts/bfabric_setResourceStatus_available.py
diff --git a/...bric/scripts/bfabric_setWorkunitStatus.py → ...bric_scripts/bfabric_setWorkunitStatus.py b/...bric/scripts/bfabric_setWorkunitStatus.py → ...bric_scripts/bfabric_setWorkunitStatus.py
diff --git a/...ric/scripts/bfabric_slurm_queue_status.py → ...ric_scripts/bfabric_slurm_queue_status.py b/...ric/scripts/bfabric_slurm_queue_status.py → ...ric_scripts/bfabric_slurm_queue_status.py
diff --git a/...fabric/scripts/bfabric_upload_resource.py → ...fabric_scripts/bfabric_upload_resource.py b/...fabric/scripts/bfabric_upload_resource.py → ...fabric_scripts/bfabric_upload_resource.py
diff --git a/...ts/bfabric_upload_submitter_executable.py → ...ts/bfabric_upload_submitter_executable.py b/...ts/bfabric_upload_submitter_executable.py → ...ts/bfabric_upload_submitter_executable.py
diff --git a/...c/scripts/bfabric_wrapper_creator_yaml.py → ...c_scripts/bfabric_wrapper_creator_yaml.py b/...c/scripts/bfabric_wrapper_creator_yaml.py → ...c_scripts/bfabric_wrapper_creator_yaml.py
diff --git a/...scripts/fgcz_maxquant_scaffold-wrapper.py → ...scripts/fgcz_maxquant_scaffold-wrapper.py b/...scripts/fgcz_maxquant_scaffold-wrapper.py → ...scripts/fgcz_maxquant_scaffold-wrapper.py
diff --git a/src/bfabric/scripts/fgcz_maxquant_wrapper.py → src/bfabric_scripts/fgcz_maxquant_wrapper.py b/src/bfabric/scripts/fgcz_maxquant_wrapper.py → src/bfabric_scripts/fgcz_maxquant_wrapper.py
diff --git a/...bric/scripts/fgcz_sge_maxquant_linux.bash → ...bric_scripts/fgcz_sge_maxquant_linux.bash b/...bric/scripts/fgcz_sge_maxquant_linux.bash → ...bric_scripts/fgcz_sge_maxquant_linux.bash