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add upload_results as a config option #191

Merged
merged 14 commits into from
Sep 27, 2023
+18 −8
Merged

add upload_results as a config option #191

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f14bb6e
upload local recipes to S3
rugeli Aug 29, 2023
59b80b4
update README and add boto3 into requirements
rugeli Aug 29, 2023
565487c
lint
rugeli Aug 29, 2023
c97d5a8
rerange import order
rugeli Aug 29, 2023
d09b64a
add save_file for S3 uploads and url generation
rugeli Sep 6, 2023
2b22d68
delete redundant error msg
rugeli Sep 6, 2023
390d284
add "upload_results" in config files as an option
rugeli Sep 8, 2023
e96a996
conditionally call post_and_open_file
rugeli Sep 8, 2023
6cda9e7
add check `number_of_packings`
rugeli Sep 18, 2023
c5b9ec7
update conditional statement
rugeli Sep 25, 2023
89e9297
Merge branch 'main' into feature/upload-results-config-option
rugeli Sep 25, 2023
fa3665f
update
rugeli Sep 25, 2023
0ee1fb0
Merge branch 'feature/upload-results-config-option' of https://github…
rugeli Sep 25, 2023
17fd02f
Merge branch 'main' into feature/upload-results-config-option
rugeli Sep 26, 2023
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1 change: 1 addition & 0 deletions cellpack/autopack/loaders/config_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ class ConfigLoader(object):
"show_sphere_trees": False,
"show_progress_bar": False,
"spacing": None,
"upload_results": False,
"use_periodicity": False,
"version": 1.0,
}
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5 changes: 4 additions & 1 deletion cellpack/autopack/writers/__init__.py
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Expand Up @@ -185,7 +185,10 @@ def save_as_simularium(self, env, all_ingr_as_array, compartments):
file_name = env.helper.writeToFile(
env.result_file, env.boundingBox, env.name, env.version
)
autopack.helper.post_and_open_file(file_name)
if env.config_data.get(
"upload_results", env.config_data.get("number_of_packings", 1) <= 1
):
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two things: I don't thin env.config_data can ever be none, so I don't think you need that check
I think you could do 3 or less. I have run some multiple packings recently that I would like to see the results of.

autopack.helper.post_and_open_file(file_name)

def save_Mixed_asJson(
self,
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3 changes: 2 additions & 1 deletion cellpack/tests/packing-configs/test_parallel_config.json
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Expand Up @@ -14,5 +14,6 @@
"number_of_packings": 5,
"spacing": null,
"use_periodicity": false,
"show_sphere_trees": true
"show_sphere_trees": true,
"upload_results": false
}
3 changes: 2 additions & 1 deletion cellpack/tests/packing-configs/test_variable_count_config.json
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Expand Up @@ -13,5 +13,6 @@
"spacing": null,
"parallel": false,
"use_periodicity": false,
"show_sphere_trees": true
"show_sphere_trees": true,
"upload_results": false
}
3 changes: 2 additions & 1 deletion examples/packing-configs/pcna_parallel_packing_config.json
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Expand Up @@ -16,5 +16,6 @@
"show_progress_bar": true,
"spacing": 2.5,
"use_periodicity": false,
"show_sphere_trees": false
"show_sphere_trees": false,
"upload_results": false
}
3 changes: 2 additions & 1 deletion examples/packing-configs/peroxisome_packing_config.json
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Expand Up @@ -14,5 +14,6 @@
"spacing": 2.5,
"use_periodicity": false,
"show_sphere_trees": false,
"load_from_grid_file": false
"load_from_grid_file": true,
"upload_results": false
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all config settings should also have a default setting in the config loader

}
5 changes: 3 additions & 2 deletions examples/packing-configs/peroxisome_parallel_packing_config.json
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Expand Up @@ -18,7 +18,8 @@
"show_sphere_trees": false,
"image_export_options": {
"hollow": false,
"voxel_size": [1,1,1],
"voxel_size": [1, 1, 1],
"projection_axis": "z"
}
},
"upload_results": false
}
3 changes: 2 additions & 1 deletion examples/packing-configs/run.json
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Expand Up @@ -13,5 +13,6 @@
"use_periodicity": false,
"show_sphere_trees": false,
"load_from_grid_file": false,
"save_converted_recipe": true
"save_converted_recipe": true,
"upload_results": true
}
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