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Quick run_all_manuscript_workflow error catching #53

Merged
merged 10 commits into from
Dec 6, 2024
Merged

Quick run_all_manuscript_workflow error catching #53

merged 10 commits into from
Dec 6, 2024

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cfrick13
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@cfrick13 cfrick13 commented Dec 6, 2024 •
edited
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====== Successes ======
figure_3_s4_height_density (900.0s) (48.7GB)
figure_4_s8_volume_trajectories (66.4s) (24.1GB)
figure_5_s9_s10_local_growth (256.9s) (38.7GB)
figure_6_s11_compensation (106.4s) (24.1GB)
figure_7_s13_s14_lineage (295.8s) (24.2GB)
figure_s12_feeding_control (149.8s) (21.2GB)
figure_s15_linear_regression_model (939.2s) (24.1GB)
figure_s19_transition_point (18.7s) (24.1GB)
figure_s1_cell_health (18.4s) (21.2GB)
figure_s20_precision_error (14.9s) (5.2GB)
figure_s2_s3_s18_segmentation_model_validation (171.4s) (8.3GB)
figure_s6_s16_inhibitors (242.2s) (15.9GB)
figure_s7_growth_outliers (98.6s) (24.9GB)
====== Failures ======
figure_1_dataset (217.8s) (28.2GB). ValueError setting an array element with a sequence. The requested array has an inhomogeneous shape after 3 dimensions. T                                                  he detected shape was (1, 1, 2) + inhomogeneous part.. See stack trace above.
====== 13 succeeded 1 failed ======

chantelleleveille and others added 9 commits November 20, 2024 13:34
jcass11
jcass11 reviewed Dec 6, 2024
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nuc_morph_analysis/lib/preprocessing/global_dataset_filtering.py
@@ -393,7 +393,7 @@ def merge_datasets(df_all, df_full):
'resolution_level',
'2d_area_cyto',
'inv_cyto_density',
'density'
'density',
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Thank you!

jcass11
jcass11 reviewed Dec 6, 2024
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nuc_morph_analysis/lib/preprocessing/global_dataset_filtering.py
@@ -438,6 +438,8 @@ def remove_columns(df, column_list=COLUMNS_TO_DROP):
df : pandas.DataFrame
The dataframe with the columns removed.
"""
column_list = [col for col in column_list if col in df.columns]
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Thank you!

@jcass11
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jcass11 commented Dec 6, 2024

I think all the mypy errors are independent of the density specific edits I made and are relevant to the broader drafted changes made in the feature_documentation branch so I'm okay with leaving them for now and dealing with them in the feature_documentation branch after we merge the density deletion changes.

@cfrick13
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cfrick13 commented Dec 6, 2024

When I ran it from a fresh .venv

pdm run python run_all_manuscript_workflows.py --only figure_1_dataset

====== Successes ======
figure_1_dataset (419.3s) (46.2GB)
====== 1 succeeded  ======

@jcass11 jcass11 merged commit 08741ba into feature_doc_test_density Dec 6, 2024
1 check failed
@jcass11 jcass11 deleted the feature_doc_test_density_frick branch December 6, 2024 21:13
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@cfrick13 @jcass11 @chantelleleveille