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ccc profiling: simple file renaming
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@miltondp
miltondp committed Sep 7, 2023
1 parent 1e04d45 commit b80ed91
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Showing 21 changed files with 116 additions and 86 deletions.
0 ...ling/12_cm_optimized/06-cm_many_genes.txt → ...optimized/06_00-default-cm_many_genes.txt
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37 changes: 21 additions & 16 deletions ...iling/12_cm_optimized/06-many_genes.ipynb → ..._optimized/06_00-default-many_genes.ipynb
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"tags": []
},
"source": [
"Clustermatch run using a larger number of genes."
"CCC run using a larger number of genes."
]
},
{
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"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code\r\n"
"/opt/code\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code/libs/ccc/coef/__pycache__\r\n",
"/opt/code/libs/ccc/pytorch/__pycache__\r\n",
"/opt/code/libs/ccc/scipy/__pycache__\r\n",
"/opt/code/libs/ccc/utils/__pycache__\r\n",
"/opt/code/libs/ccc/__pycache__\r\n",
"/opt/code/libs/ccc/sklearn/__pycache__\r\n"
"/opt/code/libs/ccc/coef/__pycache__\n",
"/opt/code/libs/ccc/pytorch/__pycache__\n",
"/opt/code/libs/ccc/scipy/__pycache__\n",
"/opt/code/libs/ccc/utils/__pycache__\n",
"/opt/code/libs/ccc/__pycache__\n",
"/opt/code/libs/ccc/sklearn/__pycache__\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"find: ‘/opt/code/libs/ccc/coef/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/pytorch/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/scipy/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/utils/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/sklearn/__pycache__’: No such file or directory\r\n"
"find: ‘/opt/code/libs/ccc/coef/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/pytorch/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/scipy/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/utils/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/sklearn/__pycache__’: No such file or directory\n"
]
}
],
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}
],
"source": [
"%%prun -s cumulative -l 50 -T 06-cm_many_genes.txt\n",
"%%prun -s cumulative -l 50 -T 06_00-default-cm_many_genes.txt\n",
"func()"
]
},
Expand All @@ -588,7 +588,12 @@
"metadata": {
"jupytext": {
"cell_metadata_filter": "all,-execution,-papermill,-trusted",
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
"text_representation": {
"extension": ".py",
"format_name": "percent",
"format_version": "1.3"
}
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
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0 ...ling/12_cm_optimized/08-cm_many_genes.txt → ...zed/06_01-disable_numba-cm_many_genes.txt
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23 changes: 14 additions & 9 deletions ...iling/12_cm_optimized/08-many_genes.ipynb → ...ized/06_01-disable_numba-many_genes.ipynb
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Expand Up @@ -186,7 +186,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code\r\n"
"/opt/code\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code/libs/ccc/coef/__pycache__\r\n",
"/opt/code/libs/ccc/pytorch/__pycache__\r\n",
"/opt/code/libs/ccc/scipy/__pycache__\r\n",
"/opt/code/libs/ccc/utils/__pycache__\r\n",
"/opt/code/libs/ccc/__pycache__\r\n",
"/opt/code/libs/ccc/sklearn/__pycache__\r\n"
"/opt/code/libs/ccc/coef/__pycache__\n",
"/opt/code/libs/ccc/pytorch/__pycache__\n",
"/opt/code/libs/ccc/scipy/__pycache__\n",
"/opt/code/libs/ccc/utils/__pycache__\n",
"/opt/code/libs/ccc/__pycache__\n",
"/opt/code/libs/ccc/sklearn/__pycache__\n"
]
}
],
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}
],
"source": [
"%%prun -s cumulative -l 50 -T 08-cm_many_genes.txt\n",
"%%prun -s cumulative -l 50 -T 06_01-disable_numba-cm_many_genes.txt\n",
"func()"
]
},
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"metadata": {
"jupytext": {
"cell_metadata_filter": "all,-execution,-papermill,-trusted",
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
"text_representation": {
"extension": ".py",
"format_name": "percent",
"format_version": "1.3"
}
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
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0 ...ling/12_cm_optimized/10-cm_many_genes.txt → ...zed/06_02-use_ari_numba-cm_many_genes.txt
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37 changes: 21 additions & 16 deletions ...timized/10-many_genes-use_ari_numba.ipynb → ...ized/06_02-use_ari_numba-many_genes.ipynb
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Expand Up @@ -31,7 +31,7 @@
"tags": []
},
"source": [
"Clustermatch run using a larger number of genes."
"CCC run using a larger number of genes with `use_ari_numba=True`."
]
},
{
Expand Down Expand Up @@ -136,7 +136,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code\r\n"
"/opt/code\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code/libs/ccc/coef/__pycache__\r\n",
"/opt/code/libs/ccc/pytorch/__pycache__\r\n",
"/opt/code/libs/ccc/scipy/__pycache__\r\n",
"/opt/code/libs/ccc/utils/__pycache__\r\n",
"/opt/code/libs/ccc/__pycache__\r\n",
"/opt/code/libs/ccc/sklearn/__pycache__\r\n"
"/opt/code/libs/ccc/coef/__pycache__\n",
"/opt/code/libs/ccc/pytorch/__pycache__\n",
"/opt/code/libs/ccc/scipy/__pycache__\n",
"/opt/code/libs/ccc/utils/__pycache__\n",
"/opt/code/libs/ccc/__pycache__\n",
"/opt/code/libs/ccc/sklearn/__pycache__\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"find: ‘/opt/code/libs/ccc/coef/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/pytorch/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/scipy/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/utils/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/__pycache__’: No such file or directory\r\n",
"find: ‘/opt/code/libs/ccc/sklearn/__pycache__’: No such file or directory\r\n"
"find: ‘/opt/code/libs/ccc/coef/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/pytorch/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/scipy/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/utils/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/__pycache__’: No such file or directory\n",
"find: ‘/opt/code/libs/ccc/sklearn/__pycache__’: No such file or directory\n"
]
}
],
Expand Down Expand Up @@ -563,7 +563,7 @@
}
],
"source": [
"%%prun -s cumulative -l 50 -T 10-cm_many_genes.txt\n",
"%%prun -s cumulative -l 50 -T 06_02-use_ari_numba-cm_many_genes.txt\n",
"func()"
]
},
Expand All @@ -588,7 +588,12 @@
"metadata": {
"jupytext": {
"cell_metadata_filter": "all,-execution,-papermill,-trusted",
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
"text_representation": {
"extension": ".py",
"format_name": "percent",
"format_version": "1.3"
}
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
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0 ...y_samples-default_internal_n_clusters.txt → ...y_samples-default_internal_n_clusters.txt
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0 ...many_samples-less_internal_n_clusters.txt → ...many_samples-less_internal_n_clusters.txt
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27 changes: 16 additions & 11 deletions ...ing/12_cm_optimized/07-many_samples.ipynb → ...ptimized/07_00-default-many_samples.ipynb
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Expand Up @@ -31,7 +31,7 @@
"tags": []
},
"source": [
"Clustermatch run using a larger number of samples."
"CCC run using a larger number of samples."
]
},
{
Expand Down Expand Up @@ -136,7 +136,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code\r\n"
"/opt/code\n"
]
}
],
Expand Down Expand Up @@ -169,12 +169,12 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code/libs/ccc/coef/__pycache__\r\n",
"/opt/code/libs/ccc/pytorch/__pycache__\r\n",
"/opt/code/libs/ccc/scipy/__pycache__\r\n",
"/opt/code/libs/ccc/utils/__pycache__\r\n",
"/opt/code/libs/ccc/__pycache__\r\n",
"/opt/code/libs/ccc/sklearn/__pycache__\r\n"
"/opt/code/libs/ccc/coef/__pycache__\n",
"/opt/code/libs/ccc/pytorch/__pycache__\n",
"/opt/code/libs/ccc/scipy/__pycache__\n",
"/opt/code/libs/ccc/utils/__pycache__\n",
"/opt/code/libs/ccc/__pycache__\n",
"/opt/code/libs/ccc/sklearn/__pycache__\n"
]
}
],
Expand Down Expand Up @@ -550,7 +550,7 @@
}
],
"source": [
"%%prun -s cumulative -l 50 -T 07-cm_many_samples-default_internal_n_clusters.txt\n",
"%%prun -s cumulative -l 50 -T 07_00-default-cm_many_samples-default_internal_n_clusters.txt\n",
"func()"
]
},
Expand Down Expand Up @@ -663,7 +663,7 @@
}
],
"source": [
"%%prun -s cumulative -l 50 -T 07-cm_many_samples-less_internal_n_clusters.txt\n",
"%%prun -s cumulative -l 50 -T 07_00-default-cm_many_samples-less_internal_n_clusters.txt\n",
"func()"
]
},
Expand All @@ -688,7 +688,12 @@
"metadata": {
"jupytext": {
"cell_metadata_filter": "all,-execution,-papermill,-trusted",
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
"text_representation": {
"extension": ".py",
"format_name": "percent",
"format_version": "1.3"
}
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
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0 ...y_samples-default_internal_n_clusters.txt → ...y_samples-default_internal_n_clusters.txt
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0 ...many_samples-less_internal_n_clusters.txt → ...many_samples-less_internal_n_clusters.txt
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25 changes: 15 additions & 10 deletions ...ing/12_cm_optimized/09-many_samples.ipynb → ...ed/07_01-disable_numba-many_samples.ipynb
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Expand Up @@ -186,7 +186,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code\r\n"
"/opt/code\n"
]
}
],
Expand Down Expand Up @@ -219,12 +219,12 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/code/libs/ccc/coef/__pycache__\r\n",
"/opt/code/libs/ccc/pytorch/__pycache__\r\n",
"/opt/code/libs/ccc/scipy/__pycache__\r\n",
"/opt/code/libs/ccc/utils/__pycache__\r\n",
"/opt/code/libs/ccc/__pycache__\r\n",
"/opt/code/libs/ccc/sklearn/__pycache__\r\n"
"/opt/code/libs/ccc/coef/__pycache__\n",
"/opt/code/libs/ccc/pytorch/__pycache__\n",
"/opt/code/libs/ccc/scipy/__pycache__\n",
"/opt/code/libs/ccc/utils/__pycache__\n",
"/opt/code/libs/ccc/__pycache__\n",
"/opt/code/libs/ccc/sklearn/__pycache__\n"
]
}
],
Expand Down Expand Up @@ -600,7 +600,7 @@
}
],
"source": [
"%%prun -s cumulative -l 50 -T 09-cm_many_samples-default_internal_n_clusters.txt\n",
"%%prun -s cumulative -l 50 -T 07_01-disable_numba-cm_many_samples-default_internal_n_clusters.txt\n",
"func()"
]
},
Expand Down Expand Up @@ -730,7 +730,7 @@
}
],
"source": [
"%%prun -s cumulative -l 50 -T 09-cm_many_samples-less_internal_n_clusters.txt\n",
"%%prun -s cumulative -l 50 -T 07_01-disable_numba-cm_many_samples-less_internal_n_clusters.txt\n",
"func()"
]
},
Expand Down Expand Up @@ -772,7 +772,12 @@
"metadata": {
"jupytext": {
"cell_metadata_filter": "all,-execution,-papermill,-trusted",
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
"notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
"text_representation": {
"extension": ".py",
"format_name": "percent",
"format_version": "1.3"
}
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
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0 ...y_samples-default_internal_n_clusters.txt → ...y_samples-default_internal_n_clusters.txt
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0 ...many_samples-less_internal_n_clusters.txt → ...many_samples-less_internal_n_clusters.txt
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