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Update to v0.3.6
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@niklases
niklases committed Sep 21, 2024
1 parent 6bc8075 commit 03ae186
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Showing 36 changed files with 558 additions and 261,988 deletions.
4 changes: 2 additions & 2 deletions .gitattributes
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@@ -1,5 +1,5 @@
*.ipynb linguist-detectable=false
*.html linguist-detectable=false
#*.sto filter=lfs diff=lfs merge=lfs -text
*.sto filter=lfs diff=lfs merge=lfs -text
#*.csv filter=lfs diff=lfs merge=lfs -text
#*.params filter=lfs diff=lfs merge=lfs -text
*.params filter=lfs diff=lfs merge=lfs -text
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2 changes: 1 addition & 1 deletion .github/workflows/build.yml
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Expand Up @@ -14,7 +14,7 @@ jobs:
runs-on: [ubuntu-latest]
strategy:
matrix:
python-version: ["3.9", "3.10", "3.11"]
python-version: ["3.9", "3.10", "3.11", "3.12"]

steps:
- uses: actions/checkout@v4
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -388,3 +388,6 @@ avGFP_shortened_dca_encoded.csv
datasets/AVGFP/avGFP_shortened.csv
avGFP_dca_encoded.csv
scripts/Runtime_tests/runtimes.png
datasets/AVGFP/Recomb_Double_Split/Predictions_Hybrid_TopRecomb_Double_Split.txt
scripts/ProteinGym_runs/single_point_mut_performance_violin.png
scripts/ProteinGym_runs/multi_point_mut_performance_violin.png
93 changes: 81 additions & 12 deletions .vscode/launch.json
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Expand Up @@ -6,7 +6,7 @@
"configurations": [
{
"name": "Python: PyPEF Help",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -19,7 +19,7 @@

{
"name": "Python: PyPEF MKLSTS ANEH",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -35,7 +35,7 @@

{
"name": "Python: PyPEF MKLSTS avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -49,9 +49,26 @@
]
},

{
"name": "Python: PyPEF MKPS avGFP drecomb",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"mkps",
"--wt", "P42212_F64L.fasta",
"--input", "avGFP.csv",
"--drecomb"
]
},

{
"name": "Python: PyPEF ml -e onehot pls_loocv",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -73,7 +90,7 @@
// or
// 2. $pypef hybrid -m GREMLIN -t TS.fasl --params GREMLIN
"name": "Python: PyPEF save GREMLIN avGFP model",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -87,9 +104,27 @@
]
},

{
"name": "Python: PyPEF hybrid LS-TS GREMLIN-DCA avGFP",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"hybrid",
//"-m", "GREMLIN", // optional, not required
"--ls", "LS.fasl",
"--ts", "TS.fasl",
"--params", "GREMLIN"
]
},

{
"name": "Python: PyPEF hybrid/only-TS-zero-shot GREMLIN-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -106,7 +141,7 @@

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -121,11 +156,45 @@
]
},

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP drecomb II",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"hybrid",
"-m", "HYBRIDgremlin",
"--pmult", "--drecomb",
"--params", "GREMLIN"
]
},

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP drecomb",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"hybrid",
"-m", "GREMLIN",
"--pmult", "--drecomb",
"--params", "GREMLIN"
]
},

{ // PLMC zero-shot steps:
// 1. $pypef param_inference --params uref100_avgfp_jhmmer_119_plmc_42.6.params
// 2. $pypef hybrid -t TS.fasl --params PLMC
"name": "Python: PyPEF save PLMC avGFP model",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -140,7 +209,7 @@

{
"name": "Python: PyPEF hybrid/only-TS-zero-shot PLMC-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -157,7 +226,7 @@

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot PLMC-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -175,7 +244,7 @@

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot PLMC-DCA variant 2 avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -193,7 +262,7 @@

{
"name": "Python: PyPEF !wrong! MSA input format (STO)",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
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