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v0.3.6 merge 'dev' to 'main' #8

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merged 22 commits into from
Sep 21, 2024
Merged

v0.3.6 merge 'dev' to 'main' #8

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66f7fa1
0.3.5-dev started
niklases Aug 9, 2024
4075a2e
Dev Update DCAHybridModel:
niklases Aug 12, 2024
da21b7c
Update hybrid_model.py and variant_data.py
niklases Aug 14, 2024
30eb90f
Update License: CC BY-NC-SA 4.0 -> CC BY-SA 4.0
niklases Sep 3, 2024
b0bf4c0
Update README.md
niklases Sep 3, 2024
86b431f
Update LICENSE.md
niklases Sep 3, 2024
3da40f3
Update launch.json: Added mkps example arguments
niklases Sep 6, 2024
b70b6e0
Update launch.json
niklases Sep 6, 2024
1657455
Update hybrid model.py:
niklases Sep 6, 2024
616bf30
Dev: Update CLI run test script linux
niklases Sep 7, 2024
604f418
Dev: Update CLI run test script Windows
niklases Sep 7, 2024
fdc0506
Update .gitginore: datasets/AVGFP/Recomb_Double_Split/Predictions_Hyb…
niklases Sep 8, 2024
b125ee3
Out-commented command as takes too long (~2h)
niklases Sep 8, 2024
fc48afa
feat: add violin plot for PGym model performance test runs
niklases Sep 14, 2024
f70dc21
update PGym scripts README
niklases Sep 14, 2024
b5b8822
Add new PGym performance plots (violin plots) for N_Train = 0, 100, 2…
niklases Sep 16, 2024
5ecb918
Update README.md
niklases Sep 20, 2024
8dff626
Py 3.12 in build.yml
niklases Sep 20, 2024
300bb9c
Remove dca encoded CSV files so that on a next run no mv error occurs
niklases Sep 21, 2024
fb419ed
v0.3.5
niklases Sep 21, 2024
cf01ea4
v0.3.5 (2)
niklases Sep 21, 2024
02c9dad
v0.3.6 for Python 3.12 support
niklases Sep 21, 2024
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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",
Expand Down
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