Skip to content

Commit 8ab8a48

Browse files
niklasesniklases
authored
Merge pull request #8 from niklases/dev
v0.3.6 merge 'dev' to 'main'
2 parents 90e113b + 02c9dad commit 8ab8a48

33 files changed

+550
-675
lines changed

‎.github/imgs/multi_point_mut_performance.png‎

5.39 MB
Loading

‎.github/imgs/multi_point_mut_performance_violin.png‎

529 KB
Loading

‎.github/imgs/single_point_mut_performance.png‎

7.31 MB
Loading

‎.github/imgs/single_point_mut_performance_violin.png‎

619 KB
Loading

‎.github/workflows/build.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ jobs:
1414
runs-on: [ubuntu-latest]
1515
strategy:
1616
matrix:
17-
python-version: ["3.9", "3.10", "3.11"]
17+
python-version: ["3.9", "3.10", "3.11", "3.12"]
1818

1919
steps:
2020
- uses: actions/checkout@v4

‎.gitignore‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -388,3 +388,6 @@ avGFP_shortened_dca_encoded.csv
388388
datasets/AVGFP/avGFP_shortened.csv
389389
avGFP_dca_encoded.csv
390390
scripts/Runtime_tests/runtimes.png
391+
datasets/AVGFP/Recomb_Double_Split/Predictions_Hybrid_TopRecomb_Double_Split.txt
392+
scripts/ProteinGym_runs/single_point_mut_performance_violin.png
393+
scripts/ProteinGym_runs/multi_point_mut_performance_violin.png

‎.vscode/launch.json‎

Lines changed: 81 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
"configurations": [
77
{
88
"name": "Python: PyPEF Help",
9-
"type": "python",
9+
"type": "debugpy",
1010
"request": "launch",
1111
"env": {"PYTHONPATH": "${workspaceFolder}"},
1212
"program": "${workspaceFolder}/pypef/main.py",
@@ -19,7 +19,7 @@
1919

2020
{
2121
"name": "Python: PyPEF MKLSTS ANEH",
22-
"type": "python",
22+
"type": "debugpy",
2323
"request": "launch",
2424
"env": {"PYTHONPATH": "${workspaceFolder}"},
2525
"program": "${workspaceFolder}/pypef/main.py",
@@ -35,7 +35,7 @@
3535

3636
{
3737
"name": "Python: PyPEF MKLSTS avGFP",
38-
"type": "python",
38+
"type": "debugpy",
3939
"request": "launch",
4040
"env": {"PYTHONPATH": "${workspaceFolder}"},
4141
"program": "${workspaceFolder}/pypef/main.py",
@@ -49,9 +49,26 @@
4949
]
5050
},
5151

52+
{
53+
"name": "Python: PyPEF MKPS avGFP drecomb",
54+
"type": "debugpy",
55+
"request": "launch",
56+
"env": {"PYTHONPATH": "${workspaceFolder}"},
57+
"program": "${workspaceFolder}/pypef/main.py",
58+
"console": "integratedTerminal",
59+
"justMyCode": true,
60+
"cwd": "${workspaceFolder}/datasets/AVGFP/",
61+
"args": [
62+
"mkps",
63+
"--wt", "P42212_F64L.fasta",
64+
"--input", "avGFP.csv",
65+
"--drecomb"
66+
]
67+
},
68+
5269
{
5370
"name": "Python: PyPEF ml -e onehot pls_loocv",
54-
"type": "python",
71+
"type": "debugpy",
5572
"request": "launch",
5673
"env": {"PYTHONPATH": "${workspaceFolder}"},
5774
"program": "${workspaceFolder}/pypef/main.py",
@@ -73,7 +90,7 @@
7390
// or
7491
// 2. $pypef hybrid -m GREMLIN -t TS.fasl --params GREMLIN
7592
"name": "Python: PyPEF save GREMLIN avGFP model",
76-
"type": "python",
93+
"type": "debugpy",
7794
"request": "launch",
7895
"env": {"PYTHONPATH": "${workspaceFolder}"},
7996
"program": "${workspaceFolder}/pypef/main.py",
@@ -87,9 +104,27 @@
87104
]
88105
},
89106

107+
{
108+
"name": "Python: PyPEF hybrid LS-TS GREMLIN-DCA avGFP",
109+
"type": "debugpy",
110+
"request": "launch",
111+
"env": {"PYTHONPATH": "${workspaceFolder}"},
112+
"program": "${workspaceFolder}/pypef/main.py",
113+
"console": "integratedTerminal",
114+
"justMyCode": true,
115+
"cwd": "${workspaceFolder}/datasets/AVGFP/",
116+
"args": [
117+
"hybrid",
118+
//"-m", "GREMLIN", // optional, not required
119+
"--ls", "LS.fasl",
120+
"--ts", "TS.fasl",
121+
"--params", "GREMLIN"
122+
]
123+
},
124+
90125
{
91126
"name": "Python: PyPEF hybrid/only-TS-zero-shot GREMLIN-DCA avGFP",
92-
"type": "python",
127+
"type": "debugpy",
93128
"request": "launch",
94129
"env": {"PYTHONPATH": "${workspaceFolder}"},
95130
"program": "${workspaceFolder}/pypef/main.py",
@@ -106,7 +141,7 @@
106141

107142
{
108143
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP",
109-
"type": "python",
144+
"type": "debugpy",
110145
"request": "launch",
111146
"env": {"PYTHONPATH": "${workspaceFolder}"},
112147
"program": "${workspaceFolder}/pypef/main.py",
@@ -121,11 +156,45 @@
121156
]
122157
},
123158

159+
{
160+
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP drecomb II",
161+
"type": "debugpy",
162+
"request": "launch",
163+
"env": {"PYTHONPATH": "${workspaceFolder}"},
164+
"program": "${workspaceFolder}/pypef/main.py",
165+
"console": "integratedTerminal",
166+
"justMyCode": true,
167+
"cwd": "${workspaceFolder}/datasets/AVGFP/",
168+
"args": [
169+
"hybrid",
170+
"-m", "HYBRIDgremlin",
171+
"--pmult", "--drecomb",
172+
"--params", "GREMLIN"
173+
]
174+
},
175+
176+
{
177+
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP drecomb",
178+
"type": "debugpy",
179+
"request": "launch",
180+
"env": {"PYTHONPATH": "${workspaceFolder}"},
181+
"program": "${workspaceFolder}/pypef/main.py",
182+
"console": "integratedTerminal",
183+
"justMyCode": true,
184+
"cwd": "${workspaceFolder}/datasets/AVGFP/",
185+
"args": [
186+
"hybrid",
187+
"-m", "GREMLIN",
188+
"--pmult", "--drecomb",
189+
"--params", "GREMLIN"
190+
]
191+
},
192+
124193
{ // PLMC zero-shot steps:
125194
// 1. $pypef param_inference --params uref100_avgfp_jhmmer_119_plmc_42.6.params
126195
// 2. $pypef hybrid -t TS.fasl --params PLMC
127196
"name": "Python: PyPEF save PLMC avGFP model",
128-
"type": "python",
197+
"type": "debugpy",
129198
"request": "launch",
130199
"env": {"PYTHONPATH": "${workspaceFolder}"},
131200
"program": "${workspaceFolder}/pypef/main.py",
@@ -140,7 +209,7 @@
140209

141210
{
142211
"name": "Python: PyPEF hybrid/only-TS-zero-shot PLMC-DCA avGFP",
143-
"type": "python",
212+
"type": "debugpy",
144213
"request": "launch",
145214
"env": {"PYTHONPATH": "${workspaceFolder}"},
146215
"program": "${workspaceFolder}/pypef/main.py",
@@ -157,7 +226,7 @@
157226

158227
{
159228
"name": "Python: PyPEF hybrid/only-PS-zero-shot PLMC-DCA avGFP",
160-
"type": "python",
229+
"type": "debugpy",
161230
"request": "launch",
162231
"env": {"PYTHONPATH": "${workspaceFolder}"},
163232
"program": "${workspaceFolder}/pypef/main.py",
@@ -175,7 +244,7 @@
175244

176245
{
177246
"name": "Python: PyPEF hybrid/only-PS-zero-shot PLMC-DCA variant 2 avGFP",
178-
"type": "python",
247+
"type": "debugpy",
179248
"request": "launch",
180249
"env": {"PYTHONPATH": "${workspaceFolder}"},
181250
"program": "${workspaceFolder}/pypef/main.py",
@@ -193,7 +262,7 @@
193262

194263
{
195264
"name": "Python: PyPEF !wrong! MSA input format (STO)",
196-
"type": "python",
265+
"type": "debugpy",
197266
"request": "launch",
198267
"env": {"PYTHONPATH": "${workspaceFolder}"},
199268
"program": "${workspaceFolder}/pypef/main.py",

0 commit comments

Comments
 (0)