Upload v0.4.3

Author: niklases

.github/imgs/A0A247D711_LISMN_Stadelmann_2021_pos_aa_distr.png

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with multiple versions of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: build
+name: CI
 
 on: [push]
 
@@ -14,7 +14,10 @@ jobs:
     runs-on: [ubuntu-latest]
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    env:
+     QT_QPA_PLATFORM: offscreen
+     DISPLAY: ':99.0'
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -33,16 +36,30 @@ jobs:
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 ./pypef --count --select=E9,F63,F7,F82 --show-source --statistics
-    - name: Export Pythonpath and run PyPEF API and CLI version test with pytest
+    - name: Export Pythonpath and run tests using the main script
       run: |
-        export PYTHONPATH="${PYTHONPATH}:${PWD}" && python -m pytest tests/
+        export PYTHONPATH="${PYTHONPATH}:${PWD}" && python -m pytest ./tests/ -v -m "not pip_specific"
+    - name: Export Pythonpath and run tests using pip-installation
+      run: |
+        export PYTHONPATH=""
+        sudo apt update
+        sudo apt install -y libegl1 xvfb \
+         libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
+         libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0
+        Xvfb :99 -screen 0 1920x1080x24 -ac &
+        sleep 3
+        pip install .[gui]
+        echo $(which pypef)
+        python -m pytest ./tests/ -v -m "not main_script_specific" --log-cli-level=INFO
 
   windows:
     name: windows
     runs-on: [windows-latest]
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    env:
+      QT_QPA_PLATFORM: offscreen
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -61,7 +78,15 @@ jobs:
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 .\pypef --count --select=E9,F63,F7,F82 --show-source --statistics
-    - name: Export Pythonpath and run PyPEF API and CLI version test with pytest
+    - name: Export Pythonpath and run tests using the main script
+      shell: pwsh
+      run: |
+        $env:PYTHONPATH = "${PWD};${env:PYTHONPATH}";python -m pytest .\tests\ -v -m "not pip_specific"
+    - name: Export Pythonpath and run tests using pip-installation
       shell: pwsh
       run: |
-        $env:PYTHONPATH = "${PWD};${env:PYTHONPATH}";python -m pytest .\tests\
+        $env:PYTHONPATH = ""
+        pip install .[gui]
+        echo (Get-Command pypef).Source
+        python -m pytest .\tests -v -m "not main_script_specific" --log-cli-level=INFO
+

.github/imgs/SOX30_HUMAN_Tsuboyama_2023_7JJK_pos_aa_distr.png

@@ -9,6 +9,7 @@ Python3127/*
 python-3.12.7-amd64.exe
 run_pypef_gui.bat
 run_pypef_gui.sh
+qt_window.spec
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -40,6 +41,7 @@ scripts/ProteinGym_runs/single_point_mut_performance_violin.png
 scripts/ProteinGym_runs/multi_point_mut_performance_violin.png
 scripts/ProteinGym_runs/single_point_mut_performance.png
 scripts/ProteinGym_runs/multi_point_mut_performance.png
+scripts/ProteinGym_runs/model_saves/*
 
 scripts/ESM_finetuning/DMS_msa_files/
 scripts/ESM_finetuning/DMS_ProteinGym_substitutions/
@@ -360,6 +362,26 @@ datasets/ANEH/Predictions_Hybrid_ESM1v_Top37_ANEH_variants_prediction_set.txt
 datasets/ANEH/Pickles/HYBRIDGREMLINESM1V
 datasets/ANEH/SSM_landscape.png
 datasets/ANEH/SSM_landscape.csv
+datasets/ANEH/ANEH_72.6.params
+datasets/ANEH/HYBRIDPLMC_DE_trajectories.png
+datasets/ANEH/MLGREMLIN_DE_trajectories.png
+datasets/ANEH/MLPLMC_DE_trajectories.png
+datasets/ANEH/Predictions_MLGREMLIN_37_ANEH_variants_prediction_set.txt
+datasets/ANEH/Predictions_MLPLMC_37_ANEH_variants_prediction_set.txt
+datasets/ANEH/Diverse_Double_Split/Predictions_MLGREMLIN_TopDiverse_Double_Split.txt
+datasets/ANEH/Diverse_Double_Split/Predictions_MLPLMC_TopDiverse_Double_Split.txt
+datasets/ANEH/Pickles/HYBRIDGREMLIN
+datasets/ANEH/Pickles/HYBRIDPLMC
+datasets/ANEH/Pickles/MLGREMLIN
+datasets/ANEH/Pickles/MLPLMC
+datasets/ANEH/Recomb_Double_Split/Predictions_MLGREMLIN_TopRecomb_Double_Split.txt
+datasets/ANEH/Recomb_Double_Split/Predictions_MLPLMC_TopRecomb_Double_Split.txt
+datasets/ANEH/Recomb_Quadruple_Split/Predictions_MLGREMLIN_TopRecomb_Quadruple_Split.txt
+datasets/ANEH/Recomb_Quadruple_Split/Predictions_MLPLMC_TopRecomb_Quadruple_Split.txt
+datasets/ANEH/Recomb_Quintuple_Split/Predictions_MLGREMLIN_TopRecomb_Quintuple_Split.txt
+datasets/ANEH/Recomb_Quintuple_Split/Predictions_MLPLMC_TopRecomb_Quintuple_Split.txt
+datasets/ANEH/Recomb_Triple_Split/Predictions_MLGREMLIN_TopRecomb_Triple_Split.txt
+datasets/ANEH/Recomb_Triple_Split/Predictions_MLPLMC_TopRecomb_Triple_Split.txt
 
 datasets/AVGFP/apc.png
 datasets/AVGFP/avGFP_aaidx_encoded.csv
@@ -455,3 +477,19 @@ datasets/AVGFP/HYBRIDGREMLINESM1V_DE_trajectories.png
 datasets/AVGFP/Recomb_Double_Split/Predictions_Hybrid_ESM1v_TopRecomb_Double_Split.txt
 datasets/AVGFP/Recomb_Double_Split/Predictions_Hybrid_ProSST_TopRecomb_Double_Split.txt
 datasets/AVGFP/avGFP_shortened.csv
+datasets/AVGFP/DCA_Hybrid_Model_Performance_GREMLIN_ESM.png
+datasets/AVGFP/DCA_Hybrid_Model_Performance_Hybrid_ESM1v_ESM.png
+datasets/AVGFP/ML_Model_Performance_ONEHOT_onehot.png
+datasets/AVGFP/ML_Model_Performance_ONEHOT_PLS.png
+datasets/AVGFP/Predictions_Hybrid_ESM1v_avGFP_prediction_set.txt
+datasets/AVGFP/Predictions_Hybrid_ProSST_avGFP_prediction_set.txt
+datasets/AVGFP/Predictions_MLGREMLIN_avGFP_prediction_set.txt
+datasets/AVGFP/Predictions_ONEHOT_avGFP_prediction_set.txt
+datasets/AVGFP/CV_performance/ONEHOT_PLS_5-fold-CV.png
+datasets/AVGFP/CV_performance/ONEHOT_PLS_CV_Results.txt
+datasets/AVGFP/HYBRIDPLMC_DE_trajectories.png
+datasets/AVGFP/MLGREMLIN_DE_trajectories.png
+datasets/AVGFP/MLPLMC_DE_trajectories.png
+datasets/AVGFP/Predictions_GREMLIN_TopTS.txt
+datasets/AVGFP/Predictions_PLMC_TopTS.txt
+datasets/AVGFP/uref100_avgfp_jhmmer_119_plmc_42.6.params