Add analysis pipeline to the PYTHONPATH for github actions

KosinskiLab · Sep 25, 2024 · 31a42e6 · 31a42e6
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commit 31a42e6
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/.github/workflows/github_actions.yml b/.github/workflows/github_actions.yml
@@ -39,7 +39,7 @@ jobs:
           pip install alphapulldown==2.0.0b4
       - if: matrix.install-type == 'developer'
         run: |
-          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base pytest importlib_metadata modelcif
+          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
           conda install -c bioconda hmmer hhsuite
@@ -64,6 +64,10 @@ jobs:
           pytest -s test/test_modelcif.py
           pytest -s test/test_features_with_templates.py
           pytest -s test/test_post_prediction.py
+          export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH
+          conda install -c bioconda biopandas 
+          pip install pyrosetta-installer 
+          python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'
           pytest -s test/test_pdb_analyser.py
           pytest -s test/test_get_good_inter_pae.py
 

diff --git a/alphapulldown/analysis_pipeline/get_good_inter_pae.py b/alphapulldown/analysis_pipeline/get_good_inter_pae.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
-from .calculate_mpdockq import get_best_plddt, read_pdb, read_plddt, score_complex, calculate_mpDockQ, read_pdb_pdockq, calc_pdockq
-from .pdb_analyser import PDBAnalyser
+from calculate_mpdockq import get_best_plddt, read_pdb, read_plddt, score_complex, calculate_mpDockQ, read_pdb_pdockq, calc_pdockq
+from pdb_analyser import PDBAnalyser
 from Bio.PDB import PDBParser
 from Bio.PDB.Polypeptide import PPBuilder
 import os