Refactor tests (#15)

* refactor tests

* linting

* tweak dockerfile

* rename test folder

* Update Dockerfile and add working directory

Author: rvhonorato

Dockerfile

@@ -1,5 +1,5 @@
 #==============================================================================================
-FROM python:3.6 as base
+FROM python:3.8 as base
 
 LABEL author="Rodrigo V. Honorato <r.vargashonorato@uu.nl>"
 
@@ -10,18 +10,16 @@ RUN apt-get update && \
   && \
   apt-get clean && rm -rf /var/lib/apt/lists/*
 
-WORKDIR /opt/software
-
-# Install Whiscy
-RUN git clone https://github.com/haddocking/whiscy.git && \
-  cd whiscy && \
-  git checkout tags/v1.1.1 && \
-  cd /opt/software/whiscy/bin/protdist && \
-  sh compile.sh
+# Copy Whiscy
+WORKDIR /opt/software/whiscy
+COPY . .
 
+# install BioPython
 RUN pip install biopython==1.79
 
-WORKDIR /opt/software/whiscy/bin
+# Build protdist
+WORKDIR /opt/software/whiscy/bin/protdist
+RUN sh compile.sh
 
 # Build Muscle
 WORKDIR /opt/software/whiscy/muscle3.8.1551
@@ -30,7 +28,7 @@ RUN curl https://drive5.com/muscle/muscle_src_3.8.1551.tar.gz | tar xzv && \
   mv muscle /opt/software/whiscy/bin/muscle3.8.1551 && \
   sed -i "s/\/Users\/bjimenez\/bin\/muscle\/muscle3.8.31_i86darwin64/\/opt\/software\/whiscy\/bin\/muscle3.8.1551/g" /opt/software/whiscy/etc/local.json
 
-# Install hsspconv
+# Build hsspconv
 RUN wget https://github.com/cmbi/hssp/archive/3.1.5.tar.gz && \
   tar -zxvf 3.1.5.tar.gz && \
   cd hssp-3.1.5 && \
@@ -41,7 +39,7 @@ RUN wget https://github.com/cmbi/hssp/archive/3.1.5.tar.gz && \
   sed -i "s/\/Users\/bjimenez\/bin\/hssp\/hsspconv/\/opt\/software\/whiscy\/bin\/hsspconv/g" /opt/software/whiscy/etc/local.json
 
 
-# Install freesasa
+# Build freesasa
 RUN  wget https://github.com/mittinatten/freesasa/releases/download/2.0.3/freesasa-2.0.3.tar.gz  && \
   tar -zxvf freesasa-2.0.3.tar.gz && \
   cd freesasa-2.0.3 && \
@@ -50,9 +48,16 @@ RUN  wget https://github.com/mittinatten/freesasa/releases/download/2.0.3/freesa
 
 # WHISCY exports
 ENV WHISCY_PATH=/opt/software/whiscy
-ENV PYTHONPATH="{$PYTHONPATH}:${WHISCY_PATH}"
+ENV PYTHONPATH="${PYTHONPATH}:${WHISCY_PATH}"
 ENV WHISCY_BIN="${WHISCY_PATH}/whiscy.py"
 ENV PATH="${WHISCY_PATH}:${WHISCY_PATH}/bin/freesasa/bin:${PATH}"
+
+WORKDIR /data
+
+###############################################################################################
+# No entrypoint here because Whiscy runs multiple commands
+###############################################################################################
+
 #==============================================================================================
 
 FROM base AS test
@@ -61,6 +66,5 @@ RUN pip install pytest coverage pytest pytest-cov hypothesis
 
 WORKDIR /opt/software/whiscy
 
-COPY test/ tests/
 
 #==============================================================================================

bin/consadjust.py

@@ -2,14 +2,18 @@
 
 __version__ = 1.0
 
+import argparse
+# Logging
+import logging
 import math
 import os
 import sys
-import argparse
+
 import numpy as np
-from libwhiscy.whiscy_data import load_residue_weights, load_cons_file, load_z_table
-# Logging
-import logging
+
+from libwhiscy.whiscy_data import (load_cons_file, load_residue_weights,
+                                   load_z_table)
+
 logger = logging.getLogger("consadjust")
 logger.setLevel(logging.INFO)
 ch = logging.StreamHandler(sys.stdout)

bin/parasmooth.py

@@ -2,21 +2,23 @@
 
 __version__ = 1.0
 
-import math
-import os
 import argparse
-import sys
 # Logging
 import logging
+import math
+import os
+import sys
+
 logger = logging.getLogger("parasmooth")
 logger.setLevel(logging.INFO)
 ch = logging.StreamHandler(sys.stdout)
 ch.setLevel(logging.INFO)
 formatter = logging.Formatter('%(name)s [%(levelname)s] %(message)s')
 ch.setFormatter(formatter)
 logger.addHandler(ch)
-from libwhiscy.whiscy_data import load_cons_file, load_smoothing_parameter_file, \
-                                    load_residue_distance_matrix
+from libwhiscy.whiscy_data import (load_cons_file,
+                                   load_residue_distance_matrix,
+                                   load_smoothing_parameter_file)
 
 
 def get_weight(par, val):

bin/residue_distance.py

@@ -9,14 +9,17 @@
 
 __version__ = 1.0
 
+import argparse
+# Logging
+import logging
 import os
 import sys
-import argparse
+
 from Bio.PDB.PDBParser import PDBParser
-from libwhiscy.whiscy_data import load_conversion_table
+
 from libwhiscy.pdbutil import is_hydrogen
-# Logging
-import logging
+from libwhiscy.whiscy_data import load_conversion_table
+
 logger = logging.getLogger("residue_distance")
 logger.setLevel(logging.INFO)
 ch = logging.StreamHandler(sys.stdout)

bin/whiscy2bfactor.py

@@ -4,10 +4,9 @@
 
 __version__ = 1.0
 
+import argparse
 import os
 import sys
-import argparse
-
 
 STANDARD_TYPES = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C',
                   'GLU': 'E', 'GLN': 'Q', 'GLY': 'G', 'HIS': 'H', 'ILE': 'I',

bin/whiscy2haddock.py

@@ -8,11 +8,11 @@
 
 __version__ = 1.0
 
+import argparse
 import os
 import sys
-import argparse
-import Bio.PDB
 
+import Bio.PDB
 
 STANDARD_TYPES = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C',
                   'GLU': 'E', 'GLN': 'Q', 'GLY': 'G', 'HIS': 'H', 'ILE': 'I',

libwhiscy/access.py

@@ -1,5 +1,5 @@
-import subprocess
 import os
+import subprocess
 
 
 def calculate_accessibility(pdb_file_name, output_file_name):

libwhiscy/pam_calc.py

@@ -1,10 +1,12 @@
 import os
+
 try:
     from math import exp, isclose
 except:
     from math import exp
     from numpy import isclose
-from libwhiscy.pam_data import logpameigval, pameigvec, pameigvecinv, code
+
+from libwhiscy.pam_data import code, logpameigval, pameigvec, pameigvecinv
 
 
 class Distance():

libwhiscy/pdbutil.py

@@ -3,11 +3,12 @@
 
 import os
 import re
+
+from Bio import AlignIO
 from Bio.PDB import PDBList
+from Bio.PDB.PDBIO import Select
 from Bio.PDB.PDBParser import PDBParser
 from Bio.PDB.Polypeptide import is_aa, three_to_one
-from Bio.PDB.PDBIO import Select
-from Bio import AlignIO
 
 
 class NotAlternative(Select):

libwhiscy/quotes.py

@@ -1,6 +1,5 @@
 import random
 
-
 _quotes = {"Mark Twain": "Too much of anything is bad, but too much good whiskey is barely enough.",
           "Raymond Chandler": "There is no bad whiskey. There are only some whiskeys that aren’t as good as others.",
           "Winston Churchill": "The water was not fit to drink. To make it palatable, we had to add whisky. By diligent effort, I learned to like it.",