Merge pull request #3 from bneron/master

ready for releasing 0.1.3

Docker/Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.8.5
+
+LABEL org.label-schema.vcs-url="https://github.com/tekpinar/correlationPlus"
+LABEL org.label-schema.version="1.0.3"
+LABEL org.label-schema.description="A Python API to plot and analyze dynamical correlations of proteins."
+LABEL org.label-schema.docker.cmd="docker run -v ~:/home/correlationPlus correlation_plus <sub cmd> <args>"
+
+USER root
+
+RUN pip3 install numpy==1.19.1 matplotlib==3.3.0 scipy==1.5.2 networkx==2.4 biopython==1.77 prody==1.10.11
+RUN pip3 correlationPlus==0.1.3
+RUN useradd -m correlationPlus
+
+USER correlationPlus
+WORKDIR /home/correlationPlus
+
+ENTRYPOINT ["/bin/sh", "-c" , "correlationPlus $0 $@"]

correlationPlus/__init__.py

@@ -34,5 +34,5 @@
 
 __all__ = ['calculate', 'mapAnalysis', 'diffMap', 'centralityAnalysis']
 
-__version__ = '0.1.2'
+__version__ = '0.1.3'
 

correlationPlus/scripts/calculate.py

@@ -29,6 +29,7 @@
 
 from correlationPlus.calculate import calcENMnDCC
 
+
 def usage_calculateApp():
     """                                                                                                                                                                                       
     Show how to use this program!                                                                                                                                                             
@@ -44,6 +45,7 @@ def usage_calculateApp():
            -o: This will be your output data file. Default is correlationMap.dat. (Optional)                                                                                                    
 """)
 
+
 def handle_arguments_calculateApp():
     method   = None
     out_file = None
@@ -92,6 +94,8 @@ def handle_arguments_calculateApp():
         sel_type = "ndcc"
 
     return method, out_file, sel_type, pdb_file
+
+
 def calculateApp():
     method, out_file, sel_type, pdb_file = handle_arguments_calculateApp()
     print(f"""                                                                                                                                                                                
@@ -106,7 +110,8 @@ def calculateApp():
     #Read pdb file
     selectedAtoms = parsePDB(pdb_file, subset='ca')
     calcENMnDCC(selectedAtoms, saveMatrix=True, out_file=out_file, method=method, nmodes=100)
-    print("@> Correlation calculation finished succesfully!")
+    print("@> Correlation calculation finished successfully!")
+
 
 if __name__ == "__main__":
     calculateApp()

requirements.txt

@@ -1,5 +1,6 @@
-numpy
-matplotlib
-prody
-scipy
-networkx
+numpy==1.19.1
+matplotlib==3.3.0
+scipy==1.5.2
+networkx==2.4
+biopython==1.77
+prody==1.10.11

setup.py

@@ -30,6 +30,7 @@
       version=cp_vers,
       description=" Python package to plot and analyze dynamical correlations maps of proteins.",
       long_description=open('README.md').read(),
+      long_description_content_type="text/markdown",
       author="Mustafa Tekpinar",
       author_email="[email protected]",
       url="https://github.com/tekpinar/correlationPlus",
@@ -39,6 +40,7 @@
           'Development Status :: 4 - Beta',
           'Environment :: Console',
           'Operating System :: POSIX',
+          'Operating System :: Microsoft :: Windows',
           'Programming Language :: Python :: 3',
           'Programming Language :: Python :: 3.6',
           'Programming Language :: Python :: 3.7',