From bbd62a02ce6270708b65d09967dbeec9ffa7e096 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Fri, 11 Sep 2020 11:09:29 +0200 Subject: [PATCH 01/11] :fix: fix the description format in setup --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 25f4e54..bf18b54 100644 --- a/setup.py +++ b/setup.py @@ -30,6 +30,7 @@ version=cp_vers, description=" Python module to plot dynamical correlations maps for proteins.", long_description=open('README.md').read(), + long_description_content_type="text/markdown", author="Mustafa Tekpinar", author_email="tekpinar@buffalo.edu", url="https://github.com/tekpinar/correlationPlus", From b5749ef9dfb8bfad0528feca1f83c9fa1e33cf5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Fri, 11 Sep 2020 11:16:30 +0200 Subject: [PATCH 02/11] :fix: add windows as supported operating system --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index bf18b54..1d23dd7 100644 --- a/setup.py +++ b/setup.py @@ -40,6 +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', From 2b621c5f9ee7ef1021c74c3113cbca42c66468f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Fri, 11 Sep 2020 11:17:35 +0200 Subject: [PATCH 03/11] :arrow_up: bump version to 1.0.3 --- correlationPlus/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/correlationPlus/__init__.py b/correlationPlus/__init__.py index dc83e90..ff929c1 100644 --- a/correlationPlus/__init__.py +++ b/correlationPlus/__init__.py @@ -37,5 +37,5 @@ __all__ = ['mapAnalysis', 'diffMap', 'centralityAnalysis'] -__version__ = '0.1.0' +__version__ = '0.1.3' From 21d9c878a67d7e64a6ec120959cdcb2f367eea44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Mon, 14 Sep 2020 10:42:02 +0200 Subject: [PATCH 04/11] fix versions for dependecies this improve reproducibility --- requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/requirements.txt b/requirements.txt index 2691cba..06d7c16 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ -numpy -matplotlib -prody -scipy -networkx \ No newline at end of file +numpy==1.19.1 +matplotlib==3.3.0 +prody==1.10.11 +scipy==1.5.2 +networkx==2.4 \ No newline at end of file From d7ea1cf0fbd0e7265ebd5e5904a2a5a79270a5fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Mon, 14 Sep 2020 10:43:56 +0200 Subject: [PATCH 05/11] fix biopython version to avoid warning correlationPlus does not depend directly from biopython but prody does. and some warning a re raised with the biopython > 1.77 --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 06d7c16..8024aed 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,4 @@ +biopython==1.77 numpy==1.19.1 matplotlib==3.3.0 prody==1.10.11 From b445ebf4217abcf93eaa7ca4401c2975c287e44d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Mon, 14 Sep 2020 10:50:02 +0200 Subject: [PATCH 06/11] :art: reorganize dependencies order --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 8024aed..bde6931 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ -biopython==1.77 numpy==1.19.1 matplotlib==3.3.0 -prody==1.10.11 scipy==1.5.2 -networkx==2.4 \ No newline at end of file +networkx==2.4 +biopython==1.77 +prody==1.10.11 From a64c195d3f3ebb1c3371b76405e68c507cbffa9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Tue, 15 Sep 2020 10:52:38 +0200 Subject: [PATCH 07/11] :art: fix typo --- correlationPlus/scripts/calculate.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/correlationPlus/scripts/calculate.py b/correlationPlus/scripts/calculate.py index ee426b2..16bfa71 100644 --- a/correlationPlus/scripts/calculate.py +++ b/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() From d023be7f297f8f856d3a7e78763ed2c1e5336b78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Tue, 15 Sep 2020 11:24:15 +0200 Subject: [PATCH 08/11] :arrow_up: bump to version 0.1.3rc2 --- correlationPlus/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/correlationPlus/__init__.py b/correlationPlus/__init__.py index b1ab941..16f7ada 100644 --- a/correlationPlus/__init__.py +++ b/correlationPlus/__init__.py @@ -34,5 +34,5 @@ __all__ = ['calculate', 'mapAnalysis', 'diffMap', 'centralityAnalysis'] -__version__ = '0.1.3' +__version__ = '0.1.3rc2' From 2aaae0613ed394ad15a61e610ef52da312385292 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Tue, 15 Sep 2020 11:25:10 +0200 Subject: [PATCH 09/11] :sparkles: add dockerfile --- Docker/Dockerfile | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 Docker/Dockerfile diff --git a/Docker/Dockerfile b/Docker/Dockerfile new file mode 100644 index 0000000..cba01be --- /dev/null +++ b/Docker/Dockerfile @@ -0,0 +1,12 @@ +FROM python:3.8.5 + +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 install -i https://test.pypi.org/simple/ correlationPlus==0.1.3rc2 +RUN useradd -m correlationPlus + +USER correlationPlus +WORKDIR /home/correlationPlus + +ENTRYPOINT ["/bin/sh", "-c" , "correlationPlus $0 $@"] \ No newline at end of file From 5c1183866a31d391b9a26f7d71a5faed6b9970f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Tue, 15 Sep 2020 15:42:07 +0200 Subject: [PATCH 10/11] set version to 0.1.3 --- correlationPlus/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/correlationPlus/__init__.py b/correlationPlus/__init__.py index 16f7ada..b1ab941 100644 --- a/correlationPlus/__init__.py +++ b/correlationPlus/__init__.py @@ -34,5 +34,5 @@ __all__ = ['calculate', 'mapAnalysis', 'diffMap', 'centralityAnalysis'] -__version__ = '0.1.3rc2' +__version__ = '0.1.3' From e28486efa3b932fa22c76d33ee40379b7209df31 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Tue, 15 Sep 2020 15:42:47 +0200 Subject: [PATCH 11/11] use official pypi package to build the image add label to image --- Docker/Dockerfile | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/Docker/Dockerfile b/Docker/Dockerfile index cba01be..94149b8 100644 --- a/Docker/Dockerfile +++ b/Docker/Dockerfile @@ -1,9 +1,14 @@ 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 " + 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 install -i https://test.pypi.org/simple/ correlationPlus==0.1.3rc2 +RUN pip3 correlationPlus==0.1.3 RUN useradd -m correlationPlus USER correlationPlus