From 410b1d06d02d6322500b90b6931d433633cd074d Mon Sep 17 00:00:00 2001 From: Koen Visscher Date: Tue, 22 May 2018 10:49:17 +0200 Subject: [PATCH] reorganise test data --- .vscode/settings.json | 3 ++ Pipfile | 10 +++++- {tests => lie_topology}/data/cnf/M01.g96 | 0 .../data/cnf/md_fX_apixaban_1.cnf | 0 {tests => lie_topology}/data/cnf/renumber.sh | 0 .../data/gro/run1_combined_pbc.gro | 0 .../data/gtop/ala_ala_ala.gtop | 0 .../data/gtop/ala_cys_ala_cys_ala.gtop | 0 {tests => lie_topology}/data/ifp/2016H66.ifp | 0 {tests => lie_topology}/data/ifp/54a7.ifp | 0 .../data/md_top/54a7.aatop | 0 .../data/md_top/54a7.mdtop | 0 .../data/md_top/54a7mtb_to_aatop.py | 0 .../data/md_top/forcefield.mdtop | 0 .../data/md_top/residues.aatop | 0 {tests => lie_topology}/data/mol2/BHC2.mol2 | 0 {tests => lie_topology}/data/mtb/1007.all.mtb | 0 .../data/mtb/2016H66_pept.mtb | 0 {tests => lie_topology}/data/mtb/54a7.mtb | 0 {tests => lie_topology}/data/mtb/g235.mtb | 0 .../data/mtb/minimal.pept.mtb | 0 {tests => lie_topology}/data/pdb/peptide.pdb | 0 {tests => lie_topology}/data/sdf/BHC2.sdf | 0 {tests => lie_topology}/data/test.seq | 0 settings.yml | 2 +- setup.py | 34 ++++++++++++------- 26 files changed, 34 insertions(+), 15 deletions(-) create mode 100644 .vscode/settings.json rename {tests => lie_topology}/data/cnf/M01.g96 (100%) rename {tests => lie_topology}/data/cnf/md_fX_apixaban_1.cnf (100%) rename {tests => lie_topology}/data/cnf/renumber.sh (100%) rename {tests => lie_topology}/data/gro/run1_combined_pbc.gro (100%) rename {tests => lie_topology}/data/gtop/ala_ala_ala.gtop (100%) rename {tests => lie_topology}/data/gtop/ala_cys_ala_cys_ala.gtop (100%) rename {tests => lie_topology}/data/ifp/2016H66.ifp (100%) rename {tests => lie_topology}/data/ifp/54a7.ifp (100%) rename {tests => lie_topology}/data/md_top/54a7.aatop (100%) rename {tests => lie_topology}/data/md_top/54a7.mdtop (100%) rename {tests => lie_topology}/data/md_top/54a7mtb_to_aatop.py (100%) rename {tests => lie_topology}/data/md_top/forcefield.mdtop (100%) rename {tests => lie_topology}/data/md_top/residues.aatop (100%) rename {tests => lie_topology}/data/mol2/BHC2.mol2 (100%) rename {tests => lie_topology}/data/mtb/1007.all.mtb (100%) rename {tests => lie_topology}/data/mtb/2016H66_pept.mtb (100%) rename {tests => lie_topology}/data/mtb/54a7.mtb (100%) rename {tests => lie_topology}/data/mtb/g235.mtb (100%) rename {tests => lie_topology}/data/mtb/minimal.pept.mtb (100%) rename {tests => lie_topology}/data/pdb/peptide.pdb (100%) rename {tests => lie_topology}/data/sdf/BHC2.sdf (100%) rename {tests => lie_topology}/data/test.seq (100%) diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..fe71598 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "python.linting.pylintEnabled": false +} \ No newline at end of file diff --git a/Pipfile b/Pipfile index 09221ca..43214a3 100644 --- a/Pipfile +++ b/Pipfile @@ -5,4 +5,12 @@ name = "pypi" [packages] mdstudio = {path = "../../mdstudio/", editable = true} -local = {path = "./", editable = true} \ No newline at end of file +local = {path = "./", editable = true} + +mdstudio = {path = "../../mdstudio/", editable = true} +local = {path = "./", editable = true} +cerise_client = ">=0.2.4" +numpy = "*" +pyparsing = "*" +panedr = ">=0.2" +retrying = ">=1.3.3" \ No newline at end of file diff --git a/tests/data/cnf/M01.g96 b/lie_topology/data/cnf/M01.g96 similarity index 100% rename from tests/data/cnf/M01.g96 rename to lie_topology/data/cnf/M01.g96 diff --git a/tests/data/cnf/md_fX_apixaban_1.cnf b/lie_topology/data/cnf/md_fX_apixaban_1.cnf similarity index 100% rename from tests/data/cnf/md_fX_apixaban_1.cnf rename to lie_topology/data/cnf/md_fX_apixaban_1.cnf diff --git a/tests/data/cnf/renumber.sh b/lie_topology/data/cnf/renumber.sh similarity index 100% rename from tests/data/cnf/renumber.sh rename to lie_topology/data/cnf/renumber.sh diff --git a/tests/data/gro/run1_combined_pbc.gro b/lie_topology/data/gro/run1_combined_pbc.gro similarity index 100% rename from tests/data/gro/run1_combined_pbc.gro rename to lie_topology/data/gro/run1_combined_pbc.gro diff --git a/tests/data/gtop/ala_ala_ala.gtop b/lie_topology/data/gtop/ala_ala_ala.gtop similarity index 100% rename from tests/data/gtop/ala_ala_ala.gtop rename to lie_topology/data/gtop/ala_ala_ala.gtop diff --git a/tests/data/gtop/ala_cys_ala_cys_ala.gtop b/lie_topology/data/gtop/ala_cys_ala_cys_ala.gtop similarity index 100% rename from tests/data/gtop/ala_cys_ala_cys_ala.gtop rename to lie_topology/data/gtop/ala_cys_ala_cys_ala.gtop diff --git a/tests/data/ifp/2016H66.ifp b/lie_topology/data/ifp/2016H66.ifp similarity index 100% rename from tests/data/ifp/2016H66.ifp rename to lie_topology/data/ifp/2016H66.ifp diff --git a/tests/data/ifp/54a7.ifp b/lie_topology/data/ifp/54a7.ifp similarity index 100% rename from tests/data/ifp/54a7.ifp rename to lie_topology/data/ifp/54a7.ifp diff --git a/tests/data/md_top/54a7.aatop b/lie_topology/data/md_top/54a7.aatop similarity index 100% rename from tests/data/md_top/54a7.aatop rename to lie_topology/data/md_top/54a7.aatop diff --git a/tests/data/md_top/54a7.mdtop b/lie_topology/data/md_top/54a7.mdtop similarity index 100% rename from tests/data/md_top/54a7.mdtop rename to lie_topology/data/md_top/54a7.mdtop diff --git a/tests/data/md_top/54a7mtb_to_aatop.py b/lie_topology/data/md_top/54a7mtb_to_aatop.py similarity index 100% rename from tests/data/md_top/54a7mtb_to_aatop.py rename to lie_topology/data/md_top/54a7mtb_to_aatop.py diff --git a/tests/data/md_top/forcefield.mdtop b/lie_topology/data/md_top/forcefield.mdtop similarity index 100% rename from tests/data/md_top/forcefield.mdtop rename to lie_topology/data/md_top/forcefield.mdtop diff --git a/tests/data/md_top/residues.aatop b/lie_topology/data/md_top/residues.aatop similarity index 100% rename from tests/data/md_top/residues.aatop rename to lie_topology/data/md_top/residues.aatop diff --git a/tests/data/mol2/BHC2.mol2 b/lie_topology/data/mol2/BHC2.mol2 similarity index 100% rename from tests/data/mol2/BHC2.mol2 rename to lie_topology/data/mol2/BHC2.mol2 diff --git a/tests/data/mtb/1007.all.mtb b/lie_topology/data/mtb/1007.all.mtb similarity index 100% rename from tests/data/mtb/1007.all.mtb rename to lie_topology/data/mtb/1007.all.mtb diff --git a/tests/data/mtb/2016H66_pept.mtb b/lie_topology/data/mtb/2016H66_pept.mtb similarity index 100% rename from tests/data/mtb/2016H66_pept.mtb rename to lie_topology/data/mtb/2016H66_pept.mtb diff --git a/tests/data/mtb/54a7.mtb b/lie_topology/data/mtb/54a7.mtb similarity index 100% rename from tests/data/mtb/54a7.mtb rename to lie_topology/data/mtb/54a7.mtb diff --git a/tests/data/mtb/g235.mtb b/lie_topology/data/mtb/g235.mtb similarity index 100% rename from tests/data/mtb/g235.mtb rename to lie_topology/data/mtb/g235.mtb diff --git a/tests/data/mtb/minimal.pept.mtb b/lie_topology/data/mtb/minimal.pept.mtb similarity index 100% rename from tests/data/mtb/minimal.pept.mtb rename to lie_topology/data/mtb/minimal.pept.mtb diff --git a/tests/data/pdb/peptide.pdb b/lie_topology/data/pdb/peptide.pdb similarity index 100% rename from tests/data/pdb/peptide.pdb rename to lie_topology/data/pdb/peptide.pdb diff --git a/tests/data/sdf/BHC2.sdf b/lie_topology/data/sdf/BHC2.sdf similarity index 100% rename from tests/data/sdf/BHC2.sdf rename to lie_topology/data/sdf/BHC2.sdf diff --git a/tests/data/test.seq b/lie_topology/data/test.seq similarity index 100% rename from tests/data/test.seq rename to lie_topology/data/test.seq diff --git a/settings.yml b/settings.yml index efbd82e..c620980 100644 --- a/settings.yml +++ b/settings.yml @@ -1,3 +1,3 @@ static: vendor: mdgroup - component: topology \ No newline at end of file + component: lie_topology \ No newline at end of file diff --git a/setup.py b/setup.py index 69e8b0e..2969be9 100644 --- a/setup.py +++ b/setup.py @@ -1,12 +1,13 @@ #! /usr/bin/env python # -*- coding: utf-8 -*- -# -# package: lie_topology + +# package: lie_docking # file: setup.py # -# Part of ‘lie_topology’, providing tools for parsing and generating topology files +# Part of ‘lie_docking’, a package providing molecular docking functionality +# for the LIEStudio package. # -# Copyright © 2016 Koen M. Visscher, Marc van Dijk, VU University Amsterdam, the Netherlands +# Copyright © 2018 K.M.Visscher, VU University Amsterdam, the Netherlands # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -20,30 +21,37 @@ # See the License for the specific language governing permissions and # limitations under the License. + from setuptools import setup, find_packages distribution_name = 'lie_topology' setup( name=distribution_name, - version='1.0.0', - license='Apache Software License 2.0', - description='LIEStudio component wrapping topology parsers and writers', + version=0.1, + description='MDStudio component wrapping topology parsers and writers', author='Koen M. Visscher, VU University, Amsterdam, The Netherlands', - author_email='k.m.visscher@vu.nl', - url='https://github.com/MD-Studio/MDStudio', - keywords='LIEStudio topology molecular force fields', + author_email=['k.m.visscher@vu.nl'], + url='https://github.com/MD-Studio/lie_topology.git', + license='Apache Software License 2.0', + keywords='MDStudio molecular simulation', platforms=['Any'], packages=find_packages(), + package_data={'lie_topology': ['data/*']}, py_modules=[distribution_name], - include_package_data=True, + install_requires=['mdstudio', 'numpy'], + include_package_data=False, zip_safe=True, classifiers=[ 'Development Status :: 3 - Alpha', 'License :: OSI Approved :: Apache Software License', 'Programming Language :: Python', - 'Topic :: Utilities', + 'Topic :: Scientific/Engineering :: Chemistry', 'Operating System :: OS Independent', 'Intended Audience :: Science/Research', - ], + ], + scripts=[], + extras_require={ + 'test': ['coverage'] + } ) \ No newline at end of file