Project name change from lie_plants_docking to mdstudio_plants_docking

.gitignore

@@ -6,8 +6,8 @@ app/dist/
 data/logs/
 data/liedb/
 docs/html/
-bin/
-tmp/
+logs/
+src/
 
 # This file is different per user
 data/settings.json
@@ -60,10 +60,6 @@ coverage.xml
 *,cover
 .hypothesis/
 
-# Translations
-*.mo
-*.pot
-
 # Sphinx documentation
 docs/_build/
 
@@ -119,6 +115,81 @@ $RECYCLE.BIN/
 # Windows shortcuts
 *.lnk
 
+### Node template
+*.log
+npm-debug.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (http://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directory
+# https://docs.npmjs.com/misc/faq#should-i-check-my-node-modules-folder-into-git
+node_modules
+
+# Docker
+docker/.INSTALLING
+
+
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+.idea/
+
+## File-based project format:
+*.iws
+
+## Plugin-specific files:
+
+# IntelliJ
+/out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# files generated on merge conflicts
+*.orig
+
+# Ignore compiled typescript
+app/gulp/*.js
+app/gulp/*.map
+app/gulp/tasks/*.js
+app/gulp/tasks/*.map
+app/src/*.js
+app/src/**/*.map
+app/src/**/*.js
+app/gulpfile.js
+app/gulpfile.js.map
+app/bower_components/*
+components/*/data
+docker/.USERDONE
+/key.priv
+/key.pub
+
 # emacs
 *~
 

Dockerfile

@@ -1,13 +1,13 @@
 FROM mdstudio/mdstudio_docker3:0.0.3
 
-COPY . /home/mdstudio/lie_plants_docking
+COPY . /home/mdstudio/mdstudio_plants_docking
 
-RUN chown mdstudio:mdstudio /home/mdstudio/lie_plants_docking
+RUN chown mdstudio:mdstudio /home/mdstudio/mdstudio_plants_docking
 
-WORKDIR /home/mdstudio/lie_plants_docking
+WORKDIR /home/mdstudio/mdstudio_plants_docking
 
 RUN pip install numpy scipy && pip install .
 
 # USER mdstudio
 
-CMD ["bash", "entry_point_lie_plants_docking.sh"]
+CMD ["bash", "entry_point_mdstudio_plants_docking.sh"]

README.md

@@ -1,8 +1,11 @@
-# lie_plants_docking
+# mdstudio_plants_docking
 
-[![Build Status](https://travis-ci.org/MD-Studio/lie_plants_docking.svg?branch=master)](https://travis-ci.org/MD-Studio/lie_plants_docking) [![Docker Build Status](https://img.shields.io/docker/build/mdstudio/lie_plants_docking.svg)](https://hub.docker.com/r/mdstudio/lie_plants_docking/)
+[![Build Status](https://travis-ci.org/MD-Studio/lie_plants_docking.svg?branch=master)](https://travis-ci.org/MD-Studio/lie_plants_docking)
+[![Docker Build Status](https://img.shields.io/docker/build/mdstudio/lie_plants_docking.svg)](https://hub.docker.com/r/mdstudio/lie_plants_docking/)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/aff6245274f44a7991a3a25976ad6472)](https://www.codacy.com/app/tifonzafel/MDStudio?utm_source=github.com&utm_medium=referral&utm_content=MD-Studio/lie_plants_docking&utm_campaign=Badge_Grade)
 
-This repo containts the interface between [MDStudio](https://github.com/MD-Studio/MDStudio) and [Plants](http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html)
+This repo containts the interface between [MDStudio](https://github.com/MD-Studio/MDStudio) and 
+[Plants](http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html)
 
 ## Note
 **You should request a LICENSE to use PLANTS**, visit the [plants website](http://www.tcd.uni-konstanz.de/plants_download/).

entry_point_lie_plants_docking.sh → entry_point_mdstudio_plants_docking.sh

@@ -2,4 +2,4 @@
 
 export MD_CONFIG_ENVIRONMENTS=dev,docker
 
-python -u -m lie_plants_docking
+python -u -m mdstudio_plants_docking

lie_plants_docking/__init__.py → mdstudio_plants_docking/__init__.py

@@ -10,7 +10,7 @@
 
 import os
 
-__module__ = 'lie_plants_docking'
+__module__ = 'mdstudio_plants_docking'
 __docformat__ = 'restructuredtext'
 __version__ = '{major:d}.{minor:d}'.format(major=0, minor=1)
 __author__ = 'Marc van Dijk'

lie_plants_docking/__main__.py → mdstudio_plants_docking/__main__.py

@@ -1,5 +1,5 @@
 from mdstudio.runner import main
-from lie_plants_docking.wamp_services import DockingWampApi
+from mdstudio_plants_docking.wamp_services import DockingWampApi
 
 
 if __name__ == '__main__':

lie_plants_docking/plants_docking.py → mdstudio_plants_docking/plants_docking.py

@@ -13,10 +13,10 @@
 import os
 import csv
 
-from lie_plants_docking.docking_base import DockingBase
-from lie_plants_docking.plants_conf import PLANTS_CONF_FILE_TEMPLATE
-from lie_plants_docking.utils import cmd_runner
-from lie_plants_docking.clustering import (coords_from_mol2, ClusterStructures)
+from mdstudio_plants_docking.docking_base import DockingBase
+from mdstudio_plants_docking.plants_conf import PLANTS_CONF_FILE_TEMPLATE
+from mdstudio_plants_docking.utils import cmd_runner
+from mdstudio_plants_docking.clustering import (coords_from_mol2, ClusterStructures)
 
 
 class PlantsDocking(DockingBase):
@@ -32,7 +32,7 @@ class PlantsDocking(DockingBase):
 
     This class is compatible with PLANTS versions 1.1 and 1.2.
     If not otherwise defined, the PLANTS executable files are available
-    in the bin directory of the lie_plants_docking package suffixed by the
+    in the bin directory of the mdstudio_plants_docking package suffixed by the
     OS identifier as returned by `sys.platform`.
     Support is available for all of PLANTS default configuration options
     described in sections 1.0 of the PLANTS manual.

lie_plants_docking/schemas/endpoints/docking_request.v1.json → mdstudio_plants_docking/schemas/endpoints/docking_request.v1.json

@@ -8,7 +8,7 @@
     "workdir": {
       "type": "string",
       "description": "Directory to run the docking simulation",
-      "default": "/tmp/mdstudio/lie_plants_docking"
+      "default": "/tmp/mdstudio/mdstudio_plants_docking"
     },
     "scoring_function": {
       "type": "string",

lie_plants_docking/utils.py → mdstudio_plants_docking/utils.py

@@ -111,5 +111,5 @@ def cmd_runner(cmd, workdir):
 
 
 PLANTS_DOCKING_SCHEMA = os.path.join(
-    pkgutil.get_data('lie_plants_docking', 'schemas/endpoints/docking_request.v1.json'))
+    pkgutil.get_data('mdstudio_plants_docking', 'schemas/endpoints/docking_request.v1.json'))
 settings = _schema_to_data(json.loads(PLANTS_DOCKING_SCHEMA))

lie_plants_docking/wamp_services.py → mdstudio_plants_docking/wamp_services.py

@@ -3,8 +3,8 @@
 import os
 from autobahn.wamp import RegisterOptions
 
-from lie_plants_docking.plants_docking import PlantsDocking
-from lie_plants_docking.utils import prepare_work_dir
+from mdstudio_plants_docking.plants_docking import PlantsDocking
+from mdstudio_plants_docking.utils import prepare_work_dir
 from mdstudio.component.session import ComponentSession
 from mdstudio.api.endpoint import endpoint
 

settings.yml

@@ -1,3 +1,3 @@
 static:
   vendor: mdgroup
-  component: lie_plants_docking
+  component: mdstudio_plants_docking

setup.py

@@ -1,10 +1,10 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# package: lie_plants_docking
+# package: mdstudio_plants_docking
 # file: setup.py
 #
-# Part of ‘lie_plants_docking’, a package providing molecular docking functionality
+# Part of ‘mdstudio_plants_docking’, a package providing molecular docking functionality
 # for the LIEStudio package.
 #
 # Copyright © 2016 Marc van Dijk, VU University Amsterdam, the Netherlands
@@ -23,7 +23,7 @@
 
 from setuptools import setup, find_packages
 
-distribution_name = 'lie_plants_docking'
+distribution_name = 'mdstudio_plants_docking'
 
 setup(
     name=distribution_name,

tests/test_docking.py

@@ -9,8 +9,8 @@
 import shutil
 import unittest
 
-from lie_plants_docking.plants_docking import PlantsDocking
-from lie_plants_docking.utils import (prepare_work_dir, settings)
+from mdstudio_plants_docking.plants_docking import PlantsDocking
+from mdstudio_plants_docking.utils import (prepare_work_dir, settings)
 
 
 # Add modules in package to path so we can import them
@@ -55,7 +55,7 @@ def test_plants_faultyworkdir(self):
         is not available and cannot be created
         """
 
-        plants = PlantsDocking(workdir='/Users/_dummy_user/lie_plants_docking/tests/plants_docking',
+        plants = PlantsDocking(workdir='/Users/_dummy_user/mdstudio_plants_docking/tests/plants_docking',
                                exec_path=exec_path,
                                bindingsite_center=[7.79934, 9.49666, 3.39229])
 
@@ -68,7 +68,7 @@ def test_plants_faultyexec(self):
         """
         self.workdir = prepare_work_dir(__rootpath__, create=True)
         plants = PlantsDocking(workdir=self.workdir,
-                               exec_path='/Users/_dummy_user/lie_plants_docking/tests/plants',
+                               exec_path='/Users/_dummy_user/mdstudio_plants_docking/tests/plants',
                                bindingsite_center=[7.79934, 9.49666, 3.39229])
 
         self.assertFalse(plants.run(self.protein, self.ligand))

tests/wamp_test/test_lie_plants_docking.py

@@ -37,7 +37,7 @@ def authorize_request(self, uri, claims):
     def on_run(self):
 
         result = yield self.call(
-            u"mdgroup.lie_plants_docking.endpoint.docking",
+            u"mdgroup.mdstudio_plants_docking.endpoint.docking",
             {u"protein_file": protein_file,
              u"ligand_file": ligand_file,
              u"min_rmsd_tolerance": 3.0,