merged

Author: Stefan Doerr

.travis.yml

@@ -27,7 +27,6 @@ matrix:
       - brew install gcc
 
 install:
- - printenv
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
  - if [ "$TRAVIS_OS_NAME" == "windows" ]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
@@ -45,9 +44,9 @@ install:
 # - source activate travis-env
 
  - conda config --add channels acellera
- - conda install -c acellera toolz=0.8.0 -y -q
+ - conda install -c acellera toolz=0.8.0 -y -q 
  - conda update --all -y -q
- - conda install anaconda requests conda-build -y -q
+ - conda install anaconda anaconda-client requests conda-build -y -q
 
 
  - if [ "$TRAVIS_BRANCH" == "$TRAVIS_TAG" ]; then export BUILD_VERSION=$TRAVIS_TAG; else export BUILD_VERSION=0.0.0; fi

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-include htmd/data *
+recursive-include htmd/lib *
+include HTMD_LICENSE.txt

README.txt

@@ -0,0 +1,4 @@
+HTMD
+See https://www.htmd.org
+Installation through PyPI is experimental -- please report bugs via
+https://github.org/acellera/htmd/issues

htmd/adaptive/adaptive.py

@@ -78,11 +78,6 @@ def run(self):
                 except ProjectNotExistError:
                     logger.info('Retrieve found no previous simulations for this adaptive. Assuming this is a new adaptive run')
 
-                if epoch >= self.nepochs:
-                    logger.info('Reached maximum number of epochs ' + str(self.nepochs))
-                    self._unsetLock()
-                    return
-
                 # Checking how many simulations are in progress (queued/running) on the queue
                 try:
                     self._running = self.app.inprogress()
@@ -95,8 +90,13 @@ def run(self):
 
                 logger.info(str(self._running) + ' simulations in progress')
 
+                if epoch >= self.nepochs and self._running == 0:
+                    logger.info('Reached maximum number of epochs ' + str(self.nepochs))
+                    self._unsetLock()
+                    return
+
                 # If currently running simulations are lower than nmin start new ones to reach nmax number of sims
-                if self._running <= self.nmin:
+                if self._running <= self.nmin and epoch < self.nepochs:
                     flag = self._algorithm()
                     if flag is False:
                         self._unsetLock()

htmd/apps/acemd.py

@@ -16,9 +16,9 @@ class Acemd(ProtocolInterface):
                'coordinates': 'structure.pdb', 'velocities': 'velocity.pdb', 'consref': 'structure.pdb',
                'parmfile': 'structure.prmtop'}
 
-    def __init__(self):
+    def __init__(self, version=2):
         super().__init__()
-
+        self._version=version 
         self._files = {}
 
         # Options
@@ -43,21 +43,26 @@ def __init__(self):
         self._cmdString('pmegridspacing', 'str', '', None)
         self._cmdString('fullelectfrequency', 'str', '', None)
         self._cmdString('energyfreq', 'str', '', None)
-        self._cmdString('constraints', 'str', '', None)
-        self._cmdString('consref', 'str', '', None)
-        self._cmdString('constraintscaling', 'str', '', None)
+        if self._version == 2:
+            self._cmdString('constraints', 'str', '', None)
+            self._cmdString('consref', 'str', '', None)
+            self._cmdString('constraintscaling', 'str', '', None)
+        if self._version == 3:
+            self._cmdString('atomrestraint', 'str', '', None)
+            self._cmdString('grouprestraint', 'str', '', None)
         self._cmdString('berendsenpressure', 'str', '', None)
         self._cmdString('berendsenpressuretarget', 'str', '', None)
         self._cmdString('berendsenpressurerelaxationtime', 'str', '', None)
         self._cmdString('tclforces', 'str', '', None)
         self._cmdString('minimize', 'str', '', None)
         self._cmdString('run', 'str', '', None)
-        self._cmdString('TCL', 'str', '', None)
         self._cmdString('celldimension', 'str', '', None)
         self._cmdString('useconstantratio', 'str', '', None)
         self._cmdString('amber', 'str', '', None)
         self._cmdString('dielectric', 'str', '', None)
         self._cmdString('pairlistdist', 'str', '', None)
+        if self._version == 2:
+            self._cmdString('TCL', 'str', '', None)
 
         # Files
         self._cmdString('bincoordinates', 'str', '', None)
@@ -68,7 +73,6 @@ def __init__(self):
         self._cmdString('extendedsystem', 'str', '', None)
         self._cmdString('coordinates', 'str', '', None)
         self._cmdString('velocities', 'str', '', None)
-        self._cmdString('consref', 'str', '', None)
         self._cmdString('parmfile', 'str', '', None)
 
     def load(self, path='.'):
@@ -175,7 +179,10 @@ def show(self, quiet=False):
 
     def _writeBashRun(self, fname):
         with open(fname, 'w') as f:
-            f.write('#!/bin/bash\nacemd >log.txt 2>&1')
+            if self._version==3:
+               f.write('#!/bin/bash\nacemd3 >log.txt 2>&1')
+            else:
+               f.write('#!/bin/bash\nacemd >log.txt 2>&1')
         os.chmod(fname, 0o700)
 
     def __repr__(self):

htmd/builder/amber.py

@@ -5,6 +5,7 @@
 #
 from __future__ import print_function
 
+
 from htmd.home import home
 import numpy as np
 import os

setup.py

@@ -0,0 +1,37 @@
+from setuptools import setup
+import subprocess
+
+version=subprocess.Popen(["git", "describe", "--tags"], stdout=subprocess.PIPE ).stdout.read().decode("utf8")
+version=version.split("-")
+version=version[0]
+
+f=open( "package/htmd-deps/DEPENDENCIES", "r" )
+deps=[ 'pyEMMA<2.3' ]
+#for a in f.readlines():
+#	deps.append(a.strip().split("=")[0]) #.decode("utf8"))
+
+print("Version [%s]" % (version) )
+print("Dependencies:" )
+print(deps)
+
+setup(name='htmd',
+	version='0.15.11',
+	description='HTMD',
+	packages=['htmd', 'htmdx', 'htmd.molecule', 'htmd.parameterization', 'htmd.adaptive', 'htmd.apps', 'htmd.builder', 'htmd.clustering', 'htmd.progress', 'htmd.projections', 'htmd.protocols', 'htmd.qm', 'htmd.queues', 'htmd.data' ],
+	install_requires=deps,
+	zip_safe=False,
+	url="https://www.htmd.org",
+	maintainer="Acellera Ltd",
+	maintainer_email="[email protected]",
+	entry_points = {
+		"console_scripts": [
+			'htmdnb    = htmdx.cli:main_htmd_notebook',
+			'htmd      = htmdx.cli:main_htmd',
+			'htmd_register   = htmdx.cli:main_do_nothing',
+			'parameterize = htmd.parameterization.cli:main_parameterize',
+			'activate_license  = htmdx.cli:main_activate'
+		]
+	},
+	include_package_data=True
+	)
+

sync_conda_with_omnia.py

@@ -55,8 +55,8 @@
 
 		acellera = {"latest_version": "0" }
 
-	if omnia["latest_version"] != acellera["latest_version"]:
-		print("Syncing %s/%s version %s.." %(pp[0], p, omnia["latest_version"]) )
+	if omnia["latest_version"] > acellera["latest_version"]:
+		print("Syncing %s/%s version %s (acellera version %s).." %(pp[0], p, omnia["latest_version"], acellera["latest_version"]) )
 		for f in omnia["files"]:
 			if f["version"] == omnia["latest_version"]:
 				url = "https:" + f["download_url"]
@@ -69,11 +69,11 @@
 				print("Uploading.."  )
 				try:
 					os.getenv("ANACONDA_TOKEN_BASIC") 
-					call([ "anaconda", "upload", "-t", os.getenv("ANACONDA_TOKEN_BASIC"),"-u",  "acellera", f["basename"] ])
+					call([ "anaconda", "upload", "--force",  "-t", os.getenv("ANACONDA_TOKEN_BASIC"),"-u",  "acellera", f["basename"] ])
 				except:
 					try:
-						call([ "anaconda", "upload", "-u",  "acellera", f["basename"] ])
+						call([ "anaconda", "upload", "--force", "-u",  "acellera", f["basename"] ])
 					except:
 						print("Failed to sync")
 	else:
-		print("Package %s up to date at version %s" % ( p, omnia["latest_version"] ) )
+		print("Package %s up to date at version %s/%s" % ( p, omnia["latest_version"], acellera["latest_version"] ) )

tests/run_inline_file_tests.py

@@ -8,9 +8,7 @@
 from subprocess import call, check_output
 import sys
 
-excludedfolders = ('./tests', './doc', './htmdlib')
-excludedfiles = ('__init__.py', 'license_headers.py', 'sync_conda_with_omnia.py', 'makerelease.py')   # Trailing comma needed otherwise it's not a tuple
-
+excludedfiles = ('__init__.py', 'license_headers.py', 'setup.py', 'sync_conda_with_omnia.py', 'makerelease.py')   # Trailing comma needed otherwise it's not a tuple
 
 def excluded(name, exclusionlist):
     for e in exclusionlist: