Move data files from quickff/share to quickff/quickff/data and use pa…

…th routine from importlib.resources

HEADER

@@ -1,5 +1,5 @@
 QuickFF is a code to quickly derive accurate force fields from ab initio input.
-Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 Steven Vandenbrande <[email protected]>, 
 Jelle Wieme <[email protected]>, 
 Toon Verstraelen <[email protected]>, Center for Molecular Modeling

MANIFEST.in

@@ -0,0 +1,5 @@
+include README
+include LICENSE
+include quickff/data/*
+include quickff/data/systems/*.*
+include quickff/data/systems/*/*.*

quickff/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/cost.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/data/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# QuickFF is a code to quickly derive accurate force fields from ab initio input.
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
+# Steven Vandenbrande <[email protected]>,
+# Jelle Wieme <[email protected]>,
+# Toon Verstraelen <[email protected]>, Center for Molecular Modeling
+# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
+# stated.
+#
+# This file is part of QuickFF.
+#
+# QuickFF is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# QuickFF is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+#
+#--

quickff/io.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/log.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/paracontext.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/perturbation.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/program.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/reference.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/scripts.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/settings.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling
@@ -30,6 +30,12 @@
 from molmod.units import parse_unit
 import os
 
+try:
+    from importlib.resources import path
+except ImportError:
+    from importlib_resources import path
+
+
 __all__  = ['Settings']
 
 def is_not_none(key, value):
@@ -158,10 +164,10 @@ def __init__(self, fn=None, **kwargs):
 
         '''
         #first read general RC settings from .quickffrc file
-        from .context import context
-        self.read_config_file(context.get_fn('quickffrc'))
+        with path('quickff.data', 'quickffrc') as fn_default:
+            self.read_config_file(fn_default)
         #if a config file is provided, read settings from this file and
-        #overwrite the general RC settings
+        #overwrite the default RC settings
         if fn is not None:
             self.read_config_file(fn)
         #if settings are defined through keyword arguments to this init

quickff/tests/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# QuickFF is a code to quickly derive accurate force fields from ab initio input.
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
+# Steven Vandenbrande <[email protected]>,
+# Jelle Wieme <[email protected]>,
+# Toon Verstraelen <[email protected]>, Center for Molecular Modeling
+# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
+# stated.
+#
+# This file is part of QuickFF.
+#
+# QuickFF is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# QuickFF is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+#
+#--

quickff/tests/common.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling
@@ -33,7 +33,6 @@
 
 from quickff.io import read_abinitio
 
-from quickff.context import context
 from quickff.io import read_abinitio
 from quickff.reference import SecondOrderTaylor
 from quickff.valence import ValenceFF
@@ -43,15 +42,26 @@
 from quickff.log import log
 log.set_level('silent')
 
+try:
+    from importlib.resources import path
+except ImportError:
+    from importlib_resources import path
+
+
 __all__ = ['log', 'read_system', 'tmpdir']
 
 def read_system(name):
-    # Load system data.
-    fn = context.get_fn(os.path.join('systems', name))
-    numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn)
+    # Load system data
+    dn = 'quickff.data.systems'
+    if '/' in name:
+        words = name.split('/')
+        dn += '.%s' %('.'.join(words[:-1]))
+        name = words[-1]
+    with path(dn, name) as fn:
+        numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn)
+        fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5'))
     # Try to load charges.
     charges = None
-    fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5'))
     if len(fns_wpart) > 0:
         with h5.File(fns_wpart[0], 'r') as f:
             charges = f['charges'][:]

quickff/tests/test_examples.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling
@@ -35,10 +35,15 @@
 from quickff.tools import set_ffatypes
 from quickff.program import DeriveFF
 from quickff.settings import Settings
-from quickff.context import context
 from quickff.reference import SecondOrderTaylor
 
-from common import log, read_system, tmpdir
+from .common import log, read_system, tmpdir
+
+try:
+    from importlib.resources import path
+except ImportError:
+    from importlib_resources import path
+
 
 def test_h2():
     #frequency of H2 stretch mode in gaussian.fchk calculation is 4416.656/cm
@@ -199,8 +204,8 @@ def test_uio66zrbrick_crossterms():
         # Load input data for a ficticious system of an isolated
         # UiO-66 brick
         name = 'uio66-zr-brick/system.chk'
-        fn = context.get_fn(os.path.join('systems', name))
-        data = load_chk(fn)
+        with path(quickff.data.systems, name) as fn:
+            data = load_chk(fn)
         system = System(data['numbers'],data['pos'],charges=data['charges'],
             ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
         system.set_standard_masses()
@@ -224,4 +229,3 @@ def test_uio66zrbrick_crossterms():
                     fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
                     print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
                     if fc_diag==0.0: assert fc==0.0
-

quickff/tests/test_reference.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling
@@ -25,7 +25,7 @@
 #--
 from molmod.units import angstrom, kjmol
 
-from common import log, read_system
+from .common import log, read_system
 
 from nose import SkipTest
 

quickff/tests/test_valence.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling
@@ -32,7 +32,7 @@
 
 from itertools import permutations
 
-from common import log, read_system
+from .common import log, read_system
 
 import numpy as np
 

quickff/tools.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling

quickff/valence.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # QuickFF is a code to quickly derive accurate force fields from ab initio input.
-# Copyright (C) 2012 - 2018 Louis Vanduyfhuys <[email protected]>
+# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <[email protected]>
 # Steven Vandenbrande <[email protected]>,
 # Jelle Wieme <[email protected]>,
 # Toon Verstraelen <[email protected]>, Center for Molecular Modeling