Merge pull request #7 from theavey/ParaTemp-4-install

Test on Travis-CI using locally installed package

.travis.yml

@@ -1,8 +1,13 @@
 language: python
 
-# command to install dependencies
+python:
+  - "2.7"
+  - "3.6"
+
+# command to install dependencies and package
 install:
   - pip install -r requirements.txt
+  - python setup.py install
 # command to run tests
 script:
-  - pytest # or py.test for Python versions 3.5 and below
+  - py.test # or py.test for Python versions 3.5 and below

paratemp/coordinate_analysis.py

@@ -2,10 +2,10 @@
 
 ########################################################################
 #                                                                      #
-# This script was written by Thomas Heavey in 2017.                    #
+# This script was written by Thomas Heavey in 2018.                    #
 #        [email protected]     [email protected]                    #
 #                                                                      #
-# Copyright 2017 Thomas J. Heavey IV                                   #
+# Copyright 2017, 2018 Thomas J. Heavey IV                             #
 #                                                                      #
 # Licensed under the Apache License, Version 2.0 (the "License");      #
 # you may not use this file except in compliance with the License.     #

setup.cfg

@@ -2,3 +2,4 @@
 VCS = git
 style = pep440
 versionfile_source = paratemp/_version.py
+tag_prefix = paratemp-

setup.py

@@ -1,14 +1,16 @@
-from distutils.core import setup
+from setuptools import setup
 import versioneer
 
 setup(
     name='ParaTemp',
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
     packages=['paratemp'],
+    scripts=['check-convergence.py'],
     url='https://github.com/theavey/ParaTemp',
     license='Apache License 2.0',
     author='Thomas Heavey',
     author_email='[email protected]',
-    description='Scripts for molecular dynamics analysis and parallel tempering in GROMACS'
+    description='Scripts for molecular dynamics analysis and parallel '
+                'tempering in GROMACS'
 )

tests/test_CoordinateAnalysis.py

@@ -2,10 +2,10 @@
 
 ########################################################################
 #                                                                      #
-# This script was written by Thomas Heavey in 2017.                    #
+# This script was written by Thomas Heavey in 2018.                    #
 #        [email protected]     [email protected]                    #
 #                                                                      #
-# Copyright 2017 Thomas J. Heavey IV                                   #
+# Copyright 2017-18 Thomas J. Heavey IV                                #
 #                                                                      #
 # Licensed under the Apache License, Version 2.0 (the "License");      #
 # you may not use this file except in compliance with the License.     #
@@ -39,7 +39,7 @@ def test_matplotlib_testing_backend():
 
 
 def test_running_mean():
-    from ..paratemp.coordinate_analysis import _running_mean
+    from paratemp.coordinate_analysis import _running_mean
     tl = [0, 2, 4]
     assert (_running_mean(tl) == [1, 3]).all()
 
@@ -48,7 +48,7 @@ class TestXTCUniverse(object):
 
     @pytest.fixture
     def univ(self):
-        from ..paratemp import coordinate_analysis as ca
+        from paratemp import coordinate_analysis as ca
         _univ = ca.Universe('tests/test-data/spc2.gro',
                             'tests/test-data/t-spc2-traj.xtc',
                             temp=205.)
@@ -61,7 +61,7 @@ def univ_w_a(self, univ):
 
     @pytest.fixture
     def univ_pbc(self):
-        from ..paratemp import coordinate_analysis as ca
+        from paratemp import coordinate_analysis as ca
         _univ = ca.Universe('tests/test-data/spc2.gro',
                             'tests/test-data/spc2-traj-pbc.xtc',
                             temp=205.)
@@ -117,7 +117,7 @@ def test_calculate_distances_no_recalc(self, univ_w_a, capsys):
 
     def test_calculate_distances_yes_recalc(self, univ_w_a):
         """
-        :type univ_w_a: ParaTemp.CoordinateAnalysis.Universe
+        :type univ_w_a: paratemp.coordinate_analysis.Universe
         """
         univ_w_a.calculate_distances(a='5 5', recalculate=True)
         assert (np.array([0., 0.]) == univ_w_a.data['a']).all()
@@ -129,13 +129,13 @@ def test_distance_pbc(self, univ_pbc, ref_a_pbc_dists):
     def test_calc_fes_1d(self, univ_w_a, ref_delta_g, ref_bins, ref_delta_g_20,
                          ref_bins_20):
         """
-        :type univ_w_a: ParaTemp.CoordinateAnalysis.Universe
+        :type univ_w_a: paratemp.coordinate_analysis.Universe
         :type ref_delta_g: np.ndarray
         :type ref_bins: np.ndarray
         :type ref_delta_g_20: np.ndarray
         :type ref_bins_20: np.ndarray
         """
-        from ..paratemp.coordinate_analysis import _calc_fes_1d
+        from paratemp.coordinate_analysis import _calc_fes_1d
         delta_g_data, bins_data = _calc_fes_1d(univ_w_a.data['a'], temp=205.,
                                                bins=None)
         assert (delta_g_data == ref_delta_g).all()
@@ -147,7 +147,7 @@ def test_calc_fes_1d(self, univ_w_a, ref_delta_g, ref_bins, ref_delta_g_20,
 
     def test_fes_1d_data_str(self, univ_w_a, ref_delta_g, ref_bins):
         """
-        :type univ_w_a: ParaTemp.CoordinateAnalysis.Universe
+        :type univ_w_a: paratemp.coordinate_analysiss.Universe
         :type ref_delta_g: np.ndarray
         :type ref_bins: np.ndarray
         """
@@ -158,7 +158,7 @@ def test_fes_1d_data_str(self, univ_w_a, ref_delta_g, ref_bins):
 
     def test_fes_1d_data_data(self, univ_w_a, ref_delta_g, ref_bins):
         """
-        :type univ_w_a: ParaTemp.CoordinateAnalysis.Universe
+        :type univ_w_a: paratemp.coordinate_analysis.Universe
         :type ref_delta_g: np.ndarray
         :type ref_bins: np.ndarray
         """

tests/test_geometries.py

@@ -2,10 +2,10 @@
 
 ########################################################################
 #                                                                      #
-# This script was written by Thomas Heavey in 2017.                    #
+# This script was written by Thomas Heavey in 2018.                    #
 #        [email protected]     [email protected]                    #
 #                                                                      #
-# Copyright 2017 Thomas J. Heavey IV                                   #
+# Copyright 2017-18 Thomas J. Heavey IV                                #
 #                                                                      #
 # Licensed under the Apache License, Version 2.0 (the "License");      #
 # you may not use this file except in compliance with the License.     #
@@ -32,7 +32,7 @@ class TestXYZ(object):
 
     @pytest.fixture
     def xyz(self):
-        from ..paratemp.geometries import XYZ
+        from paratemp.geometries import XYZ
         return XYZ('tests/test-data/stil-3htmf.xyz')
 
     def test_n_atoms(self, xyz):
@@ -51,27 +51,27 @@ def pi(self):
 
     @pytest.fixture
     def x_axis_int_list(self):
-        from ..paratemp.geometries import Vector
+        from paratemp.geometries import Vector
         return Vector([1, 0, 0])
 
     @pytest.fixture
     def x_axis_float_list(self):
-        from ..paratemp.geometries import Vector
+        from paratemp.geometries import Vector
         return Vector([1., 0., 0.])
 
     @pytest.fixture
     def x_axis_int(self):
-        from ..paratemp.geometries import Vector
+        from paratemp.geometries import Vector
         return Vector(1, 0, 0)
 
     @pytest.fixture
     def y_axis(self):
-        from ..paratemp.geometries import Vector
+        from paratemp.geometries import Vector
         return Vector(0, 1, 0)
 
     @pytest.fixture
     def z_axis(self):
-        from ..paratemp.geometries import Vector
+        from paratemp.geometries import Vector
         return Vector(0, 0, 1)
 
     def test_input_int_float(self, x_axis_int_list, x_axis_float_list):

tests/test_sim_setup.py

@@ -2,10 +2,10 @@
 
 ########################################################################
 #                                                                      #
-# This script was written by Thomas Heavey in 2017.                    #
+# This script was written by Thomas Heavey in 2018.                    #
 #        [email protected]     [email protected]                    #
 #                                                                      #
-# Copyright 2017 Thomas J. Heavey IV                                   #
+# Copyright 2017-18 Thomas J. Heavey IV                                #
 #                                                                      #
 # Licensed under the Apache License, Version 2.0 (the "License");      #
 # you may not use this file except in compliance with the License.     #
@@ -30,7 +30,7 @@
 
 
 def test_job_info_from_qsub():
-    from ..paratemp.sim_setup import _job_info_from_qsub
+    from paratemp.sim_setup import _job_info_from_qsub
     job_info = _job_info_from_qsub('Your job 2306551 ("PT-NTD-CG") '
                                    'has been submitted')
     assert job_info == ('2306551', 'PT-NTD-CG', '2306551 ("PT-NTD-CG")')
@@ -62,14 +62,14 @@ def rd1030(self):
         return {10: 30}
 
     def test_update_num(self, match_10, rd1030):
-        from ..paratemp.sim_setup import _update_num
+        from paratemp.sim_setup import _update_num
         assert '=30' == _update_num(match_10, shift=10, cat_repl_dict=rd1030)
         assert '=1' == _update_num(match_10, shift=9, cat_repl_dict=dict())
         assert '=1' == _update_num(match_10, shift=9, cat_repl_dict=rd1030)
 
     def test_update_num_raises(self, match_10, match_text, match_float,
                                match_bad_few, match_bad_many):
-        from ..paratemp.sim_setup import _update_num
+        from paratemp.sim_setup import _update_num
         with pytest.raises(KeyError):
             _update_num(match_10, shift=10, cat_repl_dict=dict())
         with pytest.raises(ValueError,
@@ -102,19 +102,19 @@ def folder_dc(n_top_dc):
 class TestGetSolvCountTop(object):
 
     def test_get_solv_count_top(self, n_top_dc, folder_dc):
-        from ..paratemp.sim_setup import get_solv_count_top
+        from paratemp.sim_setup import get_solv_count_top
         assert get_solv_count_top(n_top_dc) == 361
         assert get_solv_count_top(folder=folder_dc) == 361
 
 
 class TestSetSolvCountTop(object):
 
     def test_set_solv_count_top_n(self, n_top_dc):
-        from ..paratemp.sim_setup import set_solv_count_top, get_solv_count_top
+        from paratemp.sim_setup import set_solv_count_top, get_solv_count_top
         set_solv_count_top(n_top_dc, s_count=100)
         assert get_solv_count_top(n_top_dc) == 100
 
     def test_set_solv_count_top_folder(self, folder_dc, n_top_dc):
-        from ..paratemp.sim_setup import set_solv_count_top, get_solv_count_top
+        from paratemp.sim_setup import set_solv_count_top, get_solv_count_top
         set_solv_count_top(folder=folder_dc, s_count=50)
         assert get_solv_count_top(n_top_dc) == 50

tests/test_tools.py

@@ -2,10 +2,10 @@
 
 ########################################################################
 #                                                                      #
-# This script was written by Thomas Heavey in 2017.                    #
+# This script was written by Thomas Heavey in 2018.                    #
 #        [email protected]     [email protected]                    #
 #                                                                      #
-# Copyright 2017 Thomas J. Heavey IV                                   #
+# Copyright 2017-18 Thomas J. Heavey IV                                #
 #                                                                      #
 # Licensed under the Apache License, Version 2.0 (the "License");      #
 # you may not use this file except in compliance with the License.     #
@@ -34,5 +34,5 @@ def ref_temps():
 
 
 def test_get_temps(ref_temps):
-    from ..paratemp import get_temperatures
+    from paratemp import get_temperatures
     assert (get_temperatures('tests/test-data/temperatures.dat') == ref_temps).all()