From 07d0555eef990947684ef2dbce41708f1e409289 Mon Sep 17 00:00:00 2001 From: Anders Steen Christensen Date: Wed, 7 Jun 2017 16:08:01 +0200 Subject: [PATCH 01/15] fixed bob float/int indices bug (#7) --- src/representations.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/representations.py b/src/representations.py index b907c80ea..03cc1d244 100644 --- a/src/representations.py +++ b/src/representations.py @@ -21,6 +21,7 @@ # SOFTWARE. from __future__ import print_function +from __future__ import division import numpy as np @@ -36,7 +37,7 @@ def vector_to_matrix(v): exit(1) n = v.shape[0] - l = (-1 + int(np.sqrt(8*n+1)))/2 + l = (-1 + int(np.sqrt(8*n+1)))//2 M = np.empty((l,l)) index = 0 @@ -100,10 +101,10 @@ def generate_bob(coordinates, nuclear_charges, atomtypes, size=23, asize={"O":3, if atom1 > atom2: continue if atom1 == atom2: - size = size1*(size1-1)/2 + size = size1*(size1-1)//2 feature_vector = np.zeros(size) sub_matrix = coulomb_matrix[np.ix_(pos1,pos1)] - feature_vector[:pos1.size*(pos1.size-1)/2] = sub_matrix[np.triu_indices(pos1.size, 1)] + feature_vector[:pos1.size*(pos1.size-1)//2] = sub_matrix[np.triu_indices(pos1.size, 1)] feature_vector.sort() descriptor.append(feature_vector[:]) else: From 73e277c4d1253538db06be71b696afd1f39ad9a4 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Wed, 7 Jun 2017 16:26:51 +0200 Subject: [PATCH 02/15] Changed src/ to qml/ --- {src => qml}/__init__.py | 0 {src => qml}/arad.py | 0 {src => qml}/arad_kernels.py | 0 {src => qml}/compound.py | 0 {src => qml}/data.py | 0 {src => qml}/distance.py | 0 {src => qml}/farad_kernels.f90 | 0 {src => qml}/fcho_solve.f90 | 0 {src => qml}/fdistance.f90 | 0 {src => qml}/fkernels.f90 | 0 {src => qml}/frepresentations.f90 | 0 {src => qml}/kernels.py | 0 {src => qml}/math.py | 0 {src => qml}/representations.py | 0 {src => qml}/wrappers.py | 0 setup.py | 12 ++++++------ 16 files changed, 6 insertions(+), 6 deletions(-) rename {src => qml}/__init__.py (100%) rename {src => qml}/arad.py (100%) rename {src => qml}/arad_kernels.py (100%) rename {src => qml}/compound.py (100%) rename {src => qml}/data.py (100%) rename {src => qml}/distance.py (100%) rename {src => qml}/farad_kernels.f90 (100%) rename {src => qml}/fcho_solve.f90 (100%) rename {src => qml}/fdistance.f90 (100%) rename {src => qml}/fkernels.f90 (100%) rename {src => qml}/frepresentations.f90 (100%) rename {src => qml}/kernels.py (100%) rename {src => qml}/math.py (100%) rename {src => qml}/representations.py (100%) rename {src => qml}/wrappers.py (100%) diff --git a/src/__init__.py b/qml/__init__.py similarity index 100% rename from src/__init__.py rename to qml/__init__.py diff --git a/src/arad.py b/qml/arad.py similarity index 100% rename from src/arad.py rename to qml/arad.py diff --git a/src/arad_kernels.py b/qml/arad_kernels.py similarity index 100% rename from src/arad_kernels.py rename to qml/arad_kernels.py diff --git a/src/compound.py b/qml/compound.py similarity index 100% rename from src/compound.py rename to qml/compound.py diff --git a/src/data.py b/qml/data.py similarity index 100% rename from src/data.py rename to qml/data.py diff --git a/src/distance.py b/qml/distance.py similarity index 100% rename from src/distance.py rename to qml/distance.py diff --git a/src/farad_kernels.f90 b/qml/farad_kernels.f90 similarity index 100% rename from src/farad_kernels.f90 rename to qml/farad_kernels.f90 diff --git a/src/fcho_solve.f90 b/qml/fcho_solve.f90 similarity index 100% rename from src/fcho_solve.f90 rename to qml/fcho_solve.f90 diff --git a/src/fdistance.f90 b/qml/fdistance.f90 similarity index 100% rename from src/fdistance.f90 rename to qml/fdistance.f90 diff --git a/src/fkernels.f90 b/qml/fkernels.f90 similarity index 100% rename from src/fkernels.f90 rename to qml/fkernels.f90 diff --git a/src/frepresentations.f90 b/qml/frepresentations.f90 similarity index 100% rename from src/frepresentations.f90 rename to qml/frepresentations.f90 diff --git a/src/kernels.py b/qml/kernels.py similarity index 100% rename from src/kernels.py rename to qml/kernels.py diff --git a/src/math.py b/qml/math.py similarity index 100% rename from src/math.py rename to qml/math.py diff --git a/src/representations.py b/qml/representations.py similarity index 100% rename from src/representations.py rename to qml/representations.py diff --git a/src/wrappers.py b/qml/wrappers.py similarity index 100% rename from src/wrappers.py rename to qml/wrappers.py diff --git a/setup.py b/setup.py index 0f1d42376..a68b1ddd8 100755 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ ext_farad_kernels = Extension(name = 'farad_kernels', - sources = ['src/farad_kernels.f90'], + sources = ['qml/farad_kernels.f90'], extra_f90_compile_args = COMPILER_FLAGS, extra_f77_compile_args = COMPILER_FLAGS, extra_compile_args = COMPILER_FLAGS, @@ -50,7 +50,7 @@ f2py_options=['--quiet']) ext_fcho_solve = Extension(name = 'fcho_solve', - sources = ['src/fcho_solve.f90'], + sources = ['qml/fcho_solve.f90'], extra_f90_compile_args = COMPILER_FLAGS, extra_f77_compile_args = COMPILER_FLAGS, extra_compile_args = COMPILER_FLAGS, @@ -59,7 +59,7 @@ f2py_options=['--quiet']) ext_fdistance = Extension(name = 'fdistance', - sources = ['src/fdistance.f90'], + sources = ['qml/fdistance.f90'], extra_f90_compile_args = COMPILER_FLAGS, extra_f77_compile_args = COMPILER_FLAGS, extra_compile_args = COMPILER_FLAGS, @@ -68,7 +68,7 @@ f2py_options=['--quiet']) ext_fkernels = Extension(name = 'fkernels', - sources = ['src/fkernels.f90'], + sources = ['qml/fkernels.f90'], extra_f90_compile_args = COMPILER_FLAGS, extra_f77_compile_args = COMPILER_FLAGS, extra_compile_args = COMPILER_FLAGS, @@ -77,7 +77,7 @@ f2py_options=['--quiet']) ext_frepresentations = Extension(name = 'frepresentations', - sources = ['src/frepresentations.f90'], + sources = ['qml/frepresentations.f90'], extra_f90_compile_args = COMPILER_FLAGS, extra_f77_compile_args = COMPILER_FLAGS, extra_compile_args = COMPILER_FLAGS, @@ -108,7 +108,7 @@ def setup_pepytools(): url = __url__, # set up package contents - package_dir={'qml': 'src'}, + package_dir={'qml': 'qml'}, packages=['qml'], ext_package = 'qml', ext_modules = [ From b44132318f8b838cad88c899b49428b5f70e48d9 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Wed, 7 Jun 2017 16:37:22 +0200 Subject: [PATCH 03/15] updated setup install in travis yml --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 93edf147c..746045413 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,12 +21,12 @@ install: if [ ${TRAVIS_PYTHON_VERSION:0:1} = 3 ]; then sudo apt-get install python3-numpy export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - python3 setup.py build + # python3 setup.py build python3 setup.py install elif [ ${TRAVIS_PYTHON_VERSION} = "2.7" ]; then sudo apt-get install python-numpy export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - python2 setup.py build + # python2 setup.py build python2 setup.py install else echo "ERROR: Unknown Python version." From 986526664ee2f8204da8e8068d473d82348f4c53 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Wed, 7 Jun 2017 16:42:45 +0200 Subject: [PATCH 04/15] updated pythonpath in travis yml --- .travis.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.travis.yml b/.travis.yml index 746045413..86956a332 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,6 +37,9 @@ before_script: - cd ${TRAVIS_BUILD_DIR} - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} + - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} + - echo ${PYTHONPATH} + - echo ${TRAVIS_PYTHON_VERSION} script: - nosetests -v tests/*.py From fc7370d5eb1ffda61d49efa173cb67f8eb5e1340 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Wed, 7 Jun 2017 16:49:46 +0200 Subject: [PATCH 05/15] updated pythonpath in travis yml try 2 --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 86956a332..d48193873 100644 --- a/.travis.yml +++ b/.travis.yml @@ -38,6 +38,7 @@ before_script: - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} + - export PYTHONPATH=/home/travis/virtualenv/python2.7.12/lib/python2.7/site-packages:${PYTHONPATH} - echo ${PYTHONPATH} - echo ${TRAVIS_PYTHON_VERSION} From a95e9d7b4fb44f46c49e1ab29cb21a608d770528 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Wed, 7 Jun 2017 16:58:44 +0200 Subject: [PATCH 06/15] updated pythonpath in travis yml try 3 --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index d48193873..9dec56c85 100644 --- a/.travis.yml +++ b/.travis.yml @@ -38,7 +38,7 @@ before_script: - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - - export PYTHONPATH=/home/travis/virtualenv/python2.7.12/lib/python2.7/site-packages:${PYTHONPATH} + - export PYTHONPATH=/home/travis/virtualenv/python{TRAVIS_PYTHON_VERSION}.*/lib/python{TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - echo ${PYTHONPATH} - echo ${TRAVIS_PYTHON_VERSION} From 9395794a5cd83e0344325ffd819e3b5cafe7d41c Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Wed, 7 Jun 2017 17:01:32 +0200 Subject: [PATCH 07/15] updated pythonpath in travis yml try 4 --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 9dec56c85..2120612ba 100644 --- a/.travis.yml +++ b/.travis.yml @@ -38,7 +38,7 @@ before_script: - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - - export PYTHONPATH=/home/travis/virtualenv/python{TRAVIS_PYTHON_VERSION}.*/lib/python{TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} + - export PYTHONPATH=/home/travis/virtualenv/python${TRAVIS_PYTHON_VERSION}.*/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - echo ${PYTHONPATH} - echo ${TRAVIS_PYTHON_VERSION} From 240ce296d38f9adc83560d5f2cf4fea00ca58601 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 10:34:35 +0200 Subject: [PATCH 08/15] updated setup.py --- setup.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/setup.py b/setup.py index a68b1ddd8..c3f338b6f 100755 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2016" __credits__ = ["Anders S. Christensen (2016) https://github.com/qmlcode/qml"] __license__ = "MIT" -__version__ = "0.2.3" +__version__ = "0.2.12" __maintainer__ = "Anders S. Christensen" __email__ = "andersbiceps@gmail.com" __status__ = "Beta" @@ -95,6 +95,7 @@ def setup_pepytools(): setup( name="qml", + packages=['qml'], # metadata version=__version__, @@ -103,14 +104,12 @@ def setup_pepytools(): platforms = 'Any', description = __description__, long_description = readme(), - keywords = 'Quantum Machine Learning', - download_url = "https://github.com/qmlcode/qml/archive/0.2.3.tar.gz", + keywords = ['Machine Learning', 'Quantum Chemistry'], + classifiers = [], url = __url__, # set up package contents - package_dir={'qml': 'qml'}, - packages=['qml'], - ext_package = 'qml', + # ext_package = 'qml', ext_modules = [ ext_farad_kernels, ext_fcho_solve, From 6897206de5a4f0f486bbe78e0c0dff6e6c42efc4 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 11:42:43 +0200 Subject: [PATCH 09/15] removed trusty from travis yml --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 2120612ba..a8ffbe948 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,6 @@ language: python sudo: required -dist: trusty python: - "2.7" From d5bf8ad2af38164256051116634941a7120f4809 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 11:56:06 +0200 Subject: [PATCH 10/15] printing pythonpath in travis yml try 5 --- .travis.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.travis.yml b/.travis.yml index a8ffbe948..b92fbac97 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,7 @@ language: python sudo: required +dist: trusty python: - "2.7" @@ -40,6 +41,8 @@ before_script: - export PYTHONPATH=/home/travis/virtualenv/python${TRAVIS_PYTHON_VERSION}.*/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - echo ${PYTHONPATH} - echo ${TRAVIS_PYTHON_VERSION} + - python -m site --user-site + - python -m site script: - nosetests -v tests/*.py From 08abfefbf9ae7cf095b299941a927b1cc3f073b9 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 11:59:26 +0200 Subject: [PATCH 11/15] updated pythonpath in travis yml try 5 --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index b92fbac97..7596c9d6a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -41,7 +41,6 @@ before_script: - export PYTHONPATH=/home/travis/virtualenv/python${TRAVIS_PYTHON_VERSION}.*/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - echo ${PYTHONPATH} - echo ${TRAVIS_PYTHON_VERSION} - - python -m site --user-site - python -m site script: From b780a1dcb1b10358985a98fd95558a8b314b13c2 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 12:05:58 +0200 Subject: [PATCH 12/15] updated test path --- .travis.yml | 11 ++--------- tests/test_wrappers.py | 4 ++-- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/.travis.yml b/.travis.yml index 7596c9d6a..f2771f548 100644 --- a/.travis.yml +++ b/.travis.yml @@ -34,14 +34,7 @@ install: before_script: - - cd ${TRAVIS_BUILD_DIR} - - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - - export PYTHONPATH=/home/travis/virtualenv/python${TRAVIS_PYTHON_VERSION}.*/lib/python${TRAVIS_PYTHON_VERSION}/site-packages:${PYTHONPATH} - - echo ${PYTHONPATH} - - echo ${TRAVIS_PYTHON_VERSION} - - python -m site + - cd ${TRAVIS_BUILD_DIR}/tests/ script: - - nosetests -v tests/*.py + - nosetests -v diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py index 388802ea9..b23a059af 100644 --- a/tests/test_wrappers.py +++ b/tests/test_wrappers.py @@ -27,7 +27,7 @@ def get_energies(filename): def test_arad_wrapper(): # Parse file containing PBE0/def2-TZVP heats of formation and xyz filenames - data = get_energies("tests/hof_qm7.txt") + data = get_energies("hof_qm7.txt") # Generate a list of qml.Compound() objects mols = [] @@ -35,7 +35,7 @@ def test_arad_wrapper(): for xyz_file in sorted(data.keys())[:50]: # Initialize the qml.Compound() objects - mol = qml.Compound(xyz="tests/qm7/" + xyz_file) + mol = qml.Compound(xyz="qm7/" + xyz_file) # Associate a property (heat of formation) with the object mol.properties = data[xyz_file] From a82a64be276a6d8b36a330a0933800353a0c0d05 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 12:09:04 +0200 Subject: [PATCH 13/15] debug path 1 --- .travis.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index f2771f548..71a9876e5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,9 +5,6 @@ dist: trusty python: - "2.7" - - "3.4" - - "3.5" - - "3.6" before_install: - sudo apt-get update -qq @@ -34,6 +31,7 @@ install: before_script: + - ls -lrth /home/travis/virtualenv/python2.7.12/lib/python2.7/site-packages/qml - cd ${TRAVIS_BUILD_DIR}/tests/ script: From fd2cc196271ded742469d28563d856d39ac92e6d Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 12:14:05 +0200 Subject: [PATCH 14/15] updated ext_package --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index c3f338b6f..d7f8432a2 100755 --- a/setup.py +++ b/setup.py @@ -109,7 +109,7 @@ def setup_pepytools(): url = __url__, # set up package contents - # ext_package = 'qml', + ext_package = 'qml', ext_modules = [ ext_farad_kernels, ext_fcho_solve, From acac932b4a14e002a524879b64317efadc0791e5 Mon Sep 17 00:00:00 2001 From: "Anders S. Christensen" Date: Thu, 8 Jun 2017 12:20:14 +0200 Subject: [PATCH 15/15] working travis yml --- .travis.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 71a9876e5..25af532ab 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,6 +5,9 @@ dist: trusty python: - "2.7" + - "3.4" + - "3.5" + - "3.6" before_install: - sudo apt-get update -qq @@ -13,17 +16,12 @@ install: - sudo apt-get install -qq gcc gfortran libblas-dev liblapack-dev - sudo apt-get install -qq gcc-4.8 gfortran-4.8 - - echo ${TRAVIS_PYTHON_VERSION} - | if [ ${TRAVIS_PYTHON_VERSION:0:1} = 3 ]; then sudo apt-get install python3-numpy - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - # python3 setup.py build python3 setup.py install elif [ ${TRAVIS_PYTHON_VERSION} = "2.7" ]; then sudo apt-get install python-numpy - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH} - # python2 setup.py build python2 setup.py install else echo "ERROR: Unknown Python version." @@ -31,7 +29,6 @@ install: before_script: - - ls -lrth /home/travis/virtualenv/python2.7.12/lib/python2.7/site-packages/qml - cd ${TRAVIS_BUILD_DIR}/tests/ script: