Merge pull request #71 from MineralsCloud/develop

Try to solve issue #70 and #47

.travis.yml

@@ -1,18 +1,32 @@
-dist: xenial
 language: python
-os:
-  - linux
-python:
-  - "3.6"
+matrix:
+  include:
+    - name: "Python 3.6 on Xenial Linux"
+      python: 3.6
+      dist: xenial
+    - name: "Python 3.7.1 on Xenial Linux"
+      python: 3.7
+      dist: xenial
+    - name: "Python 3.6 on macOS"
+      os: osx
+      osx_image: xcode10.1
+      language: shell
+    - name: "Python 3.7.2 on macOS"
+      os: osx
+      osx_image: xcode10.2  # Python 3.7.2 running on macOS 10.14.3
+      language: shell       # 'language: python' is an error on Travis CI macOS
 sudo: required
-before_install:
-  - sudo apt-get install libmpc-dev
 install:
-  - pip install .
-  - pip install -Iv sphinx==1.7.4
-  - pip install sphinx-autodoc-typehints
-  - pip install sphinx_bootstrap_theme
+  - pip3 install .
+  - pip3 install -U pytest
+  - pip3 install -Iv sphinx==1.7.4
+  - pip3 install sphinx-autodoc-typehints
+  - pip3 install sphinx_bootstrap_theme
 script:
+  - pytest qha/tests/test_different_phonon_dos.py
+  - pytest qha/tests/test_read_input.py
+  - pytest qha/tests/test_single_configuration.py
+  - pytest qha/tests/test_unit_conversion.py
   - cd docs/
   - make clean && make html
 deploy:

README.md

@@ -3,6 +3,7 @@
 [TOC]
 
 [![Stable docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://mineralscloud.github.io/qha/)
+[![Build Status](https://travis-ci.com/MineralsCloud/qha.svg?branch=master)](https://travis-ci.com/MineralsCloud/qha)
 
 ## Contributors
 
@@ -25,8 +26,6 @@ please check more details on [Python 3 documentation](https://docs.python.org/3/
 
 To install `qha`, currently, Python 3.6.x distributions are recommended.
 
-Please do not use Python 3.7.x at this moment, since it contains breaking changes and many Python packages don’t support Python 3.7.x yet. We may support Python 3.7.x in the future.
-
 ### Where to get it
 
 Binary installers for the latest released version are available at the PyPI.
@@ -38,7 +37,7 @@ $ pip install qha
 
 ### Dependencies
 
-- [bigfloat](https://pypi.python.org/pypi/bigfloat)
+- [mpmath](http://mpmath.org/)
 - [lazy-property](https://github.com/jackmaney/lazy-property)
 - [matplotlib](https://matplotlib.org)
 - [Numba](http://numba.pydata.org)
@@ -57,19 +56,12 @@ The source code is currently hosted on [GitHub](https://github.com/MineralsCloud
 $ pip install .
 ```
 
-Notice that you have to use Python version 3.6.x to install. If you want to install `qha` in development mode, instead run
+Notice that you have to use Python version > 3.6.x to install. If you want to install `qha` in development mode, instead run
 
 ```shell
 $ pip install -e .
 ```
 
-### Trouble shooting of installation
-
-1. Error raised about `mpfr.h` file: To solve this error, `GMP` and `MPFR` libraries are required to use `bigfloat` package.
-   * On Linux, install `libmpfr-dev` , for example, on Ubuntu type `apt-get install libmpfr-dev`;
-   * On Windows, `bigfloat` can be installed from the binary file, please check [“Unofficial Windows Binaries for Python Extension Packages”](https://www.lfd.uci.edu/~gohlke/pythonlibs/), download the version suitable for the system, for example, for a 64-bit system, use pip to install it `pip(3) install /the/path/to/bigfloat‑0.3.0‑cp36‑cp36m‑win_amd64.whl`;
-   * On macOS, install these libraries via `brew install mpfr`. Of course, you need the [Homebrew package manager](https://brew.sh) installed to run this command.
-
 ## Checking the examples
 
 To run the examples, go to `examples/ice VII/` or `examples/silicon/` directories and type in terminal:

docs/source/tutorials/installing.rst

@@ -10,8 +10,6 @@ Compatibility
 -------------
 
 ``qha`` is compatible with Python 3.6.x.
-Please do not use Python 3.7.x at this moment, since it contains breaking changes
-and many Python packages don’t support Python 3.7.x yet. We may support Python 3.7.x in the future.
 
 Our supported platforms are:
 
@@ -22,7 +20,7 @@ Our supported platforms are:
 
 Dependencies
 ------------
-- `bigfloat <https://pypi.python.org/pypi/bigfloat>`_ [#b]_
+- `mpmath <http://mpmath.org/>`_
 - `lazy-property <https://github.com/jackmaney/lazy-property>`_
 - `matplotlib <https://matplotlib.org>`_ [#m]_
 - `Numba <http://numba.pydata.org>`_
@@ -35,14 +33,6 @@ Dependencies
 
 Notes:
 
-.. [#b] ``GMP`` and ``MPFR`` libraries are required to use ``bigfloat`` package. On macOS,
-    install these libraries via ``brew install mpfr``; on Linux, install ``libmpfr-dev`` ,
-    for example, on Ubuntu use ``apt-get install libmpfr-dev``;
-    on Windows, ``bigfloat`` can be installed from the binary file, please check
-    `Unofficial Windows Binaries for Python Extension Packages <https://www.lfd.uci.edu/~gohlke/pythonlibs/>`_,
-    download the version suitable for the system, for example,for a 64-bit system,
-    use pip to install it ``pip(3) install /the/path/to/bigfloat‑0.3.0‑cp36‑cp36m‑win_amd64.whl``;
-
 .. [#m] For some systems, ``python-tkinter`` package is needed by ``matplotlib``, otherwise the plot function will not work.
 
 Installing the ``qha`` package

qha/multi_configurations/different_phonon_dos.py

@@ -118,13 +118,13 @@ def partition_functions_for_each_configuration(self):
         :return: A matrix, the partition function of each configuration of each volume.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
+        with mpmath.workprec(self.precision):
             # shape = (# of configurations, # of volumes for each configuration)
-            exp = np.vectorize(bigfloat.exp)
+            exp = np.vectorize(mpmath.exp)
             return exp(-self.aligned_free_energies_for_each_configuration / (K * self.temperature))
 
     @LazyProperty
@@ -139,13 +139,13 @@ def partition_functions_for_all_configurations(self):
         :return: A vector, the partition function of each volume.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
+        with mpmath.workprec(self.precision):
             # shape = (# of volumes,)
-            return np.array([bigfloat.exp(d) for d in
+            return np.array([mpmath.exp(d) for d in
                              logsumexp(-self.aligned_free_energies_for_each_configuration.T / (K * self.temperature),
                                        axis=1, b=self.degeneracies)])
 
@@ -160,10 +160,10 @@ def get_free_energies(self):
         :return: The free energy on a temperature-volume grid.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
-            log_z = np.array([bigfloat.log(d) for d in self.partition_functions_for_all_configurations], dtype=float)
+        with mpmath.workprec(self.precision):
+            log_z = np.array([mpmath.log(d) for d in self.partition_functions_for_all_configurations], dtype=float)
         return -K * self.temperature * log_z

qha/multi_configurations/same_phonon_dos.py

@@ -84,13 +84,13 @@ def _static_part(self) -> Vector:
         :return: The static contribution on the temperature-volume grid.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
             raise ImportError(
-                "You need to install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+                "You need to install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
-            return np.array([bigfloat.exp(d) for d in  # shape = (# of volumes for each configuration, 1)
+        with mpmath.workprec(self.precision):
+            return np.array([mpmath.exp(d) for d in  # shape = (# of volumes for each configuration, 1)
                              logsumexp(-self.static_energies / (K * self.temperature), axis=1, b=self.degeneracies)])
 
     @property
@@ -124,12 +124,12 @@ def get_free_energies(self):
         :return: The free energy on the temperature-volume grid.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
-            log_z = np.array([bigfloat.log(d) for d in self.total], dtype=float)
+        with mpmath.workprec(self.precision):
+            log_z = np.array([mpmath.log(d) for d in self.total], dtype=float)
         return -K * self.temperature * log_z
 
 

qha/tests/test_different_phonon_dos.py

@@ -2,17 +2,17 @@
 
 import os
 import unittest
+from pathlib import Path
 
 import numpy as np
-
 from qha.calculator import DifferentPhDOSCalculator
 from qha.multi_configurations.different_phonon_dos import PartitionFunction
 from qha.settings import from_yaml
 
 
 class TestPartitionFunction(unittest.TestCase):
     def setUp(self) -> None:
-        os.chdir('../../examples/ice VII/')
+        os.chdir(Path(__file__).parent.parent.parent / 'examples/ice VII/')
         self.user_settings = {}
         settings = from_yaml("settings.yaml")
 

qha/tests/test_overall_run.py

@@ -11,7 +11,7 @@
 
 class TestOverallRun(unittest.TestCase):
     def setUp(self):
-        self.root_directory = pathlib.Path('../../examples')
+        self.root_directory = pathlib.Path(__file__).parent.parent.parent / 'examples'
         self.command = 'qha run'
         self.fixed_directory = 'results.benchmark'
         self.new_results_directory = 'results.plot'

qha/tests/test_read_input.py

@@ -11,7 +11,7 @@
 
 class TestReadInput(unittest.TestCase):
     def setUp(self):
-        self.dir = pathlib.Path('../../examples')
+        self.dir = pathlib.Path(__file__).parent.parent.parent / 'examples'
 
     def test_read_si_input(self):
         file_path = self.dir / 'silicon/input'

qha/tests/test_samevdos_overall.py

@@ -11,7 +11,7 @@
 
 class TestSamePhononDOS(unittest.TestCase):
     def setUp(self):
-        self.root_directory = pathlib.Path('../../examples')
+        self.root_directory = pathlib.Path(__file__).parent.parent.parent / 'examples'
         self.command = 'qha run'
         self.fixed_directory = 'results.benchmark'
         self.new_results_directory = 'results.same_vdos_new01'

setup.py

@@ -40,14 +40,15 @@ def find_version(*file_paths):
           'Topic :: Scientific/Engineering :: Physics',
           'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
           'Programming Language :: Python :: 3.6',
+          'Programming Language :: Python :: 3.7',
       ],
-      python_requires='>=3.6, <3.7',
+      python_requires='>=3.6',
       keywords='thermodynamic-properties quasi-harmonic-approximation scientific-computation',
       install_requires=[
           'lazy_property',
+          'mpmath',
           'numba',
           'numpy',
-          'bigfloat',
           'pandas',
           'scientific-string',
           'scipy',