From 612bda9314b032852d433dd7275c0c43cf4db77f Mon Sep 17 00:00:00 2001
From: Christian Hill <xn.hill@gmail.com>
Date: Fri, 29 Jul 2022 19:52:41 +0200
Subject: [PATCH] Rearrange for pypi packaging
---
gpl.txt => LICENSE | 0
README.md | 27 --------
README.rst | 68 +++++++++++++++++++
pyproject.toml | 3 +
setup.cfg | 3 +
setup.py | 55 ++++++++++++---
{pyqn => src/pyqn}/__init__.py | 0
{pyqn => src/pyqn}/atom_unit.py | 0
{pyqn => src/pyqn}/base_unit.py | 4 +-
{pyqn => src/pyqn}/dimensions.py | 0
{pyqn => src/pyqn}/list_base_units.py | 0
{pyqn => src/pyqn}/qn_array.py | 0
{pyqn => src/pyqn}/quantity.py | 34 +++++-----
{pyqn => src/pyqn}/si.py | 0
{pyqn => src/pyqn}/symbol.py | 0
{pyqn => src/pyqn}/units.py | 0
{pyqn/tests => tests}/test_conversions.py | 2 +-
{pyqn/tests => tests}/test_quantity.py | 8 +--
{pyqn/tests => tests}/test_units.py | 4 +-
.../tests => tests}/test_units_collisions.py | 6 +-
20 files changed, 147 insertions(+), 67 deletions(-)
rename gpl.txt => LICENSE (100%)
delete mode 100644 README.md
create mode 100644 README.rst
create mode 100644 pyproject.toml
create mode 100644 setup.cfg
rename {pyqn => src/pyqn}/__init__.py (100%)
rename {pyqn => src/pyqn}/atom_unit.py (100%)
rename {pyqn => src/pyqn}/base_unit.py (99%)
rename {pyqn => src/pyqn}/dimensions.py (100%)
rename {pyqn => src/pyqn}/list_base_units.py (100%)
rename {pyqn => src/pyqn}/qn_array.py (100%)
rename {pyqn => src/pyqn}/quantity.py (93%)
rename {pyqn => src/pyqn}/si.py (100%)
rename {pyqn => src/pyqn}/symbol.py (100%)
rename {pyqn => src/pyqn}/units.py (100%)
rename {pyqn/tests => tests}/test_conversions.py (97%)
rename {pyqn/tests => tests}/test_quantity.py (94%)
rename {pyqn/tests => tests}/test_units.py (97%)
rename {pyqn/tests => tests}/test_units_collisions.py (90%)
diff --git a/gpl.txt b/LICENSE
similarity index 100%
rename from gpl.txt
rename to LICENSE
diff --git a/README.md b/README.md
deleted file mode 100644
index ce041ff..0000000
--- a/README.md
+++ /dev/null
@@ -1,27 +0,0 @@
-# pyqn
-A Python package for handling physical units and quantities.
-
-A very quick overview:
-
- In [1]: from pyqn.units import Units
-
- In [2]: u1 = Units('km')
-
- In [3]: u2 = Units('hr')
-
- In [4]: u3 = u1/u2
-
- In [5]: print(u3)
- km.hr-1
-
- In [6]: u4 = Units('m/s')
-
- In [7]: u3.conversion(u4) # OK: can convert from km/hr to m/s
- Out[7]: 0.2777777777777778
-
- In [8]: u3.conversion(u2) # Oops: can't convert from km/hr to m!
- ...
- UnitsError: Failure in units conversion: units km.hr-1[L.T-1] and hr[T] have
- different dimensions
-
-For more information and examples, see http://christianhill.co.uk/projects/pyqn
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..f5c6fe8
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,68 @@
+********************
+Introduction to PyQn
+********************
+
+
+
+PyQn is a Python package for parsing, validating, manipulating and
+transforming physical quantities and their units.
+
+Units are specified as strings using a simple and flexible syntax,
+and may be compared, output in different formats and manipulated using a
+variety of predefined Python methods.
+
+
+
+Installation:
+=============
+
+The PyQn package can be installed either from PyPI_ using pip
+
+.. code-block:: bash
+
+ python3 -m pip install pyqn
+
+or from the source by running (one of the two) from the project source directory.
+
+.. code-block:: bash
+
+ # either
+ python setup.py install
+
+ # or
+ python3 -m pip install .
+
+
+
+Examples:
+=========
+
+Units
+-----
+The units of physical quantities are represented by the ``Units`` class. A
+``Units`` object is instantiated from a valid units string and supports ions,
+isotopologues, as well as a few special species. This object contains
+attributes including the dimensions, HTML and LaTeX representations, and
+methods for conversion to different compatible units.
+
+.. code-block:: pycon
+
+ >>> from pyqn.units import Units
+ >>> u1 = Units('km')
+
+ >>> u2 = Units('hr')
+
+ >>> u3 = u1/u2
+
+ >>> print(u3)
+ km.hr-1
+
+ >>> u4 = Units('m/s')
+
+ >>> u3.conversion(u4) # OK: can convert from km/hr to m/s
+ Out[7]: 0.2777777777777778
+
+ >>> u3.conversion(u2) # Oops: can't convert from km/hr to m!
+ ...
+ UnitsError: Failure in units conversion: units km.hr-1[L.T-1] and hr[T] have
+ different dimensions
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..9f92222
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=43", "wheel"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..41cf804
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,3 @@
+[metadata]
+# This includes the license file(s) in the wheel (requires setuptools>=42)
+license_files = LICENSE
\ No newline at end of file
diff --git a/setup.py b/setup.py
index d7a39cd..ea1e683 100644
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,48 @@
from setuptools import setup, find_packages
-setup(
- name = 'pyqn',
- version = '1.2.2',
- packages = find_packages(),
- author = 'Christian Hill',
- url = 'https://github.com/xnx/pyqn',
- license = 'GPL',
- author_email = 'christian.hill@ucl.ac.uk',
-
+from pathlib import Path
- description = 'A package for managing physical units and quantities',
-)
+root = Path(__file__).parent.resolve()
+# Get the long description from the README file
+long_description = (root / "README.rst").read_text(encoding="utf-8")
+setup(
+ name="pyqn",
+ version="1.3",
+ description="A package for managing physical units and quantities",
+ long_description=long_description,
+ long_description_content_type="text/x-rst",
+ url="https://github.com/xnx/pyqn",
+ author="Christian Hill",
+ author_email="xn.hill@gmail.com",
+ classifiers=[
+ "Development Status :: 4 - Beta",
+ "Intended Audience :: Science/Research",
+ "Topic :: Scientific/Engineering :: Chemistry",
+ "Topic :: Scientific/Engineering :: Physics",
+ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.6",
+ "Programming Language :: Python :: 3.7",
+ "Programming Language :: Python :: 3.8",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3 :: Only",
+ "Operating System :: OS Independent",
+ ],
+ keywords="chemistry, units, physical quantities, unit conversion",
+ package_dir={"": "src"},
+ packages=find_packages(where="src"),
+ python_requires=">=3.6",
+ install_requires=[
+ "pyparsing>=2.3",
+ 'importlib-resources>=1.0; python_version < "3.7.0"',
+ ],
+ extras_require={"dev": ["black", "pytest-cov", "tox", "ipython"]},
+ # package_data will include all the resolved globs into both the wheel and sdist
+ #package_data={},
+ # no need for MANIFEST.in, which should be reserved only for build-time files
+ project_urls={
+ "Bug Reports": "https://github.com/xnx/pyqn/issues",
+ },
+)
diff --git a/pyqn/__init__.py b/src/pyqn/__init__.py
similarity index 100%
rename from pyqn/__init__.py
rename to src/pyqn/__init__.py
diff --git a/pyqn/atom_unit.py b/src/pyqn/atom_unit.py
similarity index 100%
rename from pyqn/atom_unit.py
rename to src/pyqn/atom_unit.py
diff --git a/pyqn/base_unit.py b/src/pyqn/base_unit.py
similarity index 99%
rename from pyqn/base_unit.py
rename to src/pyqn/base_unit.py
index 3fee18e..833c4a7 100644
--- a/pyqn/base_unit.py
+++ b/src/pyqn/base_unit.py
@@ -111,7 +111,7 @@ def __str__(self):
BaseUnit('k', 'kayser', 'wavenumber', 100., '', 'k', d_length**-1),
BaseUnit('D', 'debye', 'electric dipole moment', 1.e-21/299792458., '', 'D',
d_charge * d_length),
-BaseUnit('hbar', 'hbar', 'angular momentum', 1.05457148e-34, '', '\hbar',
+BaseUnit('hbar', 'hbar', 'angular momentum', 1.05457148e-34, '', r'\hbar',
Dimensions(L=2, M=1, T=-1)),
BaseUnit('e', 'electron charge', 'charge', 1.602176565e-19, '', 'e', d_charge),
]),
@@ -144,7 +144,7 @@ def __str__(self):
('Non-SI units of length, area and volume', [
# Non-SI length units
-BaseUnit('Å', 'angstrom', 'length', 1.e-10, '', '\AA', d_length),
+BaseUnit('Å', 'angstrom', 'length', 1.e-10, '', r'\AA', d_length),
BaseUnit('a0', 'bohr', 'length', 5.2917721092e-11, '', 'a_0', d_length),
# Non-SI area units
BaseUnit('b', 'barn', 'area', 1.e-28, '', 'b', d_area),
diff --git a/pyqn/dimensions.py b/src/pyqn/dimensions.py
similarity index 100%
rename from pyqn/dimensions.py
rename to src/pyqn/dimensions.py
diff --git a/pyqn/list_base_units.py b/src/pyqn/list_base_units.py
similarity index 100%
rename from pyqn/list_base_units.py
rename to src/pyqn/list_base_units.py
diff --git a/pyqn/qn_array.py b/src/pyqn/qn_array.py
similarity index 100%
rename from pyqn/qn_array.py
rename to src/pyqn/qn_array.py
diff --git a/pyqn/quantity.py b/src/pyqn/quantity.py
similarity index 93%
rename from pyqn/quantity.py
rename to src/pyqn/quantity.py
index 61d38ce..077a1ac 100644
--- a/pyqn/quantity.py
+++ b/src/pyqn/quantity.py
@@ -22,7 +22,7 @@
import re
import math
-import numpy as np
+#import numpy as np
from .symbol import Symbol
from .units import Units, UnitsError
@@ -167,21 +167,21 @@ def convert_units_to(self, new_units, force=None):
else:
return Quantity(value = self.value*fac, units = new_units)
- def draw_from_dist(self, shape=None):
- """
- Return a value or number array of values drawn from the normal
- distribution described by this Quantity's mean and standard
- deviation. shape is the shape of the NumPy array to return, or
- None (the default) to return a single scalar value from the
- distribution.
-
- """
-
- if self.sd is None:
- raise ValueError('Quantity instance {} has no defined standard'
- ' deviation.'.format(self.name))
-
- return np.random.normal(loc=self.value, scale=self.sd, size=shape)
+# def draw_from_dist(self, shape=None):
+# """
+# Return a value or number array of values drawn from the normal
+# distribution described by this Quantity's mean and standard
+# deviation. shape is the shape of the NumPy array to return, or
+# None (the default) to return a single scalar value from the
+# distribution.
+#
+# """
+#
+# if self.sd is None:
+# raise ValueError('Quantity instance {} has no defined standard'
+# ' deviation.'.format(self.name))
+#
+# return np.random.normal(loc=self.value, scale=self.sd, size=shape)
def __add__(self, other):
"""
@@ -311,7 +311,7 @@ def parse(self, s_quantity, name=None, units=None, sd=None,
else:
s_mantsd = s_valsd
exp = 0
- patt = '([+-]?\d*\.?\d*)\(?(\d+)?\)?'
+ patt = r'([+-]?\d*\.?\d*)\(?(\d+)?\)?'
m = re.match(patt, s_mantsd)
if not m:
raise QuantityError('Failed to parse string into quantity:\n'\
diff --git a/pyqn/si.py b/src/pyqn/si.py
similarity index 100%
rename from pyqn/si.py
rename to src/pyqn/si.py
diff --git a/pyqn/symbol.py b/src/pyqn/symbol.py
similarity index 100%
rename from pyqn/symbol.py
rename to src/pyqn/symbol.py
diff --git a/pyqn/units.py b/src/pyqn/units.py
similarity index 100%
rename from pyqn/units.py
rename to src/pyqn/units.py
diff --git a/pyqn/tests/test_conversions.py b/tests/test_conversions.py
similarity index 97%
rename from pyqn/tests/test_conversions.py
rename to tests/test_conversions.py
index 558cf32..2c91aa0 100644
--- a/pyqn/tests/test_conversions.py
+++ b/tests/test_conversions.py
@@ -6,7 +6,7 @@
# Unit tests for unit conversions within the Units class.
import unittest
-from ..units import Units, UnitsError
+from pyqn.units import Units, UnitsError
class UnitsConversionCheck(unittest.TestCase):
"""Unit tests for unit conversions within the Units class."""
diff --git a/pyqn/tests/test_quantity.py b/tests/test_quantity.py
similarity index 94%
rename from pyqn/tests/test_quantity.py
rename to tests/test_quantity.py
index c0111b4..f1864f9 100644
--- a/pyqn/tests/test_quantity.py
+++ b/tests/test_quantity.py
@@ -1,7 +1,7 @@
import unittest
-from ..quantity import Quantity, QuantityError
-from ..dimensions import Dimensions, d_energy
-from ..units import UnitsError
+from pyqn.quantity import Quantity, QuantityError
+from pyqn.dimensions import Dimensions, d_energy
+from pyqn.units import UnitsError
class QuantityManipulations(unittest.TestCase):
def test_quantity_init(self):
@@ -77,4 +77,4 @@ def test_quantity_conversion(self):
pass
if __name__ == '__main__':
- unittest.main()
\ No newline at end of file
+ unittest.main()
diff --git a/pyqn/tests/test_units.py b/tests/test_units.py
similarity index 97%
rename from pyqn/tests/test_units.py
rename to tests/test_units.py
index 26cb7bc..1e80d35 100644
--- a/pyqn/tests/test_units.py
+++ b/tests/test_units.py
@@ -6,8 +6,8 @@
# Unit tests for the Units class.
import unittest
-from ..units import Units
-from ..dimensions import Dimensions,d_energy
+from pyqn.units import Units
+from pyqn.dimensions import Dimensions,d_energy
class UnitsCheck(unittest.TestCase):
"""Unit tests for the Units class."""
diff --git a/pyqn/tests/test_units_collisions.py b/tests/test_units_collisions.py
similarity index 90%
rename from pyqn/tests/test_units_collisions.py
rename to tests/test_units_collisions.py
index c52f6b6..f198d86 100644
--- a/pyqn/tests/test_units_collisions.py
+++ b/tests/test_units_collisions.py
@@ -8,9 +8,9 @@
# of "min" for minutes.
import unittest
-from ..units import Units
-from ..base_unit import base_units
-from ..si import si_prefixes
+from pyqn.units import Units
+from pyqn.base_unit import base_units
+from pyqn.si import si_prefixes
class ConflictsCheck(unittest.TestCase):
"""