restructure pkg & drop support for python 2.7, 3.4

.gitignore

@@ -1,11 +1,10 @@
 *.pyc
+*.egg-info/
 /.coverage
-/*.egg-info/
-/dist/
-/docs/build/
 /.pytest_cache/
 /.cache/
 /.tox/
+/dist/
+/docs/build/
 /htmlcov/
 /poetry.lock
-/setup.py

.travis.yml

@@ -2,24 +2,17 @@ language: python
 dist: xenial
 matrix:
   include:
-    - python: 2.7
-      env: TOXENV=py27-coverage-codecov
-    - python: 3.4
-      env: TOXENV=py34
-    - python: 3.5
-      env: TOXENV=py35
     - python: 3.6
       env: TOXENV=py36
     - python: 3.7
-      env: TOXENV=py37-coverage-codecov
+      env: TOXENV=py37-codecov
     - python: 3.6
       stage: deploy
       env: TOXENV=docs
 before_install:
-  - pip install tox tox-venv
+  - pip install poetry tox tox-venv
   - |
     if [[ $TOXENV != docs ]]; then
-      pip install poetry
       source .travis/install-mopac.sh
     fi
 install: true

docs/_static/custom.css

@@ -0,0 +1 @@
+.katex { font-size: 1em; }

docs/conf.py

@@ -1,43 +1,33 @@
 import datetime
-import os
-import sys
-from unittest.mock import MagicMock
 
-import toml
+from importlib_metadata import metadata
 
-sys.path.insert(0, os.path.abspath('..'))
-
-
-class Mock(MagicMock):
-    @classmethod
-    def __getattr__(cls, name):
-        return MagicMock()
-
-
-MOCK_MODULES = ['numpy', 'numpy.linalg']
-sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
-
-metadata = toml.load(open('../pyproject.toml'))['tool']['poetry']
+md = metadata('pyberny')
 
 project = 'berny'
-version = metadata['version']
-author = ' '.join(metadata['authors'][0].split()[:-1])
-description = metadata['description']
+author = md['Author']
+release = version = md['Version']
+description = md['Summary']
+year_range = (2016, datetime.date.today().year)
+year_str = (
+    str(year_range[0])
+    if year_range[0] == year_range[1]
+    else f'{year_range[0]}-{year_range[1]}'
+)
+copyright = f'{year_str}, {author}'
 
+master_doc = 'index'
 extensions = [
+    'sphinx.ext.githubpages',
     'sphinx.ext.autodoc',
     'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinxcontrib.katex',
 ]
-source_suffix = '.rst'
-master_doc = 'index'
-copyright = f'2017-{datetime.date.today().year}, {author}'
-release = version
-language = None
 exclude_patterns = ['build', '.DS_Store']
-pygments_style = 'sphinx'
-todo_include_todos = True
+
 html_theme = 'alabaster'
 html_theme_options = {
     'description': description,
@@ -47,12 +37,17 @@ def __getattr__(cls, name):
     'badge_branch': 'master',
     'codecov_button': True,
     'travis_button': True,
+    'fixed_sidebar': True,
+    'page_width': '60em',
 }
 html_sidebars = {
     '**': ['about.html', 'navigation.html', 'relations.html', 'searchbox.html']
 }
-htmlhelp_basename = f'{project}doc'
+html_static_path = ['_static']
+
 autodoc_default_options = {'special-members': '__call__'}
+todo_include_todos = True
+pygments_style = 'sphinx'
 
 
 def skip_namedtuples(app, what, name, obj, skip, options):

pyproject.toml

@@ -1,18 +1,18 @@
-[tool.black]
-target-version = "py27"
-skip-string-normalization = true
+[build-system]
+requires = ["poetry>=0.12"]
+build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "pyberny"
-version = "0.5.0"
+version = "0.6.0"
 description = "Molecular/crystal structure optimizer"
 readme = "README.md"
 authors = ["Jan Hermann <[email protected]>"]
 repository = "https://github.com/jhrmnn/pyberny"
 documentation = "https://jhrmnn.github.io/pyberny"
 license = "MPL-2.0"
 packages = [
-    { include = "berny" },
+    { include = "berny", from = "src" },
 ]
 classifiers = [
     "Environment :: Console",
@@ -23,30 +23,31 @@ classifiers = [
 ]
 
 [tool.poetry.dependencies]
-python = "~2.7 || ^3.4"
+python = "^3.5"
 numpy = "^1.15"
 pytest = { version = "^3.6", optional = true }
-sphinx = { version = "^1.7", optional = true }
 coverage = { version = "^4.5", optional = true }
-toml = { version = "^0.10.0", optional = true }
+sphinx = { version = "^2.2", optional = true }
+sphinxcontrib-katex = { version = "^0.5.1", optional = true }
+importlib-metadata = { version = "^1.5.0", optional = true }
 
 [tool.poetry.extras]
-test = ["pytest"]
-cov = ["coverage"]
-doc = ["sphinx", "toml"]
+test = ["pytest", "coverage"]
+doc = ["sphinx", "sphinxcontrib-katex", "importlib-metadata"]
 
 [tool.poetry.dev-dependencies]
 flake8 = "^3.5"
-flake8-bugbear = { version = "^18.8", python = "^3.5" }
-flake8-comprehensions = "^1.4"
-flake8-quotes = "^1.0"
+flake8-bugbear = ">=18.8"
+flake8-comprehensions = ">=1.4"
+flake8-quotes = "^2"
+black = { version = ">=19-beta.0", python = "^3.6" }
+pep8-naming = ">=0.7"
 isort = "^4.3"
-pydocstyle = "^3.0"
-black = { version = "^19-beta.0", allow-prereleases = true, python = "^3.6" }
+pydocstyle = "^5.0.1"
 
 [tool.poetry.scripts]
 berny = "berny.cli:main"
 
-[build-system]
-requires = ["poetry>=0.12"]
-build-backend = "poetry.masonry.api"
+[tool.black]
+target-version = ["py36"]
+skip-string-normalization = true

setup.cfg

@@ -1,8 +1,8 @@
 [flake8]
 max-complexity = 12
 max-line-length = 80
-ignore = E501,W503,E741,E203
-select = C,E,F,W,B,B9,Q0
+ignore = E501,W503,E741,E203,N803,N806,N802
+select = C,E,F,N,W,B,B9,Q0
 
 [isort]
 multi_line_output = 3
@@ -11,10 +11,11 @@ line_length = 85
 sections = FUTURE,STDLIB,TYPING,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
 known_typing = typing, typing_extensions
 no_lines_before = TYPING
+combine_as_imports = true
 
 [pydocstyle]
 add-ignore = D100,D104,D105,D106,D107,D202
-match-dir = berny
+match-dir = src/berny
 ignore-decorators = wraps
 
 [tool:pytest]
@@ -23,35 +24,34 @@ filterwarnings =
 
 [tox:tox]
 minversion = 3.3
-requires = tox-venv
-envlist = py27
+envlist = py37
 
 [testenv]
 skip_install = true
-setenv =
-    coverage: EXTRAS1 = -E cov
 whitelist_externals =
     poetry
+setenv =
+    codecov: COVPREFIX = coverage run -m
 deps =
     codecov: codecov
+commands_pre =
+    poetry install --no-dev -E test
 commands =
-    poetry install --no-dev -E test {env:EXTRAS1:}
-    !coverage: pytest -v
-    coverage: coverage run -m pytest -v
+    {env:COVPREFIX:} pytest -v tests
     codecov: codecov
 passenv =
     MOPACDIR
     codecov: TOXENV CI TRAVIS TRAVIS_*
 
-[coverage:run]
-branch = true
-source = berny
-
 [testenv:docs]
-whitelist_externals = touch
-deps =
-    sphinx
-    toml
+whitelist_externals =
+    poetry
+    touch
+commands_pre =
+    poetry install --no-dev -E doc
 commands =
     sphinx-build -d "{toxworkdir}/docs_doctree" docs docs/build
-    touch docs/build/.nojekyll
+
+[coverage:run]
+branch = true
+source = berny

berny/Math.py → src/berny/Math.py

@@ -91,7 +91,7 @@ def quart_min(p):
         return minim, np.polyval(p, minim)
 
     # discriminant of d^2y/dx^2=0
-    D = -(g0 + g1) ** 2 - 2 * g0 * g1 + 6 * (y1 - y0) * (g0 + g1) - 6 * (y1 - y0) ** 2
+    D = -((g0 + g1) ** 2) - 2 * g0 * g1 + 6 * (y1 - y0) * (g0 + g1) - 6 * (y1 - y0) ** 2
     if D < 1e-11:
         return None, None
     else:

berny/__init__.py → src/berny/__init__.py

@@ -2,6 +2,6 @@
 from .berny import Berny
 from .coords import angstrom
 from .geomlib import Geometry
-from .optimizers import optimize
+from .optimize import optimize
 
 __all__ = ['optimize', 'Berny', 'geomlib', 'Geometry', 'angstrom']

berny/berny.py → src/berny/berny.py

@@ -2,8 +2,8 @@
 # License, v. 2.0. If a copy of the MPL was not distributed with this
 # file, You can obtain one at http://mozilla.org/MPL/2.0/.
 import logging
-import sys
 from collections import namedtuple
+from collections.abc import Generator
 from itertools import chain
 
 import numpy as np
@@ -13,11 +13,6 @@
 from . import Math
 from .coords import InternalCoords
 
-if sys.version_info[:2] >= (3, 5):
-    from collections.abc import Generator
-else:
-    from ._py2 import Generator  # noqa
-
 __version__ = '0.3.0'
 __all__ = ['Berny']
 
@@ -79,14 +74,7 @@ class State(object):
 
     Point = namedtuple('Point', 'q E g')
 
-    def __init__(
-        self,
-        geom,
-        debug=False,
-        restart=None,
-        maxsteps=100,
-        **params
-    ):
+    def __init__(self, geom, debug=False, restart=None, maxsteps=100, **params):
         self._debug = debug
         self._maxsteps = maxsteps
         self._converged = False

berny/geomlib.py → src/berny/geomlib.py

@@ -222,7 +222,8 @@ def rho(self):
         r"""
         Calculate a measure of covalentness.
 
-        Returns :math:`\rho_{ij}:=\exp\big(-R_{ij}/(R_i^\text{cov}+R_j^\text{cov})\big)`.
+        Returns
+        :math:`\rho_{ij}:=\exp\big(-R_{ij}/(R_i^\text{cov}+R_j^\text{cov})\big)`.
         """
         geom = self.supercell()
         dist = geom.dist(geom)