reorganize python tooling

.gitignore

@@ -1,8 +1,11 @@
 *.pyc
-*.egg-info
-/build/
+/.coverage
+/*.egg-info/
 /dist/
 /docs/build/
 /.pytest_cache/
 /.cache/
 /.tox/
+/htmlcov/
+/pyproject.lock
+/setup.py

.travis.yml

@@ -0,0 +1,37 @@
+language: python
+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
+      dist: xenial
+      sudo: required
+    - python: 3.6
+      stage: deploy
+      env: TOXENV=docs
+before_install:
+  - pip install tox tox-venv
+  - |
+    if [[ $TOXENV != docs ]]; then
+      pip --upgrade pip"<=18.0"
+      curl -sSL https://raw.githubusercontent.com/sdispater/poetry/master/get-poetry.py | python
+      source .travis/install-mopac.sh
+    fi
+install: true
+script: tox
+deploy:
+  provider: pages
+  skip-cleanup: true
+  github-token: $GITHUB_TOKEN
+  keep-history: true
+  local-dir: docs/build
+  on:
+    branch: master
+    condition: $TOXENV = docs

.travis/install-mopac.sh

@@ -0,0 +1,5 @@
+wget $MOPAC_DOWNLOAD_URL $MOPAC_PASSWORD_URL
+unzip MOPAC2016_for_Linux_64_bit.zip
+chmod +x MOPAC2016.exe
+export PATH="$PATH:$PWD/.travis"
+export MOPACDIR="$PWD"

.travis/mopac

@@ -0,0 +1,4 @@
+#!/bin/bash
+export LD_LIBRARY_PATH=$MOPACDIR
+export MOPAC_LICENSE=$MOPACDIR
+$MOPACDIR/MOPAC2016.exe "$@"

berny/solvers.py

@@ -35,7 +35,7 @@ def MopacSolver(cmd='mopac', method='PM7', workdir=None):
             input_file = os.path.join(tmpdir, 'job.mop')
             with open(input_file, 'w') as f:
                 f.write(mopac_input)
-            subprocess.check_output([cmd, input_file])
+            subprocess.check_call([cmd, input_file])
             with open(os.path.join(tmpdir, 'job.out')) as f:
                 energy = float(next(l for l in f if 'TOTAL ENERGY' in l).split()[3])*ev
                 next(l for l in f if 'FINAL  POINT  AND  DERIVATIVES' in l)

docs/conf.py

@@ -1,6 +1,26 @@
-#!/usr/bin/env python3
+import os
+import sys
 import datetime
-import pkg_resources
+from unittest.mock import MagicMock
+
+import toml
+
+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']
+
+project = 'pyberny'
+version = metadata['version']
+author = ' '.join(metadata['authors'][0].split()[:-1])
+description = metadata['description']
 
 extensions = [
     'sphinx.ext.autodoc',
@@ -10,21 +30,21 @@
 ]
 source_suffix = '.rst'
 master_doc = 'index'
-project = 'pyberny'
-author = 'Jan Hermann'
 copyright = f'2017-{datetime.date.today().year}, {author}'
-version = pkg_resources.require(project)[0].version
 release = version
 language = None
 exclude_patterns = ['build', '.DS_Store']
 pygments_style = 'sphinx'
 todo_include_todos = True
 html_theme = 'alabaster'
 html_theme_options = {
-    'description': 'Molecular geometry optimizer',
+    'description': description,
     'github_button': True,
     'github_user': 'azag0',
     'github_repo': 'pyberny',
+    'badge_branch': 'master',
+    'codecov_button': True,
+    'travis_button': True,
 }
 html_sidebars = {
     '**': [

pyproject.toml

@@ -0,0 +1,33 @@
+[tool.poetry]
+name = "pyberny"
+version = "0.3.4"
+description = "Molecular/crystal structure optimizer"
+readme = "README.md"
+authors = ["Jan Hermann <[email protected]>"]
+repository = "https://github.com/azag0/pyberny"
+documentation = "https://janhermann.cz/pyberny"
+license = "MPL-2.0"
+packages = [
+    { include = "berny" },
+]
+classifiers = [
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+
+[tool.poetry.dependencies]
+python = "~2.7 || ^3.4"
+numpy = "^1.15"
+
+[tool.poetry.dev-dependencies]
+pytest = "^3.6"
+sphinx = "^1.7"
+flake8 = "^3.5"
+toml = "^0.10.0"
+coverage = "^4.5"
+
+[tool.poetry.scripts]
+berny = "berny.cli:main"

setup.cfg

@@ -0,0 +1,36 @@
+[flake8]
+ignore = E226,E501,E741
+
+[tool:pytest]
+filterwarnings =
+    ignore::PendingDeprecationWarning
+
+[tox:tox]
+minversion = 3.3
+requires = tox-venv
+envlist = py27
+
+[testenv]
+skip_install = true
+whitelist_externals = poetry
+deps =
+    pytest
+    coverage: coverage
+    codecov: codecov
+commands =
+    poetry install --no-dev
+    !coverage: pytest -v
+    coverage: coverage run --source=berny --branch -m pytest -v
+    codecov: codecov
+passenv =
+    MOPACDIR
+    codecov: TOXENV CI TRAVIS TRAVIS_*
+
+[testenv:docs]
+whitelist_externals = touch
+deps =
+    sphinx
+    toml
+commands =
+    sphinx-build -d "{toxworkdir}/docs_doctree" docs docs/build
+    touch docs/build/.nojekyll