New upstream version 0.15.4 (c3946f59) · Commits · Debian Med / python-cobra

.travis.yml

+35 −34

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ install:
		- pip install --upgrade pip setuptools wheel tox tox-travis

		script:
		- tox -- --benchmark-skip --cov-report xml --cov-report term
		- travis_wait tox -- --benchmark-skip --cov-report xml --cov-report term
		- bash <(curl -s https://codecov.io/bash)

		stages:
		@@ -41,30 +41,31 @@ stages:
		#before_deploy:
		# - source scripts/prepare_notes.sh

		jobs:
		include:
		- stage: deploy
		python: "3.6"
		install:
		- pip install --upgrade pip setuptools wheel
		script:
		- echo "Deploying..."
		deploy:
		- provider: pypi
		skip_cleanup: true
		distributions: sdist bdist_wheel
		install: skip
		script:
		- echo "Deploying COBRApy to PyPI."
		user: cobrapy
		password: $PYPI_PASSWORD
		on:
		tags: true
		repo: $GITHUB_REPO
		user: cobrapy
		password: $PYPI_PASSWORD
		- provider: script
		skip_cleanup: true
		install: skip
		script: scripts/deploy_website.sh
		on:
		tags: true
		repo: $GITHUB_REPO
		- provider: releases
		skip_cleanup: true
		install: skip
		script:
		- echo "Releasing COBRApy to GitHub."
		api_key: $GITHUB_TOKEN
		body: "Please see https://github.com/opencobra/cobrapy/tree/${TRAVIS_TAG}/release-notes/${TRAVIS_TAG}.md for the full release notes."
		on:

appveyor.yml

+14 −39

Original line number	Diff line number	Diff line
		@@ -4,57 +4,32 @@ branches:
		- devel
		- /^[0-9]+\.[0-9]+\.[0-9]+[.0-9ab]*$/

		environment:

		global:
		PIP_CACHE_DIR: "pip_cache"
		PIP_DISABLE_PIP_VERSION_CHECK: "yes"
		clone_depth: 2

		environment:
		matrix:
		- PYTHON: "C:\\Miniconda-x64"
		CONDA: true

		- PYTHON: "C:\\Miniconda36-x64"
		CONDA: true

		- PYTHON: "C:\\Python27-x64"
		TOXENV: py27

		TOXENV: py36
		- PYTHON: "C:\\Miniconda37-x64"
		TOXENV: py37
		- PYTHON: "C:\\Python36-x64"
		TOXENV: py36

		matrix:
		fast_finish: true

		clone_depth: 2

		init:
		- "ECHO %PYTHON%"
		- "set PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
		- python -V

		cache:
		- pip_cache -> appveyor.yml

		- '%LOCALAPPDATA%\pip\Cache'

		install:
		- ps: \|
		if ($env:CONDA -eq "true") {
		conda config --set always_yes yes --set changeps1 no;
		conda config --add channels conda-forge
		conda install -q pip setuptools wheel numpy scipy;
		pip install -r develop-requirements.txt;
		pip install .
		} else {
		pip install --upgrade setuptools wheel tox
		}
		platform: x64

		build: off

		install:
		- set PATH=%PYTHON%;%PYTHON%\Scripts;%PYTHON%\Library\bin;%PATH%"
		- "ECHO %PYTHON%"
		- python --version
		- python -m pip install --upgrade --disable-pip-version-check pip setuptools wheel tox

		test_script:
		- ps: \|
		if ($env:CONDA -eq "true") {
		pytest --benchmark-skip cobra/test
		} else {
		tox
		}
		- tox

cobra/init.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -13,9 +13,10 @@ from cobra.core import (
		Species)
		from cobra import flux_analysis
		from cobra import io
		from cobra import sampling
		from cobra.util import show_versions

		__version__ = "0.14.2"
		__version__ = "0.15.4"

		# set the warning format to be prettier and fit on one line
		_cobra_path = _dirname(_abspath(__file__))

cobra/core/init.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -9,5 +9,6 @@ from cobra.core.metabolite import Metabolite
		from cobra.core.model import Model
		from cobra.core.object import Object
		from cobra.core.reaction import Reaction
		from cobra.core.solution import LegacySolution, Solution, get_solution
		from cobra.core.group import Group
		from cobra.core.solution import Solution, LegacySolution, get_solution
		from cobra.core.species import Species

cobra/core/configuration.py

+49 −4

Original line number	Diff line number	Diff line
		@@ -34,6 +34,8 @@ class BaseConfiguration(object):
		solver : {"glpk", "cplex", "gurobi"}
		The default solver for new models. The solver choices are the ones
		provided by `optlang` and solvers installed in your environment.
		tolerance: float
		The default tolerance for the solver being used (default 1E-09).
		lower_bound : float
		The standard lower bound for reversible reactions (default -1000).
		upper_bound : float
		@@ -50,8 +52,10 @@ class BaseConfiguration(object):

		def __init__(self):
		self._solver = None
		self.tolerance = 1E-07
		self.lower_bound = None
		self.upper_bound = None

		# Set the default solver from a preferred order.
		for name in ["gurobi", "cplex", "glpk"]:
		try:
		@@ -60,7 +64,9 @@ class BaseConfiguration(object):
		continue
		else:
		break

		self.bounds = -1000.0, 1000.0

		try:
		self.processes = cpu_count()
		except NotImplementedError:
		@@ -99,10 +105,49 @@ class BaseConfiguration(object):
		self.upper_bound = bounds[1]

		def __repr__(self):
		return "solver: {}\nlower_bound: {}\nupper_bound: {}\n" \
		"processes: {}".format(
		interface_to_str(self.solver), self.lower_bound,
		self.upper_bound, self.processes)
		return """
		solver: {solver}
		solver tolerance: {tolerance}
		lower_bound: {lower_bound}
		upper_bound: {upper_bound}
		processes: {processes}""".format(
		solver=interface_to_str(self.solver),
		tolerance=self.tolerance,
		lower_bound=self.lower_bound,
		upper_bound=self.upper_bound,
		processes=self.processes,
		)

		def _repr_html_(self):
		return """
		<table>
		<tr>
		<td><strong>Solver</strong></td>
		<td>{solver}</td>
		</tr>
		<tr>
		<td><strong>Solver tolerance</strong></td>
		<td>{tolerance}</td>
		</tr>
		<tr>
		<td><strong>Lower bound</strong></td>
		<td>{lower_bound}</td>
		</tr>
		<tr>
		<td><strong>Upper bound</strong></td>
		<td>{upper_bound}</td>
		</tr>
		<tr>
		<td><strong>Processes</strong></td>
		<td>{processes}</td>
		</tr>
		</table>""".format(
		solver=interface_to_str(self.solver),
		tolerance=self.tolerance,
		lower_bound=self.lower_bound,
		upper_bound=self.upper_bound,
		processes=self.processes,
		)


		class Configuration(with_metaclass(Singleton, BaseConfiguration)):