Reset commit history

.gitattributes

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+docs/* linguist-vendored

.gitignore

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+build
+dist
+biosteam.egg-info
+**/__pycache__
+*.pyc
+*.pyo
+.gitignore
+.pypirc
+dist
+MANIFEST
+.coverage
+.coveralls.yml
+htmlcov
+_build
+.cache
+__pycache__
+prof
+*Pyreverse*
+monkeytype.sqlite3
+*.spyproject*
+
+# Docs #
+########
+# No need to save these files
+docs/tutorial/.ipynb_checkpoints
+docs/.ipynb_checkpoints
+docs/_build/*
+docs/_static/*
+docs/_templates/*
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+*.idea
+ # Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+#*.gz
+*.iso
+*.jar
+*.rar
+#*.tar
+#*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# mac OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+surfaces

.readthedocs.yml

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+# .readthedocs.yml
+
+build:
+  image: latest
+
+python:
+  version 3.7:
+  setup_py_install: true

.travis.yml

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+language: c
+os:
+  - linux
+compiler:
+  - "3.7"
+  - "3.8"
+branches:
+  only:
+  - master
+matrix:
+  fast_finish: true
+notifications:
+  email: false
+install:
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then CONDA_OS='Linux'; else CONDA_OS='MacOSX'; fi;
+  - wget http://repo.continuum.io/miniconda/Miniconda3-latest-${CONDA_OS}-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda create -q -n test-environment python=$CC numpy pandas scipy matplotlib pytest sympy pytz
+  - source activate test-environment
+  - pip install -r requirements_test.txt
+  - python setup.py -q install
+  - rm -rf biosteam
+script:
+  - py.test . -v --cov-report html --cov=biosteam --cov-report term-missing -m "not slow"
+after_success:
+  - coveralls

AUTHORS.rst

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+The BioSTEAM Project Contributors is composed of:
+
+* Yoel Cortes-Pena (Main BioSTEAM author and maintainer)
+
+* Developers who have contributed in person and through email, including:
+
+  * Bugrah Mirsat Sahin
+
+  * Lisa Pardini
+
+  * Brent Scheidemantle
+
+  * Rui Shi
+
+  * Sarang Sunil Bhagwat
+
+  * Yalin Li
+
+* All other developers that have contributed to the biosteam repository:
+
+      https://github.com/BioSTEAMDevelopmentGroup/biosteam/graphs/contributors

LICENSE.txt

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+===================================================================================================
+The BioSTEAM project is under the University of Illinois/NCSA Open Source License
+===================================================================================================
+
+Copyright (c) 2019-2020 Yoel Cortes-Peña and Jeremy Guest. All rights reserved.
+
+Developed by: Yoel Cortes-Peña and BioSTEAM Development Group
+              University of Illinois at Urbana-Champaign
+              https://illinois.edu/
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal with the Software without restriction, 
+including without limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is 
+furnished to do so, subject to the following conditions:
+
+* Redistributions of source code must retain the above copyright notice, this list of conditions
+  and the following disclaimers.
+
+* Redistributions in binary form must reproduce the above copyright notice, this list of
+  conditions and the following disclaimers in the documentation and/or other materials provided
+  with the distribution.
+
+* Neither the names of Yoel Cortes-Peña, Jeremy Guest, the University of Illinois, nor the names
+  of its contributors may be used to endorse or promote products derived from this Software
+  without specific prior written permission.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, 
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
+
+
+===================================================================================================
+Legacy MIT Licence (Versions 0.1-0.9)
+===================================================================================================
+
+Copyright (c) 2018-2019 Yoel Rene Cortes-Pena <yoelcortes@gmail.com> and Jeremy Guest
+<jsguest@illinois.edu>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction,
+including without limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or 
+substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT 
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, 
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT
+OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

MANIFEST.in

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+include LICENSE.txt AUTHORS README.rst pytest.ini 
+recursive-include biosteam *
+recursive-include tests *
+global-exclude .spyproject
+global-exclude tests/.spyproject/*
+global-exclude tests/.spyproject
+global-exclude *__pycache__*
+global-exclude *.py[co]
+global-exclude *.nbi
+global-exclude *.nbc
+global-exclude *.coverage
+global-exclude *.so
+global-exclude *.ipynb_checkpoints
+global-exclude ipynb_checkpoints
+global-exclude *-checkpoint.ipynb
+global-exclude *checkpoint*
+global-exclude .*ipynb_checkpoints*
+prune thermosteam/__pycache__
+recursive-exclude docs *ipynb_checkpoints

README.rst

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+=========================================================================
+BioSTEAM: The Biorefinery Simulation and Techno-Economic Analysis Modules
+=========================================================================
+
+.. image:: http://img.shields.io/pypi/v/biosteam.svg?style=flat
+   :target: https://pypi.python.org/pypi/biosteam
+   :alt: Version_status
+.. image:: http://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
+   :target: https://biosteam.readthedocs.io/en/latest/
+   :alt: Documentation
+.. image:: http://img.shields.io/badge/license-UIUC-blue.svg?style=flat
+   :target: https://github.com/BioSTEAMDevelopmentGroup/biosteam/blob/master/LICENSE.txt
+   :alt: license
+.. image:: https://img.shields.io/pypi/pyversions/biosteam.svg
+   :target: https://pypi.python.org/pypi/biosteam
+   :alt: Supported_versions
+.. image:: https://zenodo.org/badge/164639830.svg
+   :target: https://zenodo.org/badge/latestdoi/164639830
+.. image:: https://coveralls.io/repos/github/BioSTEAMDevelopmentGroup/biosteam/badge.svg?branch=master
+   :target: https://coveralls.io/github/BioSTEAMDevelopmentGroup/biosteam?branch=master
+
+
+.. contents::
+
+What is BioSTEAM?
+-----------------
+
+BioSTEAM is a fast and flexible package for the design, simulation, and techno-economic analysis of biorefineries under uncertainty [1]_. BioSTEAM's framework is built to streamline and automate early-stage technology evaluations and to enable rigorous sensitivity and uncertainty analyses. Complete biorefinery configurations are available at the `Bioindustrial-Park <https://github.com/BioSTEAMDevelopmentGroup/biosteam>`_ GitHub repository, BioSTEAM's premier repository for biorefinery models and results. The long-term growth and maintenance of BioSTEAM is supported through both community-led development and the research institutions invested in BioSTEAM, including the `Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) <https://cabbi.bio/>`_. Through its open-source and community-lead platform, BioSTEAM aims to foster communication and transparency within the biorefinery research community for an integrated effort to expedite the evaluation of candidate biofuels and bioproducts.
+
+
+Installation
+------------
+
+Get the latest version of BioSTEAM from `PyPI <https://pypi.python.org/pypi/biosteam/>`__. If you have an installation of Python with pip, simple install it with:
+
+    $ pip install biosteam
+
+To get the git version, run:
+
+    $ git clone git://github.com/BioSTEAMDevelopmentGroup/biosteam
+
+For help on common installtion issues, please visit the `documentation <https://biosteam.readthedocs.io/en/latest/Installation.html>`__.
+
+Documentation
+-------------
+
+BioSTEAM's documentation is available on the web:
+
+    http://biosteam.readthedocs.io/
+
+Bug reports
+-----------
+
+To report bugs, please use the BioSTEAM's Bug Tracker at:
+
+    https://github.com/BioSTEAMDevelopmentGroup/biosteam
+
+
+License information
+-------------------
+
+See ``LICENSE.txt`` for information on the terms & conditions for usage
+of this software, and a DISCLAIMER OF ALL WARRANTIES.
+
+Although not required by the BioSTEAM license, if it is convenient for you,
+please cite BioSTEAM if used in your work. Please also consider contributing
+any changes you make back, and benefit the community.
+
+
+About the authors
+-----------------
+
+BioSTEAM was created and developed by `Yoel Cortes-Pena <http://engineeringforsustainability.com/yoelcortespena>`__ as part of the `Guest Group <http://engineeringforsustainability.com/>`__ and the `Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) <https://cabbi.bio/>`__ at the `University of Illinois at Urbana-Champaign (UIUC) <https://illinois.edu/>`__. 
+
+References
+----------
+.. [1] Cortes-Peña, Y.; Kumar, D.; Singh, V.; Guest, J. S. BioSTEAM: A Fast and Flexible Platform for the Design, Simulation, and Techno-Economic Analysis of Biorefineries under Uncertainty. ACS Sustainable Chem. Eng. 2020. https://doi.org/10.1021/acssuschemeng.9b07040.
+
+

biosteam/__init__.py

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+# -*- coding: utf-8 -*-
+# BioSTEAM: The Biorefinery Simulation and Techno-Economic Analysis Modules
+# Copyright (C) 2020, Yoel Cortes-Pena <yoelcortes@gmail.com>
+# 
+# This module is under the UIUC open-source license. See 
+# github.com/BioSTEAMDevelopmentGroup/biosteam/blob/master/LICENSE.txt
+# for license details.
+"""
+"""
+
+__version__ = '2.20.23'
+
+#: Chemical engineering plant cost index (defaults to 567.5 at 2017)
+CE = 567.5 
+
+# %% Initialize BioSTEAM 
+
+from flexsolve import speed_up
+from ._heat_utility import HeatUtility, UtilityAgent
+from ._power_utility import PowerUtility
+from ._unit import Unit
+from ._system import System
+from ._tea import CombinedTEA, TEA
+from ._flowsheet import Flowsheet, main_flowsheet
+from ._network import Network
+from . import utils
+from . import units
+from . import evaluation
+from . import exceptions
+from . import process_tools
+from . import examples
+from . import report
+from . import digraph
+
+__all__ = ('Unit', 'PowerUtility', 'HeatUtility', 'UtilityAgent',
+           'System', 'TEA', 'CombinedTEA', 'utils', 'units', 'evaluation', 
+           'main_flowsheet', 'Flowsheet', 'CE', 'Chemical', 'Chemicals', 'Stream',
+           'MultiStream', 'settings', 'Network', 'exceptions', 'speed_up', 'report',
+           'digraph', 'process_tools', 'examples', *units.__all__, *evaluation.__all__
+)
+
+from thermosteam import Chemical, Chemicals, Thermo, Stream, MultiStream, settings
+from .evaluation import *
+from .units import *

biosteam/_facility.py

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+# -*- coding: utf-8 -*-
+# BioSTEAM: The Biorefinery Simulation and Techno-Economic Analysis Modules
+# Copyright (C) 2020, Yoel Cortes-Pena <yoelcortes@gmail.com>
+# 
+# This module is under the UIUC open-source license. See 
+# github.com/BioSTEAMDevelopmentGroup/biosteam/blob/master/LICENSE.txt
+# for license details.
+"""
+"""
+from ._unit import Unit
+
+__all__ = ('Facility',)
+
+def get_network_priority(facility):
+    return facility.network_priority
+
+class Facility(Unit, isabstract=True,
+               new_graphics=False):
+
+    @staticmethod
+    def ordered_facilities(facilities):
+        """Return facilitied ordered according to their network priority."""
+        return sorted(facilities, key=get_network_priority)
+
+    def __init_subclass__(cls,
+                          isabstract=False,
+                          new_graphics=True):
+        super().__init_subclass__(isabstract,
+                                  new_graphics)
+        if not hasattr(cls, 'network_priority'):
+            raise NotImplementedError('Facility subclasses must implement a '
+                                      '`network_priority` attribute to designate '
+                                      'the order of simulation relative to other '
+                                      'facilities')
+
+    def __init__(self, ID='', ins=None, outs=(), thermo=None):
+        Unit.__init__(self, ID, ins, outs, thermo)
+        self._system = None
+
+    @property
+    def system(self):
+        return self._system
+