Resolved travis conflicts

.travis.yml

@@ -20,47 +20,28 @@ install:
     if [ ! -f "src" ]; then
       mkdir src;
     fi;
-    version=$(python -V 3>&1);
-    if [ -n "$version" ]; then 
-      pip install Cython; 
-      if [ ! -f "$HOME/qsopt-ex/esolver" ]; then
-        ( cd src/;
-          git clone https://github.com/jonls/qsopt-ex.git;
-          cd qsopt-ex/;
-          ./bootstrap;
-          mkdir build && cd build;
-          ../configure --prefix="$HOME/qsopt-ex" && make install;
-          cd $HOME );
-      fi;
-      if [ ! -f "$HOME/python-qsoptex" ]; then
-        ( cd src/;
-          git clone https://github.com/jonls/python-qsoptex.git;
-          cd python-qsoptex/;
-          ./setup.py install;
-          cd $HOME );
-      fi;
-      pip install python-qsoptex;
-      export CPATH="$HOME/qsopt-ex/include:$CPATH";
-      export LIBRARY_PATH="$HOME/qsopt-ex/lib:$LIBRARY_PATH";
-      export LD_LIBRARY_PATH="$HOME/qsopt-ex/lib:$LD_LIBRARY_PATH";
-    else 
-      if [ ! -f "$HOME/get-pip.py" ]; then
+
+    pip install Cython; 
+    if [ ! -f "$HOME/qsopt-ex/esolver" ]; then
       ( cd src/;
-        curl -O https://bootstrap.pypa.io/pip/2.7/get-pip.py;
-        python get-pip.py;
-        python -m pip install --upgrade "pip < 19.2" );
-      fi;
-      if [ ! -f "$HOME/qsopt_ex-2.5.10.3/bin/esolver" ]; then 
-        ( cd src/; 
-          curl -LO https://github.com/jonls/qsopt-ex/releases/download/v2.5.10.3/qsopt_ex-2.5.10.3.tar.xz;
-          tar -xvaf qsopt_ex-2.5.10.3.tar.xz; 
-          cd qsopt_ex-2.5.10.3/; 
-          ./configure --prefix="$HOME/qsopt_ex-2.5.10.3" && make install ); 
-      fi;
-      export CPATH="$HOME/qsopt_ex-2.5.10.3/include:$CPATH"; 
-      export LIBRARY_PATH="$HOME/qsopt_ex-2.5.10.3/lib:$LIBRARY_PATH"; 
-      export LD_LIBRARY_PATH="$HOME/qsopt_ex-2.5.10.3/lib:$LD_LIBRARY_PATH";
+        git clone https://github.com/jonls/qsopt-ex.git;
+        cd qsopt-ex/;
+        ./bootstrap;
+        mkdir build && cd build;
+        ../configure --prefix="$HOME/qsopt-ex" && make install;
+        cd $HOME );
     fi;
+    if [ ! -f "$HOME/python-qsoptex" ]; then
+      ( cd src/;
+        git clone https://github.com/jonls/python-qsoptex.git;
+        cd python-qsoptex/;
+        ./setup.py install;    
+        cd $HOME );
+    fi;
+    pip install python-qsoptex;
+    export CPATH="$HOME/qsopt-ex/include:$CPATH";
+    export LIBRARY_PATH="$HOME/qsopt-ex/lib:$LIBRARY_PATH";
+    export LD_LIBRARY_PATH="$HOME/qsopt-ex/lib:$LD_LIBRARY_PATH";
   fi;
 - pip install tox coveralls
 - pip install tox-travis
@@ -70,18 +51,6 @@ after_success: coveralls
 matrix:
   include:
   - env: TOXENV=flake
-  - env: TOXENV=py27-nosolver,coverage
-    python: '2.7'
-  - env: TOXENV=py27-glpk,coverage
-    python: '2.7'
-  - env: TOXENV=py27-qsoptex,coverage
-    python: '2.7'
-  - env: TOXENV=py35-nosolver,coverage
-    python: '3.5'
-  - env: TOXENV=py35-glpk,coverage
-    python: '3.5'
-  - env: TOXENV=py35-qsoptex,coverage
-    python: '3.5'
   - env: TOXENV=py36-nosolver,coverage
     python: '3.6'
   - env: TOXENV=py36-glpk,coverage

NEWS.md

@@ -1,8 +1,10 @@
-v1.1.2 (2021-05-10)  
+
+v1.1.2 (2021-05-10)
 ------------------
-
+
+- Drops support for Python 2.7 (deprecated Jan. 01, 2020), 3.3, and 3.4
 - Adds the --phin and --phout options to the `tmfa` command
-- Adds descriptive counts of the number of reactions and compounds
+- Adds descriptive counts of the number of reactions and compounds 
   curated in the _manual curation_ option of `modelmapping`
 
 

docs/conf.py

@@ -67,7 +67,7 @@
 
 # General information about the project.
 project = u'PSAMM'
-copyright = u'2015-2017, PSAMM developers'
+copyright = u'2015-2021, PSAMM developers'
 author = u'PSAMM developers'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -124,7 +124,7 @@
 todo_include_todos = False
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/2.7', None)
+    'python': ('https://docs.python.org/3', None)
 }
 
 autodoc_member_order = 'bysource'

docs/development.rst

@@ -22,27 +22,22 @@ for coding style (PEP8) and building documentation, use tox_:
     $ tox
 
 When testing with tox, the local path for the Cplex python module must be
-provided in the environment variables ``CPLEX_PYTHON2_PACKAGE`` and
-``CPLEX_PYTHON3_PACKAGE`` for Python 2 and Python 3, respectively. For example:
+provided in the environment variables ``CPLEX_PYTHON3_PACKAGE`` for Python 3.
+For example:
 
 .. code-block:: shell
 
-    $ export CPLEX_PYTHON2_PACKAGE=/path/to/IBM/ILOG/CPLEX_StudioXXX/cplex/python/2.7/x86-64_osx
-    $ export CPLEX_PYTHON3_PACKAGE=/path/to/IBM/ILOG/CPLEX_StudioXXX/cplex/python/3.4/x86-64_osx
-    $ tox -e py27-cplex,py34-cplex
+    $ export CPLEX_PYTHON3_PACKAGE=/path/to/IBM/ILOG/CPLEX_StudioXXX/cplex/python/3.7/x86-64_osx
+    $ tox -e py37-cplex
 
-.. note::
-
-    Python 3 support was added in a recent release of Cplex. Older versions
-    only support Python 2.
 
 Similarly, the local path to the Gurobi package must be specified in the
 environment variable ``GUROBI_PYTHON_PACKAGE``:
 
 .. code-block:: shell
 
     $ export GUROBI_PYTHON_PACKAGE=/Library/gurobi604/mac64
-    $ tox -e py27-gurobi
+    $ tox -e py37-gurobi
 
 Adding new tests
 ----------------

docs/install.rst

@@ -64,7 +64,7 @@ the virtual environment:
 1. Locate the directory where Cplex was installed (e.g. ``/path/to/IBM/ILOG/CPLEX_StudioXXX``).
 2. Locate the appropriate subdirectory based on your platform and Python
    version: ``cplex/python/<version>/<platform>``
-   (e.g. ``cplex/python/2.7/x86-64_osx``).
+   (e.g. ``cplex/python/3.7/x86-64_osx``).
 3. Use ``pip`` to install the package from this directory using the following
    command.
 
@@ -76,11 +76,6 @@ the virtual environment:
 Further documentation on installing Cplex can be found in
 `the Cplex documentation <http://www-01.ibm.com/support/docview.wss?uid=swg21444285>`_.
 
-.. note::
-
-    Python 3 support was added in a recent release of Cplex. Older versions
-    only support Python 2. If you are using Python 3 make sure that you have
-    the latest version of Cplex installed.
 
 Gurobi
 ------
@@ -111,23 +106,8 @@ Python bindings are required for PSAMM to use the GLPK library.
 QSopt_ex
 --------
 
-QSopt_ex is supported through `python-qsoptex`_ which requires `GnuMP`_ and
-the `QSopt_ex library`_. After installing these libraries the Python bindings
-can be installed using ``pip``:
-
-.. code-block:: shell
-
-    (env) $ pip install python-qsoptex
-
-.. _Virtualenv: https://virtualenv.pypa.io/
-.. _python-qsoptex: https://pypi.python.org/pypi/python-qsoptex
-.. _GnuMP: https://gmplib.org/
-.. _QSopt_ex library: https://github.com/jonls/qsopt-ex
-
-The installation method	detailed above is only supported on Python 3.4 or lower.
-If you want to use this	solver with later versions of Python, you must first   
-install this `python-qsoptex_higherPython`_, a different library for this solver,
-and different bindings from `QSopt_ex_higherPython`_ 
+QSopt_ex is supported through `python-qsoptex`_ which requires `python-qsoptex_higherPython`_
+and `QSopt_ex_higherPython`_ . This can be installed using ``pip``:
 
 .. code-block:: shell
 
@@ -148,7 +128,6 @@ is shown below:
    :header-rows: 1
 
    * - Solver
-     - Python 2.7
      - Python 3.5
      - Python 3.6
      - Python 3.7
@@ -158,21 +137,17 @@ is shown below:
      - Yes
      - Yes
      - Yes
-     - Yes
    * - Qsopt_ex
      - Yes
      - Yes
      - Yes
      - Yes
-     - Yes
    * - Gurobi
-     - Yes
      - Yes
      - No
      - No
      - No
    * - GLPK
-     - Yes
      - No
      - Yes
      - Yes
@@ -192,7 +167,7 @@ global parameters you might require before choosing a solver.
    * - Solver
      - feasibility tolerance
      - optimality tolerance
-     - inegrality tolerance
+     - integrality tolerance
      - threads
    * - Cplex
      - Yes

docs/tutorial/psamm-install.rst

@@ -73,13 +73,7 @@ the ``psamm-tutorial`` folder:
 In this command, ``<PATH>`` should be substituted by the directory path to
 where you created the ``psamm-tutorial``. This will change your current
 directory to the ``psamm-tutorial`` directory. Then, you can create a virtual
-environment for Python 2 in the ``psamm-tutorial`` directory:
-
-.. code-block:: shell
-
-    $ virtualenv psamm-env
-
-For Python 3, use the following command instead:
+environment in the ``psamm-tutorial`` directory:
 
 .. code-block:: shell
 
@@ -235,19 +229,21 @@ will be different):
     (psamm-env) $ cd /Library/gurobi604/mac64/
     (psamm-env) $ python setup.py install
 
-The QSopt_ex solver can also be used with PSAMM. To install this solver, Python 3.4 or
-lower is required. You will first need to install Qsopt_ex on your computer and
+The QSopt_ex solver can also be used with PSAMM. To install this solver, Python 3.5 or
+higher is required. You will first need to install Qsopt_ex on your computer and
 afterwards the Python bindings (`python-qsoptex`) can be installed in the virtual
 environment:
 
 .. code-block:: shell
 
-    (psamm-env) $ pip install python-qsoptex
+    (env) $ pip install cython
+    (env) $ pip install python-qsoptex
 
 Please see the `python-qsoptex documentation`_ for more information on
 installing both the library and the Python bindings.
 
-.. _`python-qsoptex documentation`: https://github.com/jonls/python-qsoptex
+.. _python-qsoptex_higherPython: https://github.com/jonls/python-qsoptex.git
+.. _QSopt_ex_higherPython: https://github.com/jonls/qsopt-ex.git
 
 .. note::
     The QSopt_ex solver does not support Integer LP problems and as a result

setup.py

@@ -65,9 +65,6 @@
         (
             'License :: OSI Approved :: '
             'GNU General Public License v3 or later (GPLv3+)'),
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.3',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
@@ -129,7 +126,5 @@
         'pandas'
     ],
     extras_require={
-        'docs': ['sphinx', 'sphinx_rtd_theme', 'mock'],
-        ':python_version=="2.7"': ['enum34'],
-        ':python_version=="3.3"': ['enum34']
+        'docs': ['sphinx', 'sphinx_rtd_theme', 'mock']
     })

tox.ini

@@ -1,8 +1,5 @@
 [tox]
 envlist =
-    py27-{nosolver,qsoptex,glpk},
-    py33-{nosolver,qsoptex,glpk},
-    py34-{nosolver,qsoptex,glpk},
     py35-{nosolver,qsoptex,glpk},
     py36-{nosolver,qsoptex,glpk},
     py37-{nosolver,qsoptex,glpk},
@@ -23,9 +20,8 @@ setenv =
     glpk: PSAMM_SOLVER=glpk
 deps =
     coverage~=4.0
-    py27-cplex: {env:CPLEX_PYTHON2_PACKAGE}
     py35-cplex: {env:CPLEX_PYTHON3_PACKAGE}
-    py{33,34,35,36,37}-qsoptex: cython
+    py{35,36,37}-qsoptex: cython
     qsoptex: python-qsoptex>=0.5
     gurobi: {env:GUROBI_PYTHON_PACKAGE}
     glpk: swiglpk==1.2.13