diff --git a/README.md b/README.md index 201b1f9..a0d5fdd 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,9 @@ Can be easily installed using **pip**: pip install carveme ``` -Additionally, you must install diamond and CPLEX (please check the documentation for details). +Additionally, you must install: + - diamond (conda install -c bioconda diamond) + - IBM CPLEX or Gurobi solver (full versions with respective academic licenses) ### Credits and License diff --git a/carveme/__init__.py b/carveme/__init__.py index 720e5c5..f4019cd 100755 --- a/carveme/__init__.py +++ b/carveme/__init__.py @@ -4,7 +4,7 @@ from reframed import set_default_solver from reframed.solvers.solver import default_parameters, Parameter -__version__ = '1.5.1' +__version__ = '1.5.2' project_dir = os.path.abspath(os.path.dirname(__file__)) + '/' diff --git a/docs/installation.rst b/docs/installation.rst index 8418c31..1e1c9fb 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -4,10 +4,6 @@ Installation ============ -**CarveMe** currently supports Python 3.6 and 3.7. -We recommend using the `Anaconda python -distribution `_. - CarveMe can be easily installed using the **pip** package manager: .. code-block:: console @@ -17,10 +13,11 @@ CarveMe can be easily installed using the **pip** package manager: Additionally, you must manually install two external dependencies: - diamond_ (conda install -c bioconda diamond) -- IBM CPLEX_ Optimizer +- either the IBM CPLEX_ Optimizer or the Gurobi_ Optimizer .. _diamond: https://github.com/bbuchfink/diamond .. _CPLEX: https://www.ibm.com/analytics/cplex-optimizer +.. _Gurobi: https://www.gurobi.com/downloads/gurobi-software/ Note that you will need to register with IBM to obtain an `academic license for CPLEX `_. diff --git a/setup.py b/setup.py index 5c6b11e..1c4a697 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ readme = readme_file.read() requirements = [ - "reframed>=1.2.1", + "reframed>=1.4.0", "pandas>=1.0", ] @@ -74,7 +74,7 @@ setup( name='carveme', - version='1.5.1', + version='1.5.2', description="CarveMe: automated metabolic model reconstruction", long_description=readme, author="Daniel Machado", @@ -106,6 +106,9 @@ 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', 'License :: OSI Approved :: Apache Software License', ], setup_requires=['setuptools_scm']