From 7a513aef3e46673daabb0dfc7a6af34cc91f643b Mon Sep 17 00:00:00 2001 From: Keith Dufault-Thompson Date: Wed, 4 Mar 2020 16:42:40 -0500 Subject: [PATCH 1/3] Updated docs building and installed pyaml in travis.yml --- .travis.yml | 1 + docs/api/graph.rst | 6 ------ docs/conf.py | 2 +- psamm/mapmaker.py | 2 +- 4 files changed, 3 insertions(+), 8 deletions(-) delete mode 100644 docs/api/graph.rst diff --git a/.travis.yml b/.travis.yml index 702e9970..491b61bb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -32,6 +32,7 @@ install: - pip install tox coveralls - pip install tox-travis - pip install --upgrade six + - pip install pyaml script: tox -v after_success: coveralls matrix: diff --git a/docs/api/graph.rst b/docs/api/graph.rst deleted file mode 100644 index 34fb1e46..00000000 --- a/docs/api/graph.rst +++ /dev/null @@ -1,6 +0,0 @@ - -``psamm.graph`` -- Graph Related Functions -=========================================== - -.. automodule:: psamm.graph - :members: diff --git a/docs/conf.py b/docs/conf.py index ad1d287a..56084be2 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -134,7 +134,7 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'sphinx_rtd_theme' +html_theme = 'classic' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the diff --git a/psamm/mapmaker.py b/psamm/mapmaker.py index 551b115b..f95b2658 100644 --- a/psamm/mapmaker.py +++ b/psamm/mapmaker.py @@ -109,7 +109,7 @@ def predict_compound_pairs(reaction, compound_formula, solver, epsilon=1e-5, weight_func: Optional function that returns a weight for a formula element (should handle specific Atom and Radical objects). By default, the standard MapMaker weights will be used - (H=0, R=40, N=0.4, O=0.4, P=0.4, *=1). + (H=0, R=40, N=0.4, O=0.4, P=0.4, All Others=1). """ elements = set() for compound, value in reaction.compounds: From 32ba8a8e37014d0de3e78e8a9c313bc239d88119 Mon Sep 17 00:00:00 2001 From: Keith Dufault-Thompson Date: Thu, 5 Mar 2020 17:04:51 -0500 Subject: [PATCH 2/3] updated travis build to new coveralls version --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 491b61bb..3dace7c4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -33,6 +33,7 @@ install: - pip install tox-travis - pip install --upgrade six - pip install pyaml + - pip install --upgrade coveralls script: tox -v after_success: coveralls matrix: From ae9e96cd56433c289cc803794de6e657aa1efc1a Mon Sep 17 00:00:00 2001 From: Keith Dufault-Thompson Date: Thu, 5 Mar 2020 20:55:59 -0500 Subject: [PATCH 3/3] removed coverage version specification in tox.ini --- tox.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index 5c4db17f..66dafb9b 100644 --- a/tox.ini +++ b/tox.ini @@ -21,7 +21,7 @@ setenv = gurobi: PSAMM_SOLVER=gurobi glpk: PSAMM_SOLVER=glpk deps = - coverage~=4.0 + coverage py27-cplex: {env:CPLEX_PYTHON2_PACKAGE} py35-cplex: {env:CPLEX_PYTHON3_PACKAGE} qsoptex: python-qsoptex>=0.5