Chore upgrade all (#262)

* Dropping Python2 support

* Dropping Python 2 support, fixing typos

* Removed six from RTD requirements

* Typo parenthesis

* Fixing same typo on same line...

* Extracting first unique element of dictionary by list()

* Fixed typo

* Fixed wrong translation from iteritems

* Removed Python2 travis tests

* chore: update networkx

* chore: pin optlang for cobrapy 0.20

* chore: update pandas

* chore: downgrade networks lower requirement so that is py3.5 compatible

* docs: update package metadata

* Dropping Python2 support

* Dropping Python 2 support, fixing typos

* Extracting first unique element of dictionary by list()

* Fixed typo

* chore: update networkx

* chore: pin optlang for cobrapy 0.20

* chore: update pandas

* chore: downgrade networks lower requirement so that is py3.5 compatible

* docs: update package metadata

* style: apply flake8

* test: upgrade CI for 3.6,3.7,3.8

* docs: remove support for py35

* test: update travis dist to xenial

* test: remove six as dependency for tests

* fix: use the right tox envs

* test: force export TRAVIS to children processes

* test: pass travis variable through tox

* test: fix env variables tox

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 sudo: required
-dist: trusty
+dist: xenial
 
 env:
   global:
@@ -9,12 +9,14 @@ env:
 matrix:
   fast_finish: true
   include:
-    - python: '3.5'
+    - python: '3.6'
       env: TOXENV=flake8
-    - python: '3.5'
-      env: TOXENV=py35
     - python: '3.6'
       env: TOXENV=py36
+    - python: '3.7'
+      env: TOXENV=py37
+    - python: '3.8'
+      env: TOXENV=py38
 
 branches:
  only:

cameo/flux_analysis/structural.py

@@ -176,7 +176,7 @@ def find_coupled_reactions_nullspace(model, ns=None, tol=1e-10):
         left = non_blocked_ns[i]
         group = next((g for g in groups if reaction_i in g), None)
         if group:
-            reaction_i = next(l for l, c in group.items() if c == 1)
+            reaction_i = next(reac for reac, c in group.items() if c == 1)
             left = non_blocked_ns[reaction_index[reaction_i]]
         else:
             group = {reaction_i: 1}

cameo/network_analysis/networkx_based.py

@@ -98,5 +98,5 @@ def remove_highly_connected_nodes(network, max_degree=10, ignore=[]):
     -------
     None
     """
-    to_remove = [node for node, degree in network.degree_iter() if degree > max_degree and node not in ignore]
+    to_remove = [node for node, degree in network.degree if degree > max_degree and node not in ignore]
     network.remove_nodes_from(to_remove)

cameo/strain_design/deterministic/flux_variability_based.py

@@ -476,7 +476,7 @@ def __init__(self, solutions, phase_plane, reference_fva, **kwargs):
         self.reference_fva = reference_fva
         self.solutions = solutions
         self.groups = self.solutions.groupby(
-            ('biomass', 'production'), as_index=False, sort=False
+            ['biomass', 'production'], as_index=False, sort=False
         )
 
     @classmethod
@@ -525,7 +525,7 @@ def _generate_designs(cls, solutions, reference_fva):
             A list of cameo.core.strain_design.StrainDesign for each DataFrame in solutions.
         """
         designs = []
-        for _, solution in solutions.groupby(('biomass', 'production'), as_index=False, sort=False):
+        for _, solution in solutions.groupby(['biomass', 'production'], as_index=False, sort=False):
             targets = []
             relevant_targets = solution[
                 (solution['normalized_gaps'].abs() > non_zero_flux_threshold) & (

cameo/strain_design/pathway_prediction/pathway_predictor.py

@@ -162,8 +162,10 @@ def __str__(self):
         for i, pathway in enumerate(self.pathways):
             string += 'Pathway No. {}'.format(i + 1)
             for reaction in pathway.reactions:
-                string += '{}, {}:'.format(reaction.id, reaction.name,
-                                           reaction.build_reaction_string(use_metabolite_names=True))
+                string += '{}, {}: {}'.format(
+                    reaction.id, reaction.name,
+                    reaction.build_reaction_string(use_metabolite_names=True)
+                )
         return string
 
     def plot(self, grid=None, width=None, height=None, title=None):

cameo/util.py

@@ -496,8 +496,8 @@ def partition(ite, n):
     return [list(islice(iterator, 0, round(division * (i + 1)) - round(division * i))) for i in range(n)]
 
 
-def flatten(l):
-    return [item for sublist in l for item in sublist]
+def flatten(input_list):
+    return [item for sublist in input_list for item in sublist]
 
 
 def generate_colors(n):

requirements.txt

@@ -1 +1 @@
--e .
+-e . --use-feature=2020-resolver

setup.py

@@ -26,14 +26,14 @@
 requirements = ['numpy>=1.9.1',
                 'scipy>=0.14.0',
                 'blessings>=1.5.1',
-                'pandas>=0.24.0',
+                'pandas>=1.1.3',
                 'ordered-set>=1.2',
                 'cobra>=0.11.1',
                 'future>=0.15.2',
-                'optlang>=1.2.1',
+                'optlang==1.4.2',
                 'numexpr>=2.4',
                 'requests>=2.10.0',
-                'networkx==1.9.1',
+                'networkx>=2.4',
                 'escher>=1.1.2',
                 'IProgress>=0.4',
                 'inspyred>=1.0',
@@ -85,9 +85,9 @@
     classifiers=[
         'Development Status :: 3 - Alpha',
         'Topic :: Utilities',
-        'Programming Language :: Python :: 2.5',
-        'Programming Language :: Python :: 2.6',
-        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
         'License :: OSI Approved :: Apache Software License'
     ],
 )

tests/test_network_analysis.py

@@ -27,24 +27,24 @@ def test_distance_based_on_molecular_formula(salmonella):
 
 
 def test_model_to_network(salmonella):
-    assert model_to_network(salmonella).edges() == reactions_to_network(salmonella.reactions).edges()
+    assert model_to_network(salmonella).edges == reactions_to_network(salmonella.reactions).edges
     network = model_to_network(salmonella)
-    assert len(network.nodes()) == 1761
-    assert len(network.edges()) == 4924
+    assert len(network.nodes) == 1761
+    assert len(network.edges) == 4924
     network = model_to_network(salmonella, max_distance=1.)
     # nodes = network.nodes()
     # print(set(nodes).difference(set(core_model_one.metabolites)))
     # print(set(core_model_one.metabolites).difference(set(nodes)))
-    assert len(network.nodes()) == 1800
-    assert len(network.edges()) == 12853
+    assert len(network.nodes) == 1800
+    assert len(network.edges) == 12853
 
 
 def test_remove_highly_connected_nodes(salmonella):
     network = model_to_network(salmonella)
     assert salmonella.metabolites.atp_c in network.nodes()
     assert salmonella.metabolites.adp_c in network.nodes()
     remove_highly_connected_nodes(network, max_degree=10, ignore=[salmonella.metabolites.atp_c])
-    assert len(network.nodes()) == 1671
-    assert len(network.edges()) == 2342
+    assert len(network.nodes) == 1671
+    assert len(network.edges) == 2342
     assert salmonella.metabolites.atp_c in network.nodes()
     assert salmonella.metabolites.adp_c not in network.nodes()

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = flake8, py27, py34, py35, py36
+envlist = flake8, py36, py37, py38
 
 [testenv]
 deps =
@@ -8,6 +8,8 @@ deps =
     pytest-benchmark
 whitelist_externals =
     obabel
+setenv =
+  TRAVIS = True
 commands =
     pytest --cov=cameo {posargs: -v -rsx --cov-report=xml --cov-report=term --benchmark-skip tests}
 
@@ -16,6 +18,7 @@ skip_install = True
 deps = flake8
 commands = flake8 cameo
 
+
 [pytest]
 filterwarnings =
     ignore::DeprecationWarning:cobra.core.reaction
@@ -45,7 +48,6 @@ known_first_party = cameo
 known_third_party =
     cobra
     future
-    six
 
 [coverage:paths]
 source =