Merge pull request #26 from EPFL-LCSB/dev

VER: 0.9 - RedGEM is Here!
Thanks to a lot of work from @PtichapronRouge and @Redlinkk 

This release includes (finally!) a Python implementation of our redGEM[1] and lumpGEM[2] papers for systematic genome-scale metabolic model reduction.
The code is still in development, so any feedback is welcome :)

This version also features:

* Repaired autodocumentation
* Faster relaxation
* Lots of code cleanup
* Minor fixes

[1] Ataman, Meric, et al. "redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models." PLoS computational biology 13.7 (2017): e1005444.
https://doi.org/10.1371/journal.pcbi.1005444

[2] Ataman, Meric, and Vassily Hatzimanikatis. "lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites." PLoS computational biology 13.7 (2017): e1005513.
https://doi.org/10.1371/journal.pcbi.1005513

.gitignore

@@ -1,9 +1,13 @@
 # Pycharm folders
 .idea/*
+.idea/
 cobra_docker/work/.idea/*
 *___jb_old___
 *___jb_tmp___
 
+# Docker temp files
+docker/temp/
+
 ###########################################
 ###	Standard Python	.gitignore	###
 ###########################################

doc/Makefile

@@ -3,10 +3,11 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = python -msphinx
+SPHINXBUILD   = python3 -msphinx
 SPHINXPROJ    = pytfa
 SOURCEDIR     = .
 BUILDDIR      = _build
+AUTODIR       = _autogen
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -17,4 +18,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -21,7 +21,34 @@
 import sys
 sys.path.insert(0, os.path.abspath('..'))
 
+# In order to build documentation that requires libraries to import
+class Mock(object):
+    def __init__(self, *args, **kwargs):
+        return
+
+    def __call__(self, *args, **kwargs):
+        return Mock()
+
+    @classmethod
+    def __getattr__(cls, name):
+        if name in ('__file__', '__path__'):
+            return '/dev/null'
+        else:
+            return Mock()
+
+
+# These modules should correspond to the importable Python packages.
+MOCK_MODULES = [
+    'cobra',
+    'numpy',
+    'scipy',
+    'pandas',
+    'optlang', 'optlang.interface', 'optlang.symbolics',
+    'scipy', 'scipy.io',
+]
 
+for mod_name in MOCK_MODULES:
+    sys.modules[mod_name] = Mock()
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -35,7 +62,13 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
-    'sphinx.ext.mathjax']
+    'sphinx.ext.mathjax',
+    'autoapi.extension']
+
+
+# Document Python Code
+autoapi_type = 'python'
+autoapi_dirs = ['../pytfa']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -59,10 +92,10 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.8'
+version = '0.9'
 # The full version, including alpha/beta/rc tags.
 
-release = '0.8.1'
+release = '0.9.0-b0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/requirements.txt

@@ -0,0 +1,2 @@
+Sphinx
+sphinx-autoapi

models/.gitattributes

@@ -0,0 +1 @@
+*.mat filter=lfs diff=lfs merge=lfs -text

pytfa/analysis/sampling.py

@@ -13,7 +13,7 @@
 import numpy as np
 from sympy.core.singleton import S
 from time import  time
-from  cobra.flux_analysis.sampling import OptGPSampler, ACHRSampler, HRSampler,\
+from  cobra.sampling import OptGPSampler, ACHRSampler, HRSampler,\
                                             shared_np_array
 from optlang.interface import OPTIMAL
 
@@ -29,6 +29,8 @@ def __init__(self, model, thinning,  nproj=None, seed=None):
         # This currently has to be done to reset the solver basis which is
         # required to get deterministic warmup point generation
         # (in turn required for a working `seed` arg)
+        HRSampler.__init__(self, model, thinning, seed=seed)
+
         if model.solver.is_integer:
             raise TypeError("sampling does not work with integer problems :(")
         self.model = model.copy()
@@ -200,4 +202,4 @@ def sample(model, n, method="optgp", thinning=100, processes=1, seed=None):
     else:
         raise ValueError("method must be 'optgp' or 'achr'!")
 
-    return sampler.sample(n, fluxes = False)
+    return sampler.sample(n, fluxes = False)

pytfa/analysis/variability.py

@@ -19,6 +19,7 @@
 from cobra.core import Reaction
 from optlang.exceptions import SolverError
 from optlang.interface import INFEASIBLE
+from tqdm import tqdm
 
 from ..optim import DeltaG
 from ..optim.constraints import ForbiddenProfile
@@ -155,7 +156,7 @@ def variability_analysis(tmodel, kind='reactions', proc_num = BEST_THREAD_RATIO)
 
     results = {'min':{}, 'max':{}}
     for sense in ['min','max']:
-        for k,var in these_vars.items():
+        for k,var in tqdm(these_vars.items(), desc=sense+'imizing'):
             tmodel.logger.debug(sense + '-' + k)
             results[sense][k] = _variability_analysis_element(tmodel,var,sense)