New msmodelutl

.gitignore

@@ -57,6 +57,9 @@ coverage.xml
 *.mo
 *.pot
 
+# local cobrakbase fonts
+examples/Flux Analysis/Users/
+
 # Django stuff:
 *.log
 local_settings.py
@@ -128,5 +131,9 @@ venv.bak/
 .dmypy.json
 dmypy.json
 
+# Julia dev models
+*.mat
+*.zip
+
 # Pyre type checker
 .pyre/

.readthedocs.yaml

@@ -0,0 +1,16 @@
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+python:
+   install:
+   - requirements: docs/requirements.txt

MANIFEST.in

@@ -1,2 +1,3 @@
 include LICENSE
+Include modelseedpy/config.cfg
 graft data

README.rst

@@ -45,6 +45,7 @@ and then locally installed with ``pip``::
 
  cd path/to/modelseedpy
  pip install .
+
 
 The associated ModelSEED Database, which is required for a few packages, is simply downloaded by cloning the GitHub repository::
 

docs/requirements.txt

@@ -1,59 +1,2 @@
-anyio
-appdirs
-certifi
-charset-normalizer
-chemicals
-ChemW
-cobra
-commonmark
-cycler
-depinfo
-diskcache
-et-xmlfile
-fluids
-fonttools
-future
-h11
-httpcore
-httpx
-idna
-importlib-resources
-joblib
-kiwisolver
-matplotlib
-mpmath
-networkx
-numpy
-openpyxl
-optlang
-packaging
-pandas
-Pillow
-PubChemPy
-PuLP
-pydantic
-pyDEA
-Pygments
-pyparsing
-python-dateutil
-python-libsbml
-pytz
-requests
-rfc3986
-rich
-ruamel.yaml
-ruamel.yaml.clib
-scikit-learn
-scipy
-sigfig
-six
-sniffio
-sortedcontainers
-swiglpk
-sympy
-threadpoolctl
-typing_extensions
-urllib3
-xlrd
-xlwt-future
-zipp
+autoapi
+nbsphinx

docs/source/api.rst

@@ -1,12 +1,89 @@
-ModelSEEDpy API 
+API 
 ________________________________________________________________________
 
 The detailed documentation of all user-operable classes and functions in the ModelSEEDpy library are provided.
 
+
+core
+---------
+
+The ``core`` sub-library permits parsing and manipulating metabolic models::
+
+ from modelseedpy.core import *   
+
+
 .. toctree::
+   :includehidden:
+
+   core/biology_api
+   core/fbahelper_api
+   core/gapfillinghelper_api
+   core/msatpcorrection_api
+   core/msbuilder_api
+   core/mseditorapi_api
+   core/msgenome_api
+   core/msgapfill_api
+   core/msgenomeclassifier_api
+   core/msgrowthphenotypes_api
+   core/msmedia_api
+   core/msmodel_api
+   core/msmodelutils_api
+   core/mstemplate_api
+   core/rpcclient_api
+   core/template_api
+
+
+community
+------------
+
+The ``community`` sub-library compatibilizes transport reactions of individual models for a community model and simulates interactions amongst community members::
+
+ from modelseedpy.community import *   
+
+
+.. toctree::
+   :includehidden:
+
+   community/commkineticpkg_api
+   community/dfbapkg_api
+   community/mscommfitting_api
+   community/mscommunity_api
+   community/mscompatibility_api
 
-   contents
-   core/core_index
-   community/community_index
-   fbapkg/fbapkg_index
-   ml/ml_index
+
+fbapkg
+------------
+
+The ``fbapkg`` sub-library constrains and investigates metabolic models through Flux Balance Analysis methods::
+
+ from modelseedpy.fbapkg import *   
+
+.. toctree::
+   :includehidden:
+
+   fbapkg/bilevel_api
+   fbapkg/changeoptpkg_api
+   fbapkg/drainfluxes_api
+   fbapkg/elementuptakepkg_api
+   fbapkg/flexiblebiomass_api
+   fbapkg/fluxfitting_api
+   fbapkg/gapfillingpkg_api
+   fbapkg/kbasemedia_api
+   fbapkg/metabofba_api
+   fbapkg/proteomefitting_api
+   fbapkg/reactionuse_api
+   fbapkg/tfa_api
+
+
+ml
+------------
+
+The ``ml`` sub-library supports parsing features from genomes, with accessibility to KBase::
+
+ from modelseedpy.ml import *   
+
+
+.. toctree::
+   :includehidden:
+
+   ml/predict_phenotypes_api

docs/source/community/dfbapkg_api.rst

@@ -1,4 +1,4 @@
-dFBA Package
+dFBApkg
 --------------
 
 ++++++++++
@@ -9,7 +9,7 @@ This class defines and executes dynamic FBA simulations of COBRA models:
 
 .. code-block:: python
 
- from modelseedpy.fbapkg import dFBAPkg
+ from modelseedpy.community import dFBAPkg
  dfba = dFBAPkg(model, modelseed_db_path, solver = 'glpk', warnings = True, verbose = False, printing = False, jupyter = False)
 
 - *model* ``cobra.core.model.Model``: the CobraKBase model that will be simulated. The conversion from `standard COBRA models  <https://cobrapy.readthedocs.io/en/latest/autoapi/cobra/core/model/index.html>`_ to CobraKBase models is facilitated by the `cobrakbase` package.