Merge pull request #19 from VlachosGroup/development

Development

CHANGELOG.md

@@ -0,0 +1,12 @@
+## [1.0.0] - 2021-05-07
+- PyStan+CVODES no longer being developed; updated our PyStan installer to use the new (archived) GitHub URL
+- Updated Docker installation
+- Updated arviz syntax to align with current arviz package
+
+## [0.0.2] - 2020-07-07
+### Added
+- Initialization functionality for VI estimation
+- More detailed error messages for non-physical values
+
+## [0.0.1] - 2020-07-01
+Initial public release

Dockerfile

@@ -25,18 +25,10 @@ COPY ckbit /tmp/ckbit/ckbit
 WORKDIR /tmp/ckbit
 
 #
-# Build and install the CVODES-enabled PyStan:
+# Build and install the CVODES-enabled PyStan: and install CKBIT: and remove build folders
+# This reduces image size by reducing the last layers. 
 #
 RUN chmod +x pystan-install.sh
-RUN ./pystan-install.sh --build-root /tmp/ckbit --verbose
-
-#
-# Install CKBIT:
-#
-RUN python setup.py install
-
-#
-# Remove the CKBIT source:
-#
+RUN ./pystan-install.sh --build-root /tmp/ckbit --verbose && python setup.py install && rm -rf /tmp/ckbit
 WORKDIR /
-RUN rm -rf /tmp/ckbit
+

README.rst

@@ -8,12 +8,12 @@ by the Vlachos Research Group at the University of Delaware.
 
 Documentation
 -------------
-Please see the html files in the docs folder for the 
-documentation.
+Documentation can be found at this webiste:
+https://vlachosgroup.github.io/ckbit/
 
 Examples
 --------
-There are examples of the code in the examples 
+There are examples of the code in the Github examples 
 folder. The examples are provided in both Python scripts 
 and in Jupyter notebooks. Ensure the accompanying Excel 
 files are used as templates for data entry.
@@ -24,8 +24,8 @@ Max Cohen ([email protected])
 
 Dependencies
 ------------
-* PyStan: Interfaces with Stan for optimized Bayesian 
-  inference computation
+* PyStan2: Interfaces with Stan for optimized Bayesian 
+  inference computation - archieved repository
 * Datetime: Measures computational runtime
 * NumPy: Provides efficient array manipulation
 * Pickle: Creates and stores portable, serialized 

ckbit/__init__.py

@@ -7,7 +7,7 @@
 # present, too:
 #
 name = 'ckbit'
-__version__ = '0.0.1'
+__version__ = '1.0.0'
 
 # Pull rxn_ord, pfr, cstr, app_ea in as ckbit.<x>:
 from . import rxn_ord

ckbit/cstr.py

@@ -328,7 +328,7 @@ def MCMC(filename, model_name='cstr', pH=False, warmup=None, iters=2000, \
     print(fit)
     sample_vals = fit.extract(permuted=True)
     if trace: 
-        traceplot = arviz.plot_trace(fit)
+        traceplot = arviz.plot_trace(fit, compact=False)
         for i in range(rxns):
             traceplot[i,0].set_title('A0{}'.format(i+1))
             traceplot[i,1].set_title('A0{}'.format(i+1))

ckbit/pfr.py

@@ -376,7 +376,7 @@ def MCMC(filename, model_name='pfr', pH=False, R_units='kJ/mol/K', priors=None,\
     print(fit)
     sample_vals = fit.extract(permuted=True)
     if trace: 
-        traceplot = arviz.plot_trace(fit)
+        traceplot = arviz.plot_trace(fit, compact=False)
         for i in range(rxns):
             traceplot[i,0].set_title('A0{}'.format(i+1))
             traceplot[i,1].set_title('A0{}'.format(i+1))

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = ../../CKBIT_docs
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

docs/.buildinfo → docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: a395c92d2e6c2d205e929518967ef1b2
+config: a133afbb2356d03259dabfe987e6d9e9
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/appEa.rst.txt

@@ -0,0 +1,6 @@
+.. _appEa:
+
+Header
+******
+
+.. autofunction:: kbi.appEa	

docs/_build/html/_sources/index.rst.txt

@@ -0,0 +1,21 @@
+.. KBI documentation master file, created by
+   sphinx-quickstart on Mon Nov 18 14:07:47 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to KBI's documentation!
+===============================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   appEa
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`