rename stanmodels to survivalstan

MANIFEST.in

@@ -1 +1 @@
-recursive-include stanmodels/stan *
+recursive-include survivalstan/stan *

README.md

@@ -13,12 +13,12 @@ Installation / Usage
 
 To install use pip:
 
-    $ pip install stanmodels
+    $ pip install survivalstan
 
 
 Or clone the repo:
 
-    $ git clone https://github.com/jburos/stanmodels.git
+    $ git clone https://github.com/jburos/survivalstan.git
     $ python setup.py install
 
 Contributing
@@ -30,7 +30,7 @@ Example
 -------
 
 ```
-import stanmodels
+import survivalstan
 import stanity
 import seaborn as sb
 import matplotlib.pyplot as plt
@@ -41,27 +41,27 @@ d  = dataset.data.query('futime > 7')
 d.reset_index(level = 0, inplace = True)
 
 ## e.g. fit Weibull survival model
-testfit_wei = stanmodels.fit_stan_survival_model(
+testfit_wei = survivalstan.fit_stan_survival_model(
 	model_cohort = 'Weibull model',
-	model_code = stanmodels.stan.weibull_survival_model,
+	model_code = survivalstan.stan.weibull_survival_model,
 	df = d,
 	time_col = 'futime',
 	event_col = 'death',
 	formula = 'age + sex',
 	iter = 3000,
 	chains = 4,
-	make_inits = stanmodels.make_weibull_survival_model_inits
+	make_inits = survivalstan.make_weibull_survival_model_inits
 	)
 
 ## coefplot for Weibull coefficient estimates
 sb.boxplot(x = 'value', y = 'variable', data = testfit_wei['coefs'])
 
 
 ## e.g. fit Piecewise-exponential survival model 
-dlong = stanmodels.prep_data_long_surv(d, time_col = 'futime', event_col = 'death')
-testfit_pem = stanmodels.fit_stan_survival_model(
+dlong = survivalstan.prep_data_long_surv(d, time_col = 'futime', event_col = 'death')
+testfit_pem = survivalstan.fit_stan_survival_model(
 	model_cohort = 'PEM model',
-	model_code = stanmodels.stan.pem_survival_model,
+	model_code = survivalstan.stan.pem_survival_model,
 	df = dlong,
 	sample_col = 'index',
 	timepoint_end_col = 'end_time',

lint.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -o errexit
 
-find stanmodels test -name '*.py' \
+find survivalstan test -name '*.py' \
     | xargs pylint \
             --errors-only \
             --disable=print-statement

setup.cfg

@@ -7,6 +7,6 @@ description-file=README.md
 [versioneer]
 VCS = git
 style = pep440
-versionfile_source = stanmodels/_version.py
-versionfile_build = stanmodels/_version.py
+versionfile_source = survivalstan/_version.py
+versionfile_build = survivalstan/_version.py
 tag_prefix = ''

setup.py

@@ -20,13 +20,13 @@
 dependency_links = [x.strip().replace('git+', '') for x in all_reqs if 'git+' not in x]
 
 setup(
-    name='stanmodels',
+    name='survivalstan',
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
     description='Library of Stan Models for Computational Biology',
     long_description=long_description,
-    url='https://github.com/jburos/stanmodels',
-    download_url='https://github.com/jburos/stanmodels/tarball/' + versioneer.get_version(),
+    url='https://github.com/jburos/survivalstan',
+    download_url='https://github.com/jburos/survivalstan/tarball/' + versioneer.get_version(),
     license="http://www.apache.org/licenses/LICENSE-2.0.html",
     classifiers=[
         "Development Status :: 3 - Alpha",