diff --git a/MANIFEST.in b/MANIFEST.in index f15491c..a8a3778 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1 +1 @@ -recursive-include stanmodels/stan * +recursive-include survivalstan/stan * diff --git a/README.md b/README.md index 5fca6ac..c032951 100644 --- a/README.md +++ b/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 @@ -41,16 +41,16 @@ 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 @@ -58,10 +58,10 @@ 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', diff --git a/lint.sh b/lint.sh index 132a6c3..c9dcc39 100755 --- a/lint.sh +++ b/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 diff --git a/setup.cfg b/setup.cfg index 76ae3d3..3a7c75f 100644 --- a/setup.cfg +++ b/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 = '' diff --git a/setup.py b/setup.py index b65ad22..f596bc2 100644 --- a/setup.py +++ b/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", diff --git a/stanmodels/__init__.py b/survivalstan/__init__.py similarity index 100% rename from stanmodels/__init__.py rename to survivalstan/__init__.py diff --git a/stanmodels/_version.py b/survivalstan/_version.py similarity index 100% rename from stanmodels/_version.py rename to survivalstan/_version.py diff --git a/stanmodels/stan.py b/survivalstan/stan.py similarity index 100% rename from stanmodels/stan.py rename to survivalstan/stan.py diff --git a/stanmodels/stan/pem_survival_model.stan b/survivalstan/stan/pem_survival_model.stan similarity index 100% rename from stanmodels/stan/pem_survival_model.stan rename to survivalstan/stan/pem_survival_model.stan diff --git a/stanmodels/stan/pem_survival_model_randomwalk.stan b/survivalstan/stan/pem_survival_model_randomwalk.stan similarity index 100% rename from stanmodels/stan/pem_survival_model_randomwalk.stan rename to survivalstan/stan/pem_survival_model_randomwalk.stan diff --git a/stanmodels/stan/pem_survival_model_tvc.stan b/survivalstan/stan/pem_survival_model_tvc.stan similarity index 100% rename from stanmodels/stan/pem_survival_model_tvc.stan rename to survivalstan/stan/pem_survival_model_tvc.stan diff --git a/stanmodels/stan/pem_survival_model_varying_coefs.stan b/survivalstan/stan/pem_survival_model_varying_coefs.stan similarity index 100% rename from stanmodels/stan/pem_survival_model_varying_coefs.stan rename to survivalstan/stan/pem_survival_model_varying_coefs.stan diff --git a/stanmodels/stan/pem_survival_model_varying_coefs2.stan b/survivalstan/stan/pem_survival_model_varying_coefs2.stan similarity index 100% rename from stanmodels/stan/pem_survival_model_varying_coefs2.stan rename to survivalstan/stan/pem_survival_model_varying_coefs2.stan diff --git a/stanmodels/stan/pem_survival_model_varying_coefs3.stan b/survivalstan/stan/pem_survival_model_varying_coefs3.stan similarity index 100% rename from stanmodels/stan/pem_survival_model_varying_coefs3.stan rename to survivalstan/stan/pem_survival_model_varying_coefs3.stan diff --git a/stanmodels/stan/pem_survival_model_varying_coefs4.stan b/survivalstan/stan/pem_survival_model_varying_coefs4.stan similarity index 100% rename from stanmodels/stan/pem_survival_model_varying_coefs4.stan rename to survivalstan/stan/pem_survival_model_varying_coefs4.stan diff --git a/stanmodels/stan/weibull_survival_model.stan b/survivalstan/stan/weibull_survival_model.stan similarity index 100% rename from stanmodels/stan/weibull_survival_model.stan rename to survivalstan/stan/weibull_survival_model.stan diff --git a/stanmodels/stan/weibull_survival_model_varying_coefs.stan b/survivalstan/stan/weibull_survival_model_varying_coefs.stan similarity index 100% rename from stanmodels/stan/weibull_survival_model_varying_coefs.stan rename to survivalstan/stan/weibull_survival_model_varying_coefs.stan diff --git a/stanmodels/survival_model.py b/survivalstan/survival_model.py similarity index 100% rename from stanmodels/survival_model.py rename to survivalstan/survival_model.py