bdms-sim 0.2.0__tar.gz → 0.3.1__tar.gz

{bdms_sim-0.2.0 → bdms_sim-0.3.1}/CITATION.cff

@@ -1,7 +1,6 @@
 cff-version: 1.2.0
 title: BDMS
 message: 'If you use BDMS in your work, please cite as follows.'
-type: software
 authors:
   - given-names: William S.
     family-names: DeWitt
@@ -44,16 +43,5 @@ authors:
     affiliation: 'University of California, Irvine'
     email: vminin@uci.edu
     orcid: 'https://orcid.org/0000-0002-1917-9288'
-identifiers:
-  - type: doi
-    value: none
-    description: placeholder
-repository-code: 'https://github.com/WSDeWitt/BDMS'
+doi: 10.5281/zenodo.10467425
 url: 'https://wsdewitt.github.io/BDMS'
-abstract: >-
-  BDMS is a Python package for simulating trees from
-  birth-death-mutation-sampling (BDMS) processes. It
-  is developed by collaborators at the University of
-  California, Berkeley and the University of
-  California, Irvine, and the Fred Hutchinson Cancer.
-license: MIT

{bdms_sim-0.2.0 → bdms_sim-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bdms-sim
-Version: 0.2.0
+Version: 0.3.1
 Summary: Tree simulator for birth-death-mutation-sampling (BDMS) processes
 Project-URL: Homepage, https://github.com/WSDeWitt/BDMS
 Project-URL: Bug Tracker, https://github.com/WSDeWitt/BDMS/issues
@@ -20,8 +20,11 @@ Description-Content-Type: text/markdown
 
 [![build and test](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml)
 [![docs build and deploy](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml)
+[![PyPI package](https://github.com/WSDeWitt/BDMS/actions/workflows/publish.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/publish.yml)
+[![DOI](https://zenodo.org/badge/705416157.svg)](https://zenodo.org/doi/10.5281/zenodo.10467339)
 
 # BDMS
+
 Tree simulator for birth-death-mutation-sampling (BDMS) processes
 
 Documentation: https://wsdewitt.github.io/BDMS

{bdms_sim-0.2.0 → bdms_sim-0.3.1}/README.md

@@ -1,7 +1,10 @@
 [![build and test](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml)
 [![docs build and deploy](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml)
+[![PyPI package](https://github.com/WSDeWitt/BDMS/actions/workflows/publish.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/publish.yml)
+[![DOI](https://zenodo.org/badge/705416157.svg)](https://zenodo.org/doi/10.5281/zenodo.10467339)
 
 # BDMS
+
 Tree simulator for birth-death-mutation-sampling (BDMS) processes
 
 Documentation: https://wsdewitt.github.io/BDMS

{bdms_sim-0.2.0 → bdms_sim-0.3.1}/bdms/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.2.0"
+__version__ = "0.3.1"
 
 from .tree import TreeNode as _TreeNode
 

bdms_sim-0.3.1/docs/cite.rst

@@ -0,0 +1,24 @@
+Citing BDMS
+###########
+
+.. image:: https://zenodo.org/badge/705416157.svg
+  :target: https://zenodo.org/doi/10.5281/zenodo.10467339
+
+BDMS is developed by collaborators at UC Berkeley, UC Irvine, and Fred Hutchinson Cancer Center. If you use BDMS in your research, please cite as below.
+
+APA
+---
+
+  DeWitt, W. S., Celentano, M., Bakis, T., Ralph, D. K., Prillo, S., Matsen, F. A., IV, Song, Y. S., & Minin, V. M. BDMS [Computer software]. https://doi.org/10.5281/zenodo.10467425
+
+BibTeX
+------
+
+.. code-block:: bibtex
+
+  @software{DeWitt_BDMS,
+  author = {DeWitt, William S. and Celentano, Michael and Bakis, Thanasi and Ralph, Duncan K. and Prillo, Sebastian and Matsen, IV, Frederick A. and Song, Yun S. and Minin, Volodymyr M.},
+  doi = {10.5281/zenodo.10467425},
+  title = {{BDMS}},
+  url = {https://wsdewitt.github.io/BDMS}
+  }

bdms_sim-0.3.1/docs/install.rst

@@ -0,0 +1,24 @@
+Installation
+############
+
+Pip
+===
+
+.. image:: https://github.com/WSDeWitt/BDMS/actions/workflows/publish.yml/badge.svg
+  :target: https://github.com/WSDeWitt/BDMS/actions/workflows/publish.yml
+
+.. code-block:: bash
+
+  pip install bdms-sim
+
+
+Conda
+=====
+
+.. todo::
+  Publish Conda package
+
+Developer
+=========
+
+See :doc:`developer`.

bdms_sim-0.2.0/docs/cite.rst

@@ -1,6 +0,0 @@
-Citing BDMS
-###########
-
-.. todo::
-
-  put citation info here, someday

bdms_sim-0.2.0/docs/install.rst

@@ -1,21 +0,0 @@
-Installation
-############
-
-Pip
-===
-
-.. code-block:: bash
-
-  pip install bdms-sim
-
-
-Conda
-=====
-
-.. todo::
-  Publish Conda package
-
-Developer
-=========
-
-See :doc:`developer`.