Merge pull request #199 from hyanwong/patch-7

Update readme to cite Science paper

Author: benjeffery

CITATION.cff

@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use tsdate in your work, please cite it as below."
+authors:
+- given-names: Anthony Wilder
+  family-names: Wohns
+  orcid: "https://orcid.org/0000-0001-7353-1177"
+- given-names: Yan
+  family-names: Wong
+  orcid: "https://orcid.org/0000-0002-3536-6411"
+- given-names: Ben
+  family-names: Jeffery
+  orcid: "https://orcid.org/0000-0002-1982-6801"
+title: "Tsdate"
+version: 0.1.4
+date-released: 2021-06-30
+url: "https://github.com/tskit-dev/tsdate"
+license: MIT
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Anthony Wilder
+    family-names: Wohns
+    orcid: "https://orcid.org/0000-0001-7353-1177"
+  - given-names: Yan
+    family-names: Wong
+    orcid: "https://orcid.org/0000-0002-3536-6411"
+  - given-names: Ben
+    family-names: Jeffery
+    orcid: "https://orcid.org/0000-0002-1982-6801"
+  - given-names: Ali
+    family-names: Akbari
+    orcid: "https://orcid.org/0000-0002-5000-5876"
+  - given-names: Swapan
+    family-names: Mallick
+    orcid: "https://orcid.org/0000-0002-4531-4439"
+  - given-names: Ron
+    family-names: Pinhasi
+    orcid: "https://orcid.org/0000-0003-1629-8131"
+  - given-names: Nick
+    family-names: Patterson
+    orcid: "https://orcid.org/0000-0003-0302-684X"
+  - given-names: David
+    family-names: Reich
+    orcid: "https://orcid.org/0000-0002-7037-5292"
+  - given-names: Jerome
+    family-names: Kelleher
+    orcid: "https://orcid.org/0000-0002-7894-5253"
+  - given-names: Gil
+    family-names: McVean
+    orcid: "https://orcid.org/0000-0002-5012-4162"
+  doi: "10.1126/science.abi8264"
+  journal: "Science"
+  start: eabi8264
+  title: "A unified genealogy of modern and ancient genomes"
+  volume: 375
+  year: 2022

README.md

@@ -5,14 +5,14 @@
 [![Documentation Status](https://readthedocs.org/projects/tsdate/badge/?version=latest)](https://tsdate.readthedocs.io/en/latest/?badge=latest)
 
 ``tsdate`` is a scalable method for estimating the age of ancestral nodes in a 
-[tree sequence](https://www.youtube.com/watch?v=X1GEuQrF1jQ). The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").
+[tree sequence](https://tskit.dev/tutorials/what_is.html). The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").
 
 The method is designed to operate on the output of [tsinfer](https://tsinfer.readthedocs.io/en/latest/), which efficiently infers tree sequence *topologies* from large genetic datasets.
 
 Please refer to the [documentation](https://tsdate.readthedocs.io/en/latest/) for information on installing and using the software.
 
-The algorithm is described [in this BioRxiv preprint](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2). We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data. The code to reproduce these results can be found in [another repository](https://github.com/awohns/unified_genealogy_paper).
+The algorithm is described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2)). We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data. The code to reproduce these results can be found in [another repository](https://github.com/awohns/unified_genealogy_paper).
 
-> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2021) _A unified genealogy of modern and ancient genomes_. bioRxiv 2021.02.16.431497; doi: https://doi.org/10.1101/2021.02.16.431497
+> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) _A unified genealogy of modern and ancient genomes_. Science **375**: eabi8264; doi: https://doi.org/10.1126/science.abi8264
 
-Please cite this preprint if you use ``tsdate`` in published work.
+Please cite this paper if you use ``tsdate`` in published work.

docs/introduction.rst

@@ -5,13 +5,14 @@ Introduction
 ============
 
 ``tsdate`` is a scalable method for estimating the age of ancestral nodes in a 
-`tree sequence <https://www.youtube.com/watch?v=X1GEuQrF1jQ>`_. The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").
+`tree sequence <https://tskit.dev/tutorials/what_is.html>`_. The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").
 
 The method is designed to operate on the output of `tsinfer <https://tsinfer.readthedocs.io/en/latest/>`_, which efficiently infers tree sequence *topologies* from large genetic datasets. ``tsdate`` and  ``tsinfer`` are scalable to the largest genomic datasets currently available.
 
-The algorithm is described `in this BioRxiv preprint <https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2>`_. We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data; the code to reproduce these results can be found in `another repository <https://github.com/awohns/unified_genealogy_paper>`_.
+The algorithm is described `in this Science paper <https://www.science.org/doi/10.1126/science.abi8264>`_
+(preprint `here <https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2>`_). We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data; the code to reproduce these results can be found in `another repository <https://github.com/awohns/unified_genealogy_paper>`_.
 
-Please cite this preprint if you use ``tsdate`` in published work:
+Please cite this paper if you use ``tsdate`` in published work:
 
-> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2021) *A unified genealogy of modern and ancient genomes*. bioRxiv 2021.02.16.431497; doi: https://doi.org/10.1101/2021.02.16.431497
+> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) *A unified genealogy of modern and ancient genomes*. Science **375**: eabi8264; doi: https://doi.org/10.1126/science.abi826421
 

docs/requirements.txt

@@ -1,4 +1,5 @@
 attrs
+recommonmark
 six
 setuptools_scm 
 sphinx-argparse
@@ -8,4 +9,4 @@ numba
 tskit
 scipy
 tqdm
-appdirs
+appdirs