Merge from upstream master

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.travis.yml

@@ -0,0 +1,16 @@
+language: python
+
+cache: pip
+
+python:
+  - "3.5"
+  - "3.6"      # current default Python on Travis CI
+  - "3.7"
+  - "3.8"
+  - "3.8-dev"  # 3.8 development branch
+
+install:
+  - pip install -r requirements.txt
+  - pip install .
+script: 
+  - pytest ./tests/testsuite.py

README.md

@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.com/evogytis/baltic.svg?branch=master)](https://travis-ci.com/evogytis/baltic)
+
 # baltic
 
 baltic is a Python library for parsing phylogenetic trees. It takes newick, Nexus or nextstrain JSON trees and allows you to manipulate, explore and visualise them. baltic stands for Backronymed Adaptable Lightweight Tree Import Code if you like that sort of thing.

docs/publications.rst

@@ -8,18 +8,30 @@ Publications using baltic
 
 baltic was used in the following publications:
 
-- Miller D, Martin MA, Harel N, Kustin T, Tirosh O, Meir M, Sorek N, ..., Kopelman N, Huppert A, Koelle K, Stern A, 2020. _Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel, `medRxiv`: 2020.05.21.20104521; `doi <https://doi.org/10.1101/2020.05.21.20104521>`__.
+- Muller N, Kunze M, ..., Zeitlmann N, and Corman VM, 2021. _Severe Acute Respiratory Syndrome Coronavirus 2 Outbreak Related to a Nightclub, Germany, 2020_, `Emerging Infectious Diseases` 27(2): 645-648; `doi <https://doi.org/10.3201/eid2702.204443>`__.
+- Washington NL, Gangavarapu K, Zeller M, Bolze A, ..., Chiu C, Suchard MA, Lu JT, Lee W, Andersen KG, 2021. _Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States_, `medRxiv` 2021.02.06.21251159; `doi <https://doi.org/10.1101/2021.02.06.21251159>`__.
+- Alpert T, Lasek-Nesselquist E, Brito AF, ...,  Lauring AS, St. George K, MacCannell DR, Grubaugh ND, 2021. _Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States_, `medRxiv` 2021.02.10.21251540; `doi <https://doi.org/10.1101/2021.02.10.21251540>`__.
+- Zeller M, Gangavarapu K, Anderson C, Smither AR, ..., Kamil JP, Garry RF, Suchard MA, Andersen KG, 2021. _Emergence of an early SARS-CoV-2 epidemic in the United States_, `medRxiv` 2021.02.05.21251235; `doi <https://doi.org/10.1101/2021.02.05.21251235>`__.
+- Thomson EC, Rosen LE, Shepherd JG, ..., Corti D, Robertson DL, Snell G, 2021. _Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity_, `Cell` 184: 1-17; `doi <https://doi.org/10.1016/j.cell.2021.01.037>`__.
+- Hodcroft EB, Domman DB, Oguntuyo K, ..., Cooper VS,  Kamil JP, 2021. _Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677_, `medRxiv` 2021.02.12.21251658; `doi <https://doi.org/10.1101/2021.02.12.21251658>`__.
+- Moreno GK, Braun KM, Riemersma KK, ..., Kawaoka Y, Koelle K, O’Connor DH, Friedrich TC, 2020. _Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread_, `Nature Communications` 11, 5558; `doi <https://doi.org/10.1038/s41467-020-19346-z>`__.
+- Miller D, Martin MA, Harel N, Kustin T, Tirosh O, Meir M, Sorek N, ..., Kopelman N, Huppert A, Koelle K, Stern A, 2020. _Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel_, `Nature Communications` 11, 5518; `doi <https://doi.org/10.1038/s41467-020-19248-0>`__.
+- Moncla LH, Black A, DeBolt C, Lang M, Graff NR, Perez-Osorio AC, Mueller NF, Haselow D, Lindquist S, Bedford T, 2020. _Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State_, `medRxiv`: 2020.10.19.20215442; `doi <https://doi.org/10.1101/2020.10.19.20215442>`__.
+- Ladner JT, Larsen BB, Bowers JR, Hepp CM, ..., Worobey M, Keim P, 2020. _An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona_, `mBio` 11 (5): e02107-20; `doi <https://doi.org/10.1128/mBio.02107-20>`__.
+- Brito AF, Lais Machado C, ..., da Fonseca BAL, Wallau GL, Grubaugh ND, 2020. _Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil_, `medRxiv` 2020.08.10.20172247; `doi <https://doi.org/10.1101/2020.08.10.20172247>`__.
+- Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O’Toole Á,
+- Pereyaslov D, 2020. _Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020_, `Euro Surveillance` 25(32):pii=2001410; `doi <https://doi.org/10.2807/1560-7917.ES.2020.25.32.2001410>`__.
 - Pawestri HA, Nugraha AA, Han AX, Pratiwi E, Parker E, Richard M, van der Vliet S, Fouchier RAM, Muljono DH, de Jong MD, Setiawaty V, Eggink D, 2020. _Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015. `Virus Genes` 56(4): 417-429. `doi <https://doi.org/10.1007/s11262-020-01765-1>`__.
-- Ladner JT, Larsen BB, Bowers JR, Hepp CM, ..., Worobey M, Keim P, 2020. _Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU), __medRxiv__: 2020.05.08.20095935; `doi <https://doi.org/10.1101/2020.05.08.20095935>`__.
 - Sikkema RS, Pas S, Nieuwenhuijse DF, O'Toole A, ..., Munnink BBO, Kluytmans M, Koopmans MPG, 2020. _COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study, `Lancet Infect Dis`; `doi <https://doi.org/10.1016/S1473-3099(20)30527-2>`__.
 - Munnink BBO, Nieuwenhuijse DF, Stein M, O'Toole A, Haverkarte M, ..., Meijer A, Rambaut A, van Dissel J, Sikkema R, Timen A, Koopmans M, 2020. _Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands, `Nature Medicine`; `doi <https://doi.org/10.1038/s41591-020-0997-y>`__.
 - Müller NF, Stolz U, Dudas G, Stadler T, Vaughan TG, 2020. _Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses, `PNAS`: 117 (29) 17104-17111; `doi <https://doi.org/10.1073/pnas.1918304117>`__.
 - Venkatesh D, Brouwer A, Ellis R, Goujgoulova G, Seekings J, Brown IH, Lewis NS, 2020. _Regional transmission and reassortment of 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses in Bulgarian poultry 2017/18, `Viruses` 12(6): 605; `doi <https://dx.doi.org/10.3390/v12060605>`__.
 - Suárez-Esquivel M, Hernández-Mora G, Ruiz-Villalobos N, ..., Thomson NR, Moreno E, Guzmán-Verri C, 2020. _Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis, `PLOS Neglected Tropical Diseases` 14(4): e0008235; `doi <https://doi.org/10.1371/journal.pntd.0008235>`__.
 - Moncla LH, Bedford T, Dussart P, ..., Guan Y, Friedrich TC, Horwood PF, 2020. _Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia, `PLOS Pathogens` 16(1): e1008191; `doi <https://doi.org/10.1371/journal.ppat.1008191>`__.
 - Dudas G, Bedford T, 2020. The ability of single genes vs full genomes to resolve time and space in outbreak analysis. `BMC Evolutionary Biology` 19, 232; `doi <https://doi.org/10.1186/s12862-019-1567-0>`__.
-- Wiley R, Fakoli L, Letizia AG, Welch SR, Ladner JT, Albariño CG, Fallah M, Palacios G, 2019. _Lassa virus circulating in Liberia: a retrospective genomic characterisation, `Lancet Infect Dis`
+- Wiley R, Fakoli L, Letizia AG, Welch SR, Ladner JT, Albariño CG, Fallah M, Palacios G, 2019. _Lassa virus circulating in Liberia: a retrospective genomic characterisation, `Lancet Infect Dis` 19(12): 1371-1378; `doi <https://doi.org/10.1016/S1473-3099(19)30486-4>`__.
 - Theys K, Lemey P, Vandamme AM, Baele G, 2019. _Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases, `Front. Public Health`, 7: 208; `doi <https://doi.org/10.3389/fpubh.2019.00208>`__.
+- Grubaugh ND, Saraf S, Gangavarapu K, Watts A, ..., Isern S, Michael SF, Andersen KG, 2019. _Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic_. `Cell` 178(5): 1057-1071; `doi <https://doi.org/10.1016/j.cell.2019.07.018>`__.
 - Müller NF, Dudas G, Stadler T, 2019. _Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations, `Virus Evolution`, 5(2): vez030; `doi <https://doi.org/10.1093/ve/vez030>`__.
 - Mbala-Kingebeni P, Aziza A, Di Paola N, Wiley MR, ..., Peeters M, Palacios G, Ahuka-Mundeke S, 2019. _Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment, `Lancet Infect Dis` 19(6): 648-657; `doi <https://doi.org/10.1016/S1473-3099(19)30118-5>`__.
 - Work TM, Dagenais J, Stacy BA, Ladner JT, ..., Rameyer RA, Taylor DR, Waltzek TB, 2019. _A novel host-adapted strain of Salmonella Typhimurium causes renal disease in olive ridley turtles (Lepidochelys olivacea) in the Pacific, `Scientific Reports`  9: 9313; `doi <https://doi.org/10.1038/s41598-019-45752-5>`__.

requirements.txt

@@ -1 +1,2 @@
-numpy>=1.17
+numpy>=1.16
+matplotlib>=2.0.0 ## due to import of LineCollections

setup.py

@@ -8,10 +8,10 @@
 
 setup(
     name="baltic",
-    version="0.1.1",
+    version="0.1.7",
     packages=find_packages(),
     url="https://github.com/evogytis/baltic",
-    download_url="https://github.com/evogytis/baltic/archive/v1.0.0.tar.gz",
+    download_url="https://github.com/evogytis/baltic/archive/v0.1.7.tar.gz",
     keywords = ['phylogeny', 'visualization'],
     license="gpl-3.0",
     author="Gytis Dudas",
@@ -20,7 +20,7 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=requirements,
-    python_requires=">=3.6.*",
+    python_requires=">=3.5.*",
     include_package_data=False,
     zip_safe=False,
     # classifiers=[],