Code

Upgrade to version 3.0#291

Code

Merged

puethe merged 246 commits intomasternickjcroucher/gubbins:masterfrom masterCopy head branch name to clipboardJan 27, 2021

+2,886-783

Commits

Commits on Nov 6, 2020

• Modify to use pyjar

  nickjcroucher

  committed
  7c540cd

Commits on Nov 23, 2020

• Integrate pyjar into reconstruction

  nickjcroucher

  committed
  a6064f1

• Enable mar

  nickjcroucher

  committed
  d318008

Commits on Nov 24, 2020

• Remove unnecessary pyjar code

  nickjcroucher

  committed
  653892d

• Improve efficiency of alignment processing

  nickjcroucher

  committed
  b84c3a6

• Extract function for reconstructing individual columns

  nickjcroucher

  committed
  55a39de

• Tidy up column reconstruction

  nickjcroucher

  committed
  0bc2839

• Convert base reconstruction to pool

  nickjcroucher

  committed
  0ea6235

• Prepare for sharedmem implementation

  nickjcroucher

  committed
  4ffb71d

• Pass through number of threads to use to pyjar

  nickjcroucher

  committed
  9833e0a

• Parallelisation used shared memory

  nickjcroucher

  committed
  37097ad

• Improve parallelisation job definition

  nickjcroucher

  committed
  912c765

• Improve phylogeny SNP detection

  nickjcroucher

  committed
  b015280

Commits on Nov 25, 2020

• Changed access to shared memory object

  nickjcroucher

  committed
  07e5f53

• Improve efficiency of new alignment creation

  nickjcroucher

  committed
  91e25d6

• Heuristic for faster reconstruction

  nickjcroucher

  committed
  0ae23cd

• Tidy up parallelisation code

  nickjcroucher

  committed
  5f6fd3e

• Enable use of iqtree

  nickjcroucher

  committed
  b1e2286

• Enable ASR with fasttree

  nickjcroucher

  committed
  7456ad8

• Add validation for parameter value extraction

  nickjcroucher

  committed
  e22c4f8

• Controlled parameterisation of Fasttree

  nickjcroucher

  committed
  39efe88

Commits on Nov 26, 2020

• Enable use of rapidnj

  nickjcroucher

  committed
  31a94a8

• Enable use of raxml to fit models

  nickjcroucher

  committed
  45bd236

• Enable model fitting with fasttree

  nickjcroucher

  committed
  5ee84db

• Reorganise help message

  nickjcroucher

  committed
  d00dc13

Commits on Nov 27, 2020

• More flexible algorithm selection

  nickjcroucher

  committed
  b0cd491

Commits on Nov 28, 2020

• Added flexibility to Fasttree

  nickjcroucher

  committed
  049d1ec

• Allow for use of different substitution models with fasttree

  nickjcroucher

  committed
  3f1fc82

• Altered model options for raxml

  nickjcroucher

  committed
  84664ea

• Fix RAxML naming clash

  nickjcroucher

  committed
  51d1c7e

• Update rapidnj object

  nickjcroucher

  committed
  3461b36

• Allow for selection of initial tree builder

  nickjcroucher

  committed
  487c563

Commits on Nov 29, 2020

• Added option to use a starting star phylogeny

  nickjcroucher

  committed
  f4e81a5

• Enable pairwise comparisons

  nickjcroucher

  committed
  b0449ef

• Add nucleotide substitution models

  nickjcroucher

  committed
  61a668c

• Allow more flexible use of substitution models

  nickjcroucher

  committed
  eecdc17

Commits on Nov 30, 2020

• Process input arguments sensibly

  nickjcroucher

  committed
  6c1b1fc

Commits on Dec 2, 2020

• Update tree building command line options

  nickjcroucher

  committed
  66507ab

• Reconstruct sequences on optimised tree

  nickjcroucher

  committed
  020ecb0

• Use unrooted tree for IQtree ASR

  nickjcroucher

  committed
  47ce42a

Commits on Dec 3, 2020

• Tidy up unrooting function

  nickjcroucher

  committed
  8e99b08

• Fix for pyjar

  nickjcroucher

  committed
  e9bf2ca

Commits on Dec 4, 2020

• Minor code tidying

  nickjcroucher

  committed
  48da88e

Commits on Dec 5, 2020

• Shared memory for base positions

  nickjcroucher

  committed
  23ad59a

Commits on Dec 6, 2020

• Improved use of numpy data structures

  nickjcroucher

  committed
  d341ad7

• Merge pull request #2 from nickjcroucher/numpy_base_patterns

  Show description for f78d43d
  nickjcroucher

  authored
  f78d43d

• Merge pull request #4 from nickjcroucher/numpy_base_patterns

  Show description for c95e6a5
  nickjcroucher

  authored
  c95e6a5

• Simplify numpy data processing

  nickjcroucher

  committed
  975685d

• Merge pull request #5 from nickjcroucher/numpy_base_patterns

  Show description for 75e30e5
  nickjcroucher

  authored
  75e30e5

• Tidy up parallelisation

  nickjcroucher

  committed
  a4b0f5d

• Enable greater flexibility in model selection

  nickjcroucher

  committed
  d8f2828

• Allow input of custom models

  nickjcroucher

  committed
  e376f09

Commits on Dec 7, 2020

• Allow extra arguments to be passed to algorithms

  nickjcroucher

  committed
  acabc1a

• Added bootstrapping for rapidnj

  nickjcroucher

  committed
  ed3b6ea

• Add raxml bootstrapping

  nickjcroucher

  committed
  7641e29

Commits on Dec 8, 2020

• Add iqtree bootstrap

  nickjcroucher

  committed
  6b76dde

• Tidy up raxml bootstraps

  nickjcroucher

  committed
  f191407

• Rapidnj bootstrap tidied up

  nickjcroucher

  committed
  c58c111

• Add Fasttree bootstrapping

  nickjcroucher

  committed
  fb37b4b

• Add SH tests for ML methods

  nickjcroucher

  committed
  2930ff2

• Tidy up iqtree SH tests

  nickjcroucher

  committed
  1bd685c

• Add input argument processing

  nickjcroucher

  committed
  ab51d82

• Tidy up shared memory objects

  nickjcroucher

  committed
  8e909e7

• Tidy up input options

  nickjcroucher

  committed
  82e984c

• Add installation requirements needed for shared memory objects

  nickjcroucher

  committed
  90f460f

Commits on Dec 9, 2020

• Increase python version

  nickjcroucher

  committed
  32266ae

• Further checking of input arguments

  nickjcroucher

  committed
  f34c4fe

Commits on Dec 11, 2020

• Added in raxmlng as a tree builder

  nickjcroucher

  committed
  0c135a2

• Enable sequence reconstruction with RAxML-NG

  nickjcroucher

  committed
  72e6cf0

• Enable sequence reconstruction with RAxML-NG

  nickjcroucher

  committed
  26ea7af

• Enable bootstraps with RAxML-NG

  nickjcroucher

  committed
  183e1ad

• Bootstrap annotation using RAxML-NG as a utility

  nickjcroucher

  committed
  92bea14

• Add transfer bootstrap expectation

  nickjcroucher

  committed
  611ff45

• Simplify alignment naming

  nickjcroucher

  committed
  97c7d0a

• Simplify reconstruction filename code

  nickjcroucher

  committed
  0919caa

Commits on Dec 13, 2020

• Simplify bootstrap command

  nickjcroucher

  committed
  669a042

• Tidy up pyjar code

  nickjcroucher

  committed
  62d0ee7

Commits on Dec 17, 2020

• Add methods logging

  nickjcroucher

  committed
  c646c53

• Minor fixes to file names

  nickjcroucher

  committed
  1204660

• Allow for a different model fitter

  nickjcroucher

  committed
  26104eb

Commits on Dec 18, 2020

• Simplify algorithm selection code

  nickjcroucher

  committed
  58e8565

• Merge branch 'master' into pyjar

  nickjcroucher

  authored
  d994063

• Merge pull request #6 from nickjcroucher/pyjar

  Show description for e817f2d
  nickjcroucher

  authored
  e817f2d

• Merge branch 'master' of https://github.com/sanger-pathogens/gubbins into sanger-pathogens-master

  Show description for b0261b0
  nickjcroucher

  committed
  b0261b0

• Resolve conflicts before merging with original repository

  nickjcroucher

  committed
  8399ebd

• Update dependency installation script

  nickjcroucher

  committed
  5829f1c

• Apply patch gubbins_exe_in_usr_lib.patch

  nickjcroucher

  committed
  4a9835f

• Merge pull request #8 from nickjcroucher/patching

  Show description for 9cef4bd
  nickjcroucher

  authored
  9cef4bd

Commits on Dec 19, 2020

• Update dockerfile

  nickjcroucher

  committed
  890aa8f

• Merge pull request #9 from nickjcroucher/docker

  Show description for 1d578f1
  nickjcroucher

  authored
  1d578f1

Commits on Dec 20, 2020

• Apply patch spelling-error-in-binary.patch

  nickjcroucher

  committed
  ccc7a52

• Merge pull request #10 from nickjcroucher/patching

  Show description for f608316
  nickjcroucher

  authored
  f608316

• Update tree builder versions in Dockerfile

  nickjcroucher

  committed
  c456cc7

• Merge pull request #11 from nickjcroucher/docker

  Show description for 57b6887
  nickjcroucher

  authored
  57b6887

• Github actions for CI

  nickjcroucher

  committed
  e510adb

• Temporary testing change

  nickjcroucher

  committed
  9f0ed1f

• Remove travis CI

  nickjcroucher

  committed
  5e6bfdd

Commits on Dec 21, 2020

• Add Github actions yml

  nickjcroucher

  committed
  c37781a

• Reformat python test

  nickjcroucher

  committed
  169f6bf

• Define linux test

  nickjcroucher

  committed
  4735edc

• Remove missing packages from environment.yml

  nickjcroucher

  committed
  54dd44f

• Change check installation

  nickjcroucher

  committed
  116bdb3

Commits on Dec 22, 2020

• Change check installation

  nickjcroucher

  committed
  b1f8ea4

• Remove old test command file

  nickjcroucher

  committed
  04f64c4

• Use sudo for installation of check

  nickjcroucher

  committed
  2085131

• Use autoreconf for check installation

  nickjcroucher

  committed
  31d3201

• Install subunit as part of checks

  nickjcroucher

  committed
  de77725

• Fix to subunit installation

  nickjcroucher

  committed
  1b9c005

• Add cpuunit installation

  nickjcroucher

  committed
  3b9ba29

• Change cpuunit installation

  nickjcroucher

  committed
  9b70abf

• Add cpuunit configuration

  nickjcroucher

  committed
  8129a8a

• Reorder installations

  nickjcroucher

  committed
  92f937c

Commits on Dec 23, 2020

• Ensure C++ tests use defined, non-obsolete functions

  nickjcroucher

  committed
  c089291

• Edit ck_assert commands

  nickjcroucher

  committed
  fc01de8

Commits on Dec 27, 2020

• Add OSX test

  nickjcroucher

  committed
  0ed2ed4

• Change conda location in OSX test

  nickjcroucher

  committed
  379cd98

• Add conda install automake autoconf libtool for OSX

  nickjcroucher

  committed
  1745220

• Add conda install pkg-config openssl libevent for OSX

  nickjcroucher

  committed
  dd3c16a

• Add conda install berkeley-db4 boost boost-build for OSX

  nickjcroucher

  committed
  7d3e540

• Remove missing packages for conda install for OSX

  nickjcroucher

  committed
  6e37d4e

• Use apt install for OSX

  nickjcroucher

  committed
  7f954d5

• Use homebrew install for OSX

  nickjcroucher

  committed
  94a317b

• Add wheel as dependency

  nickjcroucher

  committed
  01c0b12

• Add wheel as a conda dependency

  nickjcroucher

  committed
  7b04310

• Add wheel to setup.py

  nickjcroucher

  committed
  cf4d2e6

• Add pip install wheel to setup.py

  nickjcroucher

  committed
  f28af88

• Add pip install scipy to setup.py

  nickjcroucher

  committed
  eab6336

• Update python test scripts

  nickjcroucher

  committed
  04ee185

• Use pytest

  nickjcroucher

  committed
  6a2ff08

• Fix conda env name

  nickjcroucher

  committed
  fed7d7e

Commits on Dec 28, 2020

• Change conda use for installation

  nickjcroucher

  committed
  a83cf24

• Change cppunit installation

  nickjcroucher

  committed
  b1be526

• Change cppunit installation

  nickjcroucher

  committed
  7ae1c76

• Change subunit configuration

  nickjcroucher

  committed
  1ff1087

• Change subunit cppunit flags

  nickjcroucher

  committed
  80797a0

• Use installation from source

  nickjcroucher

  committed
  fa8207c

Commits on Dec 29, 2020

• Add dendropy as a dependency and change error reporting

  nickjcroucher

  committed
  782f69a

• Additions to env

  nickjcroucher

  committed
  c1c6b83

• Remove functools from env

  nickjcroucher

  committed
  de10a3d

• Change libcheck install prefix

  nickjcroucher

  committed
  46d9482

• Change libcheck install prefix to conda env

  nickjcroucher

  committed
  4568afc

• Add conda to make search path

  nickjcroucher

  committed
  0b8ff4a

• Reformat flags for libtools

  nickjcroucher

  committed
  cc088dd

• Restore cppunit source installation for OSX

  nickjcroucher

  committed
  5c58d13

• Change library search path

  nickjcroucher

  committed
  50682c3

• Consistent install paths for OSX

  nickjcroucher

  committed
  7849018

Commits on Dec 30, 2020

• Add further flags for subunit

  nickjcroucher

  committed
  ba95462

• Add further flags for subunit

  nickjcroucher

  committed
  b46873d

• Add flags to gubbins configure

  nickjcroucher

  committed
  0945650

• Fix gubbins configure flags

  nickjcroucher

  committed
  b2ae16e

Commits on Dec 31, 2020

• Change gubbins make flags for OSX

  nickjcroucher

  committed
  c26bffd

• Remove source installations from OSX

  nickjcroucher

  committed
  619ab07

• Change flags to autoconfigure

  nickjcroucher

  committed
  d20d791

• Change flags to autoconfigure for Linux

  nickjcroucher

  committed
  07c84b8

Commits on Jan 1, 2021

• Remove rendundancy in installation

  nickjcroucher

  committed
  62ed708

• Edit flags for Linux installation

  nickjcroucher

  committed
  1017f00

• Edit flags for cppunit Linux installation

  nickjcroucher

  committed
  a309851

• Restore cppunit Linux installation

  nickjcroucher

  committed
  db3bb62

• Restore cppunit installation

  nickjcroucher

  committed
  c2b08d1

• Fix cppunit installation

  nickjcroucher

  committed
  116977d

• Remove unnecessary packages

  nickjcroucher

  committed
  a4e9a6c

• Prepare for merge with master

  nickjcroucher

  committed
  4f5c084

• Merge pull request #12 from nickjcroucher/ci_switch

  Show description for 6b4883d
  nickjcroucher

  authored
  6b4883d

• Test how many errors are due to version not being established

  nickjcroucher

  committed
  966f78a

• Remove obsolete tests

  nickjcroucher

  committed
  910e463

• Update expected file outputs

  nickjcroucher

  committed
  f00ace0

• Inactivate test for 3 sequences in alignment

  nickjcroucher

  committed
  f9c0c52

• Update test tree builders

  nickjcroucher

  committed
  113d85b

• Change tree_method file names

  nickjcroucher

  committed
  5c9acbd

Commits on Jan 2, 2021

• Make test tree names consistent

  nickjcroucher

  committed
  72dcaea

• Update comparator for midpoint rooting tests

  nickjcroucher

  committed
  ce424ab

• Update bifurcation test result

  nickjcroucher

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  5b6c8b7

Commits on Jan 3, 2021

• Move test file

  nickjcroucher

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  46a89a8

• Pass extra arguments to IQtree builder in test

  nickjcroucher

  committed
  ee2b692

• Fix prefix for RAxML reconstruction

  nickjcroucher

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  0d97fd5

• Update package metadata

  nickjcroucher

  committed
  b20aa88

• Fix clean up test

  nickjcroucher

  committed
  2be3dbb

Commits on Jan 4, 2021

• Fix to Debian bug #971111

  nickjcroucher

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  cc4d718

• Remove pkg_resources dependency

  nickjcroucher

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  df93d33

• Update regex search strings

  nickjcroucher

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  1b91b8e

• Restore pkg_resources as dependency of subunit

  nickjcroucher

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  256c58c

• Fix environment.yml typo

  nickjcroucher

  committed
  320c5b8

• Restore working linux subunit installation

  nickjcroucher

  committed
  3960c7b

• Remove pkg_resources error

  nickjcroucher

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  156857c

• Update linux installation commands

  nickjcroucher

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  60bace2

• Change imports into common.py

  nickjcroucher

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  a1d2f1a

• Fix description function

  nickjcroucher

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  7ff1ffb

• Change codecov installation on linux

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  4d94df4

• Change version handling

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  cbfec18

• Update codecov settings

  nickjcroucher

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  dbf1f77

• Add installation of pytest-cov

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  b3313da

• Remove codecov command

  nickjcroucher

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  76fbea3

• Move run_gubbins.py

  nickjcroucher

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  5e35e9e

• Fix raxmlng model fitting file names

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  be6ae19

• Remove unnecessary import

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• Remove unneeded file

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• Add model fitting tests

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  d5eccea

• Remove obsolete scripts directory

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• Restructure runner script

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  1d2d105

• Change version retrieval

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  24379be

Commits on Jan 5, 2021

• Remove scripts dir reference from makefile

  nickjcroucher

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  76e6e0b

• Fix null pointer warning in test

  nickjcroucher

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  526500c

• Bump version

  nickjcroucher

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  856a1cb

• Change to python 3.x and fix ambiguous test

  nickjcroucher

  committed
  b7dac21

• Fix code coverage command for python tests

  nickjcroucher

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  496cb05

• Change coverage calculation for python code

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  ebc52d4

• Change python testing to use consistent python version

  nickjcroucher

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  5d220dd

• Change paths for testing files

  nickjcroucher

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  a32154c

• Change handling of file paths in tests

  nickjcroucher

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  817a1da

• Further fixes to test data paths

  nickjcroucher

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  68083f6

• Make tests give verbose outputs

  nickjcroucher

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  d0dcf8a

• Extra clean up for tests

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  01ea19a

• Extra clean up for tests

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  affad5f

• Make clean up test verbose

  nickjcroucher

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  3180e27

• Fix clean up test

  nickjcroucher

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  30221f6

• Test for RAxML-specific problems

  nickjcroucher

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  6cc85a7

• Exit when unable to find suitable RAxML software

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  2e21266

• Define working directory

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  7895b7e

• Refine clean up function

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  d72efa3

• Fix clean up function

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  eb3a880

• Fix clean up function

  nickjcroucher

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  7c3048e

• Multi-thread tests

  nickjcroucher

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  12b9189

• Update code for selecting RAxML algorithm based on CPU

  nickjcroucher

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  3e478b2

• Simplify code coverage upload

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  83f4316

Commits on Jan 6, 2021

• Change names of intermediate files

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  0dbe412

• Introduce bootstrapping tests

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  e7b7fb4

Commits on Jan 7, 2021

• Update help message

  nickjcroucher

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Commits on Jan 19, 2021

• Use shutil to move file

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  cf21522

• Remove Makefile.in

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  2377005

• Specify versions in environment.yml

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  aa75c84

• Add missing dependencies to installation files

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• Improve memory management error message

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  77883a8

• Change menu options

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• apt-get only run with Linux

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  35b99bb

• Remove downloaded files

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  8964a69

• Make raxmlng test more stable

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  35ee8fe

Commits on Jan 25, 2021

• Clarify menu options

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  688425d

• Remove version from __init__

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  f355825

• Add to path for package search

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• Append to PATH before installation

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  abed3bc

• Edit threads argument description

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  a9c9026

Commits on Jan 27, 2021

• Merge version information

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  4474151

• Add make install to testing

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  cae86c5

• Try sudo install

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  5c87c32

• Change install prefix

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  1be6b5b

• Tidy up installation and version parsing

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