From 741d973f532e82ab25f8a8d7af03e6f085e049c3 Mon Sep 17 00:00:00 2001 From: Richard Reeve Date: Fri, 9 Apr 2021 03:27:09 +0100 Subject: [PATCH] Minor docs and automation fixes --- .github/workflows/docs.yaml | 3 --- .github/workflows/nightly.yaml | 5 ++--- .github/workflows/testing.yaml | 5 ++--- NEWS.md | 7 +++---- Project.toml | 2 +- README.md | 17 ++++++++++------- docs/src/index.md | 7 ++++--- 7 files changed, 22 insertions(+), 24 deletions(-) diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 9693b82a..f9491e3f 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -1,9 +1,6 @@ name: Documentation on: - release: - types: - - published push: branches: - dev diff --git a/.github/workflows/nightly.yaml b/.github/workflows/nightly.yaml index 56f40cf1..43c6d152 100644 --- a/.github/workflows/nightly.yaml +++ b/.github/workflows/nightly.yaml @@ -1,12 +1,11 @@ name: JuliaNightly # Nightly Scheduled Julia Nightly Run on: - release: - types: - - published push: branches: - dev + tags: + - 'v*' schedule: - cron: '0 2 * * 0' # Weekly at 2 AM UTC Sunday diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml index c766e860..35dc1a75 100644 --- a/.github/workflows/testing.yaml +++ b/.github/workflows/testing.yaml @@ -1,12 +1,11 @@ name: CI on: - release: - types: - - published push: branches: - dev + tags: + - 'v*' pull_request: jobs: diff --git a/NEWS.md b/NEWS.md index d4558fbd..3bfdf84e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,8 @@ # NEWS -- v0.4.8 to v0.4.17 - - fixing automation on new releases -- v0.4.7 - - docs +- v0.4.7 to v0.4.18 + - fixed automation on new releases + - documentation updates - v0.4.6 - add sort function, sort! can be reversed - v0.4.5 diff --git a/Project.toml b/Project.toml index baffcf18..10fe9071 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Phylo" uuid = "aea672f4-3940-5932-aa44-993d1c3ff149" author = ["Richard Reeve "] -version = "0.4.17" +version = "0.4.18" [deps] AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" diff --git a/README.md b/README.md index d05dcc9c..3de1fc0d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Phylo -*Package for creating and manipulating phylogenies* +## A package for creating and manipulating phylogenies | **Documentation** | **Build Status** | **DOI** | |:-----------------:|:--------------------------:|:--------------------------:| @@ -18,7 +18,7 @@ installed with `add`. For example: Updating git-repo `https://github.com/JuliaRegistries/General.git` Resolving package versions... Updating `~/.julia/environments/v1.6/Project.toml` - [aea672f4] + Phylo v0.4.7 + [aea672f4] + Phylo v0.4.18 Updating `~/.julia/environments/v1.6/Manifest.toml` (@v1.6) pkg> @@ -26,9 +26,9 @@ installed with `add`. For example: ## Project Status -The package is confirmed to work against the current LTS Julia v1.4 release -and the latest release on Linux, macOS, and Windows. It is also tested -against nightly. +The package is confirmed to work against Julia v1.6, the current LTS Julia +v1.4 release and the latest release on Linux, macOS, and Windows. It is also +tested against nightly. ## Contributing and Questions @@ -159,6 +159,7 @@ julia> tree = open(parsenewick, Phylo.path("H1N1.newick")) RootedTree with 507 tips, 1013 nodes and 1012 branches. Leaf names are 227, 294, 295, 110, 390, ... [501 omitted] ... and 418 ``` + And it can read nexus trees from files too: ```julia @@ -237,7 +238,7 @@ RCall.RObject{RCall.VecSxp} Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: - t10, t8, t1, t2, t6, t5, ... + t10, t8, t1, t2, t6, t5, ... Rooted; includes branch lengths. @@ -259,7 +260,7 @@ R> jt Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: - t10, t8, t1, t2, t6, t5, ... + t10, t8, t1, t2, t6, t5, ... Rooted; includes branch lengths. @@ -306,9 +307,11 @@ julia> d = DataFrame(nodename=getnodename.(tree, traversal(tree, preorder)), tra │ 198 │ tip 71 │ -0.868774 │ │ 199 │ tip 89 │ -0.30126 │ ``` + ![Continuous trait tree plot](docs/img/browniantree.png) Then a discrete trait: + ```julia julia> @enum TemperatureTrait lowTempPref midTempPref highTempPref diff --git a/docs/src/index.md b/docs/src/index.md index 62c3f710..c5cc2208 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,6 +1,6 @@ # Phylo -*A package for creating and manipulating phylogenies* +## A package for creating and manipulating phylogenies **Phylo** is a [Julia](http://www.julialang.org) package that provides functionality for generating phylogenetic trees to feed into our @@ -100,6 +100,7 @@ julia> tree = open(parsenewick, Phylo.path("H1N1.newick")) RootedTree with 507 tips, 1013 nodes and 1012 branches. Leaf names are 227, 294, 295, 110, 390, ... [501 omitted] ... and 418 ``` + And it can read nexus trees from files too: ```julia @@ -155,7 +156,7 @@ RCall.RObject{RCall.VecSxp} Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: - t10, t8, t1, t2, t6, t5, ... + t10, t8, t1, t2, t6, t5, ... Rooted; includes branch lengths. @@ -177,7 +178,7 @@ R> jt Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: - t10, t8, t1, t2, t6, t5, ... + t10, t8, t1, t2, t6, t5, ... Rooted; includes branch lengths.