Merge branch 'crsl4:master' into master

.github/workflows/CompatHelper.yml

@@ -13,4 +13,5 @@ jobs:
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
         run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -12,3 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -0,0 +1,70 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1' # will expand to the latest stable 1.x release of Julia.
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib" >> $GITHUB_ENV
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - name: install dependencie
+        run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - name: make docs
+        run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -27,12 +27,12 @@ StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
 [compat]
 BioSequences = "2.0"
-BioSymbols = "4.0"
+BioSymbols = "4.0, 5"
 CSV = "0.4, 0.5, 0.6, 0.7, 0.8"
 Combinatorics = "0.7, 1.0"
 DataFrames = "0.21, 0.22, 1.0"
 DataStructures = "0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18"
-Distributions = "0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24"
+Distributions = "0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 FASTX = "1.1"
 GLM = "1.1, 1.2, 1.3, 1.4"
 NLopt = "0.5.1, 0.6"

README.md

@@ -1,6 +1,6 @@
 # PhyloNetworks: analysis for phylogenetic networks <img src="docs/src/logo_text.png" align=right>
 
-[![Build Status](https://travis-ci.com/crsl4/PhyloNetworks.jl.svg?branch=master)](https://travis-ci.com/crsl4/PhyloNetworks.jl)
+[![Build status](https://github.com/crsl4/PhyloNetworks.jl/workflows/CI/badge.svg?branch=master)](https://github.com/crsl4/PhyloNetworks.jl/actions/workflows/ci.yml)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/stable)
 [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/dev)
 [![codecov](https://codecov.io/gh/crsl4/PhyloNetworks.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/crsl4/PhyloNetworks.jl)

docs/Project.toml

@@ -4,7 +4,7 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
-# will be added by Travis as being developed:
+# will be added by the CI platform as being developed:
 # PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
 # will be added to track master version in make.jl:
 # PhyloPlots = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"

docs/readme.md

@@ -7,7 +7,7 @@
 
 ## how it works: overview
 
-- `.travis.yml` asks to start the doc project
+- `.github/workflows/ci.yml` asks to start the doc project
   (installs R and dependencies like `PhyloPlots` & `Documenter`) and
   run `./docs/make.jl` after a successful test & build.
 - the julia script `docs/make.jl` has these steps:
@@ -42,11 +42,9 @@ is run in its own anonymous Modules.
 
 Some of these blocs may contain plots, which are going to be drawn during the
 process, requiring the use of `PhyloPlots` along with `RCall`. Hence,
-before the doc is built, the script `.travis.yml` installs `R` on the server,
+before the doc is built, `.github/workflows/ci.yml` installs `R` on the server,
 sets up the julia environment with dependencies like `PhyloPlots` before
 starting the build in itself.
-Note that, for an unknown reason, `R` must be installed *outside* of (the former) `make.sh`,
-in the main body of `.travis.sh`.
 
 ### Directory of the plots
 
@@ -130,116 +128,3 @@ big difference:
 The first version will look for a *section* header "blabla", to link to that section.
 The secon version will look for a *function* named "blabla",
 to link to the documentation for that function.
-
-## earlier versions
-
-### weave
-
-[`Weave`](https://github.com/mpastell/Weave.jl) was used to format the
-documentation pages until PhyloNetworks v0.7.0
-(see [v0.7.0 doc](http://crsl4.github.io/PhyloNetworks.jl/v0.7.0/)),
-and the saving of the plots on the Git repository was handled with an
-extra Travis environment variable DRAW_FIG.
-Instructions about this previous previous setup can be found in this very
-[docs/readme file, in v0.7.0](https://github.com/crsl4/PhyloNetworks.jl/blob/v0.7.0/docs/readme.md).
-An extra step used file [make_weave.jl](https://github.com/crsl4/PhyloNetworks.jl/blob/v0.7.0/docs/src/man/src/make_weave.jl).
-
-### mkdocs
-
-[MkDocs](http://www.mkdocs.org) was used to format the documentation pages until
-PhyloNetworks [v0.8.0](http://crsl4.github.io/PhyloNetworks.jl/v0.8.0/).
-For this:
-- `makedocs( ..., format = Markdown(), ...)`
-  created vanilla "GitHub md" files only (no html conversion),
-- `deploydocs` called `mkdocs` to turn the markdown files in `docs/build/*.md` into html files:
-
-        deploydocs(
-            repo = ...,
-            deps= Deps.pip("pygments", "mkdocs==0.17.5", "mkdocs-material==2.9.4", "python-markdown-math"),
-            make = () -> run(`mkdocs build`),
-            target = "site" # which files get copied to gh-pages
-        )
-
-    problem: Travis uses python 2, but mkdocs v1.0 needs python 3.
-  Versions of `mkdocs` and `mkdocs-material` specified manually to avoid conflicts,
-  See https://discourse.julialang.org/t/mkdocs-material-in-documenter/13764/3
-- In this conversion, the `mkdocs-material` package was used, for its "material" theme,
-  via configuration in the `mkdocs.yml` file, in `docs/`:
-
-
-```yml
-# this is for MkDocs, to turn the .md files produced by Documenter into .html files
-site_name:        PhyloNetworks.jl
-repo_url:         https://github.com/crsl4/PhyloNetworks.jl
-site_description: PhyloNetworks is a Julia package for the manipulation, visualization and inference of phylogenetic networks.
-site_author:      Claudia Solís-Lemus
-
-theme:
-  name: 'material'
-  palette:
-    primary: 'teal'
-    accent:  'teal'
-  logo: 'snaq_small.png'
-
-extra_css:
-  - assets/Documenter.css
-
-extra_javascript:
-  - https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML
-  - assets/mathjaxhelper.js
-
-markdown_extensions:
-  - extra
-  - tables
-  - fenced_code
-  - mdx_math
-  - codehilite
-
-docs_dir: 'build'
-
-nav:
-  - Home: index.md
-  - Manual:
-    - Installation: man/installation.md
-    - Input Data for SNaQ: man/inputdata.md
-    - TICR pipeline: man/ticr_howtogetQuartetCFs.md
-    - Network estimation and display: man/snaq_plot.md
-    - Network comparison and manipulation: man/dist_reroot.md
-    - Candidate Networks: man/fixednetworkoptim.md
-    - Extract Expected CFs: man/expectedCFs.md
-    - Bootstrap: man/bootstrap.md
-    - Multiple Alleles: man/multiplealleles.md
-    - Continuous Trait Evolution: man/trait_tree.md
-    - Parsimony on networks: man/parsimony.md
-  - Library:
-    - Public: lib/public.md
-    - Internals: lib/internals.md
-```
-
-to check/install MkDocs:
-
-```shell
-pip install --upgrade pip
-pip install --upgrade mkdocs
-pip install --upgrade mkdocs-material
-pip install --upgrade python-markdown-math
-```
-and check the installed versions:
-(in comments are versions that work okay together):
-```shell
-python --version # Python 3.5.5 :: Anaconda, Inc.
-mkdocs --version              # v0.17.4  v1.0.4
-pip show mkdocs-material      # v2.9.2   v3.2.0
-pip show Pygments             # v2.2.0   v2.3.1
-pip show pymdown-extensions   # v4.11    v4.11
-pip show python-markdown-math # v0.6     v0.6
-```
-
-then use mkdocs to build the site.
-this step creates a `site/` directory with html files.
-they can be viewed at http://127.0.0.1:8000 (follow instructions)
-
-```shell
-mkdocs build
-mkdocs serve
-```

test/test_phyLiNCoptimization.jl

@@ -251,12 +251,11 @@ for nohybridladder in [true, false]
     =#
     obj = PhyloNetworks.StatisticalSubstitutionModel(net, fastasimple, :JC69)
     obj.loglik = -Inf # missing otherwise, which would cause an error below
-    nullio = open("/dev/null", "w")
     γcache = PhyloNetworks.CacheGammaLiNC(obj)
     lcache = PhyloNetworks.CacheLengthLiNC(obj, 1e-6,1e-6,1e-2,1e-3, 5)
     @test_nowarn PhyloNetworks.phyLiNCone!(obj, 1, no3cycle,
             nohybridladder, 3, 2, false, false,
-            nullio, seed, 0.5, emptyconstraint,
+            devnull, seed, 0.5, emptyconstraint,
             1e-2, 1e-2, 1e-2, 1e-2, 0.0, 25.0, 0.01,0.9,
             γcache, lcache)
     @test obj.loglik > -27.45
@@ -335,11 +334,10 @@ end
 PhyloNetworks.setalpha!(obj.ratemodel, 0.48438)
 obj.loglik = -Inf # actual likelihood -56.3068141288164. Need something non-missing
 seed = 103
-nullio = open("/dev/null", "w")
 γcache = PhyloNetworks.CacheGammaLiNC(obj)
 lcache = PhyloNetworks.CacheLengthLiNC(obj, 1e-2,1e-2,1e-2,1e-2, 5)
 @test_nowarn PhyloNetworks.phyLiNCone!(obj, 2, true, true,
-        3, 2, false, false, nullio,
+        3, 2, false, false, devnull,
         seed, 0.5, c_species, 1e-2, 1e-2,
         1e-2, 1e-2, 0.0,50.0, 0.01,.9, γcache, lcache)
 @test obj.loglik > -65.4 # -65.0 with RNG from julia 1.5