diff --git a/.travis.yml b/.travis.yml index 373a2ad..e0ad769 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,9 +4,8 @@ os: - windows - osx julia: - - 1.0 - - 1.3 - #- nightly + - 1.2 + - 1.5 notifications: email: false addons: diff --git a/NEWS.md b/NEWS.md index cb148d9..c454655 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,18 @@ # master (unpublished) - no changes -# v0.16.0 (latest) +# v0.17.0 (latest) + +### general +- Julia versions < 1.2 are no longer supported; this change was necessary for the interleaved parallelism +overhaul in this version +- the interleaved parallelism backend got fixed to properly support changes introduced in Julia 1.2; +it now runs more stably and features better error reporting + +### bug fixes +- fixed occasional hangs when computing networks in parallel via the interleaved mode (issue #9) + +# v0.16.0 ### general - add explicit parallelism flag (`parallel_mode`) to `learn_network` to avoid having to remove workers when switching from multi-core to single-core computations diff --git a/Project.toml b/Project.toml index 8f2b884..9f0f05a 100644 --- a/Project.toml +++ b/Project.toml @@ -4,7 +4,7 @@ keywords = ["metagenomics", "microbiome", "probabilistic-graphical-models", "hig license = "GPL-3.0" desc = "Inference of microbial interaction networks from large-scale heterogeneous abundance data" authors = ["Janko Tackmann "] -version = "0.16.0" +version = "0.17.0" [deps] Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" @@ -37,7 +37,7 @@ JSON = "0.21" LightGraphs = "1" SimpleWeightedGraphs = "1" StatsBase = "0.32" -julia = "1" +julia = "1.2" [extras] DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" diff --git a/README.md b/README.md index 9637a66..77e57a7 100644 --- a/README.md +++ b/README.md @@ -9,15 +9,21 @@ FlashWeave predicts ecological interactions between microbes from large-scale co ## Installation ## -To install Julia, please follow instructions on https://github.com/JuliaLang/julia. The preferred way is to obtain a binary from https://julialang.org/downloads/. Make sure you install Julia 1.0 or above, the versions currently supported by FlashWeave. +To install Julia, please follow instructions on https://github.com/JuliaLang/julia. The preferred way is to obtain a binary from https://julialang.org/downloads/. Make sure you install Julia 1.2 or above, the versions currently supported by FlashWeave. In an interactive Julia session, you can then install FlashWeave after typing `]` via ```julia -(v1.0) pkg> add FlashWeave -# to run tests: (v1.0) pkg> test FlashWeave +(v1.2) pkg> add FlashWeave +# to run tests: (v1.2) pkg> test FlashWeave ``` +**Important note: from version 0.17, FlashWeave dropped support for Julia versions < 1.2. If you want to use FlashWeave with older Julia installations, make sure to install FlashWeave 0.16.0 (or lower) via `]` + `add FlashWeave@0.16.0`.** + +## Latest changes ## + +See [NEWS.md](https://github.com/meringlab/FlashWeave.jl/blob/master/NEWS.md) for the latest features and bugfixes. + ## Basic usage ## To learn an interaction network from an OTU table and (optionally) a meta data table, you can do diff --git a/test/io.jl b/test/io.jl index 6efce0b..f6281af 100644 --- a/test/io.jl +++ b/test/io.jl @@ -60,7 +60,6 @@ end end @testset "unfinished states" begin - println(tmp_path * "_unchecked.tsv") unf_dict_ld = FlashWeave.load_unfinished_variable_info(tmp_path * "_unchecked.tsv") @test begin all(all(getproperty(unf_dict_ld[i], p) == getproperty(unf_dict[i], p)