From e069dced107f65bc70db35e65ed14ed9ec5ab68f Mon Sep 17 00:00:00 2001 From: Will Tebbutt Date: Thu, 23 Feb 2023 12:26:59 +0000 Subject: [PATCH 1/5] update compat helper Upgrades compat helper to the latest version of the GHA --- .github/workflows/CompatHelper.yml | 27 +++++++++++++++++++++++---- 1 file changed, 23 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index ec31a788..93674ca4 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.github/workflows/CompatHelper.yml @@ -1,27 +1,46 @@ -name: CompatHelper +name: CompatHelper on: schedule: - cron: 0 0 * * * workflow_dispatch: - +permissions: + contents: write + pull-requests: write jobs: CompatHelper: runs-on: ubuntu-latest steps: + - name: Check if Julia is already available in the PATH + id: julia_in_path + run: which julia + continue-on-error: true + - name: Install Julia, but only if it is not already available in the PATH + uses: julia-actions/setup-julia@v1 + with: + version: '1' + arch: ${{ runner.arch }} + if: steps.julia_in_path.outcome != 'success' + - name: "Add the General registry via Git" + run: | + import Pkg + ENV["JULIA_PKG_SERVER"] = "" + Pkg.Registry.add("General") + shell: julia --color=yes {0} - name: "Install CompatHelper" run: | import Pkg name = "CompatHelper" uuid = "aa819f21-2bde-4658-8897-bab36330d9b7" - version = "2" + version = "3" Pkg.add(; name, uuid, version) shell: julia --color=yes {0} - name: "Run CompatHelper" run: | import CompatHelper - CompatHelper.main(; subdirs=["", "test", "docs"]) + CompatHelper.main() shell: julia --color=yes {0} env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }} + # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }} From f40bdee2c5d2fd44038aa722e6c26f85a47fb641 Mon Sep 17 00:00:00 2001 From: Will Tebbutt Date: Thu, 23 Feb 2023 12:52:39 +0000 Subject: [PATCH 2/5] Update .github/workflows/CompatHelper.yml Co-authored-by: David Widmann --- .github/workflows/CompatHelper.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index 93674ca4..4a99410c 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.github/workflows/CompatHelper.yml @@ -38,7 +38,7 @@ jobs: - name: "Run CompatHelper" run: | import CompatHelper - CompatHelper.main() + CompatHelper.main(; subdirs=["", "test", "docs"]) shell: julia --color=yes {0} env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From 33c0c1788ab031bbd4bd7ba84836ffebe88bc7bd Mon Sep 17 00:00:00 2001 From: Will Tebbutt Date: Thu, 23 Feb 2023 14:46:18 +0000 Subject: [PATCH 3/5] Bump patch and compat --- Project.toml | 8 ++++---- test/Project.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Project.toml b/Project.toml index 9d4554f1..91847a90 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "GPLikelihoods" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" authors = ["JuliaGaussianProcesses Team"] -version = "0.4.5" +version = "0.4.6" [deps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" @@ -19,10 +19,10 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [compat] ChainRulesCore = "1.7" Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25" -FastGaussQuadrature = "0.4" -Functors = "0.1, 0.2, 0.3" +FastGaussQuadrature = "0.4, 0.5" +Functors = "0.1, 0.2, 0.3, 0.4" InverseFunctions = "0.1.2" -IrrationalConstants = "0.1" +IrrationalConstants = "0.1, 0.2" SpecialFunctions = "1, 2" StatsFuns = "0.9.13, 1" julia = "1.6" diff --git a/test/Project.toml b/test/Project.toml index fe7dde87..6e2c7758 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -8,7 +8,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25" -Functors = "0.1, 0.2, 0.3" +Functors = "0.1, 0.2, 0.3, 0.4" StatsFuns = "0.9, 1" Zygote = "0.6" julia = "1.3" From 942c68ee2bed3b8c615eddde7de31fa27eee7bbb Mon Sep 17 00:00:00 2001 From: Simone Carlo Surace <51025924+simsurace@users.noreply.github.com> Date: Sat, 2 Sep 2023 15:00:21 +0200 Subject: [PATCH 4/5] Remove outdated comment about Wikipedia Related to https://github.com/JuliaStats/Distributions.jl/pull/1734 --- src/likelihoods/negativebinomial.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/likelihoods/negativebinomial.jl b/src/likelihoods/negativebinomial.jl index f663d4c0..df2873cb 100644 --- a/src/likelihoods/negativebinomial.jl +++ b/src/likelihoods/negativebinomial.jl @@ -18,9 +18,9 @@ defines in what parametrization the latent function is used, and contains the ot ## `NBParam` predefined types -### `NBParamProb` types with `p = invlink(f)` the probability of success -- [`NBParamSuccess`](@ref): This is the definition used in [`Distributions.jl`](https://juliastats.org/Distributions.jl/latest/univariate/#Distributions.NegativeBinomial). -- [`NBParamFailure`](@ref): This is the definition used in [Wikipedia](https://en.wikipedia.org/wiki/Negative_binomial_distribution). +### `NBParamProb` types with `p = invlink(f)` the probability of success/failure +- [`NBParamSuccess`](@ref): Here `p = invlink(f)` is the probability of success. This is the definition used in [`Distributions.jl`](https://juliastats.org/Distributions.jl/latest/univariate/#Distributions.NegativeBinomial). +- [`NBParamFailure`](@ref): Here `p = invlink(f)` is the probability of a failure ### `NBParamMean` types with `μ = invlink(f)` the mean/expected number of events From f54c19f0bbbcba6f79fc454f44674180af2741ce Mon Sep 17 00:00:00 2001 From: Simone Carlo Surace <51025924+simsurace@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:52:48 +0200 Subject: [PATCH 5/5] Improve wording in docstring --- src/likelihoods/negativebinomial.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/likelihoods/negativebinomial.jl b/src/likelihoods/negativebinomial.jl index df2873cb..d8f78a25 100644 --- a/src/likelihoods/negativebinomial.jl +++ b/src/likelihoods/negativebinomial.jl @@ -18,7 +18,7 @@ defines in what parametrization the latent function is used, and contains the ot ## `NBParam` predefined types -### `NBParamProb` types with `p = invlink(f)` the probability of success/failure +### `NBParamProb` types with `p = invlink(f)` the probability of success or failure - [`NBParamSuccess`](@ref): Here `p = invlink(f)` is the probability of success. This is the definition used in [`Distributions.jl`](https://juliastats.org/Distributions.jl/latest/univariate/#Distributions.NegativeBinomial). - [`NBParamFailure`](@ref): Here `p = invlink(f)` is the probability of a failure