Merge branch 'master' into tgf/softmax_docs

.github/workflows/CompatHelper.yml

@@ -1,20 +1,38 @@
-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"
@@ -25,3 +43,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

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"

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 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
 
 
 ### `NBParamMean` types with `μ = invlink(f)` the mean/expected number of events

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"