From efddd1f6b38292830f451495c93e7b892ddb1a7a Mon Sep 17 00:00:00 2001
From: Alex Arslan <ararslan@comcast.net>
Date: Sat, 9 Jul 2022 12:05:15 -0700
Subject: [PATCH 1/4] Don't rely on `Base.promote_op`

Its docstring explicitly says not to. Instead we can query the type of
the result of the operation on values of the given type.
---
 src/cox.jl | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/cox.jl b/src/cox.jl
index 5c08e16..f098d83 100644
--- a/src/cox.jl
+++ b/src/cox.jl
@@ -1,6 +1,6 @@
 # Some utility functions to compute Cox regression
 
-promote_nonmissing(::Type{T}) where {T} = Base.promote_op(/, T, T)
+promote_nonmissing(::Type{T}) where {T} = typeof(one(T) / one(T))
 promote_nonmissing(::Type{Union{T,Missing}}) where {T} = promote_nonmissing(T)
 
 struct CoxSum{T,N}
@@ -132,8 +132,7 @@ function _cox_fgh!(β, grad, hes, c::CoxAux{T}) where T
     update_cox!(c, β, (hes !== nothing) | (grad !== nothing))
     X, ξ, Xβ, θ, Xθ, ξθ, λ, fs, ls  =
         c.X, c.ξ, c.Xβ, c.θ, c.Xθ, c.ξθ, c.λ, c.fs, c.ls
-    R = Base.promote_op(/, T, T)
-    y = zero(R)
+    y = zero(T) / one(T)
 
     if hes !== nothing
         fill!(hes, 0)
@@ -143,7 +142,7 @@ function _cox_fgh!(β, grad, hes, c::CoxAux{T}) where T
     end
     if grad !== nothing || hes !== nothing
         # preallocate
-        Z = zeros(R, length(β))
+        Z = zeros(typeof(y), length(β))
     end
 
     @inbounds for i in 1:length(fs)

From fa54e407bdb7343278167eb94e926b1740da1736 Mon Sep 17 00:00:00 2001
From: Alex Arslan <ararslan@comcast.net>
Date: Sat, 9 Jul 2022 13:50:55 -0700
Subject: [PATCH 2/4] Remove unused dependency on PositiveFactorizations

The switch to Optim from hand-rolled Newton-Raphson removed the only use
of this package.
---
 Project.toml    | 2 --
 src/Survival.jl | 1 -
 2 files changed, 3 deletions(-)

diff --git a/Project.toml b/Project.toml
index e4f6f9b..6ba2afb 100644
--- a/Project.toml
+++ b/Project.toml
@@ -6,7 +6,6 @@ version = "0.2.2"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
-PositiveFactorizations = "85a6dd25-e78a-55b7-8502-1745935b8125"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
@@ -15,7 +14,6 @@ CategoricalArrays = "0.9"
 DataFrames = "1"
 Distributions = "0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 Optim = "1"
-PositiveFactorizations = "0.2"
 StatsBase = "0.30, 0.31, 0.32, 0.33"
 StatsModels = "0.6"
 julia = "1.2"
diff --git a/src/Survival.jl b/src/Survival.jl
index f3d1813..db7353f 100644
--- a/src/Survival.jl
+++ b/src/Survival.jl
@@ -2,7 +2,6 @@ module Survival
 
 using Distributions
 using LinearAlgebra
-using PositiveFactorizations
 using StatsBase
 using StatsModels
 using Optim

From fce52ed07029ac00059b680b1b52e0d04b1ec98c Mon Sep 17 00:00:00 2001
From: Alex Arslan <ararslan@comcast.net>
Date: Sat, 9 Jul 2022 14:03:56 -0700
Subject: [PATCH 3/4] Use property destructuring with Compat

We have a transitive dependency on Compat anyway and this simplifies
exactly one line of code so might as well.
---
 Project.toml    | 2 ++
 src/Survival.jl | 3 ++-
 src/cox.jl      | 3 +--
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/Project.toml b/Project.toml
index 6ba2afb..d4725bf 100644
--- a/Project.toml
+++ b/Project.toml
@@ -3,6 +3,7 @@ uuid = "8a913413-2070-5976-9d4c-2b364fdc2f7f"
 version = "0.2.2"
 
 [deps]
+Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
@@ -11,6 +12,7 @@ StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
 [compat]
 CategoricalArrays = "0.9"
+Compat = "3.43, 4"
 DataFrames = "1"
 Distributions = "0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 Optim = "1"
diff --git a/src/Survival.jl b/src/Survival.jl
index db7353f..0f1f948 100644
--- a/src/Survival.jl
+++ b/src/Survival.jl
@@ -1,10 +1,11 @@
 module Survival
 
+using Compat
 using Distributions
 using LinearAlgebra
+using Optim
 using StatsBase
 using StatsModels
-using Optim
 
 export
     EventTime,
diff --git a/src/cox.jl b/src/cox.jl
index f098d83..a43eb34 100644
--- a/src/cox.jl
+++ b/src/cox.jl
@@ -130,8 +130,7 @@ end
 
 function _cox_fgh!(β, grad, hes, c::CoxAux{T}) where T
     update_cox!(c, β, (hes !== nothing) | (grad !== nothing))
-    X, ξ, Xβ, θ, Xθ, ξθ, λ, fs, ls  =
-        c.X, c.ξ, c.Xβ, c.θ, c.Xθ, c.ξθ, c.λ, c.fs, c.ls
+    @compat (; X, ξ, Xβ, θ, Xθ, ξθ, λ, fs, ls) = c
     y = zero(T) / one(T)
 
     if hes !== nothing

From 84e296416caea45dd5c71a45d83bc81e825dbf31 Mon Sep 17 00:00:00 2001
From: Alex Arslan <ararslan@comcast.net>
Date: Sat, 9 Jul 2022 14:23:01 -0700
Subject: [PATCH 4/4] Require Julia 1.6, modernize CI, allow CategoricalArrays
 0.10

Currently we require Julia 1.2 but 1.6 is current LTS so we might as
well bump to that.
---
 .github/workflows/CI.yml | 27 ++++++---------------------
 Project.toml             |  4 ++--
 2 files changed, 8 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index a056b43..22af39f 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -1,12 +1,9 @@
 name: CI
 on:
-  pull_request:
-    branches:
-      - master
   push:
-    branches:
-      - master
-    tags: '*'
+    branches: [master]
+    tags: ["*"]
+  pull_request:
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -15,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.2'
+          - '1.6'
           - '1'
           - 'nightly'
         os:
@@ -49,20 +46,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: |
-          julia --project=docs -e '
-            using Documenter: doctest
-            using Survival
-            doctest(Survival)'
-      - run: julia --project=docs docs/make.jl
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-docdeploy@latest
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/Project.toml b/Project.toml
index d4725bf..062ac55 100644
--- a/Project.toml
+++ b/Project.toml
@@ -11,14 +11,14 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
 [compat]
-CategoricalArrays = "0.9"
+CategoricalArrays = "0.9, 0.10"
 Compat = "3.43, 4"
 DataFrames = "1"
 Distributions = "0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 Optim = "1"
 StatsBase = "0.30, 0.31, 0.32, 0.33"
 StatsModels = "0.6"
-julia = "1.2"
+julia = "1.6"
 
 [extras]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"