From f1ac9988333570551c91304a5225cd2d1ea77206 Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:25:52 -0400
Subject: [PATCH 1/9] Add dependabot.yml

---
 .github/dependabot.yml | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..ff6499d6
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
\ No newline at end of file

From 67d0fb4cb8b02d71e0bb098ac6d8ada96a02e0d5 Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:26:58 -0400
Subject: [PATCH 2/9] Separate docs workflow into separate file

---
 .github/workflows/CI.yml   | 32 ++++----------------------------
 .github/workflows/docs.yml | 30 ++++++++++++++++++++++++++++++
 2 files changed, 34 insertions(+), 28 deletions(-)
 create mode 100644 .github/workflows/docs.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 8339b0f1..e60584ae 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -1,11 +1,9 @@
 name: CI
 on:
   pull_request:
-    branches:
-      - master
+    branches: [master]
   push:
-    branches:
-      - master
+    branches: [master]
     tags: '*'
 jobs:
   test:
@@ -23,7 +21,7 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.version }}
@@ -34,26 +32,4 @@ jobs:
       - uses: julia-actions/julia-processcoverage@latest
       - uses: codecov/codecov-action@v3
         with:
-          file: lcov.info
-#   docs:
-#     name: Documentation
-#     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 MYPACKAGE
-#             doctest(MYPACKAGE)' # change MYPACKAGE to the name of your package
-#       - run: julia --project=docs docs/make.jl
-#         env:
-#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-#           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          file: lcov.info
\ No newline at end of file
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 00000000..66b98223
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,30 @@
+name: Documentation
+on:
+  pull_request:
+    branches: [master]
+  push:
+    branches: [master]
+    tags: '*'
+jobs:
+#   docs:
+#     name: Build Documentation
+#     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 MYPACKAGE
+#             doctest(MYPACKAGE)' # change MYPACKAGE to the name of your package
+#       - run: julia --project=docs docs/make.jl
+#         env:
+#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
\ No newline at end of file

From 78c7ae8bab345300c5c23adc5dc8403690e718da Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:28:41 -0400
Subject: [PATCH 3/9] Add docs env

---
 docs/Project.toml | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 docs/Project.toml

diff --git a/docs/Project.toml b/docs/Project.toml
new file mode 100644
index 00000000..f45c5bdc
--- /dev/null
+++ b/docs/Project.toml
@@ -0,0 +1,6 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
+
+[sources.KernelDensity]
+path = ".."

From 9189eea27729dc5eb46766753878222908b212c4 Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:32:34 -0400
Subject: [PATCH 4/9] Ignore docs build files

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index ae3a70e3..f0fe1401 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 examples/.ipynb_checkpoints/*
-Manifest.toml
\ No newline at end of file
+Manifest.toml
+docs/build/
\ No newline at end of file

From c91935a9bff2f297465d0c8459f9837cf8b82c74 Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:38:54 -0400
Subject: [PATCH 5/9] Create docs folder structure

---
 docs/make.jl      |  10 +++++
 docs/src/index.md | 108 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 118 insertions(+)
 create mode 100644 docs/make.jl
 create mode 100644 docs/src/index.md

diff --git a/docs/make.jl b/docs/make.jl
new file mode 100644
index 00000000..32d9e189
--- /dev/null
+++ b/docs/make.jl
@@ -0,0 +1,10 @@
+using Documenter
+using KernelDensity
+
+makedocs(
+    sitename = "KernelDensity.jl",
+    modules = [KernelDensity],
+)
+deploydocs(
+    repo = "github.com/JuliaStats/KernelDensity.jl.git",
+)
\ No newline at end of file
diff --git a/docs/src/index.md b/docs/src/index.md
new file mode 100644
index 00000000..abc2406d
--- /dev/null
+++ b/docs/src/index.md
@@ -0,0 +1,108 @@
+```@meta
+CurrentModule = KernelDensity
+```
+
+# KernelDensity.jl
+
+Kernel density estimators for Julia.
+
+## Usage
+
+### Univariate
+The main accessor function is `kde`:
+
+```julia
+U = kde(data)
+```
+
+will construct a `UnivariateKDE` object from the real vector `data`. The
+optional keyword arguments are
+* `boundary`: the lower and upper limits of the kde as a tuple. Due to the
+  fourier transforms used internally, there should be sufficient spacing to
+  prevent wrap-around at the boundaries.
+* `npoints`: the number of interpolation points to use. The function uses
+  fast Fourier transforms (FFTs) internally, so for optimal efficiency this
+  should be a power of 2 (default = 2048).
+* `kernel`: the distributional family from
+  [Distributions.jl](https://github.com/JuliaStats/Distributions.jl) to use as
+  the kernel (default = `Normal`). To add your own kernel, extend the internal
+  `kernel_dist` function.
+* `bandwidth`: the bandwidth of the kernel. Default is to use Silverman's
+  rule.
+
+The `UnivariateKDE` object `U` contains gridded coordinates (`U.x`) and the density
+estimate (`U.density`). These are typically sufficient for plotting.
+A related function
+
+``` kde_lscv(data) ```
+
+will construct a `UnivariateKDE` object, with the bandwidth selected by
+least-squares cross validation. It accepts the above keyword arguments, except
+`bandwidth`.
+
+
+There are also some slightly more advanced interfaces:
+```julia
+kde(data, midpoints::R) where R<:AbstractRange
+```
+allows specifying the internal grid to use. Optional keyword arguments are
+`kernel` and `bandwidth`.
+
+```julia
+kde(data, dist::Distribution)
+```
+allows specifying the exact distribution to use as the kernel. Optional
+keyword arguments are `boundary` and `npoints`.
+
+```julia
+kde(data, midpoints::R, dist::Distribution) where R<:AbstractRange
+```
+allows specifying both the distribution and grid.
+
+### Bivariate
+
+The usage mirrors that of the univariate case, except that `data` is now
+either a tuple of vectors
+```julia
+B = kde((xdata, ydata))
+```
+or a matrix with two columns
+```julia
+B = kde(datamatrix)
+```
+Similarly, the optional arguments all now take tuple arguments:
+e.g. `boundary` now takes a tuple of tuples `((xlo,xhi),(ylo,yhi))`.
+
+The `BivariateKDE` object `B` contains gridded coordinates (`B.x` and `B.y`) and the bivariate density
+estimate (`B.density`).
+
+### Interpolation
+
+The KDE objects are stored as gridded density values, with attached
+coordinates. These are typically sufficient for plotting (see above), but
+intermediate values can be interpolated using the
+[Interpolations.jl](https://github.com/tlycken/Interpolations.jl) package via the `pdf` method
+(extended from Distributions.jl).
+
+```julia
+pdf(k::UnivariateKDE, x)
+pdf(k::BivariateKDE, x, y)
+```
+
+where `x` and `y` are real numbers or arrays.
+
+If you are making multiple calls to `pdf`, it will be more efficient to
+construct an intermediate `InterpKDE` to store the interpolation structure:
+
+```julia
+ik = InterpKDE(k)
+pdf(ik, x)
+```
+
+`InterpKDE` will pass any extra arguments to `interpolate`.
+
+## API Reference
+
+```@autodocs
+Modules = [KernelDensity]
+```
\ No newline at end of file

From e06a1c6be6eb0b47ba41b0162f7d943934e84e82 Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:39:02 -0400
Subject: [PATCH 6/9] Activate docs workflow

---
 .github/workflows/docs.yml | 34 ++++++++++++----------------------
 1 file changed, 12 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 66b98223..9d38a958 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -6,25 +6,15 @@ on:
     branches: [master]
     tags: '*'
 jobs:
-#   docs:
-#     name: Build Documentation
-#     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 MYPACKAGE
-#             doctest(MYPACKAGE)' # change MYPACKAGE to the name of your package
-#       - run: julia --project=docs docs/make.jl
-#         env:
-#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-#           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
\ No newline at end of file
+   documenter:
+     name: Build Documentation
+     runs-on: ubuntu-latest
+     steps:
+       - uses: actions/checkout@v4
+       - uses: julia-actions/setup-julia@v2
+         with:
+           version: '1'
+       - uses: julia-actions/cache@v2
+       - uses: julia-actions/julia-docdeploy@v1
+         env:
+           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file

From 417ae2f216679bbfe7c5aa548f63e96fb467b174 Mon Sep 17 00:00:00 2001
From: Abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:40:15 -0400
Subject: [PATCH 7/9] Update codecov action version

---
 .github/workflows/CI.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e60584ae..3fae3229 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -30,6 +30,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
       - uses: julia-actions/julia-processcoverage@latest
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
\ No newline at end of file
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
\ No newline at end of file

From 92f5068af7024c18fa10234ef1794b87fa909233 Mon Sep 17 00:00:00 2001
From: abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:44:03 -0400
Subject: [PATCH 8/9] Add compat for Documenter.jl

---
 docs/Project.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/Project.toml b/docs/Project.toml
index f45c5bdc..4fa26b93 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -2,5 +2,8 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
 
+[compat]
+Documenter = "1"
+
 [sources.KernelDensity]
 path = ".."

From c4387a12ebef4ab2a3db8217b5dd6bbf69484ab8 Mon Sep 17 00:00:00 2001
From: abhro <5664668+abhro@users.noreply.github.com>
Date: Wed, 12 Mar 2025 11:47:56 -0400
Subject: [PATCH 9/9] Allow docs push preview (for PRs)

---
 docs/make.jl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/make.jl b/docs/make.jl
index 32d9e189..f514f5b2 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -7,4 +7,5 @@ makedocs(
 )
 deploydocs(
     repo = "github.com/JuliaStats/KernelDensity.jl.git",
-)
\ No newline at end of file
+    push_preview = true,
+)