From f6f833c5797adfef0f29b08bc37e280fbeeaa54e Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalol@seer.bio>
Date: Thu, 8 Feb 2024 00:41:30 -0800
Subject: [PATCH 1/3] CI: 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 000000000..ff6499d68
--- /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 882bf99fb3369228ba6c7a99b72ae0ee0c55368a Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalol@seer.bio>
Date: Thu, 8 Feb 2024 00:46:08 -0800
Subject: [PATCH 2/3] CI: use julia-actions/cache

---
 .github/workflows/CI.yml            | 7 +------
 .github/workflows/CI_ecosystem.yml  | 7 +------
 .github/workflows/CI_extended.yml   | 7 +------
 .github/workflows/documentation.yml | 1 +
 4 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 9dd5ab6b7..b706a4fd0 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -26,12 +26,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test_v2-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
diff --git a/.github/workflows/CI_ecosystem.yml b/.github/workflows/CI_ecosystem.yml
index 98a79eb0b..88159fd00 100644
--- a/.github/workflows/CI_ecosystem.yml
+++ b/.github/workflows/CI_ecosystem.yml
@@ -32,12 +32,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test_extended-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
diff --git a/.github/workflows/CI_extended.yml b/.github/workflows/CI_extended.yml
index 4cc24d90d..c3e7561a2 100644
--- a/.github/workflows/CI_extended.yml
+++ b/.github/workflows/CI_extended.yml
@@ -32,12 +32,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test_extended-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index e7dacab73..5e4b3e2c5 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -18,6 +18,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
+      - uses: julia-actions/cache@v1
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

From 44dca63c214e792d27b183debb3cd6d23a33d38d Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalol@seer.bio>
Date: Thu, 8 Feb 2024 00:46:47 -0800
Subject: [PATCH 3/3] CI: use julia-docdeploy

---
 .github/workflows/documentation.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 5e4b3e2c5..4164c3683 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -19,10 +19,8 @@ jobs:
         with:
           version: '1'
       - uses: julia-actions/cache@v1
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: julia --color=yes --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}