From 3c841563606be8fc03f144265f613f4754ddb79e Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:10:40 +0200
Subject: [PATCH 1/7] rename rClr based reusable workflows

---
 .../{R-CMD-check-build.yml => R-CMD-check-build-rClr.yml}         | 0
 .github/workflows/{pkgdown.yml => pkgdown-rClr.yml}               | 0
 .../{test-pkg-and-coverage.yml => test-coverage-rClr.yml}         | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{R-CMD-check-build.yml => R-CMD-check-build-rClr.yml} (100%)
 rename .github/workflows/{pkgdown.yml => pkgdown-rClr.yml} (100%)
 rename .github/workflows/{test-pkg-and-coverage.yml => test-coverage-rClr.yml} (100%)

diff --git a/.github/workflows/R-CMD-check-build.yml b/.github/workflows/R-CMD-check-build-rClr.yml
similarity index 100%
rename from .github/workflows/R-CMD-check-build.yml
rename to .github/workflows/R-CMD-check-build-rClr.yml
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown-rClr.yml
similarity index 100%
rename from .github/workflows/pkgdown.yml
rename to .github/workflows/pkgdown-rClr.yml
diff --git a/.github/workflows/test-pkg-and-coverage.yml b/.github/workflows/test-coverage-rClr.yml
similarity index 100%
rename from .github/workflows/test-pkg-and-coverage.yml
rename to .github/workflows/test-coverage-rClr.yml

From 89a6be8b88826950f7eacacec12b0f9a88bd3e72 Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:12:08 +0200
Subject: [PATCH 2/7] Add new reusable workflows for R packages + Do not
 install PKSim + Do not install rClr + use linux os

---
 .github/workflows/R-CMD-check-build.yaml      | 68 +++++++++++++++++++
 .../bump_dev_version_tag_branch.yaml          | 65 ++++++++++++++++++
 .github/workflows/pkgdown.yaml                | 45 ++++++++++++
 .github/workflows/test-coverage.yaml          | 59 ++++++++++++++++
 4 files changed, 237 insertions(+)
 create mode 100644 .github/workflows/R-CMD-check-build.yaml
 create mode 100644 .github/workflows/bump_dev_version_tag_branch.yaml
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 .github/workflows/test-coverage.yaml

diff --git a/.github/workflows/R-CMD-check-build.yaml b/.github/workflows/R-CMD-check-build.yaml
new file mode 100644
index 0000000..3762c5c
--- /dev/null
+++ b/.github/workflows/R-CMD-check-build.yaml
@@ -0,0 +1,68 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+
+on:
+  workflow_call:
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: 'c("error")'
+
+      - name: Build package
+        if: ${{ success() }}
+        run: |
+          output_dir <- file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "built_package")
+          dir.create(output_dir)
+          devtools::build(binary = TRUE, path = output_dir)
+        shell: Rscript {0}
+
+      - name: Get package package and R versions and store in environment
+        run: |
+          echo "PKG_VERSION=$(Rscript -e 'desc::desc_get_version()')" >> $GITHUB_ENV
+          echo "R_VERSION=$(Rscript -e 'cat(R.version$major, R.version$minor, sep = ".")')" >> $GITHUB_ENV
+        shell: bash
+
+      - name: Upload built package
+        if: ${{ success() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: ospsuite-v${{ env.PKG_VERSION }}-${{runner.os}}-r_${{ env.R_VERSION }}
+          path: ${{ runner.temp }}/built_package/*
diff --git a/.github/workflows/bump_dev_version_tag_branch.yaml b/.github/workflows/bump_dev_version_tag_branch.yaml
new file mode 100644
index 0000000..a26b920
--- /dev/null
+++ b/.github/workflows/bump_dev_version_tag_branch.yaml
@@ -0,0 +1,65 @@
+# This reusable workflow will, if triggered by a merge:
+#  - Bump version if the current version is development (x.y.z.9000+)
+#  - Tag the target branch with version number
+name: bump-dev-version
+
+on:
+  workflow_call:
+    inputs:
+        app-id:
+          type: string
+          required: true
+    secrets:
+        private-key:
+            type: string
+            require: true
+
+jobs:
+  bump-dev-version:
+    if: github.event_name != 'pull_request'
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions: write-all
+    steps:
+
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ inputs.app-id }}
+          private-key: ${{ secrets.private-key }}
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ steps.app-token.outputs.token }}
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install packages
+        run: |
+          install.packages("usethis")
+        shell: Rscript {0}
+
+      - name: Change DESCRIPTION file
+        run: |
+          if(usethis:::is_dev_version()){
+            desc::desc_set_version(version = usethis:::bump_version()[["dev"]])
+          }
+        shell: Rscript {0}
+
+      - name: Get package version from DESCRIPTION file and set as environment variable
+        run: |
+            echo "PKG_VERSION=$(Rscript -e 'desc::desc_get_version()')" >> $GITHUB_ENV
+        shell: bash
+
+      - uses: EndBug/add-and-commit@v9
+        if: ${{ success() }}
+        with:
+          message: '🤖 Bump version. [skip actions]'
+          default_author: github_actions
+          add: 'DESCRIPTION'
+          tag: 'v${{ env.PKG_VERSION }}'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..216b2a5
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,45 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+
+on:
+    workflow_call:
+  
+  name: pkgdown
+  
+  permissions: read-all
+  
+  jobs:
+    pkgdown:
+      runs-on: ubuntu-latest
+      # Only restrict concurrency for non-PR jobs
+      concurrency:
+        group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      permissions:
+        contents: write
+      steps:
+        - uses: actions/checkout@v4
+  
+        - uses: r-lib/actions/setup-pandoc@v2
+  
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+  
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::pkgdown, local::.
+            needs: website
+  
+        - name: Build site
+          run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          shell: Rscript {0}
+  
+        - name: Deploy to GitHub pages 🚀
+          if: github.event_name != 'pull_request'
+          uses: JamesIves/github-pages-deploy-action@v4.5.0
+          with:
+            clean: false
+            branch: gh-pages
+            folder: docs
+  
\ No newline at end of file
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..164e8b3
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,59 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+
+on:
+    workflow_call:
+  
+  name: test-coverage
+  
+  permissions: read-all
+  
+  jobs:
+    test-coverage:
+      runs-on: ubuntu-latest
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  
+      steps:
+        - uses: actions/checkout@v4
+  
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+  
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::covr, any::xml2
+            needs: coverage
+  
+        - name: Test coverage
+          run: |
+            cov <- covr::package_coverage(
+              quiet = FALSE,
+              clean = FALSE,
+              install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+            )
+            covr::to_cobertura(cov)
+          shell: Rscript {0}
+  
+        - uses: codecov/codecov-action@v4
+          with:
+            fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+            file: ./cobertura.xml
+            plugin: noop
+            disable_search: true
+            token: ${{ secrets.CODECOV_TOKEN }}
+  
+        - name: Show testthat output
+          if: always()
+          run: |
+            ## --------------------------------------------------------------------
+            find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+          shell: bash
+  
+        - name: Upload test results
+          if: failure()
+          uses: actions/upload-artifact@v4
+          with:
+            name: coverage-test-failures
+            path: ${{ runner.temp }}/package
+  
\ No newline at end of file

From 12dc24940641eda70c44ebd13562d38b8b870946 Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:15:53 +0200
Subject: [PATCH 3/7] fix typo

---
 .github/workflows/bump_dev_version_tag_branch.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/bump_dev_version_tag_branch.yaml b/.github/workflows/bump_dev_version_tag_branch.yaml
index a26b920..59e21ec 100644
--- a/.github/workflows/bump_dev_version_tag_branch.yaml
+++ b/.github/workflows/bump_dev_version_tag_branch.yaml
@@ -12,7 +12,7 @@ on:
     secrets:
         private-key:
             type: string
-            require: true
+            required: true
 
 jobs:
   bump-dev-version:

From 15c1c6f4fd518e0d319008921bad58754d962550 Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:17:01 +0200
Subject: [PATCH 4/7] fix indentation

---
 .github/workflows/bump_dev_version_tag_branch.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/bump_dev_version_tag_branch.yaml b/.github/workflows/bump_dev_version_tag_branch.yaml
index 59e21ec..4cc3bab 100644
--- a/.github/workflows/bump_dev_version_tag_branch.yaml
+++ b/.github/workflows/bump_dev_version_tag_branch.yaml
@@ -6,13 +6,13 @@ name: bump-dev-version
 on:
   workflow_call:
     inputs:
-        app-id:
+      app-id:
+        type: string
+        required: true
+    secrets:
+      private-key:
           type: string
           required: true
-    secrets:
-        private-key:
-            type: string
-            required: true
 
 jobs:
   bump-dev-version:

From ce9fedc405702a8195725c8d5a54e95b7f58e6c6 Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:19:22 +0200
Subject: [PATCH 5/7] remove type argument for secret

---
 .github/workflows/bump_dev_version_tag_branch.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/bump_dev_version_tag_branch.yaml b/.github/workflows/bump_dev_version_tag_branch.yaml
index 4cc3bab..d47e919 100644
--- a/.github/workflows/bump_dev_version_tag_branch.yaml
+++ b/.github/workflows/bump_dev_version_tag_branch.yaml
@@ -11,7 +11,6 @@ on:
         required: true
     secrets:
       private-key:
-          type: string
           required: true
 
 jobs:

From 15f9ac5b33ceccacec7dd0ea5bb8749569dddc65 Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:21:02 +0200
Subject: [PATCH 6/7] fix indentation

---
 .github/workflows/test-coverage.yaml | 107 +++++++++++++--------------
 1 file changed, 53 insertions(+), 54 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 164e8b3..78250f4 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -3,57 +3,56 @@
 on:
     workflow_call:
   
-  name: test-coverage
-  
-  permissions: read-all
-  
-  jobs:
-    test-coverage:
-      runs-on: ubuntu-latest
-      env:
-        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-  
-      steps:
-        - uses: actions/checkout@v4
-  
-        - uses: r-lib/actions/setup-r@v2
-          with:
-            use-public-rspm: true
-  
-        - uses: r-lib/actions/setup-r-dependencies@v2
-          with:
-            extra-packages: any::covr, any::xml2
-            needs: coverage
-  
-        - name: Test coverage
-          run: |
-            cov <- covr::package_coverage(
-              quiet = FALSE,
-              clean = FALSE,
-              install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
-            )
-            covr::to_cobertura(cov)
-          shell: Rscript {0}
-  
-        - uses: codecov/codecov-action@v4
-          with:
-            fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
-            file: ./cobertura.xml
-            plugin: noop
-            disable_search: true
-            token: ${{ secrets.CODECOV_TOKEN }}
-  
-        - name: Show testthat output
-          if: always()
-          run: |
-            ## --------------------------------------------------------------------
-            find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
-          shell: bash
-  
-        - name: Upload test results
-          if: failure()
-          uses: actions/upload-artifact@v4
-          with:
-            name: coverage-test-failures
-            path: ${{ runner.temp }}/package
-  
\ No newline at end of file
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

From 71788d651d1f5a63daf706682e93c048a3fafde1 Mon Sep 17 00:00:00 2001
From: Felix MIL <felix.mil@esqlabs.com>
Date: Fri, 19 Jul 2024 11:21:47 +0200
Subject: [PATCH 7/7] fix indentation

---
 .github/workflows/pkgdown.yaml | 79 +++++++++++++++++-----------------
 1 file changed, 39 insertions(+), 40 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 216b2a5..96323df 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -3,43 +3,42 @@
 on:
     workflow_call:
   
-  name: pkgdown
-  
-  permissions: read-all
-  
-  jobs:
-    pkgdown:
-      runs-on: ubuntu-latest
-      # Only restrict concurrency for non-PR jobs
-      concurrency:
-        group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
-      env:
-        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      permissions:
-        contents: write
-      steps:
-        - uses: actions/checkout@v4
-  
-        - uses: r-lib/actions/setup-pandoc@v2
-  
-        - uses: r-lib/actions/setup-r@v2
-          with:
-            use-public-rspm: true
-  
-        - uses: r-lib/actions/setup-r-dependencies@v2
-          with:
-            extra-packages: any::pkgdown, local::.
-            needs: website
-  
-        - name: Build site
-          run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-          shell: Rscript {0}
-  
-        - name: Deploy to GitHub pages 🚀
-          if: github.event_name != 'pull_request'
-          uses: JamesIves/github-pages-deploy-action@v4.5.0
-          with:
-            clean: false
-            branch: gh-pages
-            folder: docs
-  
\ No newline at end of file
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs