From 855ee072e09886838265242dcf17117dbcca6953 Mon Sep 17 00:00:00 2001
From: Stella <stella.belin@farmaci.uu.se>
Date: Fri, 25 Aug 2023 07:51:36 +0200
Subject: [PATCH] Add new main CI workflow

---
 .github/workflows/main.yaml | 158 ++++++++++++++++++++++++++++++++++++
 1 file changed, 158 insertions(+)
 create mode 100644 .github/workflows/main.yaml

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
new file mode 100644
index 0000000..623c3e3
--- /dev/null
+++ b/.github/workflows/main.yaml
@@ -0,0 +1,158 @@
+on:
+  schedule:
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+  workflow_call:
+
+name: Main CI workflow
+
+jobs:
+  deploy:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-2022, r: 'release'}
+          - {os: macOS-12, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout pharmr
+        uses: actions/checkout@v3
+        with:
+          path: pharmr_repo
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        working-directory: pharmr_repo
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - uses: actions/setup-python@v2
+        with:
+            python-version: "3.11"
+
+      - name: Restore R package cache
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        working-directory: pharmr_repo
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install png (temporary)
+        working-directory: pharmr_repo
+        if: runner.os == 'Windows'
+        run: |
+          install.packages('png', repos='https://mran.microsoft.com/snapshot/2022-11-27')
+        shell: Rscript {0}
+
+      - name: Install R dependencies
+        working-directory: pharmr_repo
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          install.packages('reticulate')
+        shell: Rscript {0}
+
+      - name: Install pharmr
+        working-directory: pharmr_repo
+        run: |
+          remotes::install_local(force=TRUE)
+        shell: Rscript {0}
+
+      - name: Checkout Pharmpy
+        uses: actions/checkout@v3
+        with:
+          repository: pharmpy/pharmpy
+          path: pharmpy_repo
+          fetch-depth: 0
+
+      - name: Set up Pharmpy release version
+        working-directory: pharmpy_repo
+        run: |
+          git checkout -b release_latest "$(git rev-list --tags --max-count=1)"
+          echo "pharmpy_version=`git describe --tags`" >> $GITHUB_ENV 
+          git branch -v
+
+      - name: Install Pharmpy in venv
+        working-directory: pharmpy_repo
+        run: |
+          python3.11 -m venv pharmpy_venv
+          source pharmpy_venv/bin/activate
+          pip install .
+
+      - name: Test Pharmpy
+        working-directory: pharmr_repo
+        run: |
+          reticulate::py_discover_config()
+          reticulate::use_python('../pharmpy_repo/pharmpy_venv/bin')
+          pharmr::print_pharmpy_version()
+        shell: Rscript {0}
+
+      - name: Install deploy dependencies
+        run: |
+          install.packages("devtools")
+        shell: Rscript {0}
+
+      - name: Update DESCRIPTION and documentation
+        working-directory: pharmr_repo/deploy
+        run: |
+          reticulate::use_python('../../pharmpy_repo/pharmpy_venv/bin')
+
+          pharmpy <- reticulate::import("pharmpy")
+          pharmpy_version <- pharmpy$`__version__`
+          desc::desc_set('Version', pharmpy_version)
+          desc::desc_set('Date', Sys.Date())
+          
+          reticulate::py_run_file('build_functions.py')
+          devtools::document()
+        shell: Rscript {0}
+
+      - name: Check
+        working-directory: pharmr_repo
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          reticulate::py_discover_config()
+          reticulate::use_python('../pharmpy_repo/pharmpy_venv/bin')
+          pharmr::print_pharmpy_version()
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: results-cran
+          path: check
+