Updating GitHub Actions

.github/pull_request_template.md

@@ -0,0 +1,14 @@
+Before you do a pull request, you should always **file an issue** and make sure the package maintainer agrees that it’s a problem, and is happy with your basic proposal for fixing it. We don’t want you to spend a bunch of time on something that we don’t think is a good idea.
+
+Additional requirements for pull requests:
+
+- Adhere to the [Developer Guidelines](https://ohdsi.github.io/MethodsLibrary/developerGuidelines.html) as well as the [OHDSI Code Style](https://ohdsi.github.io/MethodsLibrary/codeStyle.html).
+
+- If possible, add unit tests for new functionality you add.
+
+- Restrict your pull request to solving the issue at hand. Do not try to 'improve' parts of the code that are not related to the issue. If you feel other parts of the code need better organization, create a separate issue for that.
+
+- Make sure you pass R check without errors and warnings before submitting.
+
+- Always target the `develop` branch, and make sure you are up-to-date with the develop branch.
+

.github/workflows/R_CMD_check_Hades.yaml

@@ -28,6 +28,21 @@ jobs:
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+      CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+      CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+      CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+      CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+      CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+      CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
 
     steps:
       - uses: actions/checkout@v2
@@ -62,12 +77,28 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |    
+          sudo apt-get install libssh-dev
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Remove check folder if exists
+        if: runner.os == 'macOS'
+        run: unlink("check", recursive = TRUE)
+        shell: Rscript {0}
 
       - name: Check
         env:
@@ -77,20 +108,88 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v2
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}
 
   Release:
     needs: R-CMD-Check
+
+    runs-on: macOS-latest
+
+    env:
+      GH_TOKEN: ${{ secrets.GH_TOKEN }}
 
-    runs-on: ubuntu-20.04
+    if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/master' }}
 
     steps:
-      - name: First
-        if: ${{ github.event_name != 'pull_request' && github.branch == 'master' }}
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0    
+
+      - name: Check if version has increased
+        run: |
+          echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
+          
+      - name: Display new version number
+        if: ${{ env.new_version != '' }}
+        run: |
+          echo "${{ env.new_version }}" 
+          
+      - name: Create release
+        if: ${{ env.new_version != '' }}
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_TOKEN }} 
+        with:
+          tag_name: ${{ env.new_version }}
+          release_name: Release ${{ env.new_version }}
+          body: |
+            See NEWS.md for release notes.
+          draft: false
+          prerelease: false
+
+      - uses: r-lib/actions/setup-r@v1
+        if: ${{ env.new_version != '' }}
+
+      - name: Install drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          install.packages('drat')
+        shell: Rscript {0}
+
+      - name: Remove any tarballs that already exists
+        if: ${{ env.new_version != '' }}
+        run: |
+          rm -f *.tar.gz
+          
+      - name: Download package tarball
+        if: ${{ env.new_version != '' }}
+        uses: actions/download-artifact@v2
+        with:
+          name: package_tarball    
+
+      - name: Push to drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          bash deploy.sh
+
+      - name: Push to BroadSea
+        if: ${{ env.new_version != '' }}
         run: |
-          perl compare_version --tag && \
-          bash deploy.sh && \
           curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
+          

compare_versions

@@ -9,8 +9,6 @@ $r_major = $1;
 $r_minor = $2;
 $r_mod = $3;
 
-print "New R version: $r_major-$r_minor-$r_mod\n";
-
 open(GIT_VERSION, "git describe --tags |");
 $git = <GIT_VERSION>;
 close(GIT_VERSION);
@@ -20,49 +18,10 @@ $git_major = $1;
 $git_minor = $2;
 $git_mod = $3;
 
-print "Current git version: $git_major-$git_minor-$git_mod\n";
-
 if ($r_major > $git_major || $r_minor > $git_minor || $r_mod > $git_mod) {
-	$monotonic = 0;
+	$new_version = "v$r_major.$r_minor.$r_mod";
 } else {
-	$monotonic = -1;
-}
-
-if ($monotonic != 0) {
-	print "Non-monotonically increasing versions numbers\n";
-}
-
-if ($monotonic == 0 & $ARGV[0] eq "--tag") {
-
-	open(GIT_TAG, "git tag v$r_major.$r_minor.$r_mod |");
-
-	$fail = 0;
-	while ($line = <GIT_TAG>) {
-		if ($line =~ /fatal/) {
-			$fail = 1;
-		}
-		print "tag: $line";
-	} # TODO Check for errors
-	close(GIT_TAG);
-	print "tag: END\n\n";
-
-	if ($fail eq 1) {
-		exit(-1);
-	}
-
-	$cmd = "git config user.name \"Marc A. Suchard\"; " .
-	       "git config user.email \"msuchard@ucla.edu\"; " .
-	       "git tag v$r_major.$r_minor.$r_mod ; " .
-	       "git push -q https://\$GH_TOKEN\@github.com/OHDSI/\$PKG_NAME.git --tags";
-
-	print "cmd: $cmd\n";
-
-	open(GIT_PUSH, "$cmd |");
-	while ($line = <GIT_PUSH>) {
-		print "push: $line";
-	} # TODO Check for errors
-	close(GIT_PUSH);
-	print "push: END\n\n";
+	$new_version = "";
 }
 
-exit($monotonic);
+print($new_version);

deploy.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+set -o errexit -o nounset
+addToDrat(){
+  PKG_REPO=$PWD
+
+  ## Build package tar ball
+  export PKG_TARBALL=$(ls *.tar.gz)
+
+  cd ..; mkdir drat; cd drat
+
+  ## Set up Repo parameters
+  git init
+  git config user.name "Martijn Schuemie"
+  git config user.email "[email protected]"
+  git config --global push.default simple
+
+  ## Get drat repo
+  git remote add upstream "https://$GH_TOKEN@github.com/OHDSI/drat.git"
+  git fetch upstream 2>err.txt
+  git checkout gh-pages
+
+  ## Link to local R packages  
+  echo 'R_LIBS=~/Rlib' > .Renviron
+
+  Rscript -e "drat::insertPackage('$PKG_REPO/$PKG_TARBALL', \
+    repodir = '.', \
+    commit='GitHub Actions release: $PKG_TARBALL run $GITHUB_RUN_ID')"
+  git push
+
+}
+addToDrat