Add GitHub actions CI (#11)

* Add standard R-CMD-check action * Add pr-commands action * Add lint action * Add check badge to README * update changelog --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
laminlabs · Oct 4, 2024 · f6d5dcc · f6d5dcc
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,6 +3,7 @@
 ^LICENSE\.md$
 ^experiments$
 ^\.lintr$
+^\.github$
 ^CHANGELOG\.md$
 ^README\.qmd$
 ^docs$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: R-CMD-check.yaml
+
+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: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+
+    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")'
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -0,0 +1,34 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: lint.yaml
+
+permissions: read-all
+
+jobs:
+  lint:
+    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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,85 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,11 @@
 
 * Refactored the internal class data structures for better modularity and extensibility (PR #8).
 
+* Added GitHub actions to the project (PR #11):
+  - Standard R-CMD-check workflow.
+  - Linting action.
+  - Commands for roxygenizing (`/document`) and restyling the source code (`/style`).
+
 # laminr v0.0.1
 
 Initial POC implementation of the LaminDB API client for R.

diff --git a/README.md b/README.md
@@ -1,6 +1,11 @@
 # LaminDB interface in R
 
 
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/laminlabs/laminr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/laminlabs/laminr/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
 This package provides an interface to the LaminDB database. It allows
 you to query the database and download data from it.
 
@@ -201,8 +206,8 @@ artifact <- db$Artifact$get("KBW89Mf7IGcekja2hADu")
 artifact
 ```
 
-    <RichRecord>
-      Inherits from: <Artifact>
+    <Artifact>
+      Inherits from: <ArtifactRecord>
       Public:
         _accessor: active binding
         _action_targets: active binding
@@ -309,7 +314,7 @@ artifact$storage
 
     Warning: Data is missing expected fields: run_id, created_by_id
 
-    <RichRecord>
+    <Storage>
       Inherits from: <Record>
       Public:
         _previous_runs: active binding
@@ -337,7 +342,7 @@ artifact$storage
 artifact$created_by
 ```
 
-    <RichRecord>
+    <User>
       Inherits from: <Record>
       Public:
         created_artifacts: active binding
@@ -367,7 +372,7 @@ artifact$experimental_factors
     Data is missing expected fields: run_id, source_id, created_by_id
 
     [[1]]
-    <RichRecord>
+    <ExperimentalFactor>
       Inherits from: <Record>
       Public:
         _previous_runs: active binding
@@ -399,7 +404,7 @@ artifact$experimental_factors
         get_value: function (key) 
 
     [[2]]
-    <RichRecord>
+    <ExperimentalFactor>
       Inherits from: <Record>
       Public:
         _previous_runs: active binding
@@ -431,7 +436,7 @@ artifact$experimental_factors
         get_value: function (key) 
 
     [[3]]
-    <RichRecord>
+    <ExperimentalFactor>
       Inherits from: <Record>
       Public:
         _previous_runs: active binding

diff --git a/README.qmd b/README.qmd
@@ -3,6 +3,10 @@ title: LaminDB interface in R
 format: gfm
 ---
 
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/laminlabs/laminr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/laminlabs/laminr/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
 This package provides an interface to the LaminDB database. It allows you to query the database and download data from it.
 
 ## Installation