ci: build devcontainer and push

mcanouil · Nov 15, 2023 · d203a93 · d203a93
1 parent b03e34a
commit d203a93
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Showing 12 changed files with 55 additions and 42 deletions.
diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,43 +1,7 @@
 {
 	"name": "eggla",
-	"build": {
-		"dockerfile": "Dockerfile", 
-		"args": {
-			"VARIANT": "bullseye"
-		}
-	},
+	"image": "buildpack-deps:bullseye-curl",
 	"remoteUser": "vscode",
-	"features": {
-		"ghcr.io/devcontainers/features/common-utils:2": {
-			"installZsh": "true",
-			"username": "vscode",
-			"userUid": "1001",
-			"userGid": "1001",
-			"upgradePackages": "true"
-		},
-		"ghcr.io/devcontainers/features/git:1": {
-			"version": "latest",
-			"ppa": "false"
-		},
-		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
-			"version": "4.2.0",
-			"vscodeRSupport": "full",
-			"installDevTools": "false",
-			"installREnv": "true",
-			"installRMarkdown": "false"
-		},
-		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
-			"version": "prerelease",
-			"installTinyTex": "false",
-			"installChromium": "false"
-		},
-		"./bcftools": {
-			"version": "1.16"
-		},
-		"./eggla": {
-			"version": "main"
-		}
-	},
 	"customizations": {
 		"vscode": {
 			"extensions": [

diff --git a/...tainer/bcftools/devcontainer-feature.json → ...tainer/bcftools/devcontainer-feature.json b/...tainer/bcftools/devcontainer-feature.json → ...tainer/bcftools/devcontainer-feature.json
diff --git a/.devcontainer/bcftools/install.sh → .github/.devcontainer/bcftools/install.sh b/.devcontainer/bcftools/install.sh → .github/.devcontainer/bcftools/install.sh
diff --git a/.github/.devcontainer/devcontainer.json b/.github/.devcontainer/devcontainer.json
@@ -0,0 +1,48 @@
+{
+	"name": "eggla",
+	"image": "ghcr.io/mcanouil/eggla:devel",
+	"remoteUser": "vscode",
+	"remoteEnv": {
+		"PKG_SYSREQS": "true"
+	},
+	"features": {
+		"ghcr.io/devcontainers/features/common-utils:2": {
+			"installZsh": "true",
+			"username": "vscode",
+			"userUid": "1001",
+			"userGid": "1001",
+			"upgradePackages": "true"
+		},
+		"ghcr.io/devcontainers/features/git:1": {
+			"version": "latest",
+			"ppa": "false"
+		},
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "4.2.0",
+			"vscodeRSupport": "full",
+			"installDevTools": "false",
+			"installREnv": "true",
+			"installRMarkdown": "false"
+		},
+		"./bcftools": {
+			"version": "1.16"
+		},
+		"./eggla": {
+			"version": "main"
+		}
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"REditorSupport.r"
+			],
+			"settings": {
+				"r.rterm.option": [
+					"--no-save",
+					"--no-restore-data",
+					"--quiet"
+				]
+			}
+		}
+	}
+}
diff --git a/.devcontainer/eggla/R/lock.R → .github/.devcontainer/eggla/R/lock.R b/.devcontainer/eggla/R/lock.R → .github/.devcontainer/eggla/R/lock.R
diff --git a/.devcontainer/eggla/R/pkg.lock → .github/.devcontainer/eggla/R/pkg.lock b/.devcontainer/eggla/R/pkg.lock → .github/.devcontainer/eggla/R/pkg.lock
diff --git a/.devcontainer/eggla/bin/plink2 → .github/.devcontainer/eggla/bin/plink2 b/.devcontainer/eggla/bin/plink2 → .github/.devcontainer/eggla/bin/plink2
diff --git a/...container/eggla/devcontainer-feature.json → ...container/eggla/devcontainer-feature.json b/...container/eggla/devcontainer-feature.json → ...container/eggla/devcontainer-feature.json
diff --git a/.devcontainer/eggla/install.sh → .github/.devcontainer/eggla/install.sh b/.devcontainer/eggla/install.sh → .github/.devcontainer/eggla/install.sh
@@ -77,7 +77,8 @@ check_packages curl \
     libfribidi-dev \
     libv8-dev \
     libudunits2-dev \
-    libfftw3-dev
+    libfftw3-dev \
+    libgit2-dev
 
 install_pak() {
     local version=$1
@@ -102,9 +103,11 @@ echo "Install R packages..."
 mkdir /tmp/r-packages
 pushd /tmp/r-packages
 
+
 install_pak "auto"
 
-su "${USERNAME}" -c "R -q -e \"pak::lockfile_install(update = TRUE)\""
+cp ${FEATURE_DIR}/R/pkg.lock pkg.lock
+su "${USERNAME}" -c "R -q -e \"n <- 0; while(inherits(try(pak::lockfile_install(update = TRUE), silent = TRUE), 'try-error') && n < 3) n <- n + 1\""
 
 if [ "${EGGLA_VERSION}" = "main" ]; then
     su "${USERNAME}" -c "R -q -e \"pak::pkg_install('mcanouil/eggla', upgrade = FALSE, dependencies = TRUE)\""

diff --git a/.devcontainer/eggla/tests/eggla-example.R → ....devcontainer/eggla/tests/eggla-example.R b/.devcontainer/eggla/tests/eggla-example.R → ....devcontainer/eggla/tests/eggla-example.R
diff --git a/.github/workflows/devcontainer.yml b/.github/workflows/devcontainer.yml
@@ -14,7 +14,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  build-docker:
+  build-devcontainer:
     runs-on: ubuntu-latest
     if: |
       github.event_name == 'workflow_dispatch' ||