devcontainer

.devcontainer/devcontainer.json

@@ -1,5 +1,9 @@
 {
 	"image": "mcr.microsoft.com/devcontainers/base:ubuntu",
+	"runArgs": [
+        "-v", "/etc/timezone:/etc/timezone:ro",
+        "-v", "/etc/localtime:/etc/localtime:ro"
+    ],
 	"features": {
 		"ghcr.io/devcontainers/features/github-cli:1": {},
 		"ghcr.io/devcontainers/features/common-utils:2": {
@@ -20,5 +24,9 @@
 			}
 		}
 	},
-	"onCreateCommand": "bash .devcontainer/onCreate.sh"
+	"onCreateCommand": "bash .devcontainer/onCreate.sh",
+	"postCreateCommand": "bash .devcontainer/postCreate.sh",
+	"mounts": [
+		"source=${localEnv:MY_DEVCONTAINERS_SECRETS_DIR},target=/home/vscode/secrets,type=bind,ro,consistency=cached"
+	]
 }

.devcontainer/onCreate.sh

@@ -11,8 +11,8 @@ mkdir -p ~/.oh-my-zsh/completions
 echo "autoload -U compinit" >> ~/.zshrc
 echo "compinit -i" >> ~/.zshrc
 
-# Directory to store Rfam data (set in LocalPreferences.toml)
-mkdir -p ~/data/Rfam
-
 # Install Julia packages, registries, ...
-/home/vscode/.juliaup/bin/julia .devcontainer/onCreate.jl
+/home/vscode/.juliaup/bin/julia .devcontainer/onCreate.jl
+
+# Fix permissions for Julia Base, stdlibs (see https://github.com/JuliaLang/juliaup/issues/865, https://github.com/JuliaLang/julia/pull/51150/files)
+find /home/vscode/.julia/juliaup/*/share/julia/{base,stdlib} -type f -name '*.jl' -exec chmod 444 {} \;

.devcontainer/postCreate.sh

@@ -0,0 +1,3 @@
+# Authenticate GitHub CLI
+gh auth login -h github.com --with-token < /home/vscode/secrets/gh_token_classic.txt
+#gh auth setup-git