fix conda in container

.devcontainer/devcontainer.json

@@ -2,26 +2,29 @@
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.194.0/containers/docker-existing-dockerfile
 {
 	"name": "mc-prediction",
-	"image": "ghcr.io/kasperskytte/mc-prediction:main",
+	// "image": "ghcr.io/kasperskytte/mc-prediction:main",
 
-	// "build": {
-	// 	// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-	// 	"dockerfile": "../Dockerfile"
-	// },
+	"build": {
+		// Sets the run context to one level up instead of the .devcontainer folder.
+		"context": "..",
+		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+	 	"dockerfile": "../Dockerfile"
+	},
 
-	"initializeCommand": "docker pull ghcr.io/kasperskytte/mc-prediction:main",
+	// "initializeCommand": "docker pull ghcr.io/kasperskytte/mc-prediction:main",
 
 	// Set *default* container specific settings.json values on container create.
 	"settings": {
+		"python.defaultInterpreterPath": "/opt/conda/envs/mc-prediction/bin/python3.8",
 		"r.bracketedPaste": true,
-		"r.rterm.linux": "/usr/local/bin/radian", //Use this only for Linux
-		"r.lsp.path": "/usr/local/bin/R",
+		"r.rterm.linux": "/opt/conda/envs/mc-prediction/bin/radian",
+		"r.lsp.path": "/opt/conda/envs/mc-prediction/bin/R",
 		"r.lsp.debug": true,
 		"r.lsp.diagnostics": true,
 		"r.rterm.option": [
 			"--no-save",
 			"--no-restore",
-			"--r-binary=/usr/local/bin/R"
+			"--r-binary=/opt/conda/envs/mc-prediction/bin/R"
 	  ]
 	},
 
@@ -53,9 +56,6 @@
 	// Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root.
 	// "remoteUser": "vscode",
 
-	// Don't override entrypoint
-	"overrideCommand": false,
-
 	// Uncomment to keep the container running when disconnecting from it
 	"shutdownAction": "none"
 }

Dockerfile

@@ -66,7 +66,10 @@ RUN export DEBIAN_FRONTEND=noninteractive \
 RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py38_23.11.0-2-Linux-x86_64.sh -O /opt/miniconda.sh \
   && /bin/bash /opt/miniconda.sh -b -p /opt/conda \
   && rm -rf /opt/miniconda.sh \
-  && conda env create -f /opt/environment.yml -n mc-prediction
+  && conda env create -f /opt/environment.yml -n mc-prediction \
+  && ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
+  && echo "conda activate mc-prediction" >> ~/.bashrc
 
 # Make RUN commands use the new environment
 SHELL ["conda", "run", "-n", "mc-prediction", "/bin/bash", "-c"]

renv.lock

@@ -1115,6 +1115,11 @@
       ],
       "Hash": "3d5108641f47470611a32d0bdf357a72"
     },
+    "languageserver": {
+      "Package": "languageserver",
+      "Version": "0.3.16",
+      "Source": "Repository"
+    },
     "later": {
       "Package": "later",
       "Version": "1.3.1",