mamba-org · atrawog · Feb 5, 2024
diff --git a/.devcontainer/apt-devel.txt b/.devcontainer/apt-devel.txt
@@ -0,0 +1,19 @@
+build-essential
+sudo
+git
+apt-transport-https
+vim
+htop
+sysstat
+lsof
+nmap
+ca-certificates
+curl
+gnupg
+lsb-release
+software-properties-common
+apt-file
+util-linux
+iproute2
+iputils-ping
+procps
diff --git a/.devcontainer/config.toml b/.devcontainer/config.toml
@@ -0,0 +1,17 @@
+[sqlalchemy]
+database_url = "sqlite:///./quetz.sqlite"
+
+[session]
+# openssl rand -hex 32
+secret = "d859fc0c3554e47bdd6a8c1c27971f397dda673dbf263d30c349fb870ef7cd43"
+https_only = false
+
+[logging]
+level = "DEBUG"
+file = "quetz.log"
+
+[users]
+admins = ["dummy:alice"]
+
+[profiling]
+enable_sampling = false
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,52 @@
+{
+	"name": "quetz/frontend",
+	"containerEnv": {
+		"TZ": "Europe/Paris",
+		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+	},
+	"workspaceMount": "source=${localWorkspaceFolder},target=/workspace,type=bind",
+	"workspaceFolder": "/workspace",
+	"updateRemoteUserUID": true,
+
+	"build": {
+		"dockerfile": "../Dockerfile",
+		"context": "../",
+		"args": {
+			// "CONTAINER_WORKSPACE_FOLDER": "/workspace",
+			// "NEW_MAMBA_USER": "jovian",
+			// "NEW_MAMBA_USER_ID": "1010",
+			// "NEW_MAMBA_USER_GID": "1010",
+		},
+	},
+	"extensions": [	
+				"ms-python.python",
+				"ms-python.vscode-pylance",
+				"ms-toolsai.jupyter",
+				"ms-azuretools.vscode-docker",
+				"ms-vscode.makefile-tools",
+				"ms-vscode-remote.remote-containers",
+				"ms-vscode-remote.vscode-remote-extensionpack",
+				"GitHub.copilot",
+				"GitHub.copilot-chat",
+				],
+	"remoteUser": "jovian",
+	"settings": { 
+		"terminal.integrated.shell.linux": "/bin/bash",
+        "terminal.integrated.shellArgs.linux": ["-c"],
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "terminal.integrated.profiles.linux": {
+            "bash": {
+                "path": "/bin/bash"
+            }
+        },
+		"files.autoSave": "afterDelay",
+		"python.pythonPath": "/opt/conda/bin/python",
+		"python.defaultInterpreterPath": "/opt/conda/bin/python",
+		"jupyter.interactiveWindow.textEditor.magicCommandsAsComments": true,
+		"python.terminal.activateEnvironment": false	
+	  },
+	"mounts": [
+		"source=${localWorkspaceFolder}/.devcontainer/.cache,target=/home/jovian/.cache,type=bind,consistency=cached"
+    ],
+	"postCreateCommand": "sh /usr/local/bin/startup.sh"
+}
diff --git a/.devcontainer/fix-permissions.sh b/.devcontainer/fix-permissions.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Check if the user can execute commands with sudo
+if sudo -l &>/dev/null; then
+    echo "User has sudo privileges. Proceeding with file and directory checks."
+
+    # Get the current user's UID and GID
+    USER_UID=$(id -u)
+    USER_GID=$(id -g)
+
+    sudo chown -R $USER_UID:$USER_GID /data
+    sudo chown -R $USER_UID:$USER_GID $MAMBA_ROOT_PREFIX
+
+else
+    echo "User does not have sudo privileges. Exiting script."
+fi
diff --git a/.devcontainer/startup.sh b/.devcontainer/startup.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+cd /data/quetz && quetz start . --port 8000 --host 0.0.0.0 --proxy-headers --reload --log-level=trace
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,102 @@
+# syntax=docker/dockerfile:1.2
+
+ARG BASE_IMAGE=debian:bookworm-slim
+FROM --platform=$BUILDPLATFORM $BASE_IMAGE AS fetch
+ARG VERSION=1.5.3
+
+RUN rm -f /etc/apt/apt.conf.d/docker-*
+RUN --mount=type=cache,target=/var/cache/apt,id=apt-deb12 apt-get update && apt-get install -y --no-install-recommends bzip2 ca-certificates curl
+
+RUN if [ "$BUILDPLATFORM" = 'linux/arm64' ]; then \
+    export ARCH='aarch64'; \
+  else \
+    export ARCH='64'; \
+  fi; \
+  curl -L "https://micro.mamba.pm/api/micromamba/linux-${ARCH}/${VERSION}" | \
+  tar -xj -C "/tmp" "bin/micromamba"
+
+
+FROM --platform=$BUILDPLATFORM $BASE_IMAGE as micromamba
+
+ARG MAMBA_ROOT_PREFIX="/opt/conda"
+ARG MAMBA_EXE="/bin/micromamba"
+
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV MAMBA_ROOT_PREFIX=$MAMBA_ROOT_PREFIX
+ENV MAMBA_EXE=$MAMBA_EXE
+ENV PATH="${PATH}:${MAMBA_ROOT_PREFIX}/bin"
+
+COPY --from=fetch /etc/ssl/certs/ca-certificates.crt /etc/ssl/certs/ca-certificates.crt
+COPY --from=fetch /tmp/bin/micromamba "$MAMBA_EXE"
+
+ARG MAMBA_USER=jovian
+ARG MAMBA_USER_ID=1000
+ARG MAMBA_USER_GID=1000
+
+ENV MAMBA_USER=$MAMBA_USER
+ENV MAMBA_USER_ID=$MAMBA_USER_ID
+ENV MAMBA_USER_GID=$MAMBA_USER_GID
+
+RUN groupadd -g "${MAMBA_USER_GID}" "${MAMBA_USER}" && \
+    useradd -m -u "${MAMBA_USER_ID}" -g "${MAMBA_USER_GID}" -s /bin/bash "${MAMBA_USER}"
+RUN mkdir -p "${MAMBA_ROOT_PREFIX}/environments" && \
+    chown "${MAMBA_USER}:${MAMBA_USER}" "${MAMBA_ROOT_PREFIX}"
+
+ARG CONTAINER_WORKSPACE_FOLDER=/workspace
+RUN mkdir -p "${CONTAINER_WORKSPACE_FOLDER}"
+WORKDIR "${CONTAINER_WORKSPACE_FOLDER}"
+
+USER $MAMBA_USER
+RUN micromamba shell init --shell bash --prefix=$MAMBA_ROOT_PREFIX
+SHELL ["/bin/bash", "--rcfile", "/$MAMBA_USER/.bashrc", "-c"]
+
+
+FROM micromamba AS core
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /opt/conda/environments/environment.yml
+RUN --mount=type=cache,target=$MAMBA_ROOT_PREFIX/pkgs,id=mamba-pkgs micromamba install -y --override-channels -c conda-forge -n base -f /opt/conda/environments/environment.yml
+
+
+FROM core as core-devel
+
+USER root
+COPY --chown=$MAMBA_USER:$MAMBA_USER .devcontainer/apt-devel.txt /opt/conda/environments/apt-devel.txt
+RUN --mount=type=cache,target=/var/cache/apt,id=apt-deb12 apt-get update && xargs apt-get install -y < /opt/conda/environments/apt-devel.txt
+
+RUN usermod -aG sudo $MAMBA_USER
+RUN echo "$MAMBA_USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+COPY .devcontainer/fix-permissions.sh /bin/fix-permissions.sh
+RUN chmod +x /bin/fix-permissions.sh && \
+    echo 'export MAMBA_USER_ID=$(id -u)' >> /home/$MAMBA_USER/.bashrc && \
+    echo 'export MAMBA_USER_GID=$(id -g)' >> /home/$MAMBA_USER/.bashrc && \
+    echo "/bin/fix-permissions.sh" >> /home/$MAMBA_USER/.bashrc && \
+    echo "micromamba activate" >> /home/$MAMBA_USER/.bashrc
+
+RUN mkdir -p /code && chown -R $MAMBA_USER:$MAMBA_USER /code
+RUN mkdir -p /data && chown -R $MAMBA_USER:$MAMBA_USER /data
+
+COPY .devcontainer/startup.sh /usr/local/bin/startup.sh
+RUN chmod +x /usr/local/bin/startup.sh
+ENTRYPOINT ["startup.sh"]
+
+USER $MAMBA_USER
+
+RUN cd /code && git clone https://github.com/mamba-org/quetz.git
+RUN cd /code/quetz/plugins/quetz_runexports && pip install . --no-cache
+RUN cd /code/quetz/plugins/quetz_repodata_patching && pip install . --no-cache
+RUN cd /code/quetz/plugins/quetz_current_repodata && pip install . --no-cache
+RUN cd /code/quetz/plugins/quetz_repodata_zchunk && pip install . --no-cache
+RUN cd /code/quetz/plugins/quetz_transmutation && pip install . --no-cache
+RUN pip install git+https://git@github.com/regro/libcflib@master --no-deps
+RUN cd /code/quetz/plugins/quetz_harvester && pip install . --no-cache --no-deps
+RUN cd /code/quetz/plugins/quetz_tos && pip install . --no-cache --no-deps
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER . /code/quetz-frontend
+RUN pip install -e /code/quetz-frontend
+RUN quetz-frontend link-frontend --development
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER .devcontainer/config.toml /data
+RUN cd /data && quetz create --create-conf /data/quetz
+
+EXPOSE 8000
diff --git a/environment.yml b/environment.yml
@@ -5,3 +5,8 @@ dependencies:
   - quetz
   - nodejs=16
   - yarn=1.22
+  - sqlalchemy
+  - sqlalchemy-utils
+  - conda-build
+  - psycopg2
+  - xattr
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		cd /data/quetz && quetz start . --port 8000 --host 0.0.0.0 --proxy-headers --reload --log-level=trace