Merge pull request #6 from datamol-io/devcontainer

Add Devcontainer configuration

.devcontainer/bashrc

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+source /usr/lib/git-core/git-sh-prompt
+
+# Bash prompt
+GIT_PS1_SHOWUNTRACKEDFILES=1
+GIT_PS1_SHOWDIRTYSTATE=1
+if [ $(whoami) = root ]; then
+    SYMBOL="#"
+else
+    SYMBOL="$"
+fi
+PS1='\[\033[01;32m\]\u\[\033[0m\] \[\033[1;34m\]\h \[\033[1;35m\]\W\[\033[1;31m\]$(__git_ps1 " (%s)") \[\033[0m\]$SYMBOL '

.devcontainer/dev.Dockerfile

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+FROM ghcr.io/mamba-org/micromamba:jammy
+
+# Take root for the system-wide setup
+USER root
+
+# Install system-wide packages with `apt`
+RUN export DEBIAN_FRONTEND=noninteractive && apt update --fix-missing && \
+    apt install --no-install-recommends -y \
+    ca-certificates \
+    moreutils \
+    bash-completion \
+    less \
+    watch \
+    git \
+    patch \
+    git-lfs \
+    nano \
+    jq \
+    gnupg2 \
+    openssh-client \
+    file \
+    htop \
+    zip \
+    unzip \
+    p7zip-full \
+    curl \
+    wget \
+    lsof \
+    iputils-ping \
+    iproute2 \
+    net-tools \
+    dnsutils \
+    socat \
+    telnet \
+    && apt clean && rm -rf /var/lib/apt/lists/*
+
+# Install bash completions
+RUN mkdir -p /etc/bash_completion.d \
+    && sh -c "curl -L https://raw.githubusercontent.com/docker/compose/1.29.2/contrib/completion/bash/docker-compose > /etc/bash_completion.d/docker-compose" \
+    && sh -c "curl -L https://raw.githubusercontent.com/docker/cli/v20.10.13/contrib/completion/bash/docker > /etc/bash_completion.d/docker" \
+    && sh -c "curl -L https://raw.githubusercontent.com/git/git/v2.35.1/contrib/completion/git-completion.bash > /etc/bash_completion.d/git"
+
+# Make sure everyone can access the workspaces directory.
+ENV WORKSPACES_DIR="/workspaces"
+RUN : \
+    && mkdir --parents --mode=777 "${WORKSPACES_DIR}" \
+    && chown "$MAMBA_USER:$MAMBA_USER" "${WORKSPACES_DIR}"
+
+# Sane defaults for Git
+RUN : \
+    # Switch default editor from vim to nano
+    && git config --system core.editor nano \
+    # Prevent unintentional merges
+    # <https://blog.sffc.xyz/post/185195398930/why-you-should-use-git-pull-ff-only-git-is-a>
+    && git config --system pull.ff only \
+    # Use default branch name "main" instead of "master"
+    && git config --system init.defaultBranch main \
+    # Initialize Git LFS
+    && git lfs install --system --skip-repo \
+    ;
+
+# Go back to regular user
+USER $MAMBA_USER
+
+# Install git prompt
+# NOTE(hadim): likely a bit hacky
+COPY --chown=$MAMBA_USER:$MAMBA_USER .devcontainer/bashrc /tmp/bashrc
+RUN cat /tmp/bashrc >> ~/.bashrc
+
+# Install the Conda packages
+ARG CONDA_ENV_FILE
+COPY --chown=$MAMBA_USER:$MAMBA_USER ${CONDA_ENV_FILE} /tmp/${CONDA_ENV_FILE}
+RUN micromamba install --yes --name base --file /tmp/${CONDA_ENV_FILE} \
+    && micromamba clean --all --yes
+
+# Activate the conda environment for the Dockerfile.
+# <https://github.com/mamba-org/micromamba-docker#running-commands-in-dockerfile-within-the-conda-environment>
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# Create and set the workspace folder
+ARG CONTAINER_WORKSPACE_FOLDER=/workspaces/default-workspace-folder
+RUN mkdir -p "${CONTAINER_WORKSPACE_FOLDER}"
+WORKDIR "${CONTAINER_WORKSPACE_FOLDER}"

.devcontainer/devcontainer.json

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+{
+    "name": "medchem",
+    "containerEnv": {
+        "TZ": "America/Montreal",
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}",
+        "CONTAINER_WORKSPACE_FOLDER": "${containerWorkspaceFolder}"
+    },
+    "remoteUser": "mambauser",
+    "runArgs": [
+        "--hostname",
+        "devcontainer"
+        // // Warning: loading .env into the environment will undermine the ability
+        // // to use .env to dynamically adjust the unspecified values.
+        // "--env-file", ".env"
+    ],
+    "build": {
+        "dockerfile": "dev.Dockerfile",
+        "context": "../",
+        "args": {
+            "CONTAINER_WORKSPACE_FOLDER": "${containerWorkspaceFolder}",
+            "CONDA_ENV_FILE": "env.yml"
+        }
+    },
+    // Use 'forwardPorts' to make a list of ports inside the container available locally.
+    "forwardPorts": [],
+    // allow the entrypoint to run
+    // "overrideCommand": false,
+    // Use 'postCreateCommand' to run commands after the container is created.
+    "postCreateCommand": "pip install -e .",
+    // Customize the way VS Code is started when running in the container
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "ms-toolsai.jupyter",
+                "ms-azuretools.vscode-docker",
+                "ms-vsliveshare.vsliveshare",
+                "donjayamanne.githistory",
+                "mutantdino.resourcemonitor",
+                "github.copilot",
+                "davidanson.vscode-markdownlint"
+            ],
+            "settings": {
+                // Disable telemetry
+                "telemetry.enableTelemetry": false,
+                // For linting (code format checking), disable pylint and enable
+                // pydocstyle for docstrings and flake8 for code.
+                "python.linting.pylintEnabled": false,
+                "python.linting.pydocstyleEnabled": false,
+                "python.linting.flake8Enabled": false,
+                // Turn on "black" for automatic code formatting
+                "python.formatting.provider": "black",
+                // Disable barely usable scrollbar
+                "workbench.editor.wrapTabs": true,
+                // Use Pylance
+                "python.languageServer": "Pylance",
+                "python.analysis.typeCheckingMode": "basic",
+                // Path of the default Python environment
+                "python.pythonPath": "/opt/conda/bin/python",
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                // Disable the "conda activate base" command when opening a new terminal
+                "python.terminal.activateEnvironment": false,
+                // Make sure that key combos like Ctrl+K are not intercepted by VS Code
+                // when using the terminal
+                "terminal.integrated.allowChords": false,
+                "terminal.integrated.inheritEnv": false
+            }
+        }
+    }
+}