Add .devcontainer (#243)

.devcontainer/Dockerfile

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+ARG BASE_IMAGE=git-515d637-jammy
+FROM ghcr.io/mamba-org/micromamba-devcontainer:$BASE_IMAGE
+
+# Ensure that all users have read-write access to all files created in the subsequent commands.
+ARG DOCKERFILE_UMASK=0000
+
+# Install the fix-permissions script
+ADD --chmod=755 https://raw.githubusercontent.com/jupyter/docker-stacks/d8c60bc42cad227c5a35214a43a29c157c0a345e/images/docker-stacks-foundation/fix-permissions /usr/local/bin/fix-permissions
+
+# Create a fixed group for /opt/conda in case the user GID changes
+RUN sudo groupadd --gid 46328 mamba-admin && sudo usermod -aG mamba-admin "${MAMBA_USER}"
+
+# Install the Conda packages.
+ARG ENVIRONMENT_YAML=environment.yml
+COPY --chown=$MAMBA_USER:$MAMBA_USER ${ENVIRONMENT_YAML} /tmp/environment.yml
+RUN echo "use_lockfiles: false" >> ~/.mambarc && \
+    micromamba config append channels conda-forge && \
+    micromamba install --yes --name base --file /tmp/environment.yml && \
+    micromamba clean --all --force-pkgs-dirs --yes && \
+    sudo -E "NB_GID=mamba-admin" fix-permissions "${MAMBA_ROOT_PREFIX}"
+
+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}"
+
+# On WSL the repo is mounted with permissions 1000:1000, but the mambauser inside the container has a different UID.
+# So we change the UID of the mambauser inside the container to match the UID of the user on the host.
+USER root
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+RUN groupmod --gid $USER_GID $MAMBA_USER \
+    && usermod --uid $USER_UID --gid $USER_GID $MAMBA_USER \
+    && chown -R $USER_UID:$USER_GID /home/$MAMBA_USER
+
+# Install SLURM and Munge
+RUN apt-get update && apt-get install -y \
+    slurm-wlm \
+    munge \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up SLURM configuration
+COPY .devcontainer/slurm.conf /etc/slurm/slurm.conf
+RUN chmod 644 /etc/slurm/slurm.conf && \
+    mkdir -p /var/spool/slurmd && \
+    mkdir -p /var/run/slurm && \
+    mkdir -p /var/log/slurm && \
+    mkdir -p /var/lock/slurm && \
+    mkdir -p /var/spool/slurm && \
+    chown -R slurm:slurm /var/spool/slurmd /var/run/slurm /var/log/slurm /var/lock/slurm /var/spool/slurm
+
+# Create a startup script to ensure SLURM services are running
+RUN echo '#!/bin/bash' > /usr/local/bin/startup.sh && \
+    echo 'service munge start' >> /usr/local/bin/startup.sh && \
+    echo 'service slurmd start' >> /usr/local/bin/startup.sh && \
+    echo 'service slurmctld start' >> /usr/local/bin/startup.sh && \
+    echo 'exec "$@"' >> /usr/local/bin/startup.sh && \
+    chmod +x /usr/local/bin/startup.sh
+
+USER root
+
+CMD ["/bin/bash"]

.devcontainer/devcontainer.json

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+{
+    "name": "micromamba",
+    "runArgs": [
+        "--hostname",
+        "devcontainer",
+        "--name",
+        "${localEnv:USER}_devcontainer_micromamba",
+        "--privileged"  // Add this to allow SLURM to manage processes
+    ],
+    "containerEnv": {
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}",
+        "CONTAINER_WORKSPACE_FOLDER": "${containerWorkspaceFolder}"
+    },
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": "..",
+        "args": {
+            "CONTAINER_WORKSPACE_FOLDER": "${containerWorkspaceFolder}",
+            "BASE_IMAGE": "git-515d637-jammy",
+            "ENVIRONMENT_YAML": "environment.yml"
+        }
+    },
+    "overrideCommand": true, // allow the entrypoint to run
+    "mounts": [
+        "source=pre-commit-cache-${localEnv:USER},target=/home/mambauser/.cache/pre-commit,type=volume",
+        "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind,consistency=cached",
+        "source=${localWorkspaceFolder}/.devcontainer/slurm.conf,target=/etc/slurm-llnl/slurm.conf,type=bind"
+    ],
+    "remoteUser": "mambauser",
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-python.mypy-type-checker",
+                "charliermarsh.ruff",
+                "ms-toolsai.jupyter",
+                "ms-azuretools.vscode-docker",
+                "donjayamanne.githistory",
+                "eamodio.gitlens",
+                "mutantdino.resourcemonitor",
+                "github.copilot",
+                "davidanson.vscode-markdownlint"
+            ],
+            "settings": {
+                // Files to completely exclude from view
+                // (see also search.exclude and files.watcherExclude)
+                "files.exclude": {
+                    // Ignore cached files
+                    "**/__pycache__": true,
+                    // Ignore files created for development installs
+                    "**/*.egg-info": true,
+                    // Ignore Jupyter checkpoint files
+                    "**/.ipynb_checkpoints": true,
+                    // Ignore cache directory, except for files which start with . (e.g. .gitignore)
+                    ".devcontainer/cache/*/[!\\.]*": true
+                },
+                "[python]": {
+                    "editor.defaultFormatter": "charliermarsh.ruff"
+                },
+                "ruff.path": [
+                    "/opt/conda/bin/ruff"
+                ],
+                "ruff.interpreter": [
+                    "/opt/conda/bin/python"
+                ],
+                // Ruler for "black"-formatted line widths
+                "editor.rulers": [
+                    88
+                ],
+                // Disable barely usable scrollbar
+                "workbench.editor.wrapTabs": true,
+                // Turn on autosave
+                "files.autoSave": "afterDelay",
+                // Show whitespace as tiny grey dots
+                "editor.renderWhitespace": "boundary",
+                // Use Pylance
+                "python.languageServer": "Pylance",
+                "python.analysis.typeCheckingMode": "basic",
+                // Interpret lines beginning with "# !%" as ipython magic commands
+                "jupyter.interactiveWindow.textEditor.magicCommandsAsComments": true,
+                // Path of the default Python environment
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                // Disable the "conda activate base" command when opening a new terminal
+                "python.terminal.activateEnvironment": false,
+                // Automatically keep Git up-to-date with remotes
+                "git.autofetch": "all",
+                // Make sure that key combos like Ctrl+K are not intercepted by VS Code
+                // when using the terminal
+                "terminal.integrated.allowChords": false,
+                "extensions.verifySignature": false
+            }
+        }
+    },
+    "postCreateCommand": "sudo /usr/local/bin/startup.sh && sudo scontrol show config && sudo scontrol show nodes && sudo scontrol show partitions",
+    "postStartCommand": "pip install -e ."
+}

.devcontainer/slurm.conf

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+ClusterName=devcluster
+SlurmctldHost=localhost
+MpiDefault=none
+ProctrackType=proctrack/linuxproc
+ReturnToService=1
+SlurmctldPidFile=/var/run/slurmctld.pid
+SlurmdPidFile=/var/run/slurmd.pid
+SlurmdSpoolDir=/var/spool/slurmd
+SlurmUser=slurm
+StateSaveLocation=/var/spool/slurm
+SwitchType=switch/none
+TaskPlugin=task/affinity
+InactiveLimit=0
+KillWait=30
+MinJobAge=300
+SlurmctldTimeout=120
+SlurmdTimeout=300
+Waittime=0
+SchedulerType=sched/backfill
+SelectType=select/cons_res
+SelectTypeParameters=CR_Core
+
+# COMPUTE NODES
+NodeName=localhost NodeAddr=127.0.0.1 CPUs=1 State=UNKNOWN
+PartitionName=debug Nodes=localhost Default=YES MaxTime=INFINITE State=UP