ucgmsim-workflow 2026.9.1__tar.gz

ucgmsim_workflow-2026.9.1/.github/workflows/ci.yml

@@ -0,0 +1,12 @@
+name: CI
+on: [pull_request]
+
+jobs:
+  ci:
+    uses: ucgmsim/meta-ci-action/.github/workflows/ci.yml@v1
+    with:
+      package-dir: workflow
+      system-packages: "gmt libgmt-dev ghostscript"
+      enable-coverage: true
+      cov-package: workflow
+      cov-fail-under: 95

ucgmsim_workflow-2026.9.1/.github/workflows/claude-review.yml

@@ -0,0 +1,11 @@
+name: Claude PR Review
+
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  review:
+    uses: ucgmsim/meta-ci-action/.github/workflows/claude-review.yml@v1
+    secrets:
+      claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}

ucgmsim_workflow-2026.9.1/.github/workflows/container.yml

@@ -0,0 +1,79 @@
+name: Build, Test in Container, and Upload
+
+# Runs after a release is published to PyPI (called from publish-PyPI.yml),
+# or manually to rebuild the image for an existing PyPI release.
+on:
+  workflow_call:
+    inputs:
+      version:
+        description: 'ucgmsim-workflow version on PyPI to install'
+        required: true
+        type: string
+      ref:
+        description: 'Git ref to take the tests from (defaults to the triggering ref)'
+        required: false
+        type: string
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'ucgmsim-workflow version on PyPI to install'
+        required: true
+        type: string
+
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: earthquakesuc/workflow-bootstrap
+
+jobs:
+  build-test-upload:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+
+      # PyPI can take a little while to serve a freshly uploaded release.
+      - name: Wait for the release to appear on PyPI
+        run: |
+          for _ in $(seq 30); do
+            if curl -sf "https://pypi.org/pypi/ucgmsim-workflow/${{ inputs.version }}/json" > /dev/null; then
+              exit 0
+            fi
+            sleep 10
+          done
+          echo "ucgmsim-workflow ${{ inputs.version }} not found on PyPI" >&2
+          exit 1
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: earthquakesuc
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value=${{ inputs.version }}
+            type=raw,value=latest
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./container/Dockerfile
+          build-args: |
+            WORKFLOW_VERSION=${{ inputs.version }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Run pytest
+        run: |
+          docker run --rm \
+            -v ${{ github.workspace }}:/mnt \
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ inputs.version }} \
+            bash -c "pytest /mnt/tests"

ucgmsim_workflow-2026.9.1/.github/workflows/publish-PyPI.yml

@@ -0,0 +1,91 @@
+name: Publish to PyPI
+run-name: Publish Python Package to PyPI for release ${{ github.event.release.tag_name || inputs.tag_name || github.ref_name }}
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      tag_name:
+        description: 'Git tag to checkout and publish'
+        required: false
+        type: string
+
+jobs:
+  build:
+    name: Build distribution 📦
+    # Pure Python, so one py3-none-any wheel serves every interpreter and
+    # platform: no build matrix and no cibuildwheel.
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.version.outputs.version }}
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4.1.0
+        with:
+          ref: ${{ inputs.tag_name || github.ref }}
+          # setuptools-scm derives the version from the tag, so it needs the full
+          # history rather than a shallow clone.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Build wheel and source distribution
+        run: |
+          python3 -m pip install build
+          python3 -m build
+
+      - name: Get the package version
+        id: version
+        # The wheel filename carries the normalised version setuptools-scm
+        # derived from the tag, which is what the container installs.
+        run: |
+          wheel=$(basename dist/*.whl)
+          echo "version=$(echo "$wheel" | cut -d- -f2)" >> "$GITHUB_OUTPUT"
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ucgmsim-workflow
+
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: dist
+
+  build-container:
+    name: Build and push the container
+    needs:
+    - build
+    - publish-to-pypi
+    uses: ./.github/workflows/container.yml
+    with:
+      version: ${{ needs.build.outputs.version }}
+      ref: ${{ inputs.tag_name || github.ref }}
+    secrets: inherit

ucgmsim_workflow-2026.9.1/.gitignore

@@ -0,0 +1,191 @@
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+
+docker/runner/EMOD3D/
+docker/runner/nshmdb.db
+docker/runner/genslip_velocity_model.vmod
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+
+# Devenv
+.devenv*
+devenv.local.nix
+
+# direnv
+.direnv
+
+# pre-commit
+.pre-commit-config.yaml

ucgmsim_workflow-2026.9.1/.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+known_first_party=qcore,empirical,nshmdb,IM_calculation,mera,source_modelling

ucgmsim_workflow-2026.9.1/PKG-INFO

@@ -0,0 +1,43 @@
+Metadata-Version: 2.4
+Name: ucgmsim-workflow
+Version: 2026.9.1
+Summary: Next generation workflow powered by cylc.
+Author: QuakeCoRE
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+Requires-Dist: im-calculation<2026.09.01,>=2025.12.5
+Requires-Dist: velocity-modelling>=2026.2.1
+Requires-Dist: nshmdb>=2026.09.1
+Requires-Dist: oq_wrapper>=2025.12.3
+Requires-Dist: qcore-utils>=2025.12.2
+Requires-Dist: source_modelling>=2026.08.1
+Requires-Dist: geopandas
+Requires-Dist: pandas[hdf5,parquet]
+Requires-Dist: pyyaml
+Requires-Dist: xarray[io]
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: shapely
+Requires-Dist: tqdm
+Requires-Dist: typer
+Requires-Dist: requests
+Requires-Dist: schema
+Requires-Dist: structlog
+Requires-Dist: psutil
+Requires-Dist: parse>=1.21.0
+Requires-Dist: rich>=14.3.2
+Provides-Extra: test
+Requires-Dist: pytest>=6.0.0; extra == "test"
+Requires-Dist: hypothesis[numpy]>=6.0.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: coverage[toml]; extra == "test"
+Provides-Extra: types
+Requires-Dist: pandas-stubs; extra == "types"
+Requires-Dist: types-geopandas; extra == "types"
+Requires-Dist: types-requests; extra == "types"
+Requires-Dist: scipy-stubs; extra == "types"
+Provides-Extra: dev
+Requires-Dist: ruff>=0.16.5; extra == "dev"
+Requires-Dist: deptry; extra == "dev"
+Requires-Dist: ty>=0.0.75; extra == "dev"
+Requires-Dist: numpydoc; extra == "dev"

ucgmsim_workflow-2026.9.1/container/Dockerfile

@@ -0,0 +1,84 @@
+# Bootstrap Dockerfile
+FROM ubuntu:latest
+
+# Set noninteractive mode for apt
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Update package lists and install build dependencies
+RUN apt-get update && apt-get install -y \
+        build-essential \
+        cmake \
+        curl \
+        gfortran \
+        git \
+        pkg-config \
+        libfftw3-dev \
+        libpapi-dev \
+        libopenmpi-dev \
+        openmpi-bin \
+        openmpi-common \
+        libopenblas-openmp-dev \
+        libhdf5-dev \
+        libssl-dev \
+        zlib1g-dev \
+        libbz2-dev \
+        libreadline-dev \
+        libsqlite3-dev \
+        libffi-dev \
+        liblzma-dev \
+        libexpat1-dev \
+        libpq-dev \
+        gdal-bin \
+        libgdal-dev \
+        libgdbm-dev \
+        libgdbm-compat-dev \
+        libncurses5-dev \
+        libncursesw5-dev \
+        uuid-dev \
+        libnss3-dev \
+        libedit-dev \
+        libuuid1 \
+        libdb5.3-dev \
+        lzma \
+        tcl-dev \
+        gdb \
+        lcov \
+        ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create software directories (removed uv directory)
+RUN mkdir -p /sw/cargo /sw/rust /sw/python /sw/venv
+
+# Python installation
+ARG PYTHON_VERSION=3.13.12
+RUN curl -o /tmp/Python-${PYTHON_VERSION}.tar.xz \
+        https://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tar.xz && \
+    cd /tmp && \
+    tar xf Python-${PYTHON_VERSION}.tar.xz && \
+    cd Python-${PYTHON_VERSION} && \
+    ./configure --prefix=/sw/python --enable-optimizations && \
+    make -j$(nproc) && \
+    make install && \
+    cd /tmp && \
+    rm -rf Python-${PYTHON_VERSION}*
+
+# Set Environment Paths
+ENV RUSTUP_HOME=/sw/rust
+ENV CARGO_HOME=/sw/cargo
+ENV VIRTUAL_ENV="/sw/venv"
+# Added /sw/python/bin to path early to ensure we use the compiled python
+ENV PATH="$VIRTUAL_ENV/bin:/sw/python/bin:/sw/cargo/bin:$PATH"
+ENV LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"
+
+# Install Rust
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+
+# Setup Virtual Environment and Install via pip
+# openquake.engine 3.26+ requires gdal~=3.13.1, which is sdist-only and refuses to
+# build against the libgdal 3.12.2 that Ubuntu ships. Cap it until libgdal catches up.
+ARG WORKFLOW_VERSION
+RUN test -n "${WORKFLOW_VERSION}" || { echo "WORKFLOW_VERSION build arg is required" >&2; exit 1; } && \
+    python3 -m venv $VIRTUAL_ENV && \
+    pip install --no-cache-dir --upgrade pip setuptools wheel && \
+    pip install --no-cache-dir "ucgmsim-workflow==${WORKFLOW_VERSION}" "openquake.engine<3.26" --no-binary=h5py && \
+    chmod -R a+rX /sw

ucgmsim_workflow-2026.9.1/container/runner.def

@@ -0,0 +1,23 @@
+Bootstrap: docker
+From: earthquakesuc/workflow-bootstrap:latest
+
+%files
+    EMOD3D /EMOD3D
+
+%post
+    cd /EMOD3D && \
+      mkdir build && cd build && \
+      cmake -DHF_TIME_WINDOW=off -DUSE_FFTW=on -DCMAKE_C_FLAGS="-march=x86-64 -mtune=generic -std=gnu89" .. && \
+      make -j $(nproc) genslip_v5.6.2 srf2stoch generic_slip2srf \
+                      hb_high_binmod_v6.0.3
+
+    cd /
+    # Keep only the EMOD3D tools folder and compiled binaries
+    find /EMOD3D -mindepth 1 -maxdepth 1 ! -name "tools" -exec rm -rf {} \;
+
+%environment
+    export RUSTUP_HOME=/sw/rust
+    export CARGO_HOME=/sw/cargo
+    export PATH="/sw/venv/bin:/EMOD3D/tools:/sw/cargo/bin:/sw/python/bin:$PATH"
+    export VIRTUAL_ENV="/sw/venv"
+    export LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"

ucgmsim_workflow-2026.9.1/cylc/flow.cylc

@@ -0,0 +1,69 @@
+[scheduler]
+    allow implicit tasks = True
+[scheduling]
+    [[graph]]
+        R1 = """
+            """
+[runtime]
+    [[root]]
+        platform = mahuika-slurm
+        pre-script = """
+        module load Apptainer
+        """
+        [[[directives]]]
+            --account = nesi00213
+    [[nshm_to_realisation]]
+        platform = localhost
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif nshm2022-to-realisation /nshmdb.db 0 /share/realisation.json develop
+    [[realisation_to_srf]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif realisation-to-srf /share/realisation.json /share/realisation.srf
+    [[generate_stoch]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif generate-stoch /share/realisation.srf /share/realisation.stoch
+    [[generate_velocity_model_parameters]]
+        platform = localhost
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif generate-velocity-model-parameters /share/realisation.json
+    [[generate_velocity_model]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif sh -c "generate-velocity-model /share/realisation.json --use-nzcvm --num-threads ${SLURM_CPUS_PER_TASK:-32} --work-directory /share"
+        [[[directives]]]
+                --cpus-per-task = 32
+                --time = 01:00:00
+    [[convert_vm_hdf5_to_emod3d]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif convert-vm-hdf5-to-emod3d /share/velocity_model.h5 /share/Velocity_Model
+        [[[directives]]]
+                --cpus-per-task = 4 # While we only use 4 threads, consider increasing this to allocate more memory per task, as the conversion can be memory intensive. For MN5, setting this 112 will give entire 256GB of the node to the task.
+                --time = 02:00:00
+    [[generate_station_coordinates]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif generate-station-coordinates /share/realisation.json /share/stations
+    [[generate_model_coordinates]]
+        platform = localhost
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif generate-model-coordinates /share/realisation.json /share/model
+    [[create_e3d_par]]
+        platform = localhost
+        script = apptainer exec /nesi/nobackup/nesi00213/containers/runner_latest.sif create-e3d-par $CYLC_WORKFLOW_SHARE_DIR/realisation.json $CYLC_WORKFLOW_SHARE_DIR/realisation.srf $CYLC_WORKFLOW_SHARE_DIR/Velocity_Model $CYLC_WORKFLOW_SHARE_DIR/stations $CYLC_WORKFLOW_SHARE_DIR/model $CYLC_WORKFLOW_SHARE_DIR/LF --emod3d-path /nesi/project/nesi00213/opt/maui/hybrid_sim_tools/emod3d-mpi_v3.0.8 --scratch-ffp $CYLC_WORKFLOW_SHARE_DIR/LF
+    [[run_emod3d]]
+        platform = maui-xc-slurm
+        pre-script = ""
+        script = srun /nesi/project/nesi00213/opt/maui/hybrid_sim_tools/emod3d-mpi_v3.0.8 -args "par=$CYLC_WORKFLOW_SHARE_DIR/LF/e3d.par"
+        [[[directives]]]
+            --ntasks = 80
+            --hint = nomultithread
+            --time = 00:30:00
+    [[run_hf]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif run-hf /share/realisation.json /share/realisation.stoch /share/stations/stations.ll /share/realisation.hf
+        [[directives]]
+            --cpus-per-task = 128
+            --time = 01:00:00
+    [[plot_ts]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif plot-ts /share/LF/OutBin /share/simulation.m4v
+        
+    [[run_bb]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif bb-sim /share/realisation.json /share/stations/stations.ll /stations.vs30 /share/LF/OutBin /share/realisation.hf /share/Velocity_Model /share/realisation.bb /out
+        [[directives]]
+            --cpus-per-task = 128
+            --time = 01:00:00
+
+    [[im_calc]]
+        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share" /nesi/nobackup/nesi00213/containers/runner_latest.sif im-calc /share/realisation.json /share/realisation.bb /share/im_calc.csv
+        [[directives]]
+            --cpus-per-task = 128
+            --time = 01:00:00

ucgmsim_workflow-2026.9.1/cylc/workflow-setup

@@ -0,0 +1,75 @@
+#!/usr/bin/env bash
+
+CYLC_LATEST_VERSION=$(cylc list-versions | grep "^[0-9]" | sort -r | head -n 1)
+
+# export the correct environment variables to the users bashrc file
+grep -q 'export PROJECT=nesi00213' ~/.bashrc || echo 'export PROJECT=nesi00213' >>~/.bashrc
+grep -q "export CYLC_VERSION=$CYLC_LATEST_VERSION" ~/.bashrc || echo "export CYLC_VERSION=$CYLC_LATEST_VERSION" >>~/.bashrc
+test -d ~/cylc-src -a -d ~/cylc-run || mkdir ~/cylc-src ~/cylc-run
+
+# If the user does not already have an ssh key generated on NeSI login
+# nodes, then we must do so.
+if ! compgen -G "$HOME/.ssh/id_*.pub" >/dev/null; then
+    echo "You are about to be prompted for an ssh key password."
+    echo "You must hit enter (twice) to ensure the key does not have one."
+    sleep 1
+    ssh-keygen
+fi
+
+# In order for cylc to manage jobs via SSH it needs password-less
+# login via SSH, we do that by authorizing the local SSH keys to
+# login.
+
+cat ~/.ssh/id_*.pub >>~/.ssh/authorized_keys
+
+# These permissions must be set for the ssh keys to work.
+chmod 700 ~/.ssh
+chmod 600 ~/.ssh/id_*
+chmod 644 ~/.ssh/id_*.pub
+chmod 750 ~
+
+# Jupyter Notebook Setup
+mkdir -p ~/.cylc/uiserver
+# Beginning with port=21300, so we don't try to give a user a
+# privileged port, find a port that is unique among nesi00213 project
+# members. Configure cylc to host the gui on that port. The port needs
+# to be unique because users will port-forward this port when they
+# connect to the jupyter lab notebook upon executing cylc gui.
+if ! grep -q "$USER=" /nesi/nobackup/nesi00213/cylc_port_maps; then
+    NEXT_WORKFLOW_PORT=$(awk -F= 'BEGIN{port=21299} { if ($2>port) port=$2 fi } END {print port + 1}' /nesi/nobackup/nesi00213/cylc_port_maps)
+
+    cat <<EOF >~/.cylc/uiserver/jupyter_config.py
+c.ServerApp.open_browser=False
+c.ServerApp.port=$NEXT_WORKFLOW_PORT
+EOF
+    # Record the cylc port map so that the next user can find a unique
+    # port for themselves.
+    echo "$USER=$NEXT_WORKFLOW_PORT" >>/nesi/nobackup/nesi00213/cylc_port_maps
+else
+    NEXT_WORKFLOW_PORT=$(grep "$USER=" /nesi/nobackup/nesi00213/cylc_port_maps | cut -d= -f2)
+fi
+
+cat <<EOF
+You are correctly setup for Cylc $CYLC_LATEST_VERSION.
+Check that your ssh configuration is working correctly by executing on mahuika:
+
+	ssh mahuika02 echo Hello from Mahuika02
+
+If this command does not prompt for a password, you are good to go.
+
+To connect to cylc gui run:
+
+On mahuika:
+	cylc gui
+
+Take note of the url cylc asks you to copy and paste, the one with "127.0.0.1" in the output. It will look something like:
+
+	http://127.0.0.1:$NEXT_WORKFLOW_PORT/cylc?token=99122750aca901546a5d10ffc2d65b27
+
+but your token will vary.
+
+On your machine:
+	ssh -N -L $NEXT_WORKFLOW_PORT:localhost:$NEXT_WORKFLOW_PORT mahuika
+
+Then open the url cylc asked you to copy and paste earlier.
+EOF