add dockerfile and workflow to build a marimo

Author: alinelena

.github/workflows/docker-jupyter-image.yml

@@ -1,4 +1,4 @@
-name: ghcr
+name: ghcr-jupyter
 on:
   push:
 #    branches: [ "main" ]

.github/workflows/docker-marimo-image.yml

@@ -0,0 +1,33 @@
+name: ghcr-marimo
+on:
+  push:
+#    branches: [ "main" ]
+#  pull_request:
+#    branches: [ "main" ]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+    steps:
+      - name: 'clone the repo'
+        uses: actions/checkout@v4
+      - name: 'login to ghcr'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./containers
+          file: ./containers/Dockerfile.marimo
+          push: true
+          tags: |
+            ghcr.io/stfc/janus-core/marimo:${{ github.sha }}
+            ghcr.io/stfc/janus-core/marimo:latest

containers/Dockerfile.marimo

@@ -0,0 +1,66 @@
+FROM python:3.12-slim
+
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+
+LABEL maintainer="Alin Elena <[email protected]>"
+ARG UID="1001"
+ARG GID="100"
+
+ENV user=drFaustroll
+ENV group=drFaustroll
+RUN useradd -m ${user}
+WORKDIR /app
+
+USER root
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt update --yes && \
+    apt upgrade --yes && \
+    apt install --yes --no-install-recommends \
+    ca-certificates \
+    locales \
+    sudo \
+    tini \
+    wget bzip2 curl git gcc g++ make cmake   && \
+    apt clean && rm -rf /var/lib/apt/lists/* && \
+    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+
+ARG marimo_version=0.14.16
+ENV MARIMO_SKIP_UPDATE_CHECK=1
+ENV UV_SYSTEM_PYTHON=1
+RUN uv pip install --no-cache-dir marimo==${marimo_version} && \
+  mkdir -p /app/data && \
+  chown -R ${user}:${group} /app
+
+COPY --chown=${user}:${group} assets/tutorials tutorials
+
+ENV PORT=8842
+EXPOSE $PORT
+
+ENV HOST=0.0.0.0
+
+RUN uv pip install --no-cache-dir marimo[recommended,lsp,sql] altair pandas python-lsp-server websockets \
+  duckdb \
+  sqlglot \
+  vegafusion vl-convert-python \
+  ruff \
+  openai \
+  nbformat \
+  pytest
+RUN uv pip install --no-cache-dir 'janus-core[all]@git+https://github.com/stfc/janus-core.git@main'
+RUN uv pip install  --no-cache-dir cuequivariance==0.5.1 \
+  cuequivariance-torch==0.5.1 \
+  cuequivariance-ops-torch-cu12==0.5.1 \
+  torchvision \
+  pack-mm \
+  seaborn \
+  data-tutorials \
+  pymatviz \
+  opentsne \
+  pymatgen \
+  pymatviz \
+  git+https://github.com/imagdau/aseMolec@main
+
+CMD marimo edit --no-token -p $PORT --host $HOST

containers/assets/tutorials/geometry.py

@@ -0,0 +1,124 @@
+from __future__ import annotations
+
+import marimo
+
+__generated_with = "0.14.16"
+app = marimo.App(width="medium")
+
+
+@app.cell
+def _():
+    from ase.build import bulk
+    from ase.io import read, write
+    import marimo as mo
+    from pymatgen.io.ase import AseAtomsAdaptor
+    import pymatviz as view
+
+    from janus_core.calculations.geom_opt import GeomOpt
+
+    return AseAtomsAdaptor, GeomOpt, bulk, mo, read, view, write
+
+
+@app.cell
+def _(bulk, write):
+    device = "cpu"
+    a = 6.0
+    NaCl = bulk(
+        "NaCl", crystalstructure="rocksalt", cubic=True, orthorhombic=True, a=a
+    ) * (2, 2, 2)
+    NaCl.rattle(stdev=0.1, seed=2042)
+    write("NaCl.extxyz", NaCl)
+    return (NaCl,)
+
+
+@app.cell
+def _(AseAtomsAdaptor, NaCl, view):
+    struct = AseAtomsAdaptor().get_structure(NaCl)
+
+    s_widget = view.StructureWidget(
+        structure=struct, show_bonds=True, bonding_strategy="nearest_neighbor"
+    )
+    s_widget
+    return
+
+
+@app.cell
+def _(mo):
+    # Create a form with multiple elements
+    form = (
+        mo.md("""
+        **Geomtry Optimisation**
+
+        Upload Structure {structure}
+
+        optimize {optimize}
+
+        {fmax}
+
+        ML model :{model}
+    """)
+        .batch(
+            structure=mo.ui.file(label="Structure"),
+            fmax=mo.ui.number(label="fmax", value=0.01),
+            optimize=mo.ui.radio(
+                options={"Just coordinates": 1, "Cell vectors only": 2, "Full": 3},
+                value="Full",  # initial value
+                label="choose a methood",
+            ),
+            model=mo.ui.dropdown(
+                options={
+                    "MACE_MP-small": ("mace_mp", "small"),
+                    "MACE_MP-medium": ("mace_mp", "medium"),
+                },
+                value="MACE_MP-small",
+            ),
+        )
+        .form(
+            show_clear_button=True,
+            bordered=True,
+            submit_button_disabled=False,
+            submit_button_tooltip="start the calculation",
+        )
+    )
+    form
+    return (form,)
+
+
+@app.cell
+def _(form):
+    settings = form.value
+    print(settings)
+    return (settings,)
+
+
+@app.cell
+def _(GeomOpt, form, mo, read, settings):
+    mo.stop(form.value is None, mo.md("Upload a file and submit"))
+
+    from io import BytesIO
+
+    x = settings["structure"][0]
+    m = read(BytesIO(x.contents), format="cif")
+
+    model = settings["model"]
+    optimized_NaCl = GeomOpt(
+        struct=m,
+        model=model[1],
+        arch=model[0],
+        fmax=settings["fmax"],
+        optimizer="FIRE",
+        write_traj=True,
+    )
+
+    optimized_NaCl.run()
+    return (m,)
+
+
+@app.cell
+def _(m):
+    m
+    return
+
+
+if __name__ == "__main__":
+    app.run()

containers/assets/tutorials/hello.py

@@ -0,0 +1,14 @@
+from __future__ import annotations
+
+import marimo
+
+app = marimo.App()
+
+
+@app.cell
+def __():
+    return
+
+
+if __name__ == "__main__":
+    app.run()

pyproject.toml

@@ -171,7 +171,7 @@ pythonpath = ["."]
 source=["janus_core"]
 
 [tool.ruff]
-exclude = ["conf.py", "*ipynb"]
+exclude = ["conf.py", "*ipynb","containers/assets/tutorials/*.py"]
 target-version = "py310"
 
 [tool.ruff.lint]