Added jupyter notebook runner

Added new packages to dockerfile

Dockerfile

@@ -1,3 +1,3 @@
 FROM docker.io/continuumio/miniconda3:24.5.0-0
-RUN conda install numpy matplotlib h5py
-RUN python -m pip install hdfmap
+RUN conda install -c conda-forge numpy matplotlib h5py hdf5plugin imageio jupyter nbconvert nbformat papermill
+RUN python -m pip install hdfmap nexus2srs

jupyter_notebook_script.yaml

@@ -0,0 +1,46 @@
+apiVersion: argoproj.io/v1alpha1
+kind: ClusterWorkflowTemplate
+metadata:
+  name: mmg-test-python
+spec:
+  entrypoint: mmg-test-python
+  templates:
+    - name: notebook
+      script:
+        image: ghcr.io/diamondlightsource/magnetic-materials-workflows:0.1.0-rc4
+        command:
+          - jupyter-nbconvert
+          - --execute
+          - --stdin
+          - --to
+          - html
+          - --output
+          - notebook
+          - --output-dir
+          - /outputs
+        source: |
+          {{ .Files.Get "notebooks/notebook.ipynb" | fromJson | toPrettyJson | nindent 10 }}
+        volumeMounts:
+          - name: outputs
+            mountPath: /outputs
+  volumeClaimTemplates:
+    - metadata:
+        name: tmpdir
+      spec:
+        accessModes: [ "ReadWriteOnce" ]
+        resources:
+          requests:
+            storage: 1Gi
+        storageClassName: local-path
+  arguments:
+    parameters:
+      - name: visitdir
+        valueFrom:
+          configMapKeyRef:
+            name: sessionspaces
+            key: data_directory
+  volumes:
+    - name: session
+      hostPath:
+        path: "{{ workflow.parameters.visitdir }}"
+        type: Directory

notebooks/mmg_test_processor.ipynb

@@ -0,0 +1,175 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "0552e358",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Processor requirements\n",
+    "# The first two cells must be code cells, inpath and outpath define the scan file location and output location\n",
+    "inpath = \"\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "e6a617f0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "outpath = \"\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4d8b6081",
+   "metadata": {},
+   "source": [
+    "# Test Processor\n",
+    "\n",
+    "Load some modules and see what is available"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b06a18c7-499d-4536-8e36-fbf4cedd28d3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(inpath)\n",
+    "print(outpath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "92330199",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def module_info():\n",
+    "    import sys\n",
+    "    out = 'Python version %s' % sys.version\n",
+    "    out += '\\n at: %s' % sys.executable\n",
+    "    # Modules\n",
+    "    import numpy\n",
+    "    out += '\\n     numpy version: %s' % numpy.__version__\n",
+    "    import h5py\n",
+    "    out += '\\n      h5py version: %s' % h5py.__version__\n",
+    "    try:\n",
+    "        import imageio\n",
+    "        out += '\\n   imageio version: %s' % imageio.__version__\n",
+    "    except ImportError:\n",
+    "        out += '\\n   imageio version: None'\n",
+    "    try:\n",
+    "        import hdf5plugin\n",
+    "        out += '\\nhdf5plugin version: %s' % hdf5plugin.version\n",
+    "    except ImportError:\n",
+    "        out += '\\nhdf5plugin version: None'\n",
+    "    try:\n",
+    "        import matplotlib\n",
+    "        out += '\\nmatplotlib version: %s' % matplotlib.__version__\n",
+    "    except ImportError:\n",
+    "        out += '\\nmatplotlib version: None'\n",
+    "    try:\n",
+    "        import lmfit\n",
+    "        out += '\\n     lmfit version: %s' % lmfit.__version__\n",
+    "    except ImportError:\n",
+    "        out += '\\n     lmfit version: None'\n",
+    "    try:\n",
+    "        import hdfmap\n",
+    "        out += '\\n    hdfmap version: %s' % hdfmap.__version__\n",
+    "    except ImportError:\n",
+    "        out += '\\n    hdfmap version: None'\n",
+    "    try:\n",
+    "        import nexus2srs\n",
+    "        out += '\\n nexus2srs version: %s' % nexus2srs.__version__\n",
+    "    except ImportError:\n",
+    "        out += '\\n nexus2srs version: None'\n",
+    "    \n",
+    "    import os\n",
+    "    out += '\\nRunning in directory: %s\\n' % os.path.abspath('.')\n",
+    "    return out"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "ac437f62",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Python version 3.11.3 | packaged by conda-forge | (main, Apr  6 2023, 08:57:19) [GCC 11.3.0]\n",
+      " at: /dls_sw/apps/python/miniforge/4.10.0-0/envs/python3.11/bin/python3.11\n",
+      "     numpy version: 1.24.3\n",
+      "      h5py version: 3.8.0\n",
+      "   imageio version: 2.28.1\n",
+      "hdf5plugin version: 4.1.2\n",
+      "matplotlib version: 3.7.1\n",
+      "     lmfit version: 1.2.1\n",
+      "    hdfmap version: 0.7.0\n",
+      " nexus2srs version: None\n",
+      "Running in directory: /dls_sw/i06/scripts/gda-zocalo/notebooks\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(module_info())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "id": "496f9973",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['In', 'Out', '_', '_11', '__', '___', '__builtin__', '__builtins__', '__doc__', '__loader__', '__name__', '__package__', '__spec__', '_dh', '_i', '_i1', '_i10', '_i11', '_i12', '_i13', '_i14', '_i15', '_i16', '_i17', '_i18', '_i19', '_i2', '_i20', '_i21', '_i3', '_i4', '_i5', '_i6', '_i7', '_i8', '_i9', '_ih', '_ii', '_iii', '_oh', 'exit', 'get_ipython', 'inpath', 'module_info', 'open', 'outpath', 'quit']\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(dir())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "88d9c494",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

python_script.yaml

@@ -26,7 +26,7 @@ spec:
         value: | 
           print(f"Scan command: {cmd}")
     script:
-      image: ghcr.io/diamondlightsource/magnetic-materials-workflows:0.1.0-rc2
+      image: ghcr.io/diamondlightsource/magnetic-materials-workflows:0.1.0-rc3
       volumeMounts:
         - name: session
           mountPath: "{{ workflow.parameters.visitdir }}"
@@ -42,3 +42,7 @@ spec:
         cmd = scan('scan_command')
 
         {{inputs.parameters.python-code}}
+    outputs:
+      artifacts:
+        - name: 'some data'
+          path: '/tmp/data.json'