final adjustments before production-ready

daniel-sintef · Jun 9, 2023 · 60ea6e1 · 60ea6e1
1 parent a62a17a
commit 60ea6e1
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Showing 6 changed files with 19 additions and 183 deletions.
diff --git a/openapi.yml b/openapi.yml
@@ -12,16 +12,16 @@ info:
       - email
       - openid
       - profile
-    callback: https://materials-marketplace.aiidalab.net/hub/oauth_callback
-  x-external-hostname: https://materials-marketplace.aiidalab.net
+    callback: https://aiidalab.materials-marketplace.eu/hub/oauth_callback
+  x-external-hostname: https://aiidalab.materials-marketplace.eu
   # x-image: https://raw.githubusercontent.com/aiidalab/aiidalab-qe/v20.12.0/miscellaneous/logos/QE.jpg
   x-contacts:
     - [email protected]
   x-products:
     - name: AiiDAlab UC3 App
       productId: 55305f0c-f1a1-4ee3-8c31-a31c45b61af3
 servers:
-  - url: https://materials-marketplace.aiidalab.net
+  - url: https://aiidalab.materials-marketplace.eu
 
 paths:
   /hub/user-redirect/apps/apps/aiidalab-mp-uc3/uc3.ipynb:

diff --git a/setup.cfg b/setup.cfg
@@ -26,7 +26,7 @@ python_requires = >=3.7
 install_requires =
     aiida-core~=2.1,<3
     aiidalab>=21.09.0
-    aiidalab-widgets-base==2.0.0b1
+    aiidalab-widgets-base==2.0.0
 
 [flake8]
 ignore =

diff --git a/setup.py b/setup.py
@@ -28,7 +28,7 @@ def gitlab_token(source: "Optional[Union[Path, str]]" = None) -> str:
             f"aiida-marketusercase3 @ git+https://github.com/daniel-sintef/aiida-marketusercase3.git@master",
             "aiida-core~=2.1,<3",
             "aiidalab>=21.09.0",
-            "aiidalab-widgets-base==2.0.0b1",
+            "aiidalab-widgets-base==2.0.0",
         ]
     )
 )
diff --git a/uc3.ipynb b/uc3.ipynb
@@ -132,171 +132,6 @@
     "    ]\n",
     ")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#display(monitorprocess_step)\n",
-    "#monitorprocess_step.process = \"8cc8cbe9-81ab-4821-8dad-b25e73de9327\"\n",
-    "#monitorprocess_step.output\n",
-    "#monitorprocess_step.state\n",
-    "#monitorprocess_step.state\n",
-    "#display(widget)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "39bc69ef0cab47d0824e4081e23a6b6b",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "64ea8cc9144b437a87359bfd027545f3",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "AppLayout(children=(DisplayFinalOutput(children=(Output(),), layout=Layout(grid_area='center')),), layout=Layo…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "import json\n",
-    "import uuid\n",
-    "import logging\n",
-    "import subprocess\n",
-    "from copy import copy\n",
-    "from pathlib import Path\n",
-    "\n",
-    "import ipywidgets as ipw\n",
-    "import shortuuid\n",
-    "import traitlets\n",
-    "from aiida.engine import ProcessState, submit\n",
-    "from aiida.orm import ArrayData, Code, Dict, Str, ProcessNode, load_code, load_node\n",
-    "from aiida.plugins import CalculationFactory\n",
-    "from aiidalab_widgets_base import (\n",
-    "    AiidaNodeViewWidget,\n",
-    "    ProcessMonitor,\n",
-    "    ProcessNodesTreeWidget,\n",
-    "    WizardAppWidgetStep,\n",
-    ")\n",
-    "\n",
-    "from uc3.base_widgets_mod import ComputationalResourcesWidget\n",
-    "import matplotlib.pyplot as plt\n",
-    "from io import BytesIO\n",
-    "import base64\n",
-    "\n",
-    "from ipywidgets import AppLayout, Button, Layout, Label\n",
-    "import numpy as np\n",
-    "from numpy import random\n",
-    "from scipy import ndimage\n",
-    "from traitlets import HasTraits, Instance, observe\n",
-    "\n",
-    "class TestOutput(HasTraits):\n",
-    "    area_flux = ndimage.gaussian_filter(random.normal(50, 5, size=(512, 512)), sigma=10).ravel()\n",
-    "    volume_flux = ndimage.gaussian_filter(random.normal(100, 10, size=(512, 512)), sigma=10).ravel()\n",
-    "    particle_size = ndimage.gaussian_filter(random.normal(10, 2, size=(512, 512)), sigma=10).ravel()\n",
-    "    \n",
-    "    def get_array(self, foo):\n",
-    "        return [1,2,3,4,5]\n",
-    "\n",
-    "class DisplayFinalOutput(ipw.VBox, WizardAppWidgetStep):\n",
-    "\n",
-    "#     output = traitlets.Instance(ArrayData, allow_none=True)\n",
-    "    output = traitlets.Instance(TestOutput, allow_none=True)\n",
-    "\n",
-    "    def __init__(self, **kwargs):\n",
-    "        self.output_figure = plt.figure()\n",
-    "        self.final_output = ipw.Output()\n",
-    "\n",
-    "        super().__init__([self.final_output], **kwargs)\n",
-    "\n",
-    "    @traitlets.observe(\"output\")\n",
-    "    def _call_observe(self, change):\n",
-    "        self._observe_configuration(self, change)\n",
-    "\n",
-    "    def _observe_configuration(self, _, change):\n",
-    "        \"Format and show the user inputs.\"\n",
-    "        if change[\"new\"]:\n",
-    "            output = self.output\n",
-    "            area_flux = output.get_array(\"area_flux\")\n",
-    "            volume_flux = output.get_array(\"volume_flux\")\n",
-    "            particle_size = output.get_array(\"particle_size\")\n",
-    "            display_dict = {\n",
-    "                \"Area Flux\": area_flux,\n",
-    "                \"Volume Flux\": volume_flux,\n",
-    "                \"Particle Size\": particle_size,\n",
-    "            }\n",
-    "\n",
-    "            # Create a plot of the data\n",
-    "            x = [1, 2, 3, 4, 5]\n",
-    "            y = [2, 4, 5, 6, 7]\n",
-    "            plt.plot(x, y)\n",
-    "            plt.xlabel('X axis')\n",
-    "            plt.ylabel('Y axis')\n",
-    "\n",
-    "            # Save the plot to a buffer\n",
-    "            buffer = BytesIO()\n",
-    "            plt.savefig(buffer, format='svg')\n",
-    "            plt.close()\n",
-    "\n",
-    "            # Convert the buffer to a base64-encoded string and create the SVG image\n",
-    "            svg_data = buffer.getvalue().decode()\n",
-    "            base64_data = base64.b64encode(svg_data.encode()).decode()\n",
-    "            svg_image = f'<img src=\"data:image/svg+xml;base64,{base64_data}\">'\n",
-    "\n",
-    "            # Show the user inputs and the plot\n",
-    "            self.final_output.clear_output(wait=True)\n",
-    "            with self.final_output:\n",
-    "#                 display(ipw.HTML(f\"<h4>Configuration</h4><pre>{json.dumps(display_dict, indent=2)}</pre>\"))\n",
-    "                display(ipw.HTML(svg_image))\n",
-    "\n",
-    "            self.state = self.State.SUCCESS\n",
-    "        else:\n",
-    "            self.final_output.value = (\n",
-    "                \"<h4>Configuration</h4>[Please configure user inputs]\"\n",
-    "            )\n",
-    "\n",
-    "\n",
-    "output_data = TestOutput()\n",
-    "\n",
-    "output_widget = DisplayFinalOutput(output=output_data)\n",
-    "\n",
-    "AppLayout(center=output_widget)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -315,7 +150,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.8.10"
   },
   "vscode": {
    "interpreter": {

diff --git a/uc3_ap2.ipynb b/uc3_ap2.ipynb
@@ -116,12 +116,12 @@
     "  ['amf', 'amf', 0],\n",
     "  ['macropor', 'macropor', 0],\n",
     "  ['macrotor', 'macrotor', 0],\n",
-    "  ['k1', 'k1', 0],\n",
-    "  ['ea1', 'ea1', 0],\n",
-    "  ['k2', 'k2', 0],\n",
-    "  ['ea2', 'ea2', 0],\n",
-    "  ['koeq', 'koeq', 0],\n",
-    "  ['dhh20', 'dhh20', 0]\n",
+    "  ['k1', 'k1', 16676.31155],\n",
+    "  ['ea1', 'ea1', 96636],\n",
+    "  ['k2', 'k2', 6210120111],\n",
+    "  ['ea2', 'ea2', 133788],\n",
+    "  ['koeq', 'koeq', 1593.272279],\n",
+    "  ['dhh20', 'dhh20', -4880]\n",
     "])\n",
     "\n",
     "\n",

diff --git a/uc3_ap3.ipynb b/uc3_ap3.ipynb
@@ -108,19 +108,20 @@
     "\n",
     "computer_code_setup_step = ComputerCodeSetupStep(auto_advance=True)\n",
     "configure_userinput_step = ConfigureUserInputStep(auto_advance=True, description_label_default=[  \n",
+    "  ['dmf', 'dmf', 0],\n",
     "  ['gfr', 'gfr', 0],\n",
     "  ['ch4mf', 'ch4mf', 0],\n",
     "  ['h2omf', 'h2omf', 0],\n",
     "  ['surfa', 'surfa', 0],\n",
     "  ['amf', 'amf', 0],\n",
     "  ['macropor', 'macropor', 0],\n",
     "  ['macrotor', 'macrotor', 0],\n",
-    "  ['k1', 'k1', 0],\n",
-    "  ['ea1', 'ea1', 0],\n",
-    "  ['k2', 'k2', 0],\n",
-    "  ['ea2', 'ea2', 0],\n",
-    "  ['koeq', 'koeq', 0],\n",
-    "  ['dhh20', 'dhh20', 0]\n",
+    "  ['k1', 'k1', 16676.31155],\n",
+    "  ['ea1', 'ea1', 96636],\n",
+    "  ['k2', 'k2', 6210120111],\n",
+    "  ['ea2', 'ea2', 133788],\n",
+    "  ['koeq', 'koeq', 1593.272279],\n",
+    "  ['dhh20', 'dhh20', -4880]\n",
     "])\n",
     "\n",
     "\n",