Merge pull request #5 from FAIRmat-NFDI/3-improve-step-data-model

3 improve step data model
FAIRmat-NFDI · Nov 6, 2024 · 95b3e9e · 95b3e9e
2 parents 4a22454 + 9c6bf79
commit 95b3e9e
Show file tree

Hide file tree

Showing 11 changed files with 2,557 additions and 1,133 deletions.
diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
@@ -5,10 +5,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.12
     - name: Install dependencies
       run: |
         pip install --upgrade pip
@@ -27,10 +27,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.12
     - name: Build the package
       run: |
         pip install --upgrade pip

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ NOMAD plugin for driving experiments/simulations using bayesian optimization
 
 ----
 
-This `nomad`_ plugin was generated with `Cookiecutter`_ along with `@nomad`_'s `cookiecutter-nomad-plugin`_ template.
+This `nomad` plugin was generated with `Cookiecutter` along with `@nomad`'s `cookiecutter-nomad-plugin` template.
 
 
 ### Install
@@ -70,7 +70,7 @@ on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/pac
 
 ### Documentation on Github pages
 
-To deploy documentation on Github pages, make sure to [enable GitHub pages via the repo settings](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site#publishing-from-a-branch). 
+To deploy documentation on Github pages, make sure to [enable GitHub pages via the repo settings](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site#publishing-from-a-branch).
 
 To view the documentation locally, install the documentation related packages using:
 
@@ -85,7 +85,7 @@ mkdocs serve
 
 ### Template update
 
-We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests. 
+We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests.
 
 To run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project).
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -27,7 +27,7 @@ maintainers = [
 license = { file = "LICENSE" }
 dependencies = [
     "nomad-lab>=1.3.0",
-    "baybe",
+    "baybe>=0.11.2",
     "structlog",
 ]
 
@@ -67,7 +67,6 @@ exclude = [
 line-length = 88
 indent-width = 4
 
-
 [tool.ruff.lint]
 select = [
     # pycodestyle

diff --git a/src/nomad_bayesian_optimization/apps/tasks.py b/src/nomad_bayesian_optimization/apps/tasks.py
@@ -16,22 +16,17 @@
     search_quantities=SearchQuantities(include=[f'*#{schema_name}']),
     columns=[
         Column(quantity='entry_create_time', selected=True),
-        Column(quantity=f'data.optimization.finished#{schema_name}', selected=True),
-        Column(quantity=f'data.optimization.status#{schema_name}', selected=True),
+        Column(quantity=f'data.status#{schema_name}', selected=True),
         Column(quantity=f'data.objective.target.name#{schema_name}', selected=True),
         Column(
-            quantity=f'data.searchspace.continuous.parameters[*].name#{schema_name}',
-            selected=True,
-        ),
-        Column(
-            quantity=f'data.steps[*].sources[*].materials[*].substance_name#{schema_name}',
+            quantity=f'data.parameters[*].name#{schema_name}',
             selected=True,
         ),
     ],
     menu=Menu(
         items=[
             MenuItemTerms(
-                quantity=f'data.optimization.status#{schema_name}',
+                quantity=f'data.status#{schema_name}',
                 show_input=False,
             ),
             Menu(
@@ -67,33 +62,10 @@
             ),
             Menu(
                 size='xs',
-                title='Search space',
+                title='Parameters',
                 items=[
-                    Menu(
-                        title='Discrete',
-                        items=[
-                            MenuItemTerms(
-                                quantity=f'data.searchspace.discrete.parameters.name#{schema_name}',
-                            )
-                        ],
-                    ),
-                    Menu(
-                        title='Continuous',
-                        items=[
-                            MenuItemTerms(
-                                quantity=f'data.searchspace.continuous.parameters.name#{schema_name}',
-                            ),
-                            MenuItemHistogram(
-                                x=Axis(
-                                    search_quantity=f'data.searchspace.continuous.parameters.bounds.lower#{schema_name}'
-                                )
-                            ),
-                            MenuItemHistogram(
-                                x=Axis(
-                                    search_quantity=f'data.searchspace.continuous.parameters.bounds.upper#{schema_name}'
-                                )
-                            ),
-                        ],
+                    MenuItemTerms(
+                        quantity=f'data.parameters.name#{schema_name}',
                     ),
                 ],
             ),
@@ -124,16 +96,6 @@
                     ),
                 ],
             ),
-            Menu(
-                title='Optimization',
-                items=[
-                    MenuItemHistogram(
-                        x=Axis(
-                            search_quantity=f'data.optimization.n_steps#{schema_name}'
-                        )
-                    )
-                ],
-            ),
         ]
     ),
     filters_locked={'section_defs.definition_qualified_name': [schema_name]},

diff --git a/src/nomad_bayesian_optimization/example_uploads/getting_started/notebook.ipynb b/src/nomad_bayesian_optimization/example_uploads/getting_started/notebook.ipynb
@@ -130,11 +130,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/lauri/repositories/nomad-FAIR/nomad/datamodel/metainfo/simulation/__init__.py:52: DeprecationWarning: Usage of Environment is deprecated and will be removed in the future.\n",
+      "  m_env = Environment()\n"
+     ]
+    }
+   ],
    "source": [
-    "\n",
     "import numpy as np\n",
     "\n",
     "from nomad_bayesian_optimization.schema_packages.experiments import CVDExperiment\n",
@@ -190,7 +198,20 @@
    "metadata": {
     "id": "4PSMvrp-sdDL"
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "New recommendation:\n",
+      "         substrate  gas_flow_rate  temperature\n",
+      "0  Gallium nitride       0.388846    466.73735\n",
+      "Start testing recommendation...\n",
+      "Testing finished, refractive_index: 1.597450224449405\n",
+      "Optimization finished!\n"
+     ]
+    }
+   ],
    "source": [
     "import json\n",
     "\n",
@@ -222,12 +243,19 @@
     "\n",
     "# At the end of the run, lets store the whole optimization run into an entry\n",
     "archive = EntryArchive()\n",
-    "bopt = BayesianOptimization.from_baybe_campaign(campaign)\n",
+    "bopt = BayesianOptimization.from_baybe(campaign)\n",
     "archive.data = bopt\n",
     "bopt.normalize(archive, None)\n",
     "with open('example.archive.json', 'w') as fout:\n",
     "    json.dump(archive.m_to_dict(), fout, indent=2)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {