obi-notebook 0.2.dev2__tar.gz → 0.4__tar.gz

{obi_notebook-0.2.dev2 → obi_notebook-0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.2.dev2
+Version: 0.4
 Summary: convenience functions for OBI notebooks
 Author-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
 Maintainer-email: Open Brain Institute <jean-denis.courcol@epfl.ch>

{obi_notebook-0.2.dev2 → obi_notebook-0.4}/example.ipynb

@@ -3,15 +3,86 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "7eb47475-67c6-499a-a2b4-19f8a64974d0",
+   "id": "d139baec",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "production\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/mwr/Documents/repositories/obi-notebook/.venv/lib/python3.13/site-packages/obi_notebook/get_environment.py:22: RuntimeWarning: No environment specified. Using production.\n",
+      "  warnings.warn(f\"No environment specified. Using production.\",\n"
+     ]
+    }
+   ],
    "source": [
+    "import os\n",
+    "\n",
     "import obi_auth\n",
     "\n",
-    "from obi_notebook import get_entities, get_projects\n",
+    "from obi_notebook import get_entities, get_environment, get_projects\n",
+    "from obi_notebook.get_environment import VAR_ENVIRONMENT\n",
+    "\n",
+    "# Should raise warning: Environment not selected.\n",
+    "environment_str = get_environment.get_environment()\n",
+    "print(environment_str)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "304f4266",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "production\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/mwr/Documents/repositories/obi-notebook/.venv/lib/python3.13/site-packages/obi_notebook/get_environment.py:19: RuntimeWarning: Specified environment 'invalid' unknown. Using production.\n",
+      "  warnings.warn(f\"Specified environment '{var}' unknown. Using production.\",\n"
+     ]
+    }
+   ],
+   "source": [
+    "os.environ[VAR_ENVIRONMENT] = \"invalid\"\n",
     "\n",
-    "environment_str = \"staging\""
+    "# Should raise warning: Environment unknown.\n",
+    "environment_str = get_environment.get_environment()\n",
+    "print(environment_str)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "7eb47475-67c6-499a-a2b4-19f8a64974d0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "staging\n"
+     ]
+    }
+   ],
+   "source": [
+    "os.environ[VAR_ENVIRONMENT] = \"staging\"\n",
+    "environment_str = get_environment.get_environment()\n",
+    "print(environment_str)"
    ]
   },
   {
@@ -19,12 +90,12 @@
    "id": "4d984b92-cadd-4b07-9813-b2333272610f",
    "metadata": {},
    "source": [
-    "get authentication token for production"
+    "get authentication token"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "id": "323cb45c-91e3-451f-8a80-374e61433d31",
    "metadata": {},
    "outputs": [],
@@ -42,14 +113,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 5,
    "id": "77c47560-1163-4466-83fc-43abc6e0801a",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "639a72897c7045f78bb7aea5afbec767",
+       "model_id": "45fd425a2ed84685b37a3f567f960a23",
        "version_major": 2,
        "version_minor": 0
       },
@@ -62,12 +133,12 @@
     }
    ],
    "source": [
-    "project_context = get_projects.get_projects(token, env=\"staging\")"
+    "project_context = get_projects.get_projects(token)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "id": "d538dcac-1bdc-496b-8840-a7b32ea842ed",
    "metadata": {},
    "outputs": [
@@ -77,7 +148,7 @@
        "ProjectContext(project_id=UUID('32008ab5-76cf-47cd-b98b-a5013b30b533'), virtual_lab_id=UUID('1d8cccc0-f992-46aa-aac6-88e63c914314'), environment=<DeploymentEnvironment.staging: 'staging'>)"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -88,14 +159,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 7,
    "id": "93029f77-d71f-40f4-8c4d-9f23d2b650bc",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e4b6463129a546d394d57efc46d07d7c",
+       "model_id": "b92bedf59a6a49c4b0c6d9dcf5da4268",
        "version_major": 2,
        "version_minor": 0
       },
@@ -109,7 +180,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "9201fb70a891499cadada69780277194",
+       "model_id": "36957a0de8ea476f9fc97dbd665740d3",
        "version_major": 2,
        "version_minor": 0
       },
@@ -135,25 +206,22 @@
     "    default_scale=\"small\",\n",
     "    exclude_scales=[\"single\"],\n",
     "    add_columns=[\"subject.name\"],\n",
-    "    env=environment_str,\n",
     ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "id": "da699ed4-39fd-4602-b54d-58a0b58c2539",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "['b86271b6-c56f-4c26-b502-05ef5bb514b6',\n",
-       " '3877500c-126d-410c-aa09-e44831464e80',\n",
-       " 'd66cea8b-5c9d-4bfb-bbfd-ca3d5fb5f12c']"
+       "['c940188a-5408-4185-ab3b-dbb20de16621']"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -164,14 +232,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 9,
    "id": "a5f5445d-a61a-4fbe-962f-51e701434771",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "5fb0a08d2ce94d58a039c47fdd2f217f",
+       "model_id": "04360c5e3d5a4d318fa446f3e06e9853",
        "version_major": 2,
        "version_minor": 0
       },
@@ -185,7 +253,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a0c7ca20d54946f2af3e181c3adb3d70",
+       "model_id": "9247a1fde0a7438d853325c8a0eaf428",
        "version_major": 2,
        "version_minor": 0
       },
@@ -209,25 +277,22 @@
     "    project_context=project_context,\n",
     "    page_size=100,\n",
     "    add_columns=[\"mtypes\"],\n",
-    "    env=environment_str,\n",
     ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 10,
    "id": "2c9d28c4",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "['50248fe3-83bd-4c88-917b-63bcf0e01385',\n",
-       " '1c8ce2b1-3da1-4953-9b1b-bee8656000c4',\n",
-       " '15d02969-1e40-40ba-9081-d475d05897fd']"
+       "['afa2434f-1ccc-4fff-a047-d399e59768c9']"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -238,14 +303,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "id": "90757b52",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c2a91b53873b4e1fa54c161a59830f6b",
+       "model_id": "a3915f160d944f14b1a401e643b1f7e1",
        "version_major": 2,
        "version_minor": 0
       },
@@ -259,7 +324,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a08fd579c61b4377a0dd01478a5951be",
+       "model_id": "d1b44ab0d11146a1a11e3f32df4ceeba",
        "version_major": 2,
        "version_minor": 0
       },
@@ -273,7 +338,7 @@
    ],
    "source": [
     "cell_mesh_ids = []\n",
-    "circuit_ids = get_entities.get_entities(\n",
+    "cell_mesh_ids = get_entities.get_entities(\n",
     "    \"em-cell-mesh\",\n",
     "    token,\n",
     "    cell_mesh_ids,\n",
@@ -282,24 +347,23 @@
     "    show_pages=True,\n",
     "    project_context=project_context,\n",
     "    page_size=10,\n",
-    "    env=environment_str,\n",
     "    add_columns=[\"dense_reconstruction_cell_id\", \"subject.name\"],\n",
     ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "id": "6964ebe2",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "['2205be1a-a6db-4523-9a7b-0af309996583']"
+       "['e915d259-d03a-4544-8109-a86bbd4cd722']"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }

{obi_notebook-0.2.dev2 → obi_notebook-0.4}/src/obi_notebook/get_entities.py

@@ -8,6 +8,8 @@ from entitysdk import Client, models, types
 from ipydatagrid import DataGrid, TextRenderer
 from IPython.display import clear_output, display
 
+from obi_notebook.get_environment import get_environment
+
 LST_MTYPES_ = None
 LST_SPECIES_ = None
 LST_EMDATASETS_ = None
@@ -86,7 +88,7 @@ def get_entities(
     entity_type,
     token,
     result,
-    env="production",
+    env=None,
     project_context=None,
     return_entities=False,
     multi_select=True,
@@ -101,6 +103,8 @@ def get_entities(
     Note: The 'result' parameter is a mutable object (a list) that is modified in-place
       and also returned.
     """
+    if env is None:
+        env = get_environment()
     if page_size is not None:
         if page_size <= 0:
             raise ValueError("ERROR: Page size must be larger than 0!")
@@ -111,7 +115,7 @@ def get_entities(
     if exclude_scales is None:
         exclude_scales = []
 
-    subdomain = "www" if env == "production" else "staging"
+    subdomain = "cell-a" if env == "production" else "staging.cell-a"
     entity_core_url = f"https://{subdomain}.openbraininstitute.org/api/entitycore"
 
     # Widgets
@@ -295,6 +299,7 @@ def get_entities(
                         result.extend(l_ids)
 
             grid.observe(on_selection_change, names="selections")
+            grid.selections = [{"r1": 0, "r2": 0, "c1": 0, "c2": len(column_widths)}]
 
     for filter_ in filters_dict.values():
         filter_.observe(on_change, names="value")

obi_notebook-0.4/src/obi_notebook/get_environment.py

@@ -0,0 +1,25 @@
+"""Code for handling the deployment environment."""
+
+import warnings
+from os import getenv
+
+from obi_auth.typedef import DeploymentEnvironment
+
+VAR_ENVIRONMENT = "OBI_ENVIRONMENT"
+
+
+def get_environment():
+    """Try to get the environment to run in from environment variable."""
+    var = getenv(VAR_ENVIRONMENT)
+    if var is not None:
+        if var in DeploymentEnvironment._member_map_:
+            return DeploymentEnvironment(var)
+        else:
+            warnings.warn(
+                f"Specified environment '{var}' unknown. Using production.",
+                RuntimeWarning,
+                stacklevel=2,
+            )
+    else:
+        warnings.warn("No environment specified. Using production.", RuntimeWarning, stacklevel=2)
+    return DeploymentEnvironment.production

{obi_notebook-0.2.dev2 → obi_notebook-0.4}/src/obi_notebook/get_projects.py

@@ -5,17 +5,21 @@ import requests
 from entitysdk import ProjectContext
 from IPython.display import display
 
+from obi_notebook.get_environment import get_environment
+
 selected_project = None  # Global variable
 
 
-def get_projects(token, env="production"):
+def get_projects(token, env=None):
     """Returns available project for the end user."""
+    if env is None:
+        env = get_environment()
 
     def project_handler(selected, project_context):
         project_context.project_id = selected["id"]
         project_context.virtual_lab_id = selected["virtual_lab_id"]
 
-    subdomain = "www" if env == "production" else "staging"
+    subdomain = "cell-a" if env == "production" else "staging.cell-a"
 
     url = (
         f"https://{subdomain}.openbraininstitute.org/api/virtual-lab-manager/virtual-labs/projects"

{obi_notebook-0.2.dev2 → obi_notebook-0.4}/src/obi_notebook.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.2.dev2
+Version: 0.4
 Summary: convenience functions for OBI notebooks
 Author-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
 Maintainer-email: Open Brain Institute <jean-denis.courcol@epfl.ch>

{obi_notebook-0.2.dev2 → obi_notebook-0.4}/src/obi_notebook.egg-info/SOURCES.txt

@@ -11,6 +11,7 @@ uv.lock
 .github/workflows/tox.yml
 src/obi_notebook/__init__.py
 src/obi_notebook/get_entities.py
+src/obi_notebook/get_environment.py
 src/obi_notebook/get_projects.py
 src/obi_notebook.egg-info/PKG-INFO
 src/obi_notebook.egg-info/SOURCES.txt