Merge pull request #104 from hubmapconsortium/development

2.0.0 Release

VERSION

@@ -1 +1 @@
-1.8.0
+2.0.0

src/tags.json

@@ -9,5 +9,9 @@
   "salmon": "Spatial data analysed with Salmon",
   "codex": "CODEX data",
   "slide-seq": "Slide-seq data",
-  "files": "Work with HuBMAP data files"
+  "files": "Work with HuBMAP data files",
+  "hra": "Human Reference Atlas data",
+  "sc": "Single cell analysis",
+  "R": "Template written in R",
+  "zarr": "Using zarr file format"
 }

src/user_templates_api/templates/jupyter_lab/templates/blank/metadata.json

@@ -1,6 +1,6 @@
 {
-    "title": "Blank notebook",
-    "description": "Notebook only inserting UUIDs of added datasets",
+    "title": "Blank Notebook",
+    "description": "Notebook only inserting UUIDs of added datasets.",
     "tags": [
     ], 
     "is_multi_dataset_template": true,

src/user_templates_api/templates/jupyter_lab/templates/blank_r/metadata.json

@@ -0,0 +1,16 @@
+{
+  "title": "Blank Notebook",
+  "description": "Notebook only inserting UUIDs of added datasets.",
+  "tags": ["R"], 
+  "is_multi_dataset_template": true,
+  "template_format": "jinja",
+  "job_types": ["jupyter_lab_r"],
+  "examples": [
+    {
+      "title": "Workspace Tutorial datasets",
+      "description": "Create a blank notebook with a CODEX and Slideseq dataset linked.",
+      "datasets": ["69c70762689b20308bb049ac49653342", "a1d17fdd270a69c813b872a927dfa5f3"]
+    }
+  ],
+  "is_hidden": false
+}

src/user_templates_api/templates/jupyter_lab/templates/blank_r/render.py

@@ -0,0 +1,6 @@
+from user_templates_api.templates.jupyter_lab.render import JupyterLabRender
+
+
+class JupyterLabExampleJinjaRender(JupyterLabRender):
+    def __init__(self):
+        pass

src/user_templates_api/templates/jupyter_lab/templates/blank_r/template.txt

@@ -0,0 +1,12 @@
+[
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# linked datasets\n",
+    "uuids <- c('{{ uuids|join:'\', \'' }}')"
+   ]
+  }
+]

src/user_templates_api/templates/jupyter_lab/templates/codex_clustering/metadata.json

@@ -1,6 +1,6 @@
 {
     "title": "Cluster SPRM output of CODEX data and visualize with Vitessce",
-    "description": "This template shows how to cluster CODEX data and load a new clustering into Vitessce",
+    "description": "This template shows how to cluster CODEX data and load a new clustering into Vitessce.",
     "tags": [
         "codex",
         "visualization", 

src/user_templates_api/templates/jupyter_lab/templates/hra_api_tutorial/metadata.json

@@ -0,0 +1,12 @@
+{
+  "title": "Human Reference Atlas (HRA) API Tutorial",
+  "description": "This notebook shows users how to instantiate and use the HuBMAP HRA APIs.",
+  "tags": [
+    "hra",
+    "api"
+  ],
+  "is_multi_dataset_template": true,
+  "template_format": "jinja",
+  "is_hidden": false,
+  "last_modified_unix_timestamp": 1723749414
+}

src/user_templates_api/templates/jupyter_lab/templates/hra_api_tutorial/render.py

@@ -0,0 +1,6 @@
+from user_templates_api.templates.jupyter_lab.render import JupyterLabRender
+
+
+class JupyterLabExampleJinjaRender(JupyterLabRender):
+    def __init__(self):
+        pass