Support panel 1.0

.github/workflows/tests.yaml

@@ -15,20 +15,20 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11']
         exclude:
-          - os: windows-latest
-            python-version: 3.8
           - os: windows-latest
             python-version: 3.9
           - os: windows-latest
             python-version: '3.10'
-          - os: macos-latest
-            python-version: 3.8
+          - os: windows-latest
+            python-version: '3.11'
           - os: macos-latest
             python-version: 3.9
           - os: macos-latest
             python-version: '3.10'
+          - os: macos-latest
+            python-version: '3.11'
 
     env:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

DEVELOPER_GUIDE.md

@@ -18,7 +18,7 @@ Below we describe how to install and use this project for development.
 To install for development you will need to create and activate a virtual environment
 
 ```bash
-conda create --name panel-chemistry python=3.9 nodejs
+conda create --name panel-chemistry python=3.10 nodejs
 conda activate panel-chemistry
 ```
 

examples/reference/JSMEEditor.ipynb

@@ -161,7 +161,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -175,7 +175,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.4"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

examples/reference/NGLViewer.ipynb

@@ -83,14 +83,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "6e35c77b",
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    },
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "file_input = pn.widgets.FileInput(accept=','.join('.' + s for s in EXTENSIONS[1:]))\n",
@@ -183,7 +176,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -197,7 +190,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.4"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

examples/reference/Py3DMol.ipynb

@@ -307,8 +307,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.4"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
     "Topic :: Software Development :: Libraries",
 ]
 dependencies = [
-    "panel",
+    "panel>=1.0",
 ]
 dynamic = ["version"]
 
@@ -65,7 +65,7 @@ profile = "black"
 src_paths = ["src", "tests"]
 
 [tool.pylint.main]
-py-version=3.9
+py-version=3.10
 output-format = "colorized"
 max-attributes=12
 max-args=10
@@ -75,7 +75,7 @@ max-module-lines = 1000
 max-line-length=100
 
 [tool.mypy]
-python_version = "3.9"
+python_version = "3.10"
 namespace_packages = true
 explicit_package_bases = true
 mypy_path = "src"
@@ -84,11 +84,13 @@ exclude = []
 [[tool.mypy.overrides]]
 module = [
     "bokeh.*",
+    "comm.*",
     "holoviews.*",
     "hvplot.*",
     "param",
-    "pyviz_comms",
     "py3Dmol",
+    "pydantic.*",
+    "pyviz_comms",
 ]
 ignore_missing_imports = true
 

script.py

@@ -0,0 +1,49 @@
+import panel as pn 
+from panel_chemistry.pane import NGLViewer # panel_chemistry needs to be imported before you run pn.extension()
+from panel_chemistry.pane.ngl_viewer import EXTENSIONS
+
+pn.extension("ngl_viewer", sizing_mode="stretch_width")
+
+viewer = NGLViewer(object="1CRN", background_color="#F7F7F7", styles={"border": "1px solid lightgray"}, min_height=700, sizing_mode="stretch_both")
+
+settings = pn.Param(
+    viewer,
+    parameters=["object","extension","representation","color_scheme","custom_color_scheme","effect",],
+    name="⚙️ Settings"
+)
+
+file_input = pn.widgets.FileInput(accept=','.join('.' + s for s in EXTENSIONS[1:]))
+
+def filename_callback(target, event):
+    target.extension = event.new.split('.')[1]
+
+def value_callback(target, event):
+    target.object = event.new.decode('utf-8')
+
+file_input.link(viewer, callbacks={'value': value_callback, 'filename': filename_callback})
+
+header = pn.widgets.StaticText(value='<b>{0}</b>'.format("&#128190; File Input"))
+file_column = pn.layout.Column(header, file_input)
+
+layout = pn.Param(
+    viewer,
+    parameters=["sizing_mode", "width", "height", "background_color"],
+    name="&#128208; Layout"
+)
+
+pn.Row(
+    viewer,
+    pn.WidgetBox(settings, layout, width=300, sizing_mode="fixed",),
+)
+
+
+accent="#D2386C"
+
+pn.template.FastListTemplate(
+    site="Panel Chemistry", site_url="./",
+    title="NGLViewer", 
+    sidebar=[file_column, settings, layout],
+    main=[viewer],
+    accent_base_color=accent, header_background=accent,
+).servable();
+

src/panel_chemistry/__init__.py

@@ -2,4 +2,4 @@
 develop high-quality [Panel](https://awesome-panel.org) **data apps** within the domain of
 **chemistry**.
 """
-VERSION = "0.2.2"
+VERSION = "0.3.0"

src/panel_chemistry/bokeh_extensions/jsme_editor.py

@@ -1,27 +1,35 @@
 """A Bokeh model for the JSMEEditor"""
 from bokeh.core.properties import List, String
-from bokeh.models import HTMLBox
 from panel import extension
+from panel.models.layout import HTMLBox
 
 # pylint: disable=protected-access
 extension._imports["jsme"] = "panel_chemistry.bokeh_extensions.jsme_editor"
 # pylint: enable=protected-access
 
 
-class JSMEEditor(HTMLBox):
+class JSMEEditor(HTMLBox):  # pylint: disable=too-few-public-methods,too-many-ancestors
     """JSMEEditor Bokeh Model"""
 
-    __javascript__ = ["https://unpkg.com/[email protected]/jsme.nocache.js"]
+    __javascript__ = [
+        "https://cdn.jsdelivr.net/npm/[email protected]/jsme.nocache.js",
+    ]
 
-    value = String()
-    format = String()
-    subscriptions = List(String())
-    options = List(String())
+    __css__ = [
+        "https://cdn.jsdelivr.net/npm/[email protected]/gwt/chrome/mosaic.css",
+        "https://cdn.jsdelivr.net/npm/[email protected]/jsa.css",
+        "https://cdn.jsdelivr.net/npm/[email protected]/gwt/chrome/chrome.css",
+    ]
 
-    jme = String()
-    smiles = String()
-    mol = String()
-    mol3000 = String()
-    sdf = String()
+    value = String(default="")
+    format = String(default="smiles")
+    subscriptions = List(String, default=[])  # type: ignore
+    options = List(String, default=[])  # type: ignore
 
-    guicolor = String()
+    jme = String(default="")
+    smiles = String(default="")
+    mol = String(default="")
+    mol3000 = String(default="")
+    sdf = String(default="")
+
+    guicolor = String(default="#c0c0c0")