Upload folder using huggingface_hub

.gitignore

@@ -0,0 +1,12 @@
+.eggs/
+dist/
+*.pyc
+__pycache__/
+*.py[cod]
+*$py.class
+__tmp/*
+*.pyi
+.mypycache
+.ruff_cache
+node_modules
+backend/**/templates/

README.md

@@ -1,17 +1,427 @@
-
 ---
-tags: [gradio-custom-component,machine learning,reproducibility,visualization,gradio,gradio-template-File,protein]
-title: gradio_molecule3d V0.0.5
-colorFrom: purple
-colorTo: pink
-sdk: docker
+tags: [gradio-custom-component, File]
+title: gradio_molecule3d
+short_description: A gradio custom component
+colorFrom: blue
+colorTo: yellow
+sdk: gradio
 pinned: false
-license: apache-2.0
+app_file: space.py
 ---
 
+# `gradio_molecule3d`
+<a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
+
+Python library for easily interacting with trained machine learning models
+
+## Installation
+
+```bash
+pip install gradio_molecule3d
+```
+
+## Usage
+
+```python
+
+import gradio as gr
+from gradio_molecule3d import Molecule3D
+
+
+example = Molecule3D().example_value()
+
+
+reps =    [
+    {
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "stick",
+      "color": "whiteCarbon",
+      "residue_range": "",
+      "around": 0,
+      "byres": False,
+      "visible": False
+    }
+  ]
+
+
+
+def predict(x):
+    print("predict function", x)
+    print(x.name)
+    return x
+
+with gr.Blocks() as demo:
+    gr.Markdown("# Molecule3D")
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    out = Molecule3D(label="Output", reps=reps)
+
+    btn = gr.Button("Predict")
+    gr.Markdown(""" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "byres": False,
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red"
+        }
+      ]
+    </pre>
+    """)
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == "__main__":
+    demo.launch()
+
+```
+
+## `Molecule3D`
+
+### Initialization
+
+<table>
+<thead>
+<tr>
+<th align="left">name</th>
+<th align="left" style="width: 25%;">type</th>
+<th align="left">default</th>
+<th align="left">description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td align="left"><code>value</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | list[str] | Callable | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.</td>
+</tr>
+
+<tr>
+<td align="left"><code>reps</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Any | None
+```
+
+</td>
+<td align="left"><code>[]</code></td>
+<td align="left">None</td>
+</tr>
+
+<tr>
+<td align="left"><code>config</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Any | None
+```
+
+</td>
+<td align="left"><code>{
+    "backgroundColor": "white",
+    "orthographic": False,
+    "disableFog": False,
+}</code></td>
+<td align="left">dictionary of config options</td>
+</tr>
+
+<tr>
+<td align="left"><code>confidenceLabel</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>"pLDDT"</code></td>
+<td align="left">label for confidence values stored in the bfactor column of a pdb file</td>
+</tr>
+
+<tr>
+<td align="left"><code>file_count</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Literal["single", "multiple", "directory"]
+```
+
+</td>
+<td align="left"><code>"single"</code></td>
+<td align="left">if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".</td>
+</tr>
+
+<tr>
+<td align="left"><code>file_types</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+list[str] | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">List of file extensions or types of files to be uploaded (e.g. ['image', '.json', '.mp4']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.</td>
+</tr>
+
+<tr>
+<td align="left"><code>type</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Literal["filepath", "binary"]
+```
+
+</td>
+<td align="left"><code>"filepath"</code></td>
+<td align="left">Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.</td>
+</tr>
+
+<tr>
+<td align="left"><code>label</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.</td>
+</tr>
+
+<tr>
+<td align="left"><code>every</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Timer | float | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.</td>
+</tr>
+
+<tr>
+<td align="left"><code>inputs</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Component | Sequence[Component] | set[Component] | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.</td>
+</tr>
+
+<tr>
+<td align="left"><code>show_label</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if True, will display label.</td>
+</tr>
+
+<tr>
+<td align="left"><code>container</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If True, will place the component in a container - providing some extra padding around the border.</td>
+</tr>
+
+<tr>
+<td align="left"><code>scale</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.</td>
+</tr>
+
+<tr>
+<td align="left"><code>min_width</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int
+```
+
+</td>
+<td align="left"><code>160</code></td>
+<td align="left">minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.</td>
+</tr>
+
+<tr>
+<td align="left"><code>height</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | float | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.</td>
+</tr>
+
+<tr>
+<td align="left"><code>interactive</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.</td>
+</tr>
+
+<tr>
+<td align="left"><code>visible</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If False, component will be hidden.</td>
+</tr>
+
+<tr>
+<td align="left"><code>elem_id</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.</td>
+</tr>
+
+<tr>
+<td align="left"><code>elem_classes</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+list[str] | str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.</td>
+</tr>
+
+<tr>
+<td align="left"><code>render</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.</td>
+</tr>
+
+<tr>
+<td align="left"><code>key</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.</td>
+</tr>
+
+<tr>
+<td align="left"><code>showviewer</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.</td>
+</tr>
+</tbody></table>
+
+
+### Events
+
+| name | description |
+|:-----|:------------|
+| `change` | Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input. |
+| `select` | Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data |
+| `clear` | This listener is triggered when the user clears the Molecule3D using the clear button for the component. |
+| `upload` | This listener is triggered when the user uploads a file into the Molecule3D. |
+| `delete` | This listener is triggered when the user deletes and item from the Molecule3D. Uses event data gradio.DeletedFileData to carry `value` referring to the file that was deleted as an instance of FileData. See EventData documentation on how to use this event data |
+
+
+
+### User function
+
+The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both).
+
+- When used as an Input, the component only impacts the input signature of the user function.
+- When used as an output, the component only impacts the return signature of the user function.
 
-# Name: gradio_molecule3d
+The code snippet below is accurate in cases where the component is used as both an input and an output.
 
-Description: Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
+- **As output:** Is passed, passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+- **As input:** Should return, expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
 
-Install with: pip install gradio_molecule3d
+ ```python
+ def predict(
+     value: bytes | str | list[bytes] | list[str] | None
+ ) -> str | list[str] | None:
+     return value
+ ```
+ 

app.py

@@ -2,9 +2,8 @@
 import gradio as gr
 from gradio_molecule3d import Molecule3D
 
-import os
 
-example = Molecule3D().example_inputs()
+example = Molecule3D().example_value()
 
 
 reps =    [
@@ -40,25 +39,18 @@ with gr.Blocks() as demo:
         reps =    [
         {
           "model": 0,
-          "chain": "",
-          "resname": "",
           "style": "cartoon",
           "color": "whiteCarbon",
           "residue_range": "",
           "around": 0,
           "byres": False,
-          "visible": False,
         },
         {
           "model": 0,
           "chain": "A",
           "resname": "HIS",
           "style": "stick",
-          "color": "red",
-          "residue_range": "",
-          "around": 0,
-          "byres": False,
-          "visible": False,
+          "color": "red"
         }
       ]
     </pre>
@@ -66,5 +58,5 @@ with gr.Blocks() as demo:
     btn.click(predict, inputs=inp, outputs=out)
 
 
-if __name__ == '__main__':
-  demo.launch()
+if __name__ == "__main__":
+    demo.launch()

requirements.txt

@@ -1 +1 @@
-gradio_molecule3d==0.0.5
+gradio_molecule3d

space.py

@@ -3,7 +3,7 @@ import gradio as gr
 from app import demo as app
 import os
 
-_docs = {'Molecule3D': {'description': 'Creates a file component that allows uploading generic file (when used as an input) and or displaying generic files (output).', 'members': {'__init__': {'value': {'type': 'str | list[str] | Callable | None', 'default': 'None', 'description': 'Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.'}, 'reps': {'type': 'Any | None', 'default': '[]', 'description': None}, 'config': {'type': 'Any | None', 'default': '{\n    "backgroundColor": "white",\n    "orthographic": False,\n    "disableFog": False,\n}', 'description': 'dictionary of config options'}, 'confidenceLabel': {'type': 'str | None', 'default': '"pLDDT"', 'description': 'label for confidence values stored in the bfactor column of a pdb file'}, 'file_count': {'type': '"single" | "multiple" | "directory"', 'default': '"single"', 'description': 'if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".'}, 'file_types': {'type': 'list[str] | None', 'default': 'None', 'description': 'List of file extensions or types of files to be uploaded (e.g. [\'image\', \'.json\', \'.mp4\']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.'}, 'type': {'type': '"filepath" | "binary"', 'default': '"filepath"', 'description': 'Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.'}, 'label': {'type': 'str | None', 'default': 'None', 'description': 'The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.'}, 'every': {'type': 'float | None', 'default': 'None', 'description': "If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute."}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will display label.'}, 'container': {'type': 'bool', 'default': 'True', 'description': 'If True, will place the component in a container - providing some extra padding around the border.'}, 'scale': {'type': 'int | None', 'default': 'None', 'description': 'relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.'}, 'min_width': {'type': 'int', 'default': '160', 'description': 'minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.'}, 'height': {'type': 'int | float | None', 'default': 'None', 'description': 'The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.'}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.'}, 'visible': {'type': 'bool', 'default': 'True', 'description': 'If False, component will be hidden.'}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': 'An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': 'An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'render': {'type': 'bool', 'default': 'True', 'description': 'If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.'}, 'showviewer': {'type': 'bool', 'default': 'True', 'description': 'If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.'}}, 'postprocess': {'value': {'type': 'str | list[str] | None', 'description': "The output data received by the component from the user's function in the backend."}}, 'preprocess': {'return': {'type': 'bytes\n    | gradio.utils.NamedString\n    | list[bytes | gradio.utils.NamedString]\n    | None', 'description': "The preprocessed input data sent to the user's function in the backend."}, 'value': None}}, 'events': {'change': {'type': None, 'default': None, 'description': 'Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input.'}, 'select': {'type': None, 'default': None, 'description': 'Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data'}, 'clear': {'type': None, 'default': None, 'description': 'This listener is triggered when the user clears the Molecule3D using the X button for the component.'}, 'upload': {'type': None, 'default': None, 'description': 'This listener is triggered when the user uploads a file into the Molecule3D.'}}}, '__meta__': {'additional_interfaces': {}, 'user_fn_refs': {'Molecule3D': []}}}
+_docs = {'Molecule3D': {'description': 'Creates a file component that allows uploading one or more generic files (when used as an input) or displaying generic files or URLs for download (as output).\n', 'members': {'__init__': {'value': {'type': 'str | list[str] | Callable | None', 'default': 'None', 'description': 'Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.'}, 'reps': {'type': 'Any | None', 'default': '[]', 'description': None}, 'config': {'type': 'Any | None', 'default': '{\n    "backgroundColor": "white",\n    "orthographic": False,\n    "disableFog": False,\n}', 'description': 'dictionary of config options'}, 'confidenceLabel': {'type': 'str | None', 'default': '"pLDDT"', 'description': 'label for confidence values stored in the bfactor column of a pdb file'}, 'file_count': {'type': 'Literal["single", "multiple", "directory"]', 'default': '"single"', 'description': 'if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".'}, 'file_types': {'type': 'list[str] | None', 'default': 'None', 'description': 'List of file extensions or types of files to be uploaded (e.g. [\'image\', \'.json\', \'.mp4\']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.'}, 'type': {'type': 'Literal["filepath", "binary"]', 'default': '"filepath"', 'description': 'Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.'}, 'label': {'type': 'str | None', 'default': 'None', 'description': 'The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.'}, 'every': {'type': 'Timer | float | None', 'default': 'None', 'description': 'Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.'}, 'inputs': {'type': 'Component | Sequence[Component] | set[Component] | None', 'default': 'None', 'description': 'Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.'}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will display label.'}, 'container': {'type': 'bool', 'default': 'True', 'description': 'If True, will place the component in a container - providing some extra padding around the border.'}, 'scale': {'type': 'int | None', 'default': 'None', 'description': 'relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.'}, 'min_width': {'type': 'int', 'default': '160', 'description': 'minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.'}, 'height': {'type': 'int | float | None', 'default': 'None', 'description': 'The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.'}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.'}, 'visible': {'type': 'bool', 'default': 'True', 'description': 'If False, component will be hidden.'}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': 'An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': 'An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'render': {'type': 'bool', 'default': 'True', 'description': 'If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.'}, 'key': {'type': 'int | str | None', 'default': 'None', 'description': 'if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.'}, 'showviewer': {'type': 'bool', 'default': 'True', 'description': 'If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.'}}, 'postprocess': {'value': {'type': 'str | list[str] | None', 'description': 'Expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.'}}, 'preprocess': {'return': {'type': 'bytes | str | list[bytes] | list[str] | None', 'description': 'Passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.'}, 'value': None}}, 'events': {'change': {'type': None, 'default': None, 'description': 'Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input.'}, 'select': {'type': None, 'default': None, 'description': 'Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data'}, 'clear': {'type': None, 'default': None, 'description': 'This listener is triggered when the user clears the Molecule3D using the clear button for the component.'}, 'upload': {'type': None, 'default': None, 'description': 'This listener is triggered when the user uploads a file into the Molecule3D.'}, 'delete': {'type': None, 'default': None, 'description': 'This listener is triggered when the user deletes and item from the Molecule3D. Uses event data gradio.DeletedFileData to carry `value` referring to the file that was deleted as an instance of FileData. See EventData documentation on how to use this event data'}}}, '__meta__': {'additional_interfaces': {}, 'user_fn_refs': {'Molecule3D': []}}}
 
 abs_path = os.path.join(os.path.dirname(__file__), "css.css")
 
@@ -24,7 +24,7 @@ with gr.Blocks(
 <a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
 </div>
 
-Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
+Python library for easily interacting with trained machine learning models
 """, elem_classes=["md-custom"], header_links=True)
     app.render()
     gr.Markdown(
@@ -42,9 +42,8 @@ pip install gradio_molecule3d
 import gradio as gr
 from gradio_molecule3d import Molecule3D
 
-import os
 
-example = Molecule3D().example_inputs()
+example = Molecule3D().example_value()
 
 
 reps =    [
@@ -80,25 +79,18 @@ with gr.Blocks() as demo:
         reps =    [
         {
           "model": 0,
-          "chain": "",
-          "resname": "",
           "style": "cartoon",
           "color": "whiteCarbon",
           "residue_range": "",
           "around": 0,
           "byres": False,
-          "visible": False,
         },
         {
           "model": 0,
           "chain": "A",
           "resname": "HIS",
           "style": "stick",
-          "color": "red",
-          "residue_range": "",
-          "around": 0,
-          "byres": False,
-          "visible": False,
+          "color": "red"
         }
       ]
     </pre>
@@ -106,8 +98,8 @@ with gr.Blocks() as demo:
     btn.click(predict, inputs=inp, outputs=out)
 
 
-if __name__ == '__main__':
-  demo.launch()
+if __name__ == "__main__":
+    demo.launch()
 
 ```
 """, elem_classes=["md-custom"], header_links=True)
@@ -139,15 +131,12 @@ The impact on the users predict function varies depending on whether the compone
 
 The code snippet below is accurate in cases where the component is used as both an input and an output.
 
-- **As input:** Is passed, the preprocessed input data sent to the user's function in the backend.
-- **As output:** Should return, the output data received by the component from the user's function in the backend.
+- **As input:** Is passed, passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+- **As output:** Should return, expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
 
  ```python
 def predict(
-    value: bytes
-    | gradio.utils.NamedString
-    | list[bytes | gradio.utils.NamedString]
-    | None
+    value: bytes | str | list[bytes] | list[str] | None
 ) -> str | list[str] | None:
     return value
 ```

src/.gitignore

@@ -6,5 +6,7 @@ __pycache__/
 *$py.class
 __tmp/*
 *.pyi
+.mypycache
+.ruff_cache
 node_modules
-flagged
+backend/**/templates/

src/README.md

@@ -1,8 +1,18 @@
+---
+tags: [gradio-custom-component, File]
+title: gradio_molecule3d
+short_description: A gradio custom component
+colorFrom: blue
+colorTo: yellow
+sdk: gradio
+pinned: false
+app_file: space.py
+---
 
 # `gradio_molecule3d`
 <a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
 
-Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
+Python library for easily interacting with trained machine learning models
 
 ## Installation
 
@@ -17,9 +27,8 @@ pip install gradio_molecule3d
 import gradio as gr
 from gradio_molecule3d import Molecule3D
 
-import os
 
-example = Molecule3D().example_inputs()
+example = Molecule3D().example_value()
 
 
 reps =    [
@@ -55,25 +64,18 @@ with gr.Blocks() as demo:
         reps =    [
         {
           "model": 0,
-          "chain": "",
-          "resname": "",
           "style": "cartoon",
           "color": "whiteCarbon",
           "residue_range": "",
           "around": 0,
           "byres": False,
-          "visible": False,
         },
         {
           "model": 0,
           "chain": "A",
           "resname": "HIS",
           "style": "stick",
-          "color": "red",
-          "residue_range": "",
-          "around": 0,
-          "byres": False,
-          "visible": False,
+          "color": "red"
         }
       ]
     </pre>
@@ -81,8 +83,8 @@ with gr.Blocks() as demo:
     btn.click(predict, inputs=inp, outputs=out)
 
 
-if __name__ == '__main__':
-  demo.launch()
+if __name__ == "__main__":
+    demo.launch()
 
 ```
 
@@ -110,7 +112,7 @@ str | list[str] | Callable | None
 
 </td>
 <td align="left"><code>None</code></td>
-<td align="left">Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.</td>
+<td align="left">Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.</td>
 </tr>
 
 <tr>
@@ -161,7 +163,7 @@ str | None
 <td align="left" style="width: 25%;">
 
 ```python
-"single" | "multiple" | "directory"
+Literal["single", "multiple", "directory"]
 ```
 
 </td>
@@ -187,7 +189,7 @@ list[str] | None
 <td align="left" style="width: 25%;">
 
 ```python
-"filepath" | "binary"
+Literal["filepath", "binary"]
 ```
 
 </td>
@@ -213,12 +215,25 @@ str | None
 <td align="left" style="width: 25%;">
 
 ```python
-float | None
+Timer | float | None
 ```
 
 </td>
 <td align="left"><code>None</code></td>
-<td align="left">If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute.</td>
+<td align="left">Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.</td>
+</tr>
+
+<tr>
+<td align="left"><code>inputs</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Component | Sequence[Component] | set[Component] | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.</td>
 </tr>
 
 <tr>
@@ -257,7 +272,7 @@ int | None
 
 </td>
 <td align="left"><code>None</code></td>
-<td align="left">relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.</td>
+<td align="left">relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.</td>
 </tr>
 
 <tr>
@@ -283,7 +298,7 @@ int | float | None
 
 </td>
 <td align="left"><code>None</code></td>
-<td align="left">The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.</td>
+<td align="left">The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.</td>
 </tr>
 
 <tr>
@@ -351,6 +366,19 @@ bool
 <td align="left">If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.</td>
 </tr>
 
+<tr>
+<td align="left"><code>key</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.</td>
+</tr>
+
 <tr>
 <td align="left"><code>showviewer</code></td>
 <td align="left" style="width: 25%;">
@@ -372,8 +400,9 @@ bool
 |:-----|:------------|
 | `change` | Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input. |
 | `select` | Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data |
-| `clear` | This listener is triggered when the user clears the Molecule3D using the X button for the component. |
+| `clear` | This listener is triggered when the user clears the Molecule3D using the clear button for the component. |
 | `upload` | This listener is triggered when the user uploads a file into the Molecule3D. |
+| `delete` | This listener is triggered when the user deletes and item from the Molecule3D. Uses event data gradio.DeletedFileData to carry `value` referring to the file that was deleted as an instance of FileData. See EventData documentation on how to use this event data |
 
 
 
@@ -386,15 +415,12 @@ The impact on the users predict function varies depending on whether the compone
 
 The code snippet below is accurate in cases where the component is used as both an input and an output.
 
-- **As output:** Is passed, the preprocessed input data sent to the user's function in the backend.
-- **As input:** Should return, the output data received by the component from the user's function in the backend.
+- **As output:** Is passed, passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+- **As input:** Should return, expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
 
  ```python
  def predict(
-     value: bytes
-    | gradio.utils.NamedString
-    | list[bytes | gradio.utils.NamedString]
-    | None
+     value: bytes | str | list[bytes] | list[str] | None
  ) -> str | list[str] | None:
      return value
  ```

src/backend/gradio_molecule3d/molecule3d.py

@@ -5,44 +5,35 @@ from __future__ import annotations
 import tempfile
 import warnings
 from pathlib import Path
-from typing import Any, Callable, List, Literal
+from typing import TYPE_CHECKING, Any, Callable, Literal, Sequence
 
-from gradio_client.documentation import document, set_documentation_group
+import gradio_client.utils as client_utils
+from gradio_client import handle_file
+from gradio_client.documentation import document
 
+from gradio import processing_utils
 from gradio.components.base import Component
-from gradio.data_classes import FileData, GradioRootModel
+from gradio.data_classes import FileData, ListFiles
 from gradio.events import Events
 from gradio.utils import NamedString
 
-set_documentation_group("component")
+if TYPE_CHECKING:
+    from gradio.components import Timer
 
 
-class ListFiles(GradioRootModel):
-    root: List[FileData]
-
-    def __getitem__(self, index):
-        return self.root[index]
-
-    def __iter__(self):
-        return iter(self.root)
-
-
-@document()
 class Molecule3D(Component):
     """
-    Creates a file component that allows uploading generic file (when used as an input) and or displaying generic files (output).
-    Preprocessing: passes the uploaded file as a {tempfile._TemporaryFileWrapper} or {List[tempfile._TemporaryFileWrapper]} depending on `file_count` (or a {bytes}/{List[bytes]} depending on `type`)
-    Postprocessing: expects function to return a {str} path to a file, or {List[str]} consisting of paths to files.
-    Examples-format: a {str} path to a local file that populates the component.
-    Demos: zip_to_json, zip_files
+    Creates a file component that allows uploading one or more generic files (when used as an input) or displaying generic files or URLs for download (as output).
+
+    Demo: zip_files, zip_to_json
     """
 
-    EVENTS = [Events.change, Events.select, Events.clear, Events.upload]
+    EVENTS = [Events.change, Events.select, Events.clear, Events.upload, Events.delete]
 
     def __init__(
         self,
         value: str | list[str] | Callable | None = None,
-         reps: Any | None = [],
+        reps: Any | None = [],
         config: Any | None = {
     "backgroundColor": "white",
     "orthographic": False,
@@ -54,7 +45,8 @@ class Molecule3D(Component):
         file_types: list[str] | None = None,
         type: Literal["filepath", "binary"] = "filepath",
         label: str | None = None,
-        every: float | None = None,
+        every: Timer | float | None = None,
+        inputs: Component | Sequence[Component] | set[Component] | None = None,
         show_label: bool | None = None,
         container: bool = True,
         scale: int | None = None,
@@ -65,11 +57,12 @@ class Molecule3D(Component):
         elem_id: str | None = None,
         elem_classes: list[str] | str | None = None,
         render: bool = True,
-        showviewer: bool = True
+        key: int | str | None = None,
+        showviewer: bool = True      
     ):
         """
         Parameters:
-            value: Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.
+            value: Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.
             file_count: if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".
             file_types: List of file extensions or types of files to be uploaded (e.g. ['image', '.json', '.mp4']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.
             representations: list of representation objects
@@ -77,21 +70,29 @@ class Molecule3D(Component):
             confidenceLabel: label for confidence values stored in the bfactor column of a pdb file
             type: Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.
             label: The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.
-            every: If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute.
+            every: Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.
+            inputs: Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.
             show_label: if True, will display label.
             container: If True, will place the component in a container - providing some extra padding around the border.
-            scale: relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.
+            scale: relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.
             min_width: minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.
-            height: The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.
+            height: The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.
             interactive: if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.
             visible: If False, component will be hidden.
             elem_id: An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.
             elem_classes: An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.
             render: If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.
+            key: if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.
             showviewer: If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.
         """
+        file_count_valid_types = ["single", "multiple", "directory"]
         self.file_count = file_count
-        if self.file_count == "multiple":
+
+        if self.file_count not in file_count_valid_types:
+            raise ValueError(
+                f"Parameter file_count must be one of them: {file_count_valid_types}"
+            )
+        elif self.file_count in ["multiple", "directory"]:
             self.data_model = ListFiles
         else:
             self.data_model = FileData
@@ -115,6 +116,7 @@ class Molecule3D(Component):
         super().__init__(
             label=label,
             every=every,
+            inputs=inputs,
             show_label=show_label,
             container=container,
             scale=scale,
@@ -124,6 +126,7 @@ class Molecule3D(Component):
             elem_id=elem_id,
             elem_classes=elem_classes,
             render=render,
+            key=key,
             value=value,
         )
         self.type = type
@@ -133,7 +136,6 @@ class Molecule3D(Component):
         self.confidenceLabel = confidenceLabel
         self.showviewer = showviewer
 
-
     def _process_single_file(self, f: FileData) -> NamedString | bytes:
         file_name = f.path
         if self.type == "filepath":
@@ -152,25 +154,54 @@ class Molecule3D(Component):
 
     def preprocess(
         self, payload: ListFiles | FileData | None
-    ) -> bytes | NamedString | list[bytes | NamedString] | None:
+    ) -> bytes | str | list[bytes] | list[str] | None:
+        """
+        Parameters:
+            payload: molecule3d information as a FileData object, or a list of FileData objects.
+        Returns:
+            Passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+        """
         if payload is None:
             return None
+
         if self.file_count == "single":
             if isinstance(payload, ListFiles):
                 return self._process_single_file(payload[0])
-            else:
-                return self._process_single_file(payload)
+            return self._process_single_file(payload)
+        if isinstance(payload, ListFiles):
+            return [self._process_single_file(f) for f in payload]  # type: ignore
+        return [self._process_single_file(payload)]  # type: ignore
+
+    def _download_files(self, value: str | list[str]) -> str | list[str]:
+        downloaded_files = []
+        if isinstance(value, list):
+            for file in value:
+                if client_utils.is_http_url_like(file):
+                    downloaded_file = processing_utils.save_url_to_cache(
+                        file, self.GRADIO_CACHE
+                    )
+                    downloaded_files.append(downloaded_file)
+                else:
+                    downloaded_files.append(file)
+            return downloaded_files
+        if client_utils.is_http_url_like(value):
+            downloaded_file = processing_utils.save_url_to_cache(
+                value, self.GRADIO_CACHE
+            )
+            return downloaded_file
         else:
-            if isinstance(payload, ListFiles):
-                return [self._process_single_file(f) for f in payload]
-            else:
-                return [self._process_single_file(payload)]
+            return value
 
     def postprocess(self, value: str | list[str] | None) -> ListFiles | FileData | None:
+        """
+        Parameters:
+            value: Expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
+        Returns:
+            molecule3d information as a FileData object, or a list of FileData objects.
+        """
         if value is None:
             return None
-        
-        
+        value = self._download_files(value)
         if isinstance(value, list):
             return ListFiles(
                 root=[
@@ -189,18 +220,30 @@ class Molecule3D(Component):
                 size=Path(value).stat().st_size,
             )
 
-    def as_example(self, input_data: str | list | None) -> str:
-        if input_data is None:
+    def process_example(self, value: str | list | None) -> str:
+        if value is None:
             return ""
-        elif isinstance(input_data, list):
-            return ", ".join([Path(file).name for file in input_data])
+        elif isinstance(value, list):
+            return ", ".join([Path(file).name for file in value])
         else:
-            return Path(input_data).name
+            return Path(value).name
+
+    def example_payload(self) -> Any:
+        if self.file_count == "single":
+            return handle_file(
+                "https://files.rcsb.org/view/1PGA.pdb"
+            )
+        else:
+            return [
+                handle_file(
+                    "https://files.rcsb.org/view/1PGA.pdb"
+                )
+            ]
 
-    def example_inputs(self) -> Any:
+    def example_value(self) -> Any:
         if self.file_count == "single":
-            return "/home/duerr/Dev/GradioBio/molecule3d/demo/sample_file.pdf"
+            return "https://files.rcsb.org/view/1PGA.pdb"
         else:
             return [
-                "sample_file.pdf"
+                "https://files.rcsb.org/view/1PGA.pdb"
             ]

src/backend/gradio_molecule3d/templates/example/index.js

@@ -1,53 +1,68 @@
 const {
   SvelteComponent: f,
-  append: u,
-  attr: d,
-  detach: o,
-  element: y,
+  append_hydration: o,
+  attr: u,
+  children: h,
+  claim_element: c,
+  claim_text: y,
+  detach: _,
+  element: v,
   init: g,
-  insert: v,
-  noop: r,
-  safe_not_equal: c,
-  set_data: m,
-  text: b,
-  toggle_class: _
+  insert_hydration: m,
+  noop: d,
+  safe_not_equal: b,
+  set_data: A,
+  text: j,
+  toggle_class: r
 } = window.__gradio__svelte__internal;
-function A(t) {
-  let e, n = (Array.isArray(
+function w(a) {
+  let e, n = (
     /*value*/
-    t[0]
-  ) ? (
-    /*value*/
-    t[0].join(", ")
-  ) : (
-    /*value*/
-    t[0]
-  )) + "", s;
+    (a[0] ? Array.isArray(
+      /*value*/
+      a[0]
+    ) ? (
+      /*value*/
+      a[0].join(", ")
+    ) : (
+      /*value*/
+      a[0]
+    ) : "") + ""
+  ), i;
   return {
     c() {
-      e = y("div"), s = b(n), d(e, "class", "svelte-1hgn91n"), _(
+      e = v("div"), i = j(n), this.h();
+    },
+    l(l) {
+      e = c(l, "DIV", { class: !0 });
+      var t = h(e);
+      i = y(t, n), t.forEach(_), this.h();
+    },
+    h() {
+      u(e, "class", "svelte-1hgn91n"), r(
         e,
         "table",
         /*type*/
-        t[1] === "table"
-      ), _(
+        a[1] === "table"
+      ), r(
         e,
         "gallery",
         /*type*/
-        t[1] === "gallery"
-      ), _(
+        a[1] === "gallery"
+      ), r(
         e,
         "selected",
         /*selected*/
-        t[2]
+        a[2]
       );
     },
-    m(l, a) {
-      v(l, e, a), u(e, s);
+    m(l, t) {
+      m(l, e, t), o(e, i);
     },
-    p(l, [a]) {
-      a & /*value*/
-      1 && n !== (n = (Array.isArray(
+    p(l, [t]) {
+      t & /*value*/
+      1 && n !== (n = /*value*/
+      (l[0] ? Array.isArray(
         /*value*/
         l[0]
       ) ? (
@@ -56,44 +71,44 @@ function A(t) {
       ) : (
         /*value*/
         l[0]
-      )) + "") && m(s, n), a & /*type*/
-      2 && _(
+      ) : "") + "") && A(i, n), t & /*type*/
+      2 && r(
         e,
         "table",
         /*type*/
         l[1] === "table"
-      ), a & /*type*/
-      2 && _(
+      ), t & /*type*/
+      2 && r(
         e,
         "gallery",
         /*type*/
         l[1] === "gallery"
-      ), a & /*selected*/
-      4 && _(
+      ), t & /*selected*/
+      4 && r(
         e,
         "selected",
         /*selected*/
         l[2]
       );
     },
-    i: r,
-    o: r,
+    i: d,
+    o: d,
     d(l) {
-      l && o(e);
+      l && _(e);
     }
   };
 }
-function h(t, e, n) {
-  let { value: s } = e, { type: l } = e, { selected: a = !1 } = e;
-  return t.$$set = (i) => {
-    "value" in i && n(0, s = i.value), "type" in i && n(1, l = i.type), "selected" in i && n(2, a = i.selected);
-  }, [s, l, a];
+function E(a, e, n) {
+  let { value: i } = e, { type: l } = e, { selected: t = !1 } = e;
+  return a.$$set = (s) => {
+    "value" in s && n(0, i = s.value), "type" in s && n(1, l = s.type), "selected" in s && n(2, t = s.selected);
+  }, [i, l, t];
 }
-class j extends f {
+class q extends f {
   constructor(e) {
-    super(), g(this, e, h, A, c, { value: 0, type: 1, selected: 2 });
+    super(), g(this, e, E, w, b, { value: 0, type: 1, selected: 2 });
   }
 }
 export {
-  j as default
+  q as default
 };

src/demo/app.py

@@ -2,9 +2,8 @@
 import gradio as gr
 from gradio_molecule3d import Molecule3D
 
-import os
 
-example = Molecule3D().example_inputs()
+example = Molecule3D().example_value()
 
 
 reps =    [
@@ -40,25 +39,18 @@ with gr.Blocks() as demo:
         reps =    [
         {
           "model": 0,
-          "chain": "",
-          "resname": "",
           "style": "cartoon",
           "color": "whiteCarbon",
           "residue_range": "",
           "around": 0,
           "byres": False,
-          "visible": False,
         },
         {
           "model": 0,
           "chain": "A",
           "resname": "HIS",
           "style": "stick",
-          "color": "red",
-          "residue_range": "",
-          "around": 0,
-          "byres": False,
-          "visible": False,
+          "color": "red"
         }
       ]
     </pre>
@@ -66,5 +58,5 @@ with gr.Blocks() as demo:
     btn.click(predict, inputs=inp, outputs=out)
 
 
-if __name__ == '__main__':
-  demo.launch()
+if __name__ == "__main__":
+    demo.launch()

src/demo/requirements.txt

@@ -0,0 +1 @@
+gradio_molecule3d

src/demo/space.py

@@ -3,7 +3,7 @@ import gradio as gr
 from app import demo as app
 import os
 
-_docs = {'Molecule3D': {'description': 'Creates a file component that allows uploading generic file (when used as an input) and or displaying generic files (output).', 'members': {'__init__': {'value': {'type': 'str | list[str] | Callable | None', 'default': 'None', 'description': 'Default file to display, given as str file path. If callable, the function will be called whenever the app loads to set the initial value of the component.'}, 'reps': {'type': 'Any | None', 'default': '[]', 'description': None}, 'config': {'type': 'Any | None', 'default': '{\n    "backgroundColor": "white",\n    "orthographic": False,\n    "disableFog": False,\n}', 'description': 'dictionary of config options'}, 'confidenceLabel': {'type': 'str | None', 'default': '"pLDDT"', 'description': 'label for confidence values stored in the bfactor column of a pdb file'}, 'file_count': {'type': '"single" | "multiple" | "directory"', 'default': '"single"', 'description': 'if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".'}, 'file_types': {'type': 'list[str] | None', 'default': 'None', 'description': 'List of file extensions or types of files to be uploaded (e.g. [\'image\', \'.json\', \'.mp4\']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.'}, 'type': {'type': '"filepath" | "binary"', 'default': '"filepath"', 'description': 'Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.'}, 'label': {'type': 'str | None', 'default': 'None', 'description': 'The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.'}, 'every': {'type': 'float | None', 'default': 'None', 'description': "If `value` is a callable, run the function 'every' number of seconds while the client connection is open. Has no effect otherwise. Queue must be enabled. The event can be accessed (e.g. to cancel it) via this component's .load_event attribute."}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will display label.'}, 'container': {'type': 'bool', 'default': 'True', 'description': 'If True, will place the component in a container - providing some extra padding around the border.'}, 'scale': {'type': 'int | None', 'default': 'None', 'description': 'relative width compared to adjacent Components in a Row. For example, if Component A has scale=2, and Component B has scale=1, A will be twice as wide as B. Should be an integer.'}, 'min_width': {'type': 'int', 'default': '160', 'description': 'minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.'}, 'height': {'type': 'int | float | None', 'default': 'None', 'description': 'The maximum height of the file component, in pixels. If more files are uploaded than can fit in the height, a scrollbar will appear.'}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.'}, 'visible': {'type': 'bool', 'default': 'True', 'description': 'If False, component will be hidden.'}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': 'An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': 'An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'render': {'type': 'bool', 'default': 'True', 'description': 'If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.'}, 'showviewer': {'type': 'bool', 'default': 'True', 'description': 'If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.'}}, 'postprocess': {'value': {'type': 'str | list[str] | None', 'description': "The output data received by the component from the user's function in the backend."}}, 'preprocess': {'return': {'type': 'bytes\n    | gradio.utils.NamedString\n    | list[bytes | gradio.utils.NamedString]\n    | None', 'description': "The preprocessed input data sent to the user's function in the backend."}, 'value': None}}, 'events': {'change': {'type': None, 'default': None, 'description': 'Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input.'}, 'select': {'type': None, 'default': None, 'description': 'Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data'}, 'clear': {'type': None, 'default': None, 'description': 'This listener is triggered when the user clears the Molecule3D using the X button for the component.'}, 'upload': {'type': None, 'default': None, 'description': 'This listener is triggered when the user uploads a file into the Molecule3D.'}}}, '__meta__': {'additional_interfaces': {}, 'user_fn_refs': {'Molecule3D': []}}}
+_docs = {'Molecule3D': {'description': 'Creates a file component that allows uploading one or more generic files (when used as an input) or displaying generic files or URLs for download (as output).\n', 'members': {'__init__': {'value': {'type': 'str | list[str] | Callable | None', 'default': 'None', 'description': 'Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.'}, 'reps': {'type': 'Any | None', 'default': '[]', 'description': None}, 'config': {'type': 'Any | None', 'default': '{\n    "backgroundColor": "white",\n    "orthographic": False,\n    "disableFog": False,\n}', 'description': 'dictionary of config options'}, 'confidenceLabel': {'type': 'str | None', 'default': '"pLDDT"', 'description': 'label for confidence values stored in the bfactor column of a pdb file'}, 'file_count': {'type': 'Literal["single", "multiple", "directory"]', 'default': '"single"', 'description': 'if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".'}, 'file_types': {'type': 'list[str] | None', 'default': 'None', 'description': 'List of file extensions or types of files to be uploaded (e.g. [\'image\', \'.json\', \'.mp4\']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.'}, 'type': {'type': 'Literal["filepath", "binary"]', 'default': '"filepath"', 'description': 'Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.'}, 'label': {'type': 'str | None', 'default': 'None', 'description': 'The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.'}, 'every': {'type': 'Timer | float | None', 'default': 'None', 'description': 'Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.'}, 'inputs': {'type': 'Component | Sequence[Component] | set[Component] | None', 'default': 'None', 'description': 'Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.'}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will display label.'}, 'container': {'type': 'bool', 'default': 'True', 'description': 'If True, will place the component in a container - providing some extra padding around the border.'}, 'scale': {'type': 'int | None', 'default': 'None', 'description': 'relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.'}, 'min_width': {'type': 'int', 'default': '160', 'description': 'minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.'}, 'height': {'type': 'int | float | None', 'default': 'None', 'description': 'The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.'}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': 'if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.'}, 'visible': {'type': 'bool', 'default': 'True', 'description': 'If False, component will be hidden.'}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': 'An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': 'An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.'}, 'render': {'type': 'bool', 'default': 'True', 'description': 'If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.'}, 'key': {'type': 'int | str | None', 'default': 'None', 'description': 'if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.'}, 'showviewer': {'type': 'bool', 'default': 'True', 'description': 'If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.'}}, 'postprocess': {'value': {'type': 'str | list[str] | None', 'description': 'Expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.'}}, 'preprocess': {'return': {'type': 'bytes | str | list[bytes] | list[str] | None', 'description': 'Passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.'}, 'value': None}}, 'events': {'change': {'type': None, 'default': None, 'description': 'Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input.'}, 'select': {'type': None, 'default': None, 'description': 'Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data'}, 'clear': {'type': None, 'default': None, 'description': 'This listener is triggered when the user clears the Molecule3D using the clear button for the component.'}, 'upload': {'type': None, 'default': None, 'description': 'This listener is triggered when the user uploads a file into the Molecule3D.'}, 'delete': {'type': None, 'default': None, 'description': 'This listener is triggered when the user deletes and item from the Molecule3D. Uses event data gradio.DeletedFileData to carry `value` referring to the file that was deleted as an instance of FileData. See EventData documentation on how to use this event data'}}}, '__meta__': {'additional_interfaces': {}, 'user_fn_refs': {'Molecule3D': []}}}
 
 abs_path = os.path.join(os.path.dirname(__file__), "css.css")
 
@@ -24,7 +24,7 @@ with gr.Blocks(
 <a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
 </div>
 
-Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js
+Python library for easily interacting with trained machine learning models
 """, elem_classes=["md-custom"], header_links=True)
     app.render()
     gr.Markdown(
@@ -42,9 +42,8 @@ pip install gradio_molecule3d
 import gradio as gr
 from gradio_molecule3d import Molecule3D
 
-import os
 
-example = Molecule3D().example_inputs()
+example = Molecule3D().example_value()
 
 
 reps =    [
@@ -80,25 +79,18 @@ with gr.Blocks() as demo:
         reps =    [
         {
           "model": 0,
-          "chain": "",
-          "resname": "",
           "style": "cartoon",
           "color": "whiteCarbon",
           "residue_range": "",
           "around": 0,
           "byres": False,
-          "visible": False,
         },
         {
           "model": 0,
           "chain": "A",
           "resname": "HIS",
           "style": "stick",
-          "color": "red",
-          "residue_range": "",
-          "around": 0,
-          "byres": False,
-          "visible": False,
+          "color": "red"
         }
       ]
     </pre>
@@ -106,8 +98,8 @@ with gr.Blocks() as demo:
     btn.click(predict, inputs=inp, outputs=out)
 
 
-if __name__ == '__main__':
-  demo.launch()
+if __name__ == "__main__":
+    demo.launch()
 
 ```
 """, elem_classes=["md-custom"], header_links=True)
@@ -139,15 +131,12 @@ The impact on the users predict function varies depending on whether the compone
 
 The code snippet below is accurate in cases where the component is used as both an input and an output.
 
-- **As input:** Is passed, the preprocessed input data sent to the user's function in the backend.
-- **As output:** Should return, the output data received by the component from the user's function in the backend.
+- **As input:** Is passed, passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+- **As output:** Should return, expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
 
  ```python
 def predict(
-    value: bytes
-    | gradio.utils.NamedString
-    | list[bytes | gradio.utils.NamedString]
-    | None
+    value: bytes | str | list[bytes] | list[str] | None
 ) -> str | list[str] | None:
     return value
 ```

src/frontend/Example.svelte

@@ -1,7 +1,7 @@
 <script lang="ts">
 	import type { FileData } from "@gradio/client";
 
-	export let value: FileData;
+	export let value: FileData | null;
 	export let type: "gallery" | "table";
 	export let selected = false;
 </script>
@@ -11,7 +11,7 @@
 	class:gallery={type === "gallery"}
 	class:selected
 >
-	{Array.isArray(value) ? value.join(", ") : value}
+	{value ? (Array.isArray(value) ? value.join(", ") : value) : ""}
 </div>
 
 <style>

src/frontend/Index.svelte

@@ -8,27 +8,34 @@
 </script>
 
 <script lang="ts">
+  import "./style.css";
+
   import type { Gradio, SelectData } from "@gradio/utils";
   import File from "./shared/File.svelte";
   import FileUpload from "./shared/FileUpload.svelte";
-  import { type FileData } from "@gradio/client";
+  import type { FileData } from "@gradio/client";
   import { Block, UploadText } from "@gradio/atoms";
+
   import { StatusTracker } from "@gradio/statustracker";
   import type { LoadingStatus } from "@gradio/statustracker";
+
   export let elem_id = "";
   export let elem_classes: string[] = [];
   export let visible = true;
   export let value: null | FileData | FileData[];
+
   export let interactive: boolean;
   export let root: string;
   export let label: string;
   export let show_label: boolean;
   export let height: number | undefined = undefined;
+
   //Molecule3D specific arguments
   export let reps: any = [];
   export let config: any = {};
   export let confidenceLabel: string = "";
   export let showviewer: boolean = true;
+
   export let _selectable = false;
   export let loading_status: LoadingStatus;
   export let container = true;
@@ -40,20 +47,24 @@
     upload: never;
     clear: never;
     select: SelectData;
+    clear_status: LoadingStatus;
+    delete: FileData;
   }>;
-  export let file_count: string;
+  export let file_count: "single" | "multiple" | "directory";
   export let file_types: string[] = ["file"];
+
   let old_value = value;
   $: if (JSON.stringify(old_value) !== JSON.stringify(value)) {
     gradio.dispatch("change");
     old_value = value;
-    console.log("value change", value);
+
     moldata = null;
     retrieveContent(value);
   }
+
   let dragging = false;
   let pending_upload = false;
-  //check for missing keys in reps
+
   let keys_for_reps = {
     model: {
       type: Number,
@@ -198,7 +209,7 @@
 
 <Block
   {visible}
-  variant={value === null ? "dashed" : "solid"}
+  variant={value ? "solid" : "dashed"}
   border_mode={dragging ? "focus" : "base"}
   padding={false}
   {elem_id}
@@ -215,8 +226,8 @@
     status={pending_upload
       ? "generating"
       : loading_status?.status || "complete"}
+    on:clear_status={() => gradio.dispatch("clear_status", loading_status)}
   />
-
   {#if !interactive}
     <File
       on:select={({ detail }) => gradio.dispatch("select", detail)}
@@ -235,6 +246,8 @@
     />
   {:else}
     <FileUpload
+      upload={gradio.client.upload}
+      stream_handler={gradio.client.stream}
       {label}
       {show_label}
       {value}
@@ -248,8 +261,8 @@
       {confidenceLabel}
       {moldata}
       molviewer={showviewer}
+      max_file_size={gradio.max_file_size}
       on:change={({ detail }) => {
-        errors = [];
         value = detail;
       }}
       on:drag={({ detail }) => (dragging = detail)}
@@ -261,6 +274,14 @@
           "identifier not found in database, check spelling"
         )}
       on:upload={() => gradio.dispatch("upload")}
+      on:error={({ detail }) => {
+        loading_status = loading_status || {};
+        loading_status.status = "error";
+        gradio.dispatch("error", detail);
+      }}
+      on:delete={({ detail }) => {
+        gradio.dispatch("delete", detail);
+      }}
       i18n={gradio.i18n}
     >
       <UploadText i18n={gradio.i18n} type="file" />
@@ -301,93 +322,3 @@
     </div>
   {/if}
 </Block>
-
-<style>
-  .sr-only {
-    position: absolute;
-    width: 1px;
-    height: 1px;
-    padding: 0;
-    margin: -1px;
-    overflow: hidden;
-    clip: rect(0, 0, 0, 0);
-    white-space: nowrap;
-    border-width: 0;
-  }
-  .mb-4 {
-    margin-bottom: 1rem;
-  }
-  .ml-4 {
-    margin-left: 1rem;
-  }
-  .mr-3 {
-    margin-right: 0.75rem;
-  }
-  .mt-1 {
-    margin-top: 0.25rem;
-  }
-  .mt-1\.5 {
-    margin-top: 0.375rem;
-  }
-  .mt-\[2px\] {
-    margin-top: 2px;
-  }
-  .inline {
-    display: inline;
-  }
-  .flex {
-    display: flex;
-  }
-  .h-4 {
-    height: 1rem;
-  }
-  .w-4 {
-    width: 1rem;
-  }
-  .flex-shrink-0 {
-    flex-shrink: 0;
-  }
-  .list-inside {
-    list-style-position: inside;
-  }
-  .list-disc {
-    list-style-type: disc;
-  }
-  .rounded-lg {
-    border-radius: 0.5rem;
-  }
-  .bg-red-50 {
-    --tw-bg-opacity: 1;
-    background-color: rgb(254 242 242 / var(--tw-bg-opacity));
-  }
-  .m-2 {
-    margin: 0.5rem;
-  }
-  .p-4 {
-    padding: 1rem;
-  }
-  .text-sm {
-    font-size: 0.875rem;
-    line-height: 1.25rem;
-  }
-  .font-medium {
-    font-weight: 500;
-  }
-  .lowercase {
-    text-transform: lowercase;
-  }
-  .text-red-800 {
-    --tw-text-opacity: 1;
-    color: rgb(153 27 27 / var(--tw-text-opacity));
-  }
-  @media (prefers-color-scheme: dark) {
-    .dark\:bg-gray-800 {
-      --tw-bg-opacity: 1;
-      background-color: rgb(31 41 55 / var(--tw-bg-opacity));
-    }
-    .dark\:text-red-400 {
-      --tw-text-opacity: 1;
-      color: rgb(248 113 113 / var(--tw-text-opacity));
-    }
-  }
-</style>

src/frontend/gradio.config.js

@@ -0,0 +1,11 @@
+import tailwindcss from "@tailwindcss/vite";
+
+export default {
+  plugins: [tailwindcss()],
+  svelte: {
+    preprocess: [],
+  },
+  build: {
+    target: "modules",
+  },
+};

src/frontend/package.json

@@ -1,25 +1,36 @@
 {
   "name": "gradio_molecule3d",
-  "version": "0.2.1",
+  "version": "0.9.2",
   "description": "Gradio UI packages",
   "type": "module",
   "author": "",
   "license": "ISC",
   "private": false,
   "dependencies": {
-    "@gradio/atoms": "0.2.0",
-    "@gradio/client": "0.13.0",
-    "@gradio/icons": "0.2.0",
-    "@gradio/statustracker": "0.3.0",
-    "@gradio/upload": "0.3.1",
-    "@gradio/utils": "0.2.0",
-    "3dmol": "^2.0.6"
+    "@gradio/atoms": "0.9.0",
+    "@gradio/client": "1.6.0",
+    "@gradio/icons": "0.8.0",
+    "@gradio/markdown": "^0.10.1",
+    "@gradio/statustracker": "0.8.1",
+    "@gradio/upload": "0.13.1",
+    "@gradio/utils": "0.7.0",
+    "@gradio/wasm": "0.14.1",
+    "@tailwindcss/vite": "^4.0.0-alpha.30",
+    "3dmol": "^2.4.0",
+    "tailwindcss": "^4.0.0-alpha.30"
+  },
+  "devDependencies": {
+    "@gradio/preview": "0.12.0"
   },
   "main": "./Index.svelte",
   "main_changeset": true,
   "exports": {
-    ".": "./Index.svelte",
-    "./example": "./Example.svelte",
+    ".": {
+      "gradio": "./Index.svelte"
+    },
+    "./example": {
+      "gradio": "./Example.svelte"
+    },
     "./package.json": "./package.json"
   }
-}
+}

src/frontend/shared/File.svelte

@@ -3,23 +3,22 @@
   import { BlockLabel, Empty } from "@gradio/atoms";
   import { File } from "@gradio/icons";
   import FilePreview from "./FilePreview.svelte";
+  import type { I18nFormatter } from "@gradio/utils";
 
   import MolecularViewer from "./MolecularViewer.svelte";
 
-  import type { I18nFormatter } from "@gradio/utils";
-
   export let value: FileData | FileData[] | null = null;
   export let label: string;
   export let show_label = true;
   export let selectable = false;
   export let height: number | undefined = undefined;
   export let i18n: I18nFormatter;
+
   export let config = {};
   export let confidenceLabel = "";
   export let representations = [];
   export let moldata = null;
   export let molviewer = false;
-  export let errors = [];
 </script>
 
 <BlockLabel
@@ -29,10 +28,9 @@
   label={label || "File"}
 />
 
-{#if value}
+{#if value && (Array.isArray(value) ? value.length > 0 : true)}
   <FilePreview {i18n} {selectable} on:select {value} {height} />
 
-  <!-- {JSON.stringify(moldata)} -->
   {#if moldata != null && molviewer}
     <MolecularViewer {moldata} {config} {confidenceLabel} {representations} />
   {/if}

src/frontend/shared/FilePreview.svelte

@@ -1,16 +1,60 @@
 <script lang="ts">
 	import type { FileData } from "@gradio/client";
-	import { display_file_name, display_file_size } from "./utils";
+	import { prettyBytes } from "./utils";
 	import { createEventDispatcher } from "svelte";
 	import type { I18nFormatter, SelectData } from "@gradio/utils";
+	import { DownloadLink } from "@gradio/wasm/svelte";
 
 	const dispatch = createEventDispatcher<{
 		select: SelectData;
+		change: FileData[] | FileData;
+		delete: FileData;
 	}>();
 	export let value: FileData | FileData[];
 	export let selectable = false;
 	export let height: number | undefined = undefined;
 	export let i18n: I18nFormatter;
+
+	function split_filename(filename: string): [string, string] {
+		const last_dot = filename.lastIndexOf(".");
+		if (last_dot === -1) {
+			return [filename, ""];
+		}
+		return [filename.slice(0, last_dot), filename.slice(last_dot)];
+	}
+
+	$: normalized_files = (Array.isArray(value) ? value : [value]).map((file) => {
+		const [filename_stem, filename_ext] = split_filename(file.orig_name ?? "");
+		return {
+			...file,
+			filename_stem,
+			filename_ext
+		};
+	});
+
+	function handle_row_click(
+		event: MouseEvent & { currentTarget: HTMLTableRowElement },
+		index: number
+	): void {
+		const tr = event.currentTarget;
+		const should_select =
+			event.target === tr || // Only select if the click is on the row itself
+			(tr &&
+				tr.firstElementChild &&
+				event.composedPath().includes(tr.firstElementChild)); // Or if the click is on the name column
+
+		if (should_select) {
+			dispatch("select", { value: normalized_files[index].orig_name, index });
+		}
+	}
+
+	function remove_file(index: number): void {
+		const removed = normalized_files.splice(index, 1);
+		normalized_files = [...normalized_files];
+		value = normalized_files;
+		dispatch("delete", removed[0]);
+		dispatch("change", normalized_files);
+	}
 </script>
 
 <div
@@ -19,33 +63,51 @@
 >
 	<table class="file-preview">
 		<tbody>
-			{#each Array.isArray(value) ? value : [value] as file, i}
+			{#each normalized_files as file, i (file)}
 				<tr
 					class="file"
 					class:selectable
-					on:click={() =>
-						dispatch("select", {
-							value: file.orig_name,
-							index: i
-						})}
+					on:click={(event) => {
+						handle_row_click(event, i);
+					}}
 				>
-					<td>
-						{display_file_name(file)}
+					<td class="filename" aria-label={file.orig_name}>
+						<span class="stem">{file.filename_stem}</span>
+						<span class="ext">{file.filename_ext}</span>
 					</td>
 
 					<td class="download">
 						{#if file.url}
-							<a
+							<DownloadLink
 								href={file.url}
-								target="_blank"
 								download={window.__is_colab__ ? null : file.orig_name}
 							>
-								{@html display_file_size(file)}&nbsp;&#8675;
-							</a>
+								{@html file.size != null
+									? prettyBytes(file.size)
+									: "(size unknown)"}&nbsp;&#8675;
+							</DownloadLink>
 						{:else}
 							{i18n("file.uploading")}
 						{/if}
 					</td>
+
+					{#if normalized_files.length > 1}
+						<td>
+							<button
+								class="label-clear-button"
+								aria-label="Remove this file"
+								on:click={() => {
+									remove_file(i);
+								}}
+								on:keydown={(event) => {
+									if (event.key === "Enter") {
+										remove_file(i);
+									}
+								}}
+								>×
+							</button>
+						</td>
+					{/if}
 				</tr>
 			{/each}
 		</tbody>
@@ -53,26 +115,31 @@
 </div>
 
 <style>
-	td {
-		width: 45%;
+	.label-clear-button {
+		color: var(--body-text-color-subdued);
+		position: relative;
+		left: -3px;
 	}
 
-	td:last-child {
-		width: 10%;
-		text-align: right;
-	}
-	.file-preview-holder {
-		overflow-x: auto;
-		overflow-y: auto;
+	.label-clear-button:hover {
+		color: var(--body-text-color);
 	}
+
 	.file-preview {
+		table-layout: fixed;
 		width: var(--size-full);
 		max-height: var(--size-60);
 		overflow-y: auto;
 		margin-top: var(--size-1);
 		color: var(--body-text-color);
 	}
+
+	.file-preview-holder {
+		overflow: auto;
+	}
+
 	.file {
+		display: flex;
 		width: var(--size-full);
 	}
 
@@ -80,20 +147,40 @@
 		padding: var(--size-1) var(--size-2-5);
 	}
 
+	.filename {
+		flex-grow: 1;
+		display: flex;
+		overflow: hidden;
+	}
+	.filename .stem {
+		overflow: hidden;
+		text-overflow: ellipsis;
+		white-space: nowrap;
+	}
+	.filename .ext {
+		white-space: nowrap;
+	}
+
+	.download {
+		min-width: 8rem;
+		width: 10%;
+		white-space: nowrap;
+		text-align: right;
+	}
 	.download:hover {
 		text-decoration: underline;
 	}
-	.download > a {
+	.download > :global(a) {
 		color: var(--link-text-color);
 	}
 
-	.download > a:hover {
+	.download > :global(a:hover) {
 		color: var(--link-text-color-hover);
 	}
-	.download > a:visited {
+	.download > :global(a:visited) {
 		color: var(--link-text-color-visited);
 	}
-	.download > a:active {
+	.download > :global(a:active) {
 		color: var(--link-text-color-active);
 	}
 	.selectable {

src/frontend/shared/FileRetrieval.svelte

@@ -1,16 +1,19 @@
 <script lang="ts">
   import { createEventDispatcher, tick, getContext } from "svelte";
 
-  import { upload_files, upload, FileData } from "@gradio/client";
+  import { FileData } from "@gradio/client";
   import LoadingSpinner from "./loading_spinner.svelte";
   let uploaded_files;
   const dispatch = createEventDispatcher();
-  const upload_fn = getContext<typeof upload_files>("upload_files");
+
+  import type { Client } from "@Gradio Uptime/client";
+  export let upload: Client["upload"];
+
   export let root: string;
   async function handle_upload(file_data: FileData): Promise<void> {
     await tick();
     const upload_id = Math.random().toString(36).substring(2, 15);
-    uploaded_files = await upload([file_data], root, upload_id, upload_fn);
+    uploaded_files = await upload([file_data], root, upload_id);
     dispatch("load", uploaded_files[0]);
   }
   let loading = false;

src/frontend/shared/FileUpload.svelte

@@ -1,7 +1,7 @@
 <script lang="ts">
   import { createEventDispatcher, tick } from "svelte";
   import { Upload, ModifyUpload } from "@gradio/upload";
-  import type { FileData } from "@gradio/client";
+  import type { FileData, Client } from "@gradio/client";
   import { BlockLabel } from "@gradio/atoms";
   import { File } from "@gradio/icons";
   import FileRetrieval from "./FileRetrieval.svelte";
@@ -14,12 +14,15 @@
 
   export let label: string;
   export let show_label = true;
-  export let file_count = "single";
+  export let file_count: "single" | "multiple" | "directory" = "single";
   export let file_types: string[] | null = null;
   export let selectable = false;
   export let root: string;
   export let height: number | undefined = undefined;
   export let i18n: I18nFormatter;
+  export let max_file_size: number | null = null;
+  export let upload: Client["upload"];
+  export let stream_handler: Client["stream"];
 
   export let config = {};
   export let confidenceLabel = "";
@@ -31,15 +34,16 @@
     detail,
   }: CustomEvent<FileData | FileData[]>): Promise<void> {
     value = detail;
+    console.log("upload", detail);
+
     await tick();
     dispatch("change", value);
     dispatch("upload", detail);
-    console.log("upload", detail);
   }
 
   function handle_clear(): void {
     value = null;
-    moldata = null;
+    oldata = null;
     dispatch("change", null);
     dispatch("clear");
   }
@@ -53,34 +57,23 @@
     error: string;
   }>();
 
-  let accept_file_types: string | null;
-  if (file_types == null) {
-    accept_file_types = null;
-  } else {
-    file_types = file_types.map((x) => {
-      if (x.startsWith(".")) {
-        return x;
-      }
-      return x + "/*";
-    });
-    accept_file_types = file_types.join(", ");
-  }
-
   let dragging = false;
   $: dispatch("drag", dragging);
 </script>
 
-<BlockLabel
-  {show_label}
-  Icon={File}
-  float={value === null}
-  label={label || "File"}
-/>
+<BlockLabel {show_label} Icon={File} float={!value} label={label || "File"} />
 
-{#if value}
+{#if value && (Array.isArray(value) ? value.length > 0 : true)}
   <ModifyUpload {i18n} on:clear={handle_clear} absolute />
-  <FilePreview {i18n} on:select {selectable} {value} {height} />
-
+  <FilePreview
+    {i18n}
+    on:select
+    {selectable}
+    {value}
+    {height}
+    on:change
+    on:delete
+  />
   {#if moldata != null && molviewer}
     <MolecularViewer {moldata} {config} {confidenceLabel} {representations} />
   {/if}
@@ -88,14 +81,19 @@
   <FileRetrieval
     {root}
     on:load={handle_upload}
+    {upload}
     on:notfound={() => dispatch("notfound")}
   />
   <Upload
     on:load={handle_upload}
-    filetype={accept_file_types}
+    filetype={file_types}
     {file_count}
+    {max_file_size}
     {root}
     bind:dragging
+    on:error
+    {stream_handler}
+    {upload}
   >
     <slot />
   </Upload>

src/frontend/shared/MolecularViewer.svelte

@@ -1,21 +1,13 @@
 <script lang="ts">
   import * as mol from "3dmol/build/3Dmol.js";
-  let TDmol = mol.default;
+  let TDmol = mol;
 
   import { onMount, onDestroy } from "svelte";
 
-  // import RepresentationsIcon from "../static/RepresentationsIcon.svelte";
-  // import JSZip from "jszip";
-  // import { saveAs } from "file-saver";
-
   let viewer;
   export let confidenceLabel = null;
 
   export let moldata = null;
-  // [
-  // { data: propdata, name: "Input", format: "pdb", asFrames: false },
-  // { data: moldata2, name: "Output", format: "pdb", asFrames: true },
-  // ];
 
   let settings = {
     backgroundColor: {
@@ -29,13 +21,11 @@
       type: "toggle",
     },
   };
-  export let config = {};
-
-  // {
-  //   backgroundColor: "white",
-  //   orthographic: false,
-  //   disableFog: false,
-  // };
+  export let config = {
+    backgroundColor: "white",
+    orthographic: false,
+    disableFog: false,
+  };
 
   $: {
     if (view != undefined) {
@@ -159,6 +149,7 @@
             and: [selObj, { atom: ["N", "C", "O"], invert: true }],
           };
         }
+
         if (rep.style === "surface") {
           colorObj.opacity = 0.8;
           view.addSurface(TDmol.SurfaceType.VDW, colorObj, selObj);
@@ -220,7 +211,7 @@
     applyStyles(representations);
     view.zoomTo();
     view.render();
-    view.zoom(0.8, 2000);
+    view.zoom(0.9, 100);
 
     representations.forEach((rep) => {
       if (rep.color === "alphafold") {

src/frontend/shared/utils.ts

@@ -10,32 +10,3 @@ export const prettyBytes = (bytes: number): string => {
 	let unit = units[i];
 	return bytes.toFixed(1) + " " + unit;
 };
-
-export const display_file_name = (value: FileData): string => {
-	var str: string;
-	str = value.orig_name;
-	const max_length = 30;
-
-	if (str.length > max_length) {
-		const truncated_name = str.substring(0, max_length);
-		const file_extension_index = str.lastIndexOf(".");
-		if (file_extension_index !== -1) {
-			const file_extension = str.slice(file_extension_index);
-			return `${truncated_name}..${file_extension}`;
-		}
-		return truncated_name;
-	}
-	return str;
-};
-
-export const display_file_size = (value: FileData | FileData[]): string => {
-	var total_size = 0;
-	if (Array.isArray(value)) {
-		for (var file of value) {
-			if (file.size !== undefined) total_size += file.size;
-		}
-	} else {
-		total_size = value.size || 0;
-	}
-	return prettyBytes(total_size);
-};

src/frontend/style.css

@@ -0,0 +1 @@
+@import "tailwindcss";

src/pyproject.toml

@@ -8,12 +8,12 @@ build-backend = "hatchling.build"
 
 [project]
 name = "gradio_molecule3d"
-version = "0.0.5"
-description = "Molecule3D custom component to visualize pdb or sdf files using 3Dmol.js"
+version = "0.0.6"
+description = "Python library for easily interacting with trained machine learning models"
 readme = "README.md"
-license = "MIT"
+license = "Apache-2.0"
 requires-python = ">=3.8"
-authors = [{ name = "Simon Dürr", email = "dev@simonduerr.eu" }]
+authors = [{ name = "YOUR NAME", email = "YOUREMAIL@domain.com" }]
 keywords = [
   "machine learning",
   "reproducibility",
@@ -24,10 +24,9 @@ keywords = [
   "protein"
 ]
 # Add dependencies here
-dependencies = ["gradio>=4.0,<5.0"]
+dependencies = ["gradio>=4.0,<6.0"]
 classifiers = [
   'Development Status :: 3 - Alpha',
-  'License :: OSI Approved :: Apache Software License',
   'Operating System :: OS Independent',
   'Programming Language :: Python :: 3',
   'Programming Language :: Python :: 3 :: Only',
@@ -40,11 +39,12 @@ classifiers = [
   'Topic :: Scientific/Engineering :: Visualization',
 ]
 
+
 [project.optional-dependencies]
 dev = ["build", "twine"]
 
 [tool.hatch.build]
-artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates"]
+artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi"]
 
 [tool.hatch.build.targets.wheel]
 packages = ["/backend/gradio_molecule3d"]