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Dockerfile

@@ -5,6 +5,10 @@ WORKDIR /code
 
 COPY --link --chown=1000 . .
 
+RUN mkdir -p /tmp/cache/
+RUN chmod a+rwx -R /tmp/cache/
+ENV TRANSFORMERS_CACHE=/tmp/cache/ 
+
 RUN pip install --no-cache-dir -r requirements.txt
 
 ENV PYTHONUNBUFFERED=1 	GRADIO_ALLOW_FLAGGING=never 	GRADIO_NUM_PORTS=1 	GRADIO_SERVER_NAME=0.0.0.0     GRADIO_SERVER_PORT=7860 	SYSTEM=spaces

README.md

@@ -1,10 +1,17 @@
 
 ---
-tags: [gradio-custom-component, gradio-template-File]
-title: gradio_molecule3d V0.0.1
-colorFrom: gray
+tags: [gradio-custom-component,machine learning,reproducibility,visualization,gradio,gradio-template-File,protein]
+title: gradio_molecule3d V0.0.2
+colorFrom: purple
 colorTo: indigo
 sdk: docker
 pinned: false
 license: apache-2.0
 ---
+
+
+# Name: gradio_molecule3d
+
+Description: Molecule3D custom component to visualize pdb or sdf files
+
+Install with: pip install gradio_molecule3d

app.py

@@ -26,21 +26,20 @@ def predict(x):
     return x
 
 #doesn't work
-demoInterface = gr.Interface(
-    predict,
-    Molecule3D(label="Molecule3D", reps=reps),  # interactive version of your component
-    Molecule3D(),  # static version of your component
-    #examples=[[example]],  # uncomment this line to view the "example version" of your component
-)
+#demo = gr.Interface(
+#     predict,
+#     Molecule3D(label="Molecule3D", reps=reps),  # interactive version of your component
+#     Molecule3D(),  # static version of your component
+#     examples=[[example]],  # uncomment this line to view the "example version" of your component
+# )
 
 #works
 with gr.Blocks() as demo:
-    with gr.Row():
-        inp = Molecule3D("1pga.pdb",label="Molecule3D", reps=reps)
-        out = Molecule3D(label="Molecule3D", reps=reps)
+    inp = Molecule3D("demo/1pga.pdb",label="Molecule3D", reps=reps)
+    inp = Molecule3D("demo/1pga.pdb",label="Molecule3D", reps=reps, showviewer=False)
+    out = Molecule3D(label="Molecule3D", reps=reps)
     btn = gr.Button("Predict")
     btn.click(predict, inputs=inp, outputs=out)
 
-#demo.launch()
-
-demoInterface.launch()
+demo.launch()
+# blocks.launch()

requirements.txt

@@ -1 +1 @@
-gradio_molecule3d-0.0.1-py3-none-any.whl
+gradio_molecule3d-0.0.2-py3-none-any.whl

src/backend/gradio_molecule3d/molecule3d.py

@@ -65,6 +65,7 @@ class Molecule3D(Component):
         elem_id: str | None = None,
         elem_classes: list[str] | str | None = None,
         render: bool = True,
+        showviewer: bool = True
     ):
         """
         Parameters:
@@ -87,6 +88,7 @@ class Molecule3D(Component):
             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.
+            showviewer: If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.
         """
         self.file_count = file_count
         if self.file_count == "multiple":
@@ -129,6 +131,7 @@ class Molecule3D(Component):
         self.reps = reps
         self.config = config
         self.confidenceLabel = confidenceLabel
+        self.showviewer = showviewer
 
 
     def _process_single_file(self, f: FileData) -> NamedString | bytes:

src/backend/gradio_molecule3d/molecule3d.pyi

@@ -66,6 +66,7 @@ class Molecule3D(Component):
         elem_id: str | None = None,
         elem_classes: list[str] | str | None = None,
         render: bool = True,
+        showviewer: bool = True
     ):
         """
         Parameters:
@@ -88,6 +89,7 @@ class Molecule3D(Component):
             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.
+            showviewer: If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.
         """
         self.file_count = file_count
         if self.file_count == "multiple":
@@ -130,6 +132,7 @@ class Molecule3D(Component):
         self.reps = reps
         self.config = config
         self.confidenceLabel = confidenceLabel
+        self.showviewer = showviewer
 
 
     def _process_single_file(self, f: FileData) -> NamedString | bytes:
@@ -211,7 +214,6 @@ class Molecule3D(Component):
         inputs: Component | Sequence[Component] | set[Component] | None = None,
         outputs: Component | Sequence[Component] | None = None,
         api_name: str | None | Literal[False] = None,
-        status_tracker: None = None,
         scroll_to_output: bool = False,
         show_progress: Literal["full", "minimal", "hidden"] = "full",
         queue: bool | None = None,
@@ -222,7 +224,10 @@ class Molecule3D(Component):
         cancels: dict[str, Any] | list[dict[str, Any]] | None = None,
         every: float | None = None,
         trigger_mode: Literal["once", "multiple", "always_last"] | None = None,
-        js: str | None = None,) -> Dependency:
+        js: str | None = None,
+        concurrency_limit: int | None | Literal["default"] = "default",
+        concurrency_id: str | None = None,
+        show_api: bool = True) -> Dependency:
         """
         Parameters:
             fn: the function to call when this event is triggered. Often a machine learning model's prediction function. Each parameter of the function corresponds to one input component, and the function should return a single value or a tuple of values, with each element in the tuple corresponding to one output component.
@@ -240,6 +245,9 @@ class Molecule3D(Component):
             every: Run this event 'every' number of seconds while the client connection is open. Interpreted in seconds. Queue must be enabled.
             trigger_mode: If "once" (default for all events except `.change()`) would not allow any submissions while an event is pending. If set to "multiple", unlimited submissions are allowed while pending, and "always_last" (default for `.change()` event) would allow a second submission after the pending event is complete.
             js: Optional frontend js method to run before running 'fn'. Input arguments for js method are values of 'inputs' and 'outputs', return should be a list of values for output components.
+            concurrency_limit: If set, this is the maximum number of this event that can be running simultaneously. Can be set to None to mean no concurrency_limit (any number of this event can be running simultaneously). Set to "default" to use the default concurrency limit (defined by the `default_concurrency_limit` parameter in `Blocks.queue()`, which itself is 1 by default).
+            concurrency_id: If set, this is the id of the concurrency group. Events with the same concurrency_id will be limited by the lowest set concurrency_limit.
+            show_api: whether to show this event in the "view API" page of the Gradio app, or in the ".view_api()" method of the Gradio clients. Unlike setting api_name to False, setting show_api to False will still allow downstream apps to use this event. If fn is None, show_api will automatically be set to False.
         """
         ...
     
@@ -248,7 +256,6 @@ class Molecule3D(Component):
         inputs: Component | Sequence[Component] | set[Component] | None = None,
         outputs: Component | Sequence[Component] | None = None,
         api_name: str | None | Literal[False] = None,
-        status_tracker: None = None,
         scroll_to_output: bool = False,
         show_progress: Literal["full", "minimal", "hidden"] = "full",
         queue: bool | None = None,
@@ -259,7 +266,10 @@ class Molecule3D(Component):
         cancels: dict[str, Any] | list[dict[str, Any]] | None = None,
         every: float | None = None,
         trigger_mode: Literal["once", "multiple", "always_last"] | None = None,
-        js: str | None = None,) -> Dependency:
+        js: str | None = None,
+        concurrency_limit: int | None | Literal["default"] = "default",
+        concurrency_id: str | None = None,
+        show_api: bool = True) -> Dependency:
         """
         Parameters:
             fn: the function to call when this event is triggered. Often a machine learning model's prediction function. Each parameter of the function corresponds to one input component, and the function should return a single value or a tuple of values, with each element in the tuple corresponding to one output component.
@@ -277,6 +287,9 @@ class Molecule3D(Component):
             every: Run this event 'every' number of seconds while the client connection is open. Interpreted in seconds. Queue must be enabled.
             trigger_mode: If "once" (default for all events except `.change()`) would not allow any submissions while an event is pending. If set to "multiple", unlimited submissions are allowed while pending, and "always_last" (default for `.change()` event) would allow a second submission after the pending event is complete.
             js: Optional frontend js method to run before running 'fn'. Input arguments for js method are values of 'inputs' and 'outputs', return should be a list of values for output components.
+            concurrency_limit: If set, this is the maximum number of this event that can be running simultaneously. Can be set to None to mean no concurrency_limit (any number of this event can be running simultaneously). Set to "default" to use the default concurrency limit (defined by the `default_concurrency_limit` parameter in `Blocks.queue()`, which itself is 1 by default).
+            concurrency_id: If set, this is the id of the concurrency group. Events with the same concurrency_id will be limited by the lowest set concurrency_limit.
+            show_api: whether to show this event in the "view API" page of the Gradio app, or in the ".view_api()" method of the Gradio clients. Unlike setting api_name to False, setting show_api to False will still allow downstream apps to use this event. If fn is None, show_api will automatically be set to False.
         """
         ...
     
@@ -285,7 +298,6 @@ class Molecule3D(Component):
         inputs: Component | Sequence[Component] | set[Component] | None = None,
         outputs: Component | Sequence[Component] | None = None,
         api_name: str | None | Literal[False] = None,
-        status_tracker: None = None,
         scroll_to_output: bool = False,
         show_progress: Literal["full", "minimal", "hidden"] = "full",
         queue: bool | None = None,
@@ -296,7 +308,10 @@ class Molecule3D(Component):
         cancels: dict[str, Any] | list[dict[str, Any]] | None = None,
         every: float | None = None,
         trigger_mode: Literal["once", "multiple", "always_last"] | None = None,
-        js: str | None = None,) -> Dependency:
+        js: str | None = None,
+        concurrency_limit: int | None | Literal["default"] = "default",
+        concurrency_id: str | None = None,
+        show_api: bool = True) -> Dependency:
         """
         Parameters:
             fn: the function to call when this event is triggered. Often a machine learning model's prediction function. Each parameter of the function corresponds to one input component, and the function should return a single value or a tuple of values, with each element in the tuple corresponding to one output component.
@@ -314,6 +329,9 @@ class Molecule3D(Component):
             every: Run this event 'every' number of seconds while the client connection is open. Interpreted in seconds. Queue must be enabled.
             trigger_mode: If "once" (default for all events except `.change()`) would not allow any submissions while an event is pending. If set to "multiple", unlimited submissions are allowed while pending, and "always_last" (default for `.change()` event) would allow a second submission after the pending event is complete.
             js: Optional frontend js method to run before running 'fn'. Input arguments for js method are values of 'inputs' and 'outputs', return should be a list of values for output components.
+            concurrency_limit: If set, this is the maximum number of this event that can be running simultaneously. Can be set to None to mean no concurrency_limit (any number of this event can be running simultaneously). Set to "default" to use the default concurrency limit (defined by the `default_concurrency_limit` parameter in `Blocks.queue()`, which itself is 1 by default).
+            concurrency_id: If set, this is the id of the concurrency group. Events with the same concurrency_id will be limited by the lowest set concurrency_limit.
+            show_api: whether to show this event in the "view API" page of the Gradio app, or in the ".view_api()" method of the Gradio clients. Unlike setting api_name to False, setting show_api to False will still allow downstream apps to use this event. If fn is None, show_api will automatically be set to False.
         """
         ...
     
@@ -322,7 +340,6 @@ class Molecule3D(Component):
         inputs: Component | Sequence[Component] | set[Component] | None = None,
         outputs: Component | Sequence[Component] | None = None,
         api_name: str | None | Literal[False] = None,
-        status_tracker: None = None,
         scroll_to_output: bool = False,
         show_progress: Literal["full", "minimal", "hidden"] = "full",
         queue: bool | None = None,
@@ -333,7 +350,10 @@ class Molecule3D(Component):
         cancels: dict[str, Any] | list[dict[str, Any]] | None = None,
         every: float | None = None,
         trigger_mode: Literal["once", "multiple", "always_last"] | None = None,
-        js: str | None = None,) -> Dependency:
+        js: str | None = None,
+        concurrency_limit: int | None | Literal["default"] = "default",
+        concurrency_id: str | None = None,
+        show_api: bool = True) -> Dependency:
         """
         Parameters:
             fn: the function to call when this event is triggered. Often a machine learning model's prediction function. Each parameter of the function corresponds to one input component, and the function should return a single value or a tuple of values, with each element in the tuple corresponding to one output component.
@@ -351,5 +371,8 @@ class Molecule3D(Component):
             every: Run this event 'every' number of seconds while the client connection is open. Interpreted in seconds. Queue must be enabled.
             trigger_mode: If "once" (default for all events except `.change()`) would not allow any submissions while an event is pending. If set to "multiple", unlimited submissions are allowed while pending, and "always_last" (default for `.change()` event) would allow a second submission after the pending event is complete.
             js: Optional frontend js method to run before running 'fn'. Input arguments for js method are values of 'inputs' and 'outputs', return should be a list of values for output components.
+            concurrency_limit: If set, this is the maximum number of this event that can be running simultaneously. Can be set to None to mean no concurrency_limit (any number of this event can be running simultaneously). Set to "default" to use the default concurrency limit (defined by the `default_concurrency_limit` parameter in `Blocks.queue()`, which itself is 1 by default).
+            concurrency_id: If set, this is the id of the concurrency group. Events with the same concurrency_id will be limited by the lowest set concurrency_limit.
+            show_api: whether to show this event in the "view API" page of the Gradio app, or in the ".view_api()" method of the Gradio clients. Unlike setting api_name to False, setting show_api to False will still allow downstream apps to use this event. If fn is None, show_api will automatically be set to False.
         """
         ...

src/demo/app.py

@@ -26,7 +26,7 @@ def predict(x):
     return x
 
 #doesn't work
-# demo = gr.Interface(
+#demo = gr.Interface(
 #     predict,
 #     Molecule3D(label="Molecule3D", reps=reps),  # interactive version of your component
 #     Molecule3D(),  # static version of your component
@@ -36,6 +36,7 @@ def predict(x):
 #works
 with gr.Blocks() as demo:
     inp = Molecule3D("demo/1pga.pdb",label="Molecule3D", reps=reps)
+    inp = Molecule3D("demo/1pga.pdb",label="Molecule3D", reps=reps, showviewer=False)
     out = Molecule3D(label="Molecule3D", reps=reps)
     btn = gr.Button("Predict")
     btn.click(predict, inputs=inp, outputs=out)

src/frontend/Index.svelte

@@ -33,6 +33,7 @@
   export let reps: any = [];
   export let config: any = {};
   export let confidenceLabel: string = "";
+  export let showviewer: boolean = true;
 
   export let proxy_url: null | string;
   export let _selectable = false;
@@ -242,6 +243,7 @@
       {moldata}
       {errors}
       i18n={gradio.i18n}
+      molviewer={showviewer}
     />
   {:else}
     <FileUpload
@@ -257,6 +259,7 @@
       {config}
       {confidenceLabel}
       {moldata}
+      molviewer={showviewer}
       on:change={({ detail }) => {
         errors = [];
         value = detail;

src/frontend/shared/File.svelte

@@ -18,6 +18,7 @@
   export let confidenceLabel = "";
   export let representations = [];
   export let moldata = null;
+  export let molviewer = false;
   export let errors = [];
 </script>
 
@@ -32,7 +33,7 @@
   <FilePreview {i18n} {selectable} on:select {value} {height} />
 
   <!-- {JSON.stringify(moldata)} -->
-  {#if moldata != null}
+  {#if moldata != null && molviewer}
     <MolecularViewer {moldata} {config} {confidenceLabel} {representations} />
   {/if}
 {:else}

src/frontend/shared/FileUpload.svelte

@@ -25,6 +25,7 @@
   export let confidenceLabel = "";
   export let representations = [];
   export let moldata = null;
+  export let molviewer = false;
 
   async function handle_upload({
     detail,
@@ -78,7 +79,7 @@
   <ModifyUpload {i18n} on:clear={handle_clear} absolute />
   <FilePreview {i18n} on:select {selectable} {value} {height} />
 
-  {#if moldata != null}
+  {#if moldata != null && molviewer}
     <MolecularViewer {moldata} {config} {confidenceLabel} {representations} />
   {/if}
 {:else}

src/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "gradio_molecule3d"
-version = "0.0.1"
+version = "0.0.2"
 description = "Molecule3D custom component to visualize pdb or sdf files"
 readme = "README.md"
 license = "MIT"
@@ -44,7 +44,7 @@ classifiers = [
 dev = ["build", "twine"]
 
 [tool.hatch.build]
-artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi", "backend/gradio_molecule3d/templates"]
+artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates", "backend/gradio_molecule3d/templates"]
 
 [tool.hatch.build.targets.wheel]
 packages = ["/backend/gradio_molecule3d"]