Minor widget enhancements (MDAnalysis#65)

- Add documentation link in widget details page
- Add confirmation for widget delete from dashboard page
- Add duplicate and delete support of widget from widget details page

Author: PardhavMaradani

mdadash/backend/analyses/acf.py

@@ -109,6 +109,11 @@ class ACFAnalysis(WidgetBase):
     name = "ACF"
     description = "Autocorrelation Function"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.acf.html"
+    )
+
     _notes = (
         "To correctly compute positional ACF using this widget, you must supply "
         "coordinates in the unwrapped convention, also known as no-jump. That is, "

mdadash/backend/analyses/com_distance.py

@@ -90,6 +90,11 @@ class COMDistance(WidgetBase):
     name = "COMDistance"
     description = "Distance between two COMs"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.com_distance.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",

mdadash/backend/analyses/contacts.py

@@ -80,6 +80,11 @@ class Contacts(WidgetBase):
     name = "Contacts"
     description = "Contacts within a cutoff"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.contacts.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",

mdadash/backend/analyses/custom_code.py

@@ -106,6 +106,11 @@ def show(self, name, values):
     name = "Custom Code"
     description = "Custom user-defined code"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.custom_code.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",

mdadash/backend/analyses/dssp.py

@@ -68,6 +68,11 @@ class DSSPAnalysis(WidgetBase):
     name = "DSSP Analysis"
     description = "Secondary structure assignment of protein"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.dssp.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",

mdadash/backend/analyses/energies.py

@@ -75,6 +75,12 @@ class EnergyWidgetBase:
     data_key = ""
     y_label = "Energy ( kJ / mol )"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.energies.html"
+        "#mdadash.backend.analyses.energies.EnergyWidgetBase"
+    )
+
     _notes = (
         "Energies are only available for streaming trajectories and only if the "
         "simulation engine is configured to send them."
@@ -131,7 +137,7 @@ def _reset_plot_values(self):
 
     def _set_title(self):
         """Set plot title"""
-        self.ax.set_title(self.title, y=1.05)
+        self.ax.set_title(self.title)
 
     def _set_x_values(self):
         """Set the values for the x-axis"""

mdadash/backend/analyses/helix_analysis.py

@@ -89,6 +89,11 @@ class HelixAnalysis(WidgetBase):
     name = "Helix Analysis"
     description = "Helix analysis using HELANAL"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.helix_analysis.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",

mdadash/backend/analyses/hydrogen_bonds.py

@@ -111,6 +111,11 @@ class HydrogenBonds(WidgetBase):
         "of donor-hydrogen pairs."
     )
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.hydrogen_bonds.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",

mdadash/backend/analyses/janin.py

@@ -38,6 +38,10 @@ class JaninPlot(WidgetBase):
         Show allowed and marginally allowed regions
             Default: ``True``
 
+    Custom title
+        Custom title for the plot
+            Default: ''
+
     **Output**
 
     Here is an example output plot of this widget:
@@ -50,6 +54,11 @@ class JaninPlot(WidgetBase):
     name = "Janin Plot"
     description = "Dihedral angles analysis using Janin plot"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.janin.html"
+    )
+
     _inputs: ClassVar = [
         {
             "attribute": "selection",
@@ -64,24 +73,32 @@ class JaninPlot(WidgetBase):
             "description": "Show allowed and marginally allowed regions",
             "type": "bool",
         },
+        {
+            "attribute": "custom_title",
+            "name": "Custom title",
+            "description": "Custom title for the plot",
+            "type": "str",
+        },
     ]
 
     def __init__(self):
         super().__init__()
         self.selection = "protein"
         self.ref = True
         self.janin = None
+        self.title = "protein"
+        self.custom_title = None
         self._setup_plot()
 
     def _setup_plot(self):
         """Setup matplotlib plot"""
         self.fig, self.ax = plt.subplots()
         (self.plot,) = self.ax.plot([], [])
-        self.ax.grid(True)
 
     def _update_selection(self):
         """Update atom groups when selection phrase changes"""
         self.janin = Janin(self.u.select_atoms(self.selection))
+        self.title = f"{self.selection}"
 
     def on_post_connect(self):
         """on_post_connect handler"""
@@ -108,5 +125,8 @@ def run_every_frame(self):
         self.janin.plot(ax=self.ax, color="black", marker=".", ref=self.ref)
         self.ax.set_xlabel(r"$\chi_1$ (degrees)")
         self.ax.set_ylabel(r"$\chi_2$ (degrees)")
+        self.ax.set_title(
+            self.custom_title.replace("\\n", "\n") if self.custom_title else self.title
+        )
         self.fig.canvas.draw()
         display(self.fig)

mdadash/backend/analyses/msd.py

@@ -88,6 +88,11 @@ class MSDAnalysis(WidgetBase):
     name = "MSD Analysis"
     description = "Mean squared displacement analysis"
 
+    _doclink = (
+        "https://mdadash.readthedocs.io/en/latest/autosummary/"
+        "mdadash.backend.analyses.msd.html"
+    )
+
     _notes = (
         "To correctly compute MSD using this widget, you must supply coordinates "
         "in the unwrapped convention, also known as no-jump. That is, when atoms "