workbench 0.8.219__py3-none-any.whl → 0.8.231__py3-none-any.whl

workbench/themes/light/custom.css

@@ -1,17 +1,79 @@
+/* Light Theme Color Palette - Blue-Purple Blend */
+:root {
+    /* Primary colors - blue to purple blend, low saturation */
+    --wb-lightest: rgb(215, 218, 225);        /* Light blue-lavender - backgrounds */
+    --wb-light: rgb(210, 213, 220);           /* Slightly lighter - alternate rows */
+    --wb-medium: rgb(175, 185, 215);          /* Medium blue-purple - headers */
+    --wb-accent: rgb(120, 130, 180);          /* Blue-purple accent - borders */
+    --wb-dark: rgb(80, 90, 140);              /* Dark blue-purple - strong accents */
+
+    /* Text colors */
+    --wb-text-primary: rgb(45, 45, 55);       /* Primary text */
+    --wb-text-bold: rgb(80, 80, 180);          /* Bold text */
+    --wb-text-italic: rgb(120, 80, 180);        /* Italic text */
+    --wb-text-muted: rgb(95, 100, 120);       /* Muted text */
+
+    /* Semantic colors */
+    --wb-success: rgb(40, 110, 50);
+    --wb-info: rgb(60, 80, 160);
+    --wb-warning: rgb(170, 90, 10);
+    --wb-danger: rgb(180, 50, 80);
+    --wb-pink: rgb(200, 100, 200);
+
+    /* Shadows */
+    --wb-shadow: rgba(80, 80, 80, 0.15);
+
+    /* Dropdown/form colors */
+    --wb-dropdown-bg: rgba(215, 215, 215);
+    --wb-dropdown-focus: rgba(215, 215, 215);
+    --wb-dropdown-hover: rgba(215, 215, 215);
+
+    /* Container colors */
+    --wb-container-bg: rgb(215, 218, 225);
+    --wb-table-cell-bg: rgb(215, 218, 225);
+
+    /* Body gradient colors */
+    --wb-body-gradient-start: rgb(180, 195, 215);
+    --wb-body-gradient-end: rgb(195, 205, 220);
+
+    /* Table header gradient colors */
+    --wb-header-red-start: rgb(200, 120, 120);
+    --wb-header-red-end: rgb(160, 90, 90);
+    --wb-header-yellow-start: rgb(180, 175, 100);
+    --wb-header-yellow-end: rgb(140, 135, 70);
+    --wb-header-green-start: rgb(110, 170, 110);
+    --wb-header-green-end: rgb(80, 130, 80);
+    --wb-header-purple-start: rgb(160, 120, 180);
+    --wb-header-purple-end: rgb(120, 85, 140);
+}
+
 h1, h2, h3, h4 {
-    color: rgb(80, 80, 80); /* We want the headers dark gray */
+    color: var(--wb-text-primary);
 }
 
 body {
-    color: rgb(80, 80, 80); /* Dark gray text */
-    /* background: linear-gradient(90deg, rgba(240,240,240,1) 0%, rgba(240,240,240,1) 50%, rgba(150,150,195,1) 100%);*/
-    /* background: linear-gradient(90deg, rgba(200,200,220,1) 0%, rgba(150,150,195,1) 100%); */
-    background: linear-gradient(90deg, rgba(200,200,220,1) 0%, rgba(170,170,210,1) 100%);
+    color: var(--wb-text-primary);
+    background: linear-gradient(90deg, var(--wb-body-gradient-start) 0%, var(--wb-body-gradient-end) 100%);
 }
 
 /* Custom CSS to style bold text */
 b, strong {
-    color: rgb(40, 40, 40);
+    color: var(--wb-text-bold);
+}
+
+/* Custom CSS to style italic text */
+i, em {
+    color: var(--wb-text-italic);
+}
+
+/* Default link color */
+a {
+    color: rgb(40, 80, 200); /* Electric blue for links */
+}
+
+/* Hover effect */
+a:hover {
+    color: rgb(60, 100, 240); /* Brighter blue on hover */
 }
 
 /* Reduce spacing around lists */
@@ -25,104 +87,125 @@ ul, ol {
 
 /* AgGrid custom CSS */
 
-/* Adjust header background color */
-.ag-header {
-    --ag-header-background-color: rgba(150, 150, 195);
-}
-
-/* Adjust cell background */
-.ag-cell {
-    background-color: rgb(240, 240, 240);
-}
-
-/* Alternate row colors */
-.ag-row:nth-child(even) .ag-cell {
-    background-color: rgb(230, 230, 230);
-}
-
-/* Selection color for the entire row */
-.ag-row.ag-row-selected .ag-cell {
-    background-color: rgba(170, 170, 205, 1.0);
+/* AG Grid 33+ uses CSS variables for theming - set them at the theme level */
+[class*="ag-theme-"] {
+    --ag-background-color: var(--wb-lightest);
+    --ag-odd-row-background-color: var(--wb-lightest);
+    --ag-row-background-color: var(--wb-light);
+    --ag-selected-row-background-color: var(--wb-medium);
+    --ag-row-hover-color: var(--wb-light);
+    --ag-header-background-color: var(--wb-medium);
+    --ag-border-color: var(--wb-accent);
+    --ag-foreground-color: var(--wb-text-primary);
+    --ag-header-foreground-color: var(--wb-text-primary);
+
+    /* Box shadow and rounded corners */
+    box-shadow: 2px 2px 6px 5px var(--wb-shadow);
+    border-radius: 12px;
+    border: 0.5px solid var(--wb-accent);
+    margin: 0;
+    padding: 0;
 }
 
-/* There's a one pixel border around the grid that we want to remove */
+/* Remove border from the grid wrapper */
 .ag-root-wrapper {
-    border: none !important; /* Force removal with !important */
+    border: none !important;
 }
 
-
-/* Box shadow and rounded corners for all AgGrid themes */
-[class*="ag-theme-"] {
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.2); /* Drop shadow */
-    border-radius: 12px; /* Rounded corners */
-    border: 0.5px solid rgba(0, 0, 205, 0.5);
-    margin: 0;
-    padding: 0;
+/* AG Grid container - remove padding but allow shadow overflow */
+div:has(> [class*="ag-theme-"]) {
+    padding: 0 !important;
+    overflow: visible !important;
 }
 
 /* Apply styling to Workbench containers */
 .workbench-container {
-    background-color: rgba(240, 240, 240, 0.5);
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.2);
-    border-radius: 12px; /* Rounded corners */
+    background-color: var(--wb-container-bg);
+    box-shadow: 2px 2px 6px 5px var(--wb-shadow);
+    border-radius: 12px;
 }
 
 /* Apply styling to Workbench Offsets */
 .workbench-offset {
-    background-color: rgba(240, 240, 240, 0.25);
-    box-shadow: 1px 1px 3px 2px rgba(0, 0, 0, 0.2);
-    border-radius: 12px; /* Rounded corners */
-}
-
-/* Apply styling to Workbench Highlight */
-.workbench-highlight {
-    background-color: rgba(240, 240, 240, 0.5);
-    box-shadow: 1px 1px 3px 2px rgba(0, 0, 0, 0.2);
-    border-radius: 12px; /* Rounded corners */
+    box-shadow: 1px 1px 3px 2px var(--wb-shadow);
+    border-radius: 12px;
 }
 
 /* Apply styling to custom tooltips */
 .custom-tooltip {
-    background-color: rgba(240, 240, 240, 1.0);
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
-    border-radius: 25px; /* Rounded corners */
-    overflow: hidden; /* Ensure contents fit inside the rounded corners */
-    border: 2px solid rgba(128, 128, 128, 1); /* 1-pixel grey */
+    background-color: var(--wb-lightest);
+    box-shadow: 2px 2px 6px 5px var(--wb-shadow);
+    border-radius: 25px;
+    overflow: hidden;
+    border: 2px solid var(--wb-accent);
 }
 
 /* Some of the HTML/Markdown will use color hints like 'green-text' or 'blue-text' */
 .green-text {
-    color: rgb(40, 100, 40);
+    color: var(--wb-success);
 }
 
 .blue-text {
-    color: rgb(70, 70, 160);
+    color: var(--wb-info);
 }
 
 .pink-text {
-    color: rgb(200, 100, 200);
+    color: var(--wb-pink);
 }
 
 .red-text {
-    color: rgb(200, 60, 100);
+    color: var(--wb-danger);
 }
 
 .orange-text {
-    color: rgb(160, 80, 0);
+    color: var(--wb-warning);
 }
 
 .alert {
-    color: rgb(200, 60, 100);
+    color: var(--wb-danger);
 }
 
 .warning {
-    color: rgb(160, 80, 0);
+    color: var(--wb-warning);
 }
 
 .good {
-    color: rgb(40, 100, 40);
+    color: var(--wb-success);
+}
+
+/* Dropdown styling (dcc.Dropdown) - override Bootstrap's variables */
+.dash-dropdown {
+    --bs-body-bg: var(--wb-dropdown-bg);
+    --bs-body-color: var(--wb-text-primary);
+    --bs-border-color: var(--wb-accent);
+}
+
+/* Bootstrap form controls (dbc components) */
+.form-select, .form-control {
+    background-color: var(--wb-dropdown-bg) !important;
+    border: 1px solid var(--wb-accent) !important;
+    color: var(--wb-text-primary) !important;
 }
 
+.form-select:focus, .form-control:focus {
+    background-color: var(--wb-dropdown-focus) !important;
+    border-color: var(--wb-dark) !important;
+    box-shadow: 0 0 0 0.2rem var(--wb-shadow) !important;
+}
+
+.dropdown-menu {
+    background-color: var(--wb-dropdown-bg) !important;
+    border: 1px solid var(--wb-accent) !important;
+}
+
+.dropdown-item {
+    color: var(--wb-text-primary) !important;
+}
+
+.dropdown-item:hover, .dropdown-item:focus {
+    background-color: var(--wb-dropdown-hover) !important;
+    color: var(--wb-text-primary) !important;
+}
 
 /* Table styling */
 table {
@@ -131,15 +214,40 @@ table {
 
 th {
     padding: 10px;
-    border: 1px solid rgb(120, 120, 120);
-    background-color: rgba(150, 150, 195);
+    border: 1px solid var(--wb-accent);
+    background-color: var(--wb-medium);
     font-weight: bold;
     text-align: center !important;
 }
 
 td {
     padding: 5px;
-    border: 0.5px solid rgb(120, 120, 120);
-    background-color: rgba(240, 240, 240, 0.5);
+    border: 0.5px solid var(--wb-accent);
+    background-color: var(--wb-table-cell-bg);
     text-align: center !important;
 }
+
+/* AG Grid table header colors - gradient theme */
+/* Data Sources tables - red gradient */
+#main_data_sources .ag-header,
+#data_sources_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-red-start) 0%, var(--wb-header-red-end) 100%) !important;
+}
+
+/* Feature Sets tables - yellow/olive gradient */
+#main_feature_sets .ag-header,
+#feature_sets_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-yellow-start) 0%, var(--wb-header-yellow-end) 100%) !important;
+}
+
+/* Models tables - green gradient */
+#main_models .ag-header,
+#models_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-green-start) 0%, var(--wb-header-green-end) 100%) !important;
+}
+
+/* Endpoints tables - purple gradient */
+#main_endpoints .ag-header,
+#endpoints_table .ag-header {
+    background: linear-gradient(180deg, var(--wb-header-purple-start) 0%, var(--wb-header-purple-end) 100%) !important;
+}

workbench/themes/light/plotly.json

@@ -133,7 +133,7 @@
                     "ticks": ""
                 },
                 "colorscale": [
-                    [0.0, "rgb(100, 100, 200)"],
+                    [0.0, "rgba(100, 100, 200, 0.8)"],
                     [0.4, "rgb(100, 200, 100)"],
                     [0.65, "rgb(170, 170, 50)"],
                     [0.85, "rgb(200, 100, 100)"],
@@ -476,14 +476,14 @@
         },
         "colorscale": {
             "diverging": [
-                [0.0, "rgb(100, 100, 255)"],
+                [0.0, "rgba(100, 100, 255, 0.8)"],
                 [0.4, "rgb(100, 240, 100)"],
                 [0.65, "rgb(200, 200, 50)"],
                 [0.85, "rgb(255, 100, 100)"],
                 [1.0, "rgb(255, 100, 100)"]
             ],
             "sequential": [
-                [0.0, "rgb(100, 100, 200)"],
+                [0.0, "rgba(100, 100, 200, 0.8)"],
                 [0.4, "rgb(100, 200, 100)"],
                 [0.65, "rgb(170, 170, 50)"],
                 [0.85, "rgb(200, 100, 100)"],
@@ -561,8 +561,8 @@
         "mapbox": {
             "style": "light"
         },
-        "paper_bgcolor": "rgba(0, 0, 0, 0.0)",
-        "plot_bgcolor": "rgba(0, 0, 0, 0.0)",
+        "paper_bgcolor": "rgba(255, 255, 255, 0.0)",
+        "plot_bgcolor": "rgba(255, 255, 255, 0.0)",
         "polar": {
             "angularaxis": {
                 "gridcolor": "#EBF0F8",
@@ -633,25 +633,25 @@
         },
         "xaxis": {
             "automargin": true,
-            "gridcolor": "#ffffff",
+            "gridcolor": "rgba(120, 130, 160, 0.3)",
             "linecolor": "#EBF0F8",
             "ticks": "",
             "title": {
                 "standoff": 15
             },
-            "zerolinecolor": "#edeeee",
+            "zerolinecolor": "rgba(120, 130, 160, 0.4)",
             "zerolinewidth": 2,
             "gridwidth": 0.5
         },
         "yaxis": {
             "automargin": true,
-            "gridcolor": "#ffffff",
+            "gridcolor": "rgba(120, 130, 160, 0.3)",
             "linecolor": "#EBF0F8",
             "ticks": "",
             "title": {
                 "standoff": 15
             },
-            "zerolinecolor": "#edeeee",
+            "zerolinecolor": "rgba(120, 130, 160, 0.4)",
             "zerolinewidth": 2,
             "gridwidth": 0.5
         },

workbench/themes/midnight_blue/custom.css

@@ -37,48 +37,42 @@ a:hover {
 
 /* AgGrid custom CSS */
 
-/* Adjust header background color */
-.ag-header {
+/* AG Grid 33+ uses CSS variables for theming - set them at the theme level */
+[class*="ag-theme-"] {
+    --ag-background-color: rgb(54, 55, 88);
+    --ag-odd-row-background-color: rgb(54, 55, 88);
+    --ag-row-background-color: rgb(58, 59, 92);
+    --ag-selected-row-background-color: rgb(32, 75, 105);
+    --ag-row-hover-color: rgb(52, 73, 100);
     --ag-header-background-color: rgb(42, 85, 115);
-}
-
-/* Adjust cell background */
-.ag-cell {
-    background-color: rgb(57, 63, 96);
-}
-
-/* Alternate row colors */
-.ag-row:nth-child(even) .ag-cell {
-    background-color: rgb(62, 68, 101);
-}
+    --ag-border-color: rgba(80, 85, 115, 0.5);
+    --ag-foreground-color: rgb(210, 210, 210);
+    --ag-header-foreground-color: rgb(220, 220, 220);
 
-/* Selection color for the entire row */
-.ag-row.ag-row-selected .ag-cell {
-    background-color: rgb(32, 75, 105);
+    /* Box shadow and rounded corners */
+    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
+    border-radius: 12px;
+    border: 0.5px solid rgba(0, 0, 0, 0.5);
+    margin: 0;
+    padding: 0;
 }
 
-
-
-/* There's a one pixel border around the grid that we want to remove */
+/* Remove border from the grid wrapper */
 .ag-root-wrapper {
-    border: none !important; /* Force removal with !important */
+    border: none !important;
 }
 
-
-/* Box shadow and rounded corners for all AgGrid themes */
-[class*="ag-theme-"] {
-    box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
-    border-radius: 12px; /* Rounded corners */
-    border: 0.5px solid rgba(0, 0, 0, 0.5);
-    margin: 0;
-    padding: 0;
+/* AG Grid container - remove padding but allow shadow overflow */
+div:has(> [class*="ag-theme-"]) {
+    padding: 0 !important;
+    overflow: visible !important;
 }
 
 /* Apply styling to Workbench containers */
 .workbench-container {
     box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
     border-radius: 12px; /* Rounded corners */
-    background-color: rgba(45, 41, 76, 0.5); /* Dark background */
+    background-color: rgb(54, 55, 88); /* Dark background */
 }
 
 /* Apply styling to Workbench Offsets */
@@ -133,6 +127,40 @@ a:hover {
     color: rgb(100, 255, 100);
 }
 
+/* Dropdown styling (dcc.Dropdown) - override Bootstrap's --bs-body-bg variable */
+.dash-dropdown {
+    --bs-body-bg: rgb(55, 60, 90);
+    --bs-border-color: rgb(80, 85, 115);
+}
+
+
+/* Bootstrap form controls (dbc components) */
+.form-select, .form-control {
+    background-color: rgb(55, 60, 90) !important;
+    border: 1px solid rgb(80, 85, 115) !important;
+    color: rgb(210, 210, 210) !important;
+}
+
+.form-select:focus, .form-control:focus {
+    background-color: rgb(60, 65, 95) !important;
+    border-color: rgb(100, 105, 140) !important;
+    box-shadow: 0 0 0 0.2rem rgba(100, 105, 140, 0.25) !important;
+}
+
+.dropdown-menu {
+    background-color: rgb(55, 60, 90) !important;
+    border: 1px solid rgb(80, 85, 115) !important;
+}
+
+.dropdown-item {
+    color: rgb(210, 210, 210) !important;
+}
+
+.dropdown-item:hover, .dropdown-item:focus {
+    background-color: rgb(70, 75, 110) !important;
+    color: rgb(230, 230, 230) !important;
+}
+
 /* Table styling */
 table {
     width: 100%;
@@ -151,4 +179,29 @@ td {
     padding: 5px;
     border: 0.5px solid #444;
     text-align: center !important;
+}
+
+/* AG Grid table header colors - gradient theme */
+/* Data Sources tables - red gradient */
+#main_data_sources .ag-header,
+#data_sources_table .ag-header {
+    background: linear-gradient(180deg, rgb(130, 55, 55) 0%, rgb(80, 35, 35) 100%) !important;
+}
+
+/* Feature Sets tables - yellow/olive gradient */
+#main_feature_sets .ag-header,
+#feature_sets_table .ag-header {
+    background: linear-gradient(180deg, rgb(110, 105, 50) 0%, rgb(70, 65, 30) 100%) !important;
+}
+
+/* Models tables - green gradient */
+#main_models .ag-header,
+#models_table .ag-header {
+    background: linear-gradient(180deg, rgb(50, 100, 50) 0%, rgb(30, 60, 30) 100%) !important;
+}
+
+/* Endpoints tables - purple gradient */
+#main_endpoints .ag-header,
+#endpoints_table .ag-header {
+    background: linear-gradient(180deg, rgb(90, 55, 110) 0%, rgb(55, 30, 70) 100%) !important;
 }

workbench/themes/midnight_blue/plotly.json

@@ -528,7 +528,7 @@
             "style": "dark"
         },
         "paper_bgcolor": "rgba(0, 0, 0, 0.0)",
-        "plot_bgcolor": "rgba(0, 0, 0, 0.0)",
+        "plot_bgcolor": "rgb(54, 55, 88)",
         "polar": {
             "angularaxis": {
                 "gridcolor": "#506784",

workbench/utils/aws_utils.py

@@ -17,7 +17,6 @@ from botocore.exceptions import ClientError
 from sagemaker.session import Session as SageSession
 from collections.abc import Mapping, Iterable
 
-
 # Workbench Imports
 from workbench.utils.config_manager import ConfigManager
 from workbench.utils.deprecated_utils import deprecated

workbench/utils/chem_utils/mol_descriptors.py

@@ -99,7 +99,6 @@ from rdkit.ML.Descriptors import MoleculeDescriptors
 from mordred import Calculator as MordredCalculator
 from mordred import AcidBase, Aromatic, Constitutional, Chi, CarbonTypes
 
-
 logger = logging.getLogger("workbench")
 logger.setLevel(logging.DEBUG)
 

workbench/utils/chem_utils/projections.py

@@ -17,18 +17,28 @@ log = logging.getLogger("workbench")
 
 def fingerprints_to_matrix(fingerprints, dtype=np.uint8):
     """
-    Convert bitstring fingerprints to numpy matrix.
+    Convert fingerprints to numpy matrix.
+
+    Supports two formats (auto-detected):
+        - Bitstrings: "10110010..." → matrix of 0s and 1s
+        - Count vectors: "0,3,0,1,5,..." → matrix of counts (or binary if dtype=np.bool_)
 
     Args:
-        fingerprints: pandas Series or list of bitstring fingerprints
-        dtype: numpy data type (uint8 is default: np.bool_ is good for Jaccard computations
+        fingerprints: pandas Series or list of fingerprints
+        dtype: numpy data type (uint8 is default; np.bool_ for Jaccard computations)
 
     Returns:
         dense numpy array of shape (n_molecules, n_bits)
     """
-
-    # Dense matrix representation (we might support sparse in the future)
-    return np.array([list(fp) for fp in fingerprints], dtype=dtype)
+    # Auto-detect format based on first fingerprint
+    sample = str(fingerprints.iloc[0] if hasattr(fingerprints, "iloc") else fingerprints[0])
+    if "," in sample:
+        # Count vector format: comma-separated integers
+        matrix = np.array([list(map(int, fp.split(","))) for fp in fingerprints], dtype=dtype)
+    else:
+        # Bitstring format: each character is a bit
+        matrix = np.array([list(fp) for fp in fingerprints], dtype=dtype)
+    return matrix
 
 
 def project_fingerprints(df: pd.DataFrame, projection: str = "UMAP") -> pd.DataFrame: