Rebase etc

- Rebased against `main`, and fixed merged conflicts. - Updated copyright requirement - Updated how models are serialized. - Update style based on other pushes to the branch - Added `__future__` annotations - updated a few docstrings that needed an update - updated yarn lock based on changes with the marginal1d tool and the trace tool. - removed the 3rd party histogram requirement, since it is easy to calculate a histogram. - other fixes associated with merging etc.
facebookresearch · Oct 19, 2022 · 0bc5cc0 · 0bc5cc0
1 parent c509ad4
commit 0bc5cc0
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Showing 15 changed files with 69 additions and 132 deletions.
diff --git a/src/beanmachine/ppl/diagnostics/tools/__init__.py b/src/beanmachine/ppl/diagnostics/tools/__init__.py
@@ -6,7 +6,6 @@
 # flake8: noqa
 
 """Visual diagnostic tools for Bean Machine models."""
-
 import sys
 from pathlib import Path
 
@@ -16,6 +15,7 @@
     #       accepted, see https://peps.python.org/pep-0655/. This is to follow the
     #       interface objects in JavaScript that allow keys to not be required using ?.
     from typing import TypedDict
+
     from typing_extensions import NotRequired
 else:
     from typing_extensions import NotRequired, TypedDict

diff --git a/src/beanmachine/ppl/diagnostics/tools/js/src/marginal1d/callbacks.ts b/src/beanmachine/ppl/diagnostics/tools/js/src/marginal1d/callbacks.ts
@@ -72,7 +72,7 @@ export const computeStats = (
 
   // Compute the point statistics for the KDE, and create labels to display them in the
   // figures.
-  const mean = computeMean(marginalX);
+  const mean = computeMean(rawData);
   const hdiBounds = hdiInterval(rawData, hdiProbability);
   const x = [hdiBounds.lowerBound, mean, hdiBounds.upperBound];
   const y = interpolatePoints({x: marginalX, y: marginalY, points: x});

diff --git a/src/beanmachine/ppl/diagnostics/tools/js/src/stats/histogram.ts b/src/beanmachine/ppl/diagnostics/tools/js/src/stats/histogram.ts
@@ -1,4 +1,10 @@
-/* import {calculateHistogram} from 'compute-histogram'; */
+/**
+ * Copyright (c) Meta Platforms, Inc. and affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
 import {linearRange, numericalSort, shape} from './array';
 import {rankData, scaleToOne} from './dataTransformation';
 import {mean as computeMean} from './pointStatistic';

diff --git a/src/beanmachine/ppl/diagnostics/tools/js/yarn.lock b/src/beanmachine/ppl/diagnostics/tools/js/yarn.lock
@@ -106,7 +106,7 @@
     "@jridgewell/sourcemap-codec" "^1.4.10"
     "@jridgewell/trace-mapping" "^0.3.9"
 
-"@jridgewell/[email protected]", "@jridgewell/resolve-uri@^3.0.3":
+"@jridgewell/[email protected]":
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/@jridgewell/resolve-uri/-/resolve-uri-3.1.0.tgz#2203b118c157721addfe69d47b70465463066d78"
   integrity sha512-F2msla3tad+Mfht5cJq7LSXcdudKTWCVYUgw6pLFOOHSTtZlj6SWNYAp+AhuqLmWdBO2X5hPrLcu8cVP8fy28w==
@@ -201,7 +201,7 @@
   resolved "https://registry.yarnpkg.com/@types/json5/-/json5-0.0.29.tgz#ee28707ae94e11d2b827bcbe5270bcea7f3e71ee"
   integrity sha512-dRLjCWHYg4oaA77cxO64oO+7JwCwnIzkZPdrrC71jQmQtlhM556pwKo5bUzqvZndkVbeFLIIi+9TC40JNF5hNQ==
 
-"@types/node@*", "@types/node@^18.0.4":
+"@types/node@*":
   version "18.8.5"
   resolved "https://registry.yarnpkg.com/@types/node/-/node-18.8.5.tgz#6a31f820c1077c3f8ce44f9e203e68a176e8f59e"
   integrity sha512-Bq7G3AErwe5A/Zki5fdD3O6+0zDChhg671NfPjtIcbtzDNZTv4NPKMRFr7gtYPG7y+B8uTiNK4Ngd9T0FTar6Q==
@@ -218,20 +218,6 @@
   dependencies:
     "@types/jquery" "*"
 
-"@typescript-eslint/eslint-plugin@^5.30.5":
-  version "5.40.0"
-  resolved "https://registry.yarnpkg.com/@typescript-eslint/eslint-plugin/-/eslint-plugin-5.40.0.tgz#0159bb71410eec563968288a17bd4478cdb685bd"
-  integrity sha512-FIBZgS3DVJgqPwJzvZTuH4HNsZhHMa9SjxTKAZTlMsPw/UzpEjcf9f4dfgDJEHjK+HboUJo123Eshl6niwEm/Q==
-  dependencies:
-    "@typescript-eslint/scope-manager" "5.40.0"
-    "@typescript-eslint/type-utils" "5.40.0"
-    "@typescript-eslint/utils" "5.40.0"
-    debug "^4.3.4"
-    ignore "^5.2.0"
-    regexpp "^3.2.0"
-    semver "^7.3.7"
-    tsutils "^3.21.0"
-
 "@typescript-eslint/parser@^5.30.5":
   version "5.40.0"
   resolved "https://registry.yarnpkg.com/@typescript-eslint/parser/-/parser-5.40.0.tgz#432bddc1fe9154945660f67c1ba6d44de5014840"
@@ -250,16 +236,6 @@
     "@typescript-eslint/types" "5.40.0"
     "@typescript-eslint/visitor-keys" "5.40.0"
 
-"@typescript-eslint/[email protected]":
-  version "5.40.0"
-  resolved "https://registry.yarnpkg.com/@typescript-eslint/type-utils/-/type-utils-5.40.0.tgz#4964099d0158355e72d67a370249d7fc03331126"
-  integrity sha512-nfuSdKEZY2TpnPz5covjJqav+g5qeBqwSHKBvz7Vm1SAfy93SwKk/JeSTymruDGItTwNijSsno5LhOHRS1pcfw==
-  dependencies:
-    "@typescript-eslint/typescript-estree" "5.40.0"
-    "@typescript-eslint/utils" "5.40.0"
-    debug "^4.3.4"
-    tsutils "^3.21.0"
-
 "@typescript-eslint/[email protected]":
   version "5.40.0"
   resolved "https://registry.yarnpkg.com/@typescript-eslint/types/-/types-5.40.0.tgz#8de07e118a10b8f63c99e174a3860f75608c822e"
@@ -278,19 +254,6 @@
     semver "^7.3.7"
     tsutils "^3.21.0"
 
-"@typescript-eslint/[email protected]":
-  version "5.40.0"
-  resolved "https://registry.yarnpkg.com/@typescript-eslint/utils/-/utils-5.40.0.tgz#647f56a875fd09d33c6abd70913c3dd50759b772"
-  integrity sha512-MO0y3T5BQ5+tkkuYZJBjePewsY+cQnfkYeRqS6tPh28niiIwPnQ1t59CSRcs1ZwJJNOdWw7rv9pF8aP58IMihA==
-  dependencies:
-    "@types/json-schema" "^7.0.9"
-    "@typescript-eslint/scope-manager" "5.40.0"
-    "@typescript-eslint/types" "5.40.0"
-    "@typescript-eslint/typescript-estree" "5.40.0"
-    eslint-scope "^5.1.1"
-    eslint-utils "^3.0.0"
-    semver "^7.3.7"
-
 "@typescript-eslint/[email protected]":
   version "5.40.0"
   resolved "https://registry.yarnpkg.com/@typescript-eslint/visitor-keys/-/visitor-keys-5.40.0.tgz#dd2d38097f68e0d2e1e06cb9f73c0173aca54b68"
@@ -684,11 +647,6 @@ core-js-pure@^3.25.1:
   resolved "https://registry.yarnpkg.com/core-js-pure/-/core-js-pure-3.25.5.tgz#79716ba54240c6aa9ceba6eee08cf79471ba184d"
   integrity sha512-oml3M22pHM+igfWHDfdLVq2ShWmjM2V4L+dQEBs0DWVIqEm9WHCwGAlZ6BmyBQGy5sFrJmcx+856D9lVKyGWYg==
 
-create-require@^1.1.0:
-  version "1.1.1"
-  resolved "https://registry.yarnpkg.com/create-require/-/create-require-1.1.1.tgz#c1d7e8f1e5f6cfc9ff65f9cd352d37348756c333"
-  integrity sha512-dcKFX3jn0MpIaXjisoRvexIJVEKzaq7z2rZKxf+MSr9TkdmHmsU4m2lcLojrj/FHl8mk5VxMmYA+ftRkP/3oKQ==
-
 cross-spawn@^7.0.2, cross-spawn@^7.0.3:
   version "7.0.3"
   resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.3.tgz#f73a85b9d5d41d045551c177e2882d4ac85728a6"
@@ -786,11 +744,6 @@ emoji-regex@^9.2.2:
   resolved "https://registry.yarnpkg.com/emoji-regex/-/emoji-regex-9.2.2.tgz#840c8803b0d8047f4ff0cf963176b32d4ef3ed72"
   integrity sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==
 
-emoji-regex@^9.2.2:
-  version "9.2.2"
-  resolved "https://registry.yarnpkg.com/emoji-regex/-/emoji-regex-9.2.2.tgz#840c8803b0d8047f4ff0cf963176b32d4ef3ed72"
-  integrity sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==
-
 enhanced-resolve@^5.0.0, enhanced-resolve@^5.10.0:
   version "5.10.0"
   resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.10.0.tgz#0dc579c3bb2a1032e357ac45b8f3a6f3ad4fb1e6"
@@ -1630,11 +1583,6 @@ js-sdsl@^4.1.4:
   resolved "https://registry.yarnpkg.com/js-tokens/-/js-tokens-4.0.0.tgz#19203fb59991df98e3a287050d4647cdeaf32499"
   integrity sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ==
 
-"js-tokens@^3.0.0 || ^4.0.0":
-  version "4.0.0"
-  resolved "https://registry.yarnpkg.com/js-tokens/-/js-tokens-4.0.0.tgz#19203fb59991df98e3a287050d4647cdeaf32499"
-  integrity sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ==
-
 js-yaml@^4.1.0:
   version "4.1.0"
   resolved "https://registry.yarnpkg.com/js-yaml/-/js-yaml-4.1.0.tgz#c1fb65f8f5017901cdd2c951864ba18458a10602"
@@ -2008,11 +1956,6 @@ prelude-ls@^1.2.1:
   resolved "https://registry.yarnpkg.com/prelude-ls/-/prelude-ls-1.2.1.tgz#debc6489d7a6e6b0e7611888cec880337d316396"
   integrity sha512-vkcDPrRZo1QZLbn5RLGPpg/WmIQ65qoWWhcGKf/b5eplkkarX0m9z8ppCat4mlOqUsWpyNuYgO3VRyrYHSzX5g==
 
-prettier@^2.7.1:
-  version "2.7.1"
-  resolved "https://registry.yarnpkg.com/prettier/-/prettier-2.7.1.tgz#e235806850d057f97bb08368a4f7d899f7760c64"
-  integrity sha512-ujppO+MkdPqoVINuDFDRLClm7D78qbDt0/NR+wp5FqEZOoTNAjPHWj17QRhu7geIHJfcNhRk1XVQmF8Bp3ye+g==
-
 proj4@^2.7.5:
   version "2.8.0"
   resolved "https://registry.yarnpkg.com/proj4/-/proj4-2.8.0.tgz#b2cb8f3ccd56d4dcc7c3e46155cd02caa804b170"

diff --git a/src/beanmachine/ppl/diagnostics/tools/marginal1d/tool.py b/src/beanmachine/ppl/diagnostics/tools/marginal1d/tool.py
@@ -4,8 +4,7 @@
 # LICENSE file in the root directory of this source tree.
 
 """Marginal 1D diagnostic tool for a Bean Machine model."""
-
-from typing import TypeVar
+from __future__ import annotations
 
 from beanmachine.ppl.diagnostics.tools.marginal1d import utils
 from beanmachine.ppl.diagnostics.tools.utils.diagnostic_tool_base import (
@@ -16,9 +15,6 @@
 from bokeh.models.callbacks import CustomJS
 
 
-T = TypeVar("T", bound="Marginal1d")
-
-
 class Marginal1d(DiagnosticToolBaseClass):
     """
     Marginal 1D diagnostic tool.
@@ -40,10 +36,10 @@ class Marginal1d(DiagnosticToolBaseClass):
             independently from a Python server.
     """
 
-    def __init__(self: T, mcs: MonteCarloSamples) -> None:
+    def __init__(self: Marginal1d, mcs: MonteCarloSamples) -> None:
         super(Marginal1d, self).__init__(mcs)
 
-    def create_document(self: T) -> Model:
+    def create_document(self: Marginal1d) -> Model:
         # Initialize widget values using Python.
         rv_name = self.rv_names[0]
         bw_factor = 1.0

diff --git a/src/beanmachine/ppl/diagnostics/tools/marginal1d/typing.py b/src/beanmachine/ppl/diagnostics/tools/marginal1d/typing.py
@@ -4,7 +4,6 @@
 # LICENSE file in the root directory of this source tree.
 
 """Marginal 1D diagnostic tool types for a Bean Machine model."""
-
 from typing import Any, Dict, List, Union
 
 from beanmachine.ppl.diagnostics.tools import TypedDict

diff --git a/src/beanmachine/ppl/diagnostics/tools/marginal1d/utils.py b/src/beanmachine/ppl/diagnostics/tools/marginal1d/utils.py
@@ -4,7 +4,6 @@
 # LICENSE file in the root directory of this source tree.
 
 """Methods used to generate the diagnostic tool."""
-
 from typing import List
 
 import numpy as np

diff --git a/src/beanmachine/ppl/diagnostics/tools/trace/tool.py b/src/beanmachine/ppl/diagnostics/tools/trace/tool.py
@@ -4,8 +4,7 @@
 # LICENSE file in the root directory of this source tree.
 
 """Trace diagnostic tool for a Bean Machine model."""
-
-from typing import TypeVar
+from __future__ import annotations
 
 from beanmachine.ppl.diagnostics.tools.trace import utils
 from beanmachine.ppl.diagnostics.tools.utils.diagnostic_tool_base import (
@@ -16,9 +15,6 @@
 from bokeh.models.callbacks import CustomJS
 
 
-T = TypeVar("T", bound="Trace")
-
-
 class Trace(DiagnosticToolBaseClass):
     """Trace tool.
 
@@ -39,10 +35,10 @@ class Trace(DiagnosticToolBaseClass):
             independently from a Python server.
     """
 
-    def __init__(self: T, mcs: MonteCarloSamples) -> None:
+    def __init__(self: Trace, mcs: MonteCarloSamples) -> None:
         super(Trace, self).__init__(mcs)
 
-    def create_document(self: T) -> Model:
+    def create_document(self: Trace) -> Model:
         # Initialize widget values using Python.
         rv_name = self.rv_names[0]
 
@@ -88,10 +84,22 @@ def create_document(self: T) -> Model:
         # Create the widgets for the tool using Python.
         widgets = utils.create_widgets(rv_names=self.rv_names, rv_name=rv_name)
 
+        # Create the view of the tool and serialize it into HTML using static resources
+        # from Bokeh. Embedding the tool in this manner prevents external CDN calls for
+        # JavaScript resources, and prevents the user from having to know where the
+        # Bokeh server is.
+        tool_view = utils.create_view(figures=figures, widgets=widgets)
+
         # Create callbacks for the tool using JavaScript.
         callback_js = f"""
             const rvName = widgets.rv_select.value;
             const rvData = data[rvName];
+            let bw = 0.0;
+            // Remove the CSS classes that dim the tool output on initial load.
+            const toolTab = toolView.tabs[0];
+            const toolChildren = toolTab.child.children;
+            const dimmedComponent = toolChildren[1];
+            dimmedComponent.css_classes = [];
             try {{
               trace.update(
                 rvData,
@@ -125,6 +133,7 @@ def create_document(self: T) -> Model:
             "sources": sources,
             "figures": figures,
             "tooltips": tooltips,
+            "toolView": tool_view,
         }
 
         # Each widget requires slightly different JS.
@@ -149,5 +158,4 @@ def create_document(self: T) -> Model:
         widgets["bw_factor_slider"].js_on_change("value", slider_callback)
         widgets["hdi_slider"].js_on_change("value", slider_callback)
 
-        tool_view = utils.create_view(figures=figures, widgets=widgets)
         return tool_view
diff --git a/src/beanmachine/ppl/diagnostics/tools/trace/typing.py b/src/beanmachine/ppl/diagnostics/tools/trace/typing.py
@@ -4,7 +4,6 @@
 # LICENSE file in the root directory of this source tree.
 
 """Trace diagnostic tool types for a Bean Machine model."""
-
 from typing import Any, Dict, List, Union
 
 from beanmachine.ppl.diagnostics.tools import NotRequired, TypedDict

diff --git a/src/beanmachine/ppl/diagnostics/tools/trace/utils.py b/src/beanmachine/ppl/diagnostics/tools/trace/utils.py
@@ -4,7 +4,6 @@
 # LICENSE file in the root directory of this source tree.
 
 """Methods used to generate the diagnostic tool."""
-
 from typing import List
 
 from beanmachine.ppl.diagnostics.tools.trace import typing
@@ -201,21 +200,18 @@ def create_figures(rv_name: str, num_chains: int) -> typing.Figures:
         if figure_name == "marginals":
             fig.title = "Marginal"
             fig.xaxis.axis_label = rv_name
-            # fig.x_range = Range1d()
             fig.yaxis.visible = False
         elif figure_name == "forests":
             fig.title = "Forest"
             fig.xaxis.axis_label = rv_name
             fig.yaxis.axis_label = "Chain"
             fig.yaxis.minor_tick_line_color = None
             fig.yaxis.ticker.desired_num_ticks = num_chains
-            # fig.x_range = Range1d()
         elif figure_name == "traces":
             fig.title = "Trace"
             fig.xaxis.axis_label = "Draw from single chain"
             fig.yaxis.axis_label = rv_name
             fig.width = TRACE_PLOT_WIDTH
-            # fig.x_range = Range1d()
         elif figure_name == "ranks":
             fig.title = "Rank"
             fig.xaxis.axis_label = "Rank from all chains"
@@ -399,8 +395,6 @@ def add_glyphs(
     None
         Adds data bound glyphs to the given figures directly.
     """
-    # range_min = []
-    # range_max = []
     for figure_name, figure_sources in sources.items():
         fig = figures[figure_name]
         for chain_name, source in figure_sources.items():
@@ -417,11 +411,6 @@ def add_glyphs(
             # its range stable are linked to the marginal figure's range below.
             if figure_name == "marginals":
                 pass
-                # data = source["line"].data["x"]
-                # minimum = min(data) if len(data) != 0 else 0
-                # maximum = max(data) if len(data) != 0 else 1
-                # range_min.append(minimum)
-                # range_max.append(maximum)
             elif figure_name == "forests":
                 fig.add_glyph(
                     source_or_glyph=source["circle"],
@@ -437,12 +426,7 @@ def add_glyphs(
                     name=chain_glyphs["quad"]["glyph"].name,
                 )
     # Link figure ranges together.
-    # figures["marginals"].x_range = Range1d(
-    #     start=min(range_min) if len(range_min) != 0 else 0,
-    #     end=max(range_max) if len(range_max) != 0 else 1,
-    # )
     figures["forests"].x_range = figures["marginals"].x_range
-    # figures["traces"].y_range = figures["marginals"].x_range
 
 
 def create_annotations(figures: typing.Figures, num_chains: int) -> typing.Annotations:
@@ -573,21 +557,23 @@ def create_tooltips(
                     {
                         "line": HoverTool(
                             renderers=plotting_utils.filter_renderers(
-                                fig, f"{figure_name}{chain_name.title()}LineGlyph"
+                                fig,
+                                f"{figure_name}{chain_name.title()}LineGlyph",
                             ),
                             tooltips=[("Chain", "@chain"), ("Rank mean", "@rankMean")],
                         ),
                         "quad": HoverTool(
                             renderers=plotting_utils.filter_renderers(
-                                fig, f"{figure_name}{chain_name.title()}QuadGlyph"
+                                fig,
+                                f"{figure_name}{chain_name.title()}QuadGlyph",
                             ),
                             tooltips=[
                                 ("Chain", "@chain"),
                                 ("Draws", "@draws"),
                                 ("Rank", "@rank"),
                             ],
                         ),
-                    }
+                    },
                 )
     return output