Enhancements (small editing + reformatting changes)

CITATION.cff

@@ -25,13 +25,19 @@ authors:
       email: "sadie.s.niblett@usace.army.mil"
       affiliation: "U.S. Army Corps of Engineers, Risk Management Center"
       orcid: "https://orcid.org/0009-0008-8588-4816"
-    - family-names: "Gonzalez"
-      given-names: "Julian"
-      email: "julian.t.gonzalez@usace.army.mil"
-      affiliation: "U.S. Army Corps of Engineers, Risk Management Center"
-      orcid: "https://orcid.org/0009-0009-9058-7653"
     - family-names: "Smith"
       given-names: "C. Haden"
       email: "cole.h.smith@usace.army.mil"
       affiliation: "U.S. Army Corps of Engineers, Risk Management Center"
       orcid: "https://orcid.org/0000-0002-4651-9890"
+reviewers:
+    - family-names: "McGraw"
+      given-names: "Dan"
+      email: "daniel.e.mcgraw@usace.army.mil"
+      affiliation: "U.S. Army Corps of Engineers, Risk Management Center"
+      orcid: "https://orcid.org/0009-0006-4859-0179"
+    - family-names: "Gonzalez"
+      given-names: "Julian"
+      email: "julian.t.gonzalez@usace.army.mil"
+      affiliation: "U.S. Army Corps of Engineers, Risk Management Center"
+      orcid: "https://orcid.org/0009-0009-9058-7653"

notebooks/00_getting_started.ipynb

@@ -62,7 +62,7 @@
     "5. Now you should be able to select this virtual environment as a kernel. Click on the **\"Select Kernel\"** in the top right. Chose Python environments and select Python(.venv), the one you just created! If it doesn't show up right away, try reloading your window.\n",
     "6. Open the command palette (Ctrl+Shift+P or Cmd+Shift+P) and find **\"Python:Select Interpreter\"**. Chose the .venv option to tell VS code to always use this interpreter going forward.\n",
     "\n",
-    "Now we have ensured that we can use and run Python in there Jupyter notebooks. Time to get down to business in Numerics!\n",
+    "Now we have ensured that we can use and run Python in these Jupyter notebooks. Time to get down to business in Numerics!\n",
     "\n",
     "## What is Numerics?\n",
     "Numerics is a comprehensive .NET library for numerical computing and statistical analysis, developed by the U.S. Army Corps of Engineers Risk Management Center [[1]](#1). It includes:\n",
@@ -220,7 +220,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "65dc539a",
    "metadata": {
     "execution": {
@@ -230,7 +230,19 @@
      "shell.execute_reply": "2026-04-23T18:41:58.462306Z"
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "FileNotFoundException",
+     "evalue": "Unable to find assembly 'c:\\GIT\\BestFit-Python-Examples\\packages\\RMC.Numerics.2.0.1\\lib\\net8.0\\Numerics.dll'.\r\n   at Python.Runtime.CLRModule.AddReference(String name) in /home/benedikt/.cache/uv/sdists-v6/.tmpkW03e6/pythonnet-3.0.5/src/runtime/Types/ClrModule.cs:line 117\r\n   at System.RuntimeMethodHandle.InvokeMethod(ObjectHandleOnStack target, Void** arguments, ObjectHandleOnStack sig, BOOL isConstructor, ObjectHandleOnStack result)\r\n   at System.Reflection.MethodBaseInvoker.InterpretedInvoke_Method(Object obj, IntPtr* args)\r\n   at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span`1 copyOfArgs, BindingFlags invokeAttr)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mFileNotFoundException\u001b[39m                     Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[2]\u001b[39m\u001b[32m, line 5\u001b[39m\n\u001b[32m      2\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mhelper_functions\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m resolve_numerics_dll\n\u001b[32m      4\u001b[39m dll_path = resolve_numerics_dll()\n\u001b[32m----> \u001b[39m\u001b[32m5\u001b[39m \u001b[43mclr\u001b[49m\u001b[43m.\u001b[49m\u001b[43mAddReference\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mdll_path\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m      7\u001b[39m \u001b[38;5;28mprint\u001b[39m(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33m✓ Loaded Numerics from: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mdll_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m\"\u001b[39m)\n",
+      "\u001b[31mFileNotFoundException\u001b[39m: Unable to find assembly 'c:\\GIT\\BestFit-Python-Examples\\packages\\RMC.Numerics.2.0.1\\lib\\net8.0\\Numerics.dll'.\r\n   at Python.Runtime.CLRModule.AddReference(String name) in /home/benedikt/.cache/uv/sdists-v6/.tmpkW03e6/pythonnet-3.0.5/src/runtime/Types/ClrModule.cs:line 117\r\n   at System.RuntimeMethodHandle.InvokeMethod(ObjectHandleOnStack target, Void** arguments, ObjectHandleOnStack sig, BOOL isConstructor, ObjectHandleOnStack result)\r\n   at System.Reflection.MethodBaseInvoker.InterpretedInvoke_Method(Object obj, IntPtr* args)\r\n   at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span`1 copyOfArgs, BindingFlags invokeAttr)"
+     ]
+    }
+   ],
    "source": [
     "import clr\n",
     "from helper_functions import resolve_numerics_dll\n",
@@ -252,7 +264,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "b3a59cb5",
    "metadata": {
     "execution": {
@@ -291,7 +303,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "f6b4f2fd",
    "metadata": {
     "execution": {
@@ -346,7 +358,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "d51dfbec",
    "metadata": {
     "execution": {
@@ -395,7 +407,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "3c61d5ad",
    "metadata": {
     "execution": {
@@ -441,7 +453,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "b2c575cc",
    "metadata": {
     "execution": {
@@ -591,7 +603,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.10"
+   "version": "3.13.1"
   }
  },
  "nbformat": 4,

notebooks/01_distributions.ipynb

@@ -2531,7 +2531,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.10"
+   "version": "3.13.1"
   }
  },
  "nbformat": 4,

notebooks/02_distribution_fitting.ipynb

@@ -806,7 +806,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.10"
+   "version": "3.13.1"
   }
  },
  "nbformat": 4,

notebooks/03_mcmc_basics.ipynb

@@ -117,10 +117,14 @@
    },
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "✓ Setup complete\n"
+     "ename": "FileNotFoundException",
+     "evalue": "Unable to find assembly 'c:\\GIT\\BestFit-Python-Examples\\packages\\RMC.Numerics.2.0.1\\lib\\net8.0\\Numerics.dll'.\r\n   at Python.Runtime.CLRModule.AddReference(String name) in /home/benedikt/.cache/uv/sdists-v6/.tmpkW03e6/pythonnet-3.0.5/src/runtime/Types/ClrModule.cs:line 117\r\n   at System.Reflection.MethodBaseInvoker.InterpretedInvoke_Method(Object obj, IntPtr* args)\r\n   at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span`1 copyOfArgs, BindingFlags invokeAttr)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mFileNotFoundException\u001b[39m                     Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[1]\u001b[39m\u001b[32m, line 12\u001b[39m\n\u001b[32m     10\u001b[39m \u001b[38;5;66;03m# Load Numerics DLL (auto-discovered from NuGet; see notebook 00 for details)\u001b[39;00m\n\u001b[32m     11\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mhelper_functions\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m resolve_numerics_dll\n\u001b[32m---> \u001b[39m\u001b[32m12\u001b[39m \u001b[43mclr\u001b[49m\u001b[43m.\u001b[49m\u001b[43mAddReference\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mstr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mresolve_numerics_dll\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m     14\u001b[39m \u001b[38;5;66;03m# Import MCMC and distribution classes\u001b[39;00m\n\u001b[32m     15\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mNumerics\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mSampling\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mMCMC\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m RWMH, MCMCResults, LogLikelihood, MCMCSampler\n",
+      "\u001b[31mFileNotFoundException\u001b[39m: Unable to find assembly 'c:\\GIT\\BestFit-Python-Examples\\packages\\RMC.Numerics.2.0.1\\lib\\net8.0\\Numerics.dll'.\r\n   at Python.Runtime.CLRModule.AddReference(String name) in /home/benedikt/.cache/uv/sdists-v6/.tmpkW03e6/pythonnet-3.0.5/src/runtime/Types/ClrModule.cs:line 117\r\n   at System.Reflection.MethodBaseInvoker.InterpretedInvoke_Method(Object obj, IntPtr* args)\r\n   at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span`1 copyOfArgs, BindingFlags invokeAttr)"
      ]
     }
    ],
@@ -150,7 +154,6 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "id": "8f4b903e",
    "metadata": {
     "execution": {
@@ -160,7 +163,6 @@
      "shell.execute_reply": "2026-04-23T21:32:20.774600Z"
     }
    },
-   "outputs": [],
    "source": [
     "> **Note for demo users.** When calling Numerics MCMC samplers from Python via pythonnet, the samplers' internal parallel chains (`Parallel.For`) contend for Python's Global Interpreter Lock (GIL). This makes parallel execution slower than sequential. That's why every example below sets `sampler.ParallelizeChains = False`. It defaults to `True`, which works well in C# but slows the sampler down when driven from Python."
    ]
@@ -181,7 +183,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "04138f5a",
    "metadata": {
     "execution": {
@@ -255,7 +257,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "68d30485",
    "metadata": {
     "execution": {
@@ -316,7 +318,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "e8aca3ab",
    "metadata": {
     "execution": {
@@ -394,7 +396,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "165d8ce2",
    "metadata": {
     "execution": {
@@ -457,7 +459,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "59d808ac",
    "metadata": {
     "execution": {
@@ -523,7 +525,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "8b653f22",
    "metadata": {
     "execution": {
@@ -662,7 +664,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "eb20ce0a",
    "metadata": {
     "execution": {
@@ -727,7 +729,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "2a1a8d09",
    "metadata": {
     "execution": {
@@ -917,7 +919,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "066f0505",
    "metadata": {
     "execution": {
@@ -1037,7 +1039,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -1051,7 +1053,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.10"
+   "version": "3.13.1"
   }
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  "nbformat": 4,

notebooks/04_mcmc_bayesian_inference.ipynb

@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "46006368",
    "metadata": {
     "execution": {
@@ -76,7 +76,6 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "id": "d3ef7a3e",
    "metadata": {
     "execution": {
@@ -86,7 +85,6 @@
      "shell.execute_reply": "2026-04-23T19:23:09.776975Z"
     }
    },
-   "outputs": [],
    "source": [
     "> **Note for demo users.** When calling Numerics MCMC samplers from Python via pythonnet, the samplers' internal parallel chains (`Parallel.For`) contend for Python's Global Interpreter Lock (GIL). This makes parallel execution slower than sequential. That's why every example below sets `sampler.ParallelizeChains = False`. It defaults to `True`, which works well in C# but slows the sampler down when driven from Python."
    ]
@@ -105,7 +103,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "6d40f966",
    "metadata": {
     "execution": {
@@ -250,7 +248,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "9ebe9b66",
    "metadata": {
     "execution": {
@@ -436,7 +434,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "18a04004",
    "metadata": {
     "execution": {
@@ -610,7 +608,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "54366e57",
    "metadata": {
     "execution": {
@@ -798,7 +796,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "8bbd362c",
    "metadata": {
     "execution": {
@@ -1005,7 +1003,7 @@
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   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "8ecdca79",
    "metadata": {
     "execution": {
@@ -1197,7 +1195,7 @@
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   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "111be476",
    "metadata": {
     "execution": {
@@ -1479,7 +1477,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -1493,7 +1491,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.10"
+   "version": "3.13.1"
   }
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