updates packaging material

Author: kyleniemeyer

packaging-distribution.ipynb

@@ -9,8 +9,7 @@
    },
    "source": [
     "---\n",
-    "title: \"Getting Started\"\n",
-    "subtitle: \"Packaging and distributing your Python code\"\n",
+    "title: \"Packaging and distributing your Python code\"\n",
     "author: \"Kyle Niemeyer\"\n",
     "date: \"29 January 2025\"\n",
     "institute: \"Oregon State University\"\n",
@@ -209,109 +208,6 @@
     ":::"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Notebook to installable package\n",
-    "\n",
-    "## Hypothetical workflow for a researcher {.smaller}\n",
-    "\n",
-    "1. Work on idea for paper with collaborators\n",
-    "2. Do exploratory analysis in scripts and Jupyter ecosystem\n",
-    "3. As research progresses, need to write more-complicated functions and workflows\n",
-    "3. Code begins to sprawl across multiple directories\n",
-    "4. Software dependencies begin to become more complicated\n",
-    "4. The code \"works on my machine\", but what about your collaborators?\n",
-    "\n",
-    "::: {.r-fit-text .fragment}\n",
-    "**People heroically press forward, but this is painful, and not reusable**\n",
-    ":::\n",
-    "\n",
-    "## {.smaller}\n",
-    "\n",
-    "Imagine you start with a Jupyter notebook that looks like this:\n",
-    "\n",
-    "```{.python .fragment}\n",
-    "import numpy as np\n",
-    "from scipy.optimize import minimize\n",
-    "\n",
-    "# Rosenbrock function\n",
-    "def rosen(x):\n",
-    "    \"\"\"The Rosenbrock function\"\"\"\n",
-    "    return sum(100.0 * (x[1:] - x[:-1] ** 2.0) ** 2.0 + (1 - x[:-1]) ** 2.0)\n",
-    "\n",
-    "def rosen_der(x):\n",
-    "    \"\"\"Gradient of the Rosenbrock function\"\"\"\n",
-    "    xm = x[1:-1]\n",
-    "    xm_m1 = x[:-2]\n",
-    "    xm_p1 = x[2:]\n",
-    "    der = np.zeros_like(x)\n",
-    "    der[1:-1] = 200 * (xm - xm_m1**2) - 400 * (xm_p1 - xm**2) * xm - 2 * (1 - xm)\n",
-    "    der[0] = -400 * x[0] * (x[1] - x[0] ** 2) - 2 * (1 - x[0])\n",
-    "    der[-1] = 200 * (x[-1] - x[-2] ** 2)\n",
-    "    return der\n",
-    "\n",
-    "# Minimization of the Rosenbrock function with some initial guess\n",
-    "x0 = np.array([1.3, 0.7, 0.8, 1.9, 1.2])\n",
-    "result = minimize(rosen, x0, method=\"BFGS\", jac=rosen_der, options={\"disp\": True})\n",
-    "optimized_params = result.x\n",
-    "print(optimized_params)\n",
-    "```\n",
-    "\n",
-    "## Reusable science, step by step\n",
-    "\n",
-    "We can convert our notebook code into a simple importable module an and example calling it:\n",
-    "\n",
-    "``` bash\n",
-    "$ tree edit-sys-path \n",
-    "edit-sys-path\n",
-    "├── code\n",
-    "│   └── utils.py\n",
-    "└── example.py\n",
-    "\n",
-    "2 directories, 2 files\n",
-    "```\n",
-    "\n",
-    "## Reusable science, step by step\n",
-    "\n",
-    "``` python\n",
-    "# example.py\n",
-    "import sys\n",
-    "from pathlib import Path\n",
-    "\n",
-    "import numpy as np\n",
-    "from scipy.optimize import minimize\n",
-    "\n",
-    "# Make ./code/utils.py visible to sys.path\n",
-    "# sys.path position 1 should be after cwd and before activated virtual environment\n",
-    "sys.path.insert(1, str(Path().cwd() / \"code\"))\n",
-    "from utils import rosen, rosen_der\n",
-    "\n",
-    "x0 = np.array([1.3, 0.7, 0.8, 1.9, 1.2])\n",
-    "result = minimize(rosen, x0, method=\"BFGS\", jac=rosen_der, options={\"disp\": True})\n",
-    "optimized_params = result.x\n",
-    "print(optimized_params)\n",
-    "```\n",
-    "\n",
-    "## Reusable science, step by step\n",
-    "\n",
-    "- This is **already better** than having everything in a single massive file!\n",
-    "- However, now things are tied to this relative path on your computer:\n",
-    "\n",
-    "``` {.python .fragment}\n",
-    "# Make ./code/utils.py visible to sys.path\n",
-    "sys.path.insert(1, str(Path(__file__).parent / \"code\"))\n",
-    "from utils import rosen, rosen_der\n",
-    "```\n",
-    "\n",
-    "::: fragment\n",
-    "and are brittle to refactoring and change; plus, not very portable to others.\n",
-    "::: \n",
-    "\n",
-    "- But we can do better!"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},