prototypes/Complexity over Time.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# The idea\n",
    "\n",
    "In my previous blog post, we got to know the idea of \"indentation-based complexity\". We took a static view on the Linux kernel to spot the most complex areas.\n",
    "\n",
    "This time, we wanna track the evolution of the indentation-based complexity of a software system over time. We are especially interested in it's correlation between the lines of code. Because if we have a more or less stable development of the lines of codes of our system, but an increasing number of indentation per source code file, we surely got a complexity problem.\n",
    "\n",
    "Again, this analysis is higly inspired by [Adam Tornhill's book \"Software Design X-Ray\"](https://pragprog.com/book/atevol/software-design-x-rays)\n",
    ", which I currently always recommend if you want to get a deep dive into software data analysis."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# The data\n",
    "For the calculation of the evolution of our software system, we can use data from the version control system. In our case, we can get all changes to Java source code files with Git. We just need so say the right magic words, which is\n",
    "\n",
    "```git log -p -- *.java```\n",
    "\n",
    "This gives us data like the following:\n",
    "\n",
    "```\n",
    "commit e5254156eca3a8461fa758f17dc5fae27e738ab5\n",
    "Author: Antoine Rey <antoine.rey@gmail.com>\n",
    "Date:   Fri Aug 19 18:54:56 2016 +0200\n",
    "\n",
    "    Convert Controler's integration test to unit test\n",
    "\n",
    "diff --git a/src/test/java/org/springframework/samples/petclinic \n",
    "/web/CrashControllerTests.java b/src/test/java/org/springframework/samples/petclinic/web/CrashControllerTests.java\n",
    "index ee83b8a..a83255b 100644\n",
    "--- a/src/test/java/org/springframework/samples/petclinic/web/CrashControllerTests.java\n",
    "+++ b/src/test/java/org/springframework/samples/petclinic/web/CrashControllerTests.java\n",
    "@@ -1,8 +1,5 @@\n",
    " package org.springframework.samples.petclinic.web;\n",
    " \n",
    "-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;\n",
    "-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;\n",
    "-\n",
    " import org.junit.Before;\n",
    " import org.junit.Test;\n",
    " import org.junit.runner.RunWith;\n",
    "```\n",
    "\n",
    "We have the\n",
    "* commit sha  \n",
    "```    commit e5254156eca3a8461fa758f17dc5fae27e738ab5```\n",
    "* author's name  \n",
    "```    Author: Antoine Rey <antoine.rey@gmail.com>```\n",
    "* date of the commit  \n",
    "```    Date:   Fri Aug 19 18:54:56 2016 +0200```\n",
    "* commit message  \n",
    "```    Convert Controler's integration test to unit test```\n",
    "* names of the files that changes (after and before)  \n",
    "```   diff --git a/src/test/java/org/springframework/samples/petclinic \n",
    "/web/CrashControllerTests.java b/src/test/java/org/springframework/samples/petclinic/web/CrashControllerTests.java```\n",
    "* the extended index header  \n",
    "```   index ee83b8a..a83255b 100644```  \n",
    "```   --- a/src/test/java/org/springframework/samples/petclinic/web/CrashControllerTests.java\n",
    "+++ b/src/test/java/org/springframework/samples/petclinic/web/CrashControllerTests.java``` \n",
    "* and the full file diff where we can see additions or modifications (`+`) and deletions (`-`)   \n",
    "```\n",
    "    package org.springframework.samples.petclinic.web;\n",
    " \n",
    "    -import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;\n",
    "    -import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;     \n",
    "    -\n",
    "     import org.junit.Before;\n",
    "```\n",
    "We \"just\" have to get this data into our favorite data analysis framework, which is, of course, Pandas :-). We can actually do that! Let's see how!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Advanced data wangling\n",
    "Reading in such a semi-structured data is a little challenge. But we can do it with some tricks. First, we read in the whole Git diff history by standard means, using `read_csv` and the separator `\\n` to get one row per line. We make sure to give the columns a nice name as well."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "ename": "FileNotFoundError",
     "evalue": "File b'../../buschmais-spring-petclinic_fork/git_diff.log' does not exist",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-1-194884588aee>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      4\u001b[0m     \u001b[1;34m\"../../buschmais-spring-petclinic_fork/git_diff.log\"\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m     \u001b[0msep\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"\\n\"\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 6\u001b[1;33m     names=[\"raw\"])\n\u001b[0m\u001b[0;32m      7\u001b[0m \u001b[0mdiff_raw\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mhead\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m16\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mC:\\dev\\apps\\Anaconda3\\lib\\site-packages\\pandas\\io\\parsers.py\u001b[0m in \u001b[0;36mparser_f\u001b[1;34m(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skipfooter, skip_footer, doublequote, delim_whitespace, as_recarray, compact_ints, use_unsigned, low_memory, buffer_lines, memory_map, float_precision)\u001b[0m\n\u001b[0;32m    707\u001b[0m                     skip_blank_lines=skip_blank_lines)\n\u001b[0;32m    708\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 709\u001b[1;33m         \u001b[1;32mreturn\u001b[0m \u001b[0m_read\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkwds\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    710\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    711\u001b[0m     \u001b[0mparser_f\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m__name__\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mname\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mC:\\dev\\apps\\Anaconda3\\lib\\site-packages\\pandas\\io\\parsers.py\u001b[0m in \u001b[0;36m_read\u001b[1;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[0;32m    447\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    448\u001b[0m     \u001b[1;31m# Create the parser.\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 449\u001b[1;33m     \u001b[0mparser\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mTextFileReader\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    450\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    451\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[0mchunksize\u001b[0m \u001b[1;32mor\u001b[0m \u001b[0miterator\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mC:\\dev\\apps\\Anaconda3\\lib\\site-packages\\pandas\\io\\parsers.py\u001b[0m in \u001b[0;36m__init__\u001b[1;34m(self, f, engine, **kwds)\u001b[0m\n\u001b[0;32m    816\u001b[0m             \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'has_index_names'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mkwds\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'has_index_names'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    817\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 818\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_make_engine\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mengine\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    819\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    820\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mclose\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mC:\\dev\\apps\\Anaconda3\\lib\\site-packages\\pandas\\io\\parsers.py\u001b[0m in \u001b[0;36m_make_engine\u001b[1;34m(self, engine)\u001b[0m\n\u001b[0;32m   1047\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0m_make_engine\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mengine\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m'c'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1048\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;34m'c'\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1049\u001b[1;33m             \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_engine\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mCParserWrapper\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mf\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1050\u001b[0m         \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1051\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;34m'python'\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mC:\\dev\\apps\\Anaconda3\\lib\\site-packages\\pandas\\io\\parsers.py\u001b[0m in \u001b[0;36m__init__\u001b[1;34m(self, src, **kwds)\u001b[0m\n\u001b[0;32m   1693\u001b[0m         \u001b[0mkwds\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'allow_leading_cols'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mindex_col\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[1;32mFalse\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1694\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1695\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_reader\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mparsers\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mTextReader\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msrc\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1696\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1697\u001b[0m         \u001b[1;31m# XXX\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader.__cinit__\u001b[1;34m()\u001b[0m\n",
      "\u001b[1;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._setup_parser_source\u001b[1;34m()\u001b[0m\n",
      "\u001b[1;31mFileNotFoundError\u001b[0m: File b'../../buschmais-spring-petclinic_fork/git_diff.log' does not exist"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "diff_raw = pd.read_csv(\n",
    "    \"../../buschmais-spring-petclinic_fork/git_diff.log\",\n",
    "    sep=\"\\n\",\n",
    "    names=[\"raw\"])\n",
    "diff_raw.head(16)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The output is the commit data that I've describe above where each in line the text file represents one row in the DataFrame (without blank lines)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Cleansing\n",
    "We skip all the data we don't need for sure. Especially the \"extended index header\" with the two lines that being with `+++` and `---` are candidates to mix with the real diff data that begins also with a `+` or a `-`. Furtunately, we can identify these rows easily: These are the rows that begin with the row that starts with `index`. Using the `shift` operation starting at the row with `index`, we can get rid of all those lines."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "index_row = diff_raw.raw.str.startswith(\"index \")\n",
    "ignored_diff_rows = (index_row.shift(1) | index_row.shift(2))\n",
    "diff_raw = diff_raw[~(index_row | ignored_diff_rows)]\n",
    "diff_raw.head(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extracting metadata"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we extract some metadata of a commit. We can identify the different entries by using a regular expression that looks up a specific key word for each line. We extract each individual information into a new Series/column because we need it for each change line during the software's history. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff_raw['commit'] = diff_raw.raw.str.split(\"^commit \").str[1]\n",
    "diff_raw['timestamp'] = pd.to_datetime(diff_raw.raw.str.split(\"^Date: \").str[1])\n",
    "diff_raw['path'] = diff_raw.raw.str.extract(\"^diff --git.* b/(.*)\", expand=True)[0]\n",
    "diff_raw.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To assign each commit's metadata to the remaining rows, we forward fill those rows with the metadata by using the `fillna` method. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff_raw = diff_raw.fillna(method='ffill')\n",
    "diff_raw.head(8)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Identifying source code lines\n",
    "We can now focus on the changed source code lines. We can identify "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%timeit\n",
    "diff_raw.raw.str.extract(\"^\\+( *).*$\", expand=True)[0].str.len()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff_raw[\"i\"] = diff_raw.raw.str[1:].str.len() - diff_raw.raw.str[1:].str.lstrip().str.len()\n",
    "diff_raw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%timeit\n",
    "diff_raw.raw.str[0] + diff_raw.raw.str.[1:].str.lstrip().str.len()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff_raw['added'] = diff_raw.line.str.extract(\"^\\+( *).*$\", expand=True)[0].str.len()\n",
    "diff_raw['deleted'] = diff_raw.line.str.extract(\"^-( *).*$\", expand=True)[0].str.len()\n",
    "diff_raw.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For our later indentation-based complexity calculation, we have to make sure that each line"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff_raw['line'] = diff_raw.raw.str.replace(\"\\t\", \"    \")\n",
    "diff_raw.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff = \\\n",
    "    diff_raw[\n",
    "        (~diff_raw['added'].isnull()) | \n",
    "             (~diff_raw['deleted'].isnull())].copy()\n",
    "diff.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff['is_comment'] = diff.line.str[1:].str.match(r' *(//|/*\\*).*')\n",
    "diff['is_empty'] = diff.line.str[1:].str.replace(\" \",\"\").str.len() == 0\n",
    "diff['is_source'] = ~(diff['is_empty'] | diff['is_comment'])\n",
    "diff.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff.raw.str[0].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff['lines_added'] = (~diff.added.isnull()).astype('int')\n",
    "diff['lines_deleted'] = (~diff.deleted.isnull()).astype('int')\n",
    "diff.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff = diff.fillna(0)\n",
    "#diff.to_excel(\"temp.xlsx\")\n",
    "diff.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "commits_per_day = diff.set_index('timestamp').resample(\"D\").sum()\n",
    "commits_per_day.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "commits_per_day.cumsum().plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(commits_per_day.added - commits_per_day.deleted).cumsum().plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(commits_per_day.lines_added - commits_per_day.lines_deleted).cumsum().plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "diff_sum = diff.sum()\n",
    "diff_sum.lines_added - diff_sum.lines_deleted                                                    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "3913"
   ]
  }
 ],
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