Add pre-commit hook section to chapter 3

create pre-commit hooks

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+    -   id: black
+    -   id: black-jupyter

learning/03 Testing.ipynb

@@ -153,10 +153,65 @@
     "You tell Hypothesis how to generate the test data, in this case we use some numpy specifc code to generate 2 dimensional arrays with `dtype = int` and entries randomly sampled from `[1, -1]`. We use the same trick as before of checking two implementations against one another."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "91fa6842-f214-4fd3-bbe5-0f20d7d0d2cc",
+   "metadata": {},
+   "source": [
+    "## Autoformaters\n",
+    "\n",
+    "While we're doing things that will help keep our code clean and tidy in the future, I would recommend installing a code formatter like `black`. This is a program that enforces a particular formatting style on your code by simply doing it for you. At first this sounds a bit weird, but it has a few benefits:\n",
+    "\n",
+    "- It makes git diffs as small as possible because formatting changes never show up\n",
+    "- It means you never have to discuss with your collaborators about code formatting, something which can waste a lot of time!\n",
+    "\n",
+    "Here I will show you how to setup `black` as a pre-commit hook, this means it runs before you commit anything to git, which is probably the best time to do it. We'll use a helper tool called [pre-commit](https://pre-commit.com/).\n",
+    "\n",
+    "```bash\n",
+    "pip install pre-commit\n",
+    "pre-commit sample-config >> .pre-commit-config.yaml # Generate an initial config\n",
+    "```\n",
+    "Now we add some additional lines to the `.pre-commit-config.yaml` config file to setup black:\n",
+    "```yaml\n",
+    "-   repo: https://github.com/psf/black\n",
+    "    rev: 21.12b0\n",
+    "    hooks:\n",
+    "    -   id: black\n",
+    "    -   id: black-jupyter\n",
+    "```\n",
+    "And finally `pre-commit install` will make this run every time you commit to git. It's worth running it manually once the first time to check it works: `pre-commit run --all-files`. Running this I immediatly got a cryptic error that, on googling, turned out to be that something broke in version 21.12b0 of `21.12b0`. Running `precommit autoupdate` fixed this for me by updated `black` to a later version. Running `pre-commit run --all-files` a second time now gives me:\n",
+    "```bash\n",
+    "(recode) tom@TomsLaptop ReCoDE_MCMCFF % pre-commit run --all-files\n",
+    "trim trailing whitespace.................................................Passed\n",
+    "fix end of files.........................................................Passed\n",
+    "check yaml...........................................(no files to check)Skipped\n",
+    "check for added large files..............................................Passed\n",
+    "black....................................................................Passed\n",
+    "(recode) tom@TomsLaptop ReCoDE_MCMCFF % \n",
+    "```\n",
+    "\n",
+    "Now whenever you commit anything, `black` will autoformat it before it actually gets commited. I'll test this for myself by putting\n",
+    "```python\n",
+    "def ugly_litte_one_liner(a,b,c): return \" \".join([a,b,c/2. +3])\n",
+    "```\n",
+    "in a code cell below and we'll see how `black` formats it. The only gotcha here is that you have to reload jupyter notebooks from disk in order to see the changes that `black` makes."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "24874a21-b9b3-4c38-9a79-1a2b4bce88a9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def ugly_litte_one_liner(a, b, c):\n",
+    "    return \" \".join([a, b, c / 2.0 + 3])"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21270ceb-f5b7-496b-a530-2def9f70b89f",
+   "id": "2f53a760-c1b4-43bf-8774-54d2d9edc230",
    "metadata": {},
    "outputs": [],
    "source": []