merge and reorganise

d57f1519 · Toby Hodges · bfdb76b4 · 82977ee2 · d57f1519 · d57f1519
Verified Commit d57f1519 authored 5 years ago by Toby Hodges
--- a/meetings/old/Mistakes.ipynb
+++ b/meetings/old/Mistakes.ipynb
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(None, None, 1)\n"
+     ]
+    }
+   ],
+   "source": [
+    "# this can be a shortcut to assign None to multiple variables\n",
+    "x = y = z = None\n",
+    "z = 1\n",
+    "\n",
+    "print(x,y,z)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "ename": "AssertionError",
+     "evalue": "b wasn't in there!",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAssertionError\u001b[0m                            Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-5-a791a4bf8f4c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m## assert\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mmylist\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m'a'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'c'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'f'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0;32massert\u001b[0m \u001b[0;34m'b'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mmylist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"b wasn't in there!\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mAssertionError\u001b[0m: b wasn't in there!"
+     ]
+    }
+   ],
+   "source": [
+    "## assert\n",
+    "mylist = ['a', 'c', 'f']\n",
+    "assert 'b' in mylist, \"b wasn't in there!\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(['x'], ['x'], ['x'])\n"
+     ]
+    }
+   ],
+   "source": [
+    "# BAD: this is probably not what you wanted\n",
+    "u, i, o = []\n",
+    "o.append(\"x\")\n",
+    "\n",
+    "print(u,i,o)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "collapsed": false,
+    "deletable": true,
+    "editable": true,
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(True, ['a', 'x'], ['a', 'x'])\n"
+     ]
+    }
+   ],
+   "source": [
+    "# BAD: the original list you pass to the method will get updated!\n",
+    "def my_method(mutable_list=[]):\n",
+    "    mutable_list.append('x')\n",
+    "    return mutable_list\n",
+    "\n",
+    "# a list out of the my_method scope\n",
+    "a_list = ['a']\n",
+    "\n",
+    "b_list = my_method(mutable_list=a_list)\n",
+    "\n",
+    "# a_list get modified!\n",
+    "print( a_list == b_list, a_list, b_list )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Whats wrong here... \n",
+    "```bash\n",
+    "\n",
+    "conda create -n giphy python=3\n",
+    "conda install Flask\n",
+    "  (..)\n",
+    "  Package plan for installation in environment /Users/scholtal/anaconda:\n",
+    "  (..)\n",
+    "  The following packages will be UPDATED:\n",
+    "  (..)\n",
+    "  The following packages will be DOWNGRADED due to dependency conflicts:\n",
+    "  (..)\n",
+    "\n",
+    "```\n",
+    "\n",
+    "Spot the missing ``source activate giphy``...."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "defaultdict(<class 'list'>, {'a': [1, 2]})\n"
+     ]
+    }
+   ],
+   "source": [
+    "from collections import defaultdict\n",
+    "d = defaultdict(list)\n",
+    "d[\"a\"] = [1]\n",
+    "d[\"a\"].append(2)\n",
+    "print(d)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "defaultdict(<class 'int'>, {'a': 3})\n"
+     ]
+    }
+   ],
+   "source": [
+    "d = defaultdict(int)\n",
+    "d[\"a\"] += 1\n",
+    "d[\"a\"] += 2\n",
+    "print(d)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'newkey': [1], 'newkey1': [2]}"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "## without using deafaultdict\n",
+    "e = {}\n",
+    "e.setdefault(\"newkey\", []).append(1)\n",
+    "e.setdefault(\"newkey1\", []).append(2)\n",
+    "e"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'newkey': [1, 2]}"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "f = dict(newkey=[1])\n",
+    "f[\"newkey\"].append(2)\n",
+    "f"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "f"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
+%% Cell type:code id: tags:
+``` python
+# this can be a shortcut to assign None to multiple variables
+x = y = z = None
+z = 1
+print(x,y,z)
+```
+%% Output
+    (None, None, 1)
+%% Cell type:code id: tags:
+``` python
+## assert
+mylist = ['a', 'c', 'f']
+assert 'b' in mylist, "b wasn't in there!"
+```
+%% Output
+    ---------------------------------------------------------------------------
+    AssertionError                            Traceback (most recent call last)
+    <ipython-input-5-a791a4bf8f4c> in <module>()
+          1 ## assert
+          2 mylist = ['a', 'c', 'f']
+    ----> 3 assert 'b' in mylist, "b wasn't in there!"
+    AssertionError: b wasn't in there!
+%% Cell type:code id: tags:
+``` python
+# BAD: this is probably not what you wanted
+u, i, o = []
+o.append("x")
+print(u,i,o)
+```
+%% Output
+    (['x'], ['x'], ['x'])
+%% Cell type:code id: tags:
+``` python
+# BAD: the original list you pass to the method will get updated!
+def my_method(mutable_list=[]):
+    mutable_list.append('x')
+    return mutable_list
+# a list out of the my_method scope
+a_list = ['a']
+b_list = my_method(mutable_list=a_list)
+# a_list get modified!
+print( a_list == b_list, a_list, b_list )
+```
+%% Output
+    (True, ['a', 'x'], ['a', 'x'])
+%% Cell type:markdown id: tags:
+Whats wrong here...
+```bash
+conda create -n giphy python=3
+conda install Flask
+  (..)
+  Package plan for installation in environment /Users/scholtal/anaconda:
+  (..)
+  The following packages will be UPDATED:
+  (..)
+  The following packages will be DOWNGRADED due to dependency conflicts:
+  (..)
+```
+Spot the missing ``source activate giphy``....
+%% Cell type:code id: tags:
+``` python
+from collections import defaultdict
+d = defaultdict(list)
+d["a"] = [1]
+d["a"].append(2)
+print(d)
+```
+%% Output
+    defaultdict(<class 'list'>, {'a': [1, 2]})
+%% Cell type:code id: tags:
+``` python
+d = defaultdict(int)
+d["a"] += 1
+d["a"] += 2
+print(d)
+```
+%% Output
+    defaultdict(<class 'int'>, {'a': 3})
+%% Cell type:code id: tags:
+``` python
+## without using deafaultdict
+e = {}
+e.setdefault("newkey", []).append(1)
+e.setdefault("newkey1", []).append(2)
+e
+```
+%% Output
+    {'newkey': [1], 'newkey1': [2]}
+%% Cell type:code id: tags:
+``` python
+f = dict(newkey=[1])
+f["newkey"].append(2)
+f
+```
+%% Output
+    {'newkey': [1, 2]}
+%% Cell type:code id: tags:
+``` python
+f
+```
--- a/users/dinkel/django/buttondown.css
+++ b/users/dinkel/django/buttondown.css
--- a/users/dinkel/django/github.css
+++ b/users/dinkel/django/github.css
--- a/users/dinkel/django/introduction.html
+++ b/users/dinkel/django/introduction.html
--- a/users/dinkel/django/introduction.md
+++ b/users/dinkel/django/introduction.md
--- a/users/dinkel/multiprocessing/ping_subnet_map.py
+++ b/users/dinkel/multiprocessing/ping_subnet_map.py
--- a/users/dinkel/multiprocessing/ping_subnet_simple.py
+++ b/users/dinkel/multiprocessing/ping_subnet_simple.py
--- a/users/dinkel/raspberry/GPIO/BlinkenPi.ipynb
+++ b/users/dinkel/raspberry/GPIO/BlinkenPi.ipynb
--- a/users/dinkel/raspberry/GPIO/BlinkenPi.py
+++ b/users/dinkel/raspberry/GPIO/BlinkenPi.py
--- a/users/dinkel/raspberry/GPIO/PiR.ipynb
+++ b/users/dinkel/raspberry/GPIO/PiR.ipynb
--- a/users/dinkel/raspberry/GPIO/PiR.py
+++ b/users/dinkel/raspberry/GPIO/PiR.py
--- a/users/dinkel/raspberry/GPIO/gpio-pinout-rev2.jpg
+++ b/users/dinkel/raspberry/GPIO/gpio-pinout-rev2.jpg
--- a/users/dinkel/raspberry/GPIO/readme.rst
+++ b/users/dinkel/raspberry/GPIO/readme.rst
--- a/users/dinkel/virtualenv/virtualenv.pdf
+++ b/users/dinkel/virtualenv/virtualenv.pdf
--- a/users/dinkel/virtualenv/virtualenv.t2t
+++ b/users/dinkel/virtualenv/virtualenv.t2t
--- a/users/klaus/ChipSeqElli/ChiPSeqElli.ipynb
+++ b/users/klaus/ChipSeqElli/ChiPSeqElli.ipynb
--- a/users/klaus/ChipSeqElli/ChiPSeqElliLocal.ipynb
+++ b/users/klaus/ChipSeqElli/ChiPSeqElliLocal.ipynb
--- a/users/kosinski/.gitignore
+++ b/users/kosinski/.gitignore
--- a/users/zichner/.gitignore
+++ b/users/zichner/.gitignore
--- a/readme.md
+++ b/readme.md
@@ -2,7 +2,7 @@
 A group of people at EMBL Heidelberg, who share an interest in the Python programming language. You can contact the group by sending email to [python@embl.de](mailto:python@embl.de). The mailing list is managed by [Toby Hodges](mailto:toby.hodges@embl.de), [Malvika Sharan](mailto:malvika.sharan@embl.de), and [Marc Gouw](mailto:gouw@embl.de) - to join us, send an email to one of them. Meetings usually take place fortnightly, on Wednesdays at 17:00, in the Biocomputing Seminar Room (100).
-#### Ideas/suggestions for future meetings
+## Ideas/suggestions for future meetings
 Please add to this list, or email one of the mailing list managers above, to suggest/request/volunteer a topic for discussion.
@@ -10,3 +10,16 @@ Please add to this list, or email one of the mailing list managers above, to sug
 - super()
 - .py -> .ipynb
 - matplotlib 2.0
+## Jupyter Notebooks
+For some meetings you may find Jupyter notebooks that have been used in the meetings demonstrating/documenting discussions.
+## Getting Started
+```
+conda create -n epug python=3 jupyter
+source activate epug
+jupyter notebook
+```