diff --git a/talks/packages/packages.ipynb b/talks/packages/packages.ipynb
index 84bc3797483fa3f76082dface02016a90764dd77..f96cca7eba78337021c01e5b1a540448a0dc0c07 100644
--- a/talks/packages/packages.ipynb
+++ b/talks/packages/packages.ipynb
@@ -19,8 +19,10 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"import numpy as np"
@@ -47,7 +49,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"import scipy as sp"
@@ -63,7 +67,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"from scipy import optimize\n",
@@ -84,7 +90,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"import matplotlib as mpl\n",
@@ -102,7 +110,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"x = np.linspace(0, 2, 100)\n",
@@ -156,7 +166,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"import statsmodels.api as sm\n",
@@ -167,7 +179,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"df = sm.datasets.get_rdataset(\"Guerry\", \"HistData\").data\n",
@@ -177,7 +191,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"df.describe()"
@@ -186,7 +202,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"df.groupby('Region').mean()"
@@ -195,7 +213,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"results = smf.ols('Lottery ~ Literacy + np.log(Pop1831)', data=df).fit()\n",
@@ -205,7 +225,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"df['log_pop'] = np.log(df.Pop1831)\n",
@@ -215,7 +237,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"results = smf.ols('Lottery ~ Literacy + log_pop', data=df).fit()\n",
@@ -225,7 +249,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"results = smf.ols('Lottery ~ Literacy + np.log(Pop1831) + Region', data=df).fit()\n",
@@ -235,7 +261,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"results = smf.ols('Lottery ~ Literacy + np.log(Pop1831) + Region + Region * Literacy', data=df).fit()\n",
@@ -245,7 +273,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%matplotlib nbagg\n",
@@ -263,7 +293,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"import sympy as sym # no standard nickname"
@@ -272,7 +304,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"x, a, b, c = sym.symbols('x, a, b, c')\n",
@@ -282,7 +316,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"sym.integrate(x/(x**2+a*x+2), x)"
@@ -291,7 +327,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"f = sym.utilities.lambdify((x, a), sym.integrate((x**2+a*x+2), x))\n",
@@ -309,7 +347,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%%writefile test_argparse.py\n",
@@ -335,7 +375,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%run test_argparse.py 3 8 -v"
@@ -344,7 +386,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%run test_argparse.py -h"
@@ -353,7 +397,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%run test_argparse.py 3 8.5 -q"
@@ -363,13 +409,45 @@
"cell_type": "markdown",
"metadata": {},
"source": [
+ "Alternatives:\n",
+ "- [docopt](http://docopt.org/): You write a usage string, docopt will generate the parser\n",
+ "> ```\n",
+ "> # example from https://realpython.com/blog/python/comparing-python-command-line-parsing-libraries-argparse-docopt-click/\n",
+ "> \"\"\"Greeter.\n",
+ ">\n",
+ "> Usage:\n",
+ "> commands.py hello\n",
+ "> commands.py goodbye\n",
+ "> commands.py -h | --help\n",
+ ">\n",
+ "> Options:\n",
+ "> -h --help Show this screen.\n",
+ "> \"\"\"\n",
+ "> from docopt import docopt\n",
+ ">\n",
+ "> if __name__ == '__main__':\n",
+ "> arguments = docopt(__doc__)\n",
+ "> ```\n",
+ "- [clize](http://clize.readthedocs.io/en/stable/why.html): You write a function, clize will generate the parser\n",
+ "> ```\n",
+ "> from clize import run\n",
+ ">\n",
+ "> def echo(word):\n",
+ "> return word\n",
+ ">\n",
+ "> if __name__ == '__main__':\n",
+ "> run(echo)\n",
+ "> ```\n",
+ "\n",
"### [Gooey](https://github.com/chriskiehl/Gooey): GUI from command line tool"
]
},
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%%writefile test_gooey.py\n",
@@ -397,7 +475,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%run test_gooey.py"
@@ -406,7 +486,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"!gcoord_gui"
@@ -416,13 +498,19 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## [Jinja2](http://jinja.pocoo.org/docs/2.10/): HTML generation"
+ "## [Jinja2](http://jinja.pocoo.org/docs/2.10/): Templating language\n",
+ "Jinja2 allows to create templates of files with placeholders, where future content will go.\n",
+ "This allows for the creation of a large number of similar files.\n",
+ "\n",
+ "This can for example be used to produce static HTML output in a highly flexible manner."
]
},
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%%writefile image_list.jinja2\n",
@@ -458,7 +546,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"def plot_sine(amplitude, frequency):\n",
@@ -481,7 +571,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"from jinja2 import Environment, FileSystemLoader\n",
@@ -503,7 +595,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"!open image_list.html"
@@ -526,7 +620,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%%writefile wx_hello_world.py\n",
@@ -634,7 +730,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"%run wx_hello_world.py"
@@ -649,13 +747,17 @@
"- theano/tensorflow/pytorch\n",
" - keras\n",
"\n",
- "## [Pycuda](https://documen.tician.de/pycuda/): Programming the GPU"
+ "## [Pycuda](https://documen.tician.de/pycuda/): Programming the GPU\n",
+ "Wrapper around [Cuda](https://developer.nvidia.com/cuda-zone).\n",
+ "The alternative [Pyopencl](https://documen.tician.de/pyopencl/) provides a very similar wrapper around [OpenCL](https://www.khronos.org/opencl/)."
]
},
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "collapsed": true
+ },
"outputs": [],
"source": [
"import pycuda.autoinit\n",
@@ -778,11 +880,77 @@
"- [pylint](https://pypi.python.org/pypi/pylint): most extensive linter\n",
"- [pyflake](https://pypi.python.org/pypi/pyflakes): if you think pylint is too strict\n",
"- [pep8](https://pypi.python.org/pypi/pep8): just checks for style errors\n",
- "- [mypy](http://mypy-lang.org/): adding explicit typing to python"
+ "- [mypy](http://mypy-lang.org/): adding explicit typing to python\n",
+ "\n",
+ "## Web frameworks\n",
+ "- [Django2](https://www.djangoproject.com/): includes the most features, but also forces you to do things their way\n",
+ "- [Pyramid](https://trypyramid.com): Intermediate options\n",
+ "- [Flask](http://flask.pocoo.org/): Bare-bone web framework, but many extensions available\n",
+ "\n",
+ "There are also many, many libraries to interact with databases, but you will have to google those yourself.\n",
+ "\n",
+ "# Several honourable mentions\n",
+ "- [trimesh](https://github.com/mikedh/trimesh): Triangular mesh algorithms\n",
+ "- [Pillow](https://pillow.readthedocs.io/en/latest/): Read/write/manipulate a wide variety of images (png, jpg, tiff, etc.)\n",
+ "- [psychopy](http://www.psychopy.org/): equivalent of psychtoolbox (workshop coming up in April in Nottingham)\n",
+ "- [Buit-in libraries](https://docs.python.org/3/py-modindex.html)\n",
+ " - [collections](https://docs.python.org/3.6/library/collections.html): deque, OrderedDict, namedtuple, and more\n",
+ " - [datetime](https://docs.python.org/3/library/datetime.html): Basic date and time types\n",
+ " - [enum](https://docs.python.org/3/library/enum.html): Enumerators\n",
+ " - [fractions](https://docs.python.org/3/library/fractions.html): rational numbers\n",
+ " - [functools](https://docs.python.org/3/library/functools.html): caching, decorators, and support for functional programming\n",
+ " - [json](https://docs.python.org/3/library/json.html)/[ipaddress](https://docs.python.org/3/library/ipaddress.html)/[xml](https://docs.python.org/3/library/xml.html#module-xml): parsing/writing\n",
+ " - [itertools](https://docs.python.org/3/library/itertools.html): more tools to loop over sequences\n",
+ " - [logging](https://docs.python.org/3/library/logging.htm): log your output to stdout or a file (more flexible than print statements)\n",
+ " - [multiprocessing](https://docs.python.org/3/library/multiprocessing.html)\n",
+ " - [os](https://docs.python.org/3/library/os.html#module-os)/[sys](https://docs.python.org/3/library/sys.html): Miscellaneous operating system interfaces\n",
+ " - [os.path](https://docs.python.org/3/library/os.path.html)/[pathlib](https://docs.python.org/3/library/pathlib.html): utilities to deal with filesystem paths (latter provides an object-oriented interface)\n",
+ " - [pickle](https://docs.python.org/3/library/pickle.html): Store/load any python object\n",
+ " - [shutil](https://docs.python.org/3/library/shutil.html): copy/move files\n",
+ " - [subprocess](https://docs.python.org/3/library/subprocess.html): call shell commands\n",
+ " - [turtule](https://docs.python.org/3/library/turtle.html#module-turtle): teach python to your kids!\n",
+ " - [warnings](https://docs.python.org/3/library/warnings.html#module-warnings): tell people they are not using your code properly"
]
}
],
- "metadata": {},
+ "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": "3.6.2"
+ },
+ "toc": {
+ "colors": {
+ "hover_highlight": "#DAA520",
+ "running_highlight": "#FF0000",
+ "selected_highlight": "#FFD700"
+ },
+ "moveMenuLeft": true,
+ "nav_menu": {
+ "height": "417px",
+ "width": "252px"
+ },
+ "navigate_menu": true,
+ "number_sections": true,
+ "sideBar": true,
+ "threshold": 4,
+ "toc_cell": false,
+ "toc_section_display": "block",
+ "toc_window_display": false
+ }
+ },
"nbformat": 4,
"nbformat_minor": 2
}
diff --git a/talks/packages/packages.md b/talks/packages/packages.md
index 851c5065890aa015ad67da36b467cd0b7e515f8b..49f3a6d046d46a5b59133b19fc897cca8200a7c3 100644
--- a/talks/packages/packages.md
+++ b/talks/packages/packages.md
@@ -194,6 +194,36 @@ if __name__ == '__main__':
%run test_argparse.py 3 8.5 -q
```
+Alternatives:
+- [docopt](http://docopt.org/): You write a usage string, docopt will generate the parser
+> ```
+> # example from https://realpython.com/blog/python/comparing-python-command-line-parsing-libraries-argparse-docopt-click/
+> """Greeter.
+>
+> Usage:
+> commands.py hello
+> commands.py goodbye
+> commands.py -h | --help
+>
+> Options:
+> -h --help Show this screen.
+> """
+> from docopt import docopt
+>
+> if __name__ == '__main__':
+> arguments = docopt(__doc__)
+> ```
+- [clize](http://clize.readthedocs.io/en/stable/why.html): You write a function, clize will generate the parser
+> ```
+> from clize import run
+>
+> def echo(word):
+> return word
+>
+> if __name__ == '__main__':
+> run(echo)
+> ```
+
### [Gooey](https://github.com/chriskiehl/Gooey): GUI from command line tool
```
%%writefile test_gooey.py
@@ -226,7 +256,11 @@ if __name__ == '__main__':
!gcoord_gui
```
-## [Jinja2](http://jinja.pocoo.org/docs/2.10/): HTML generation
+## [Jinja2](http://jinja.pocoo.org/docs/2.10/): Templating language
+Jinja2 allows to create templates of files with placeholders, where future content will go.
+This allows for the creation of a large number of similar files.
+
+This can for example be used to produce static HTML output in a highly flexible manner.
```
%%writefile image_list.jinja2
<!DOCTYPE html>
@@ -418,6 +452,8 @@ if __name__ == '__main__':
- keras
## [Pycuda](https://documen.tician.de/pycuda/): Programming the GPU
+Wrapper around [Cuda](https://developer.nvidia.com/cuda-zone).
+The alternative [Pyopencl](https://documen.tician.de/pyopencl/) provides a very similar wrapper around [OpenCL](https://www.khronos.org/opencl/).
```
import pycuda.autoinit
import pycuda.driver as drv
@@ -444,6 +480,7 @@ multiply_them(
print(dest-a*b)
```
+Also see [pyopenGL](http://pyopengl.sourceforge.net/): graphics programming in python (used in FSLeyes)
## Testing
- [unittest](https://docs.python.org/3.6/library/unittest.html): python built-in testing
> ```
@@ -535,4 +572,34 @@ Linters check the code for any syntax errors, [style errors](https://www.python.
- [pylint](https://pypi.python.org/pypi/pylint): most extensive linter
- [pyflake](https://pypi.python.org/pypi/pyflakes): if you think pylint is too strict
- [pep8](https://pypi.python.org/pypi/pep8): just checks for style errors
-- [mypy](http://mypy-lang.org/): adding explicit typing to python
\ No newline at end of file
+- [mypy](http://mypy-lang.org/): adding explicit typing to python
+
+## Web frameworks
+- [Django2](https://www.djangoproject.com/): includes the most features, but also forces you to do things their way
+- [Pyramid](https://trypyramid.com): Intermediate options
+- [Flask](http://flask.pocoo.org/): Bare-bone web framework, but many extensions available
+
+There are also many, many libraries to interact with databases, but you will have to google those yourself.
+
+# Several honourable mentions
+- [trimesh](https://github.com/mikedh/trimesh): Triangular mesh algorithms
+- [Pillow](https://pillow.readthedocs.io/en/latest/): Read/write/manipulate a wide variety of images (png, jpg, tiff, etc.)
+- [psychopy](http://www.psychopy.org/): equivalent of psychtoolbox (workshop coming up in April in Nottingham)
+- [Buit-in libraries](https://docs.python.org/3/py-modindex.html)
+ - [collections](https://docs.python.org/3.6/library/collections.html): deque, OrderedDict, namedtuple, and more
+ - [datetime](https://docs.python.org/3/library/datetime.html): Basic date and time types
+ - [enum](https://docs.python.org/3/library/enum.html): Enumerators
+ - [fractions](https://docs.python.org/3/library/fractions.html): rational numbers
+ - [functools](https://docs.python.org/3/library/functools.html): caching, decorators, and support for functional programming
+ - [json](https://docs.python.org/3/library/json.html)/[ipaddress](https://docs.python.org/3/library/ipaddress.html)/[xml](https://docs.python.org/3/library/xml.html#module-xml): parsing/writing
+ - [itertools](https://docs.python.org/3/library/itertools.html): more tools to loop over sequences
+ - [logging](https://docs.python.org/3/library/logging.htm): log your output to stdout or a file (more flexible than print statements)
+ - [multiprocessing](https://docs.python.org/3/library/multiprocessing.html)
+ - [os](https://docs.python.org/3/library/os.html#module-os)/[sys](https://docs.python.org/3/library/sys.html): Miscellaneous operating system interfaces
+ - [os.path](https://docs.python.org/3/library/os.path.html)/[pathlib](https://docs.python.org/3/library/pathlib.html): utilities to deal with filesystem paths (latter provides an object-oriented interface)
+ - [pickle](https://docs.python.org/3/library/pickle.html): Store/load any python object
+ - [shutil](https://docs.python.org/3/library/shutil.html): copy/move files
+ - [subprocess](https://docs.python.org/3/library/subprocess.html): call shell commands
+ - [time](https://docs.python.org/3/library/time.html)/[timeit](https://docs.python.org/3/library/timeit.html): keeping track of it
+ - [turtule](https://docs.python.org/3/library/turtle.html#module-turtle): teach python to your kids!
+ - [warnings](https://docs.python.org/3/library/warnings.html#module-warnings): tell people they are not using your code properly