Notebooks to introduce biopython
License: MIT License
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In the branch;
https://github.com/tiagoantao/biopython-notebook/tree/tex-ipynb-convert
I have added a scripts folded and a script to convert the tutorial tex files to ipynb. It mostly works ok.
You can see the converted notebooks here;
https://github.com/vincentdavis/biopython-notebook/tree/tex-ipynb-convert/Tutorial
I figured this folder might also be useful for a scripts to download data files.
Is this script something you want to include?
As per the subject. As suggested by @vincentdavis.
See, for example https://github.com/bollwyvl/nosebook
The "Substitution Matrices" section of the cookbook should be merged or combimed with chapter 21 Advanced which covers Substitution Matrices.
The code seems windows dependent. Also lacks example files
If the notebook specifies python 2 the Travis CI tests exit. The python version is specified at the end of the notebook JSON as shown below. Travis CI error below.
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}Traceback (most recent call last):
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/jupyter_client/kernelspec.py", line 141, in get_kernel_spec
resource_dir = d[kernel_name.lower()]
KeyError: 'python2'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "test/test.py", line 23, in <module>
nb_executed, resources = ex.preprocess(nb, resources={})
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py", line 79, in preprocess
cwd=path)
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/jupyter_client/manager.py", line 430, in start_new_kernel
km.start_kernel(**kwargs)
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/jupyter_client/manager.py", line 231, in start_kernel
kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/jupyter_client/manager.py", line 171, in format_kernel_cmd
cmd = self.kernel_spec.argv + extra_arguments
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/jupyter_client/manager.py", line 82, in kernel_spec
self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
File "/home/travis/virtualenv/python3.5.0/lib/python3.5/site-packages/jupyter_client/kernelspec.py", line 143, in get_kernel_spec
raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: 'python2'
The command "python test/test.py" exited with 1.
Done. Your build exited with 1.Make sure this works with the binder service
Show an example with the new Post vs Get with long URLs
From Biopython news
The Bio.Entrez interface will automatically use an HTTP POST rather than HTTP GET if the URL would exceed 1000 characters. This is based on NCBI guidelines and the fact that very long queries like complex searches can otherwise trigger an HTTP Error 414 Request URI too long.
http://mybinder.org/
I am giving it a try.
I was planning on reorganizing notebook names. Mostly removing spaces and maybe even the numbering. The spaces on file names are problematic and there is really no ordering in chapter reading (save for one or two exceptions).
@vincentdavis if you are not OK with this, please say...
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