On 25 February 2015 at 11:43, Ryan Gonzalez <rymg19@gmail.com> wrote:

Ask on python-list. Also check out the FAQ and the Help page. Not sure what your problem is; Python is EXTREMELY well documented.

The core Python docs aren't bad, but getting the full scientific Python stack up and running is still challenging for most folks. Garry, while Ryan is correct that python-list or python-tutor would be a better venue for this question (python-dev is for discussing the development *of* Python, rather than *with* Python), you may also be interested to know that getting the scientific Python stack up and running has its own dedicated section in the Python Packaging User's Guide: https://packaging.python.org/en/latest/science.html In particular, it is likely to be worth your time t to look at adopting one of the downstream Scientific Python distributions, rather than attempting to use upstream Python directly: http://www.scipy.org/install.html Regards, Nick.

On Tue, Feb 24, 2015 at 7:15 PM, GARRY M CRANE <gandkcrane@msn.com> wrote:

...

I am trying to learn Python for use in computational biology. I am using the interesting book: "Computing for Biologists; Python Programming and Principles" (by Ran Libeskind-Hadas and Eliot Bush). It has an interesting and useful set of programming exercises at www.cs.hmc.edu/CFB. I am actually enjoying solving (doing) the example problems. However, I find some of the instructions non-functional for me. For example the import function does not work, nor f=open("filename.txt"). I have saved files per instructions in the programming exercise inside the Python34 folder (I am using Python 3.4 in Windows 7). But use of the f=open() command produces an error message that the requested file does not exist. I assume I have chosen a wrong location for the saved file within that Python34 folder, but trial and error has not led to a successful use of these functions. import simply leaves a blank line .. no suggestion about the problem.

Asking questions in Google and Ask about where to save Python-related files that can be used subsequently have not led to answers - just details about structuring or formatting things to be written/saved/use of the \n at end of each line, etc. Important details, but of no help. I am finding Python to be very handy at many biologic things such as working with DNA strings, etc. but I find the documentation and indexing for finding how to use many Python features exasperating. I am writing to you based on a READ ME file in my Python folder - generated when I installed Python.

FYI, I asked a few questions of one of the authors of the interesting book - who politely replied he was too busy to answer right now - the book and problems were meant for a class ... though neither the book nor problems say so. The professor hopes to get around to issues of use by non-students sometime - but not now.

Another feature I have come across so far that does not work is importation of matplotlib. I copy computed results (that otherwise would go to your plotting routine) then go to Excel and with manipulation produce a usable chart there - but at a cost of time and energy.

Your Python tool has many intriguing features - but some of the most basic functions do not work for me (even though many features do, e.g., import random does work). The failure of these features - so far as I can tell - is because of lack of description (for the general non-expert public) about where/how to install various features. Perhaps I need to reinstall from the ground up??? If so, just what should I do? If there is a less drastic solution, can you tell me about it?

Thank you for any help ... and if you could provide me a lead regarding WHERE to ask subsequent questions I would be most grateful. Sometimes, Google or Ask or a U Tube tutorial does a good job - but if one does not know the 'proper' name or term for something, it often is frustrating or impossible to get an answer. I have not heard about any comprehensive handbook for Python34 aimed at one who wants to use Python for creating programs (functions) that work - and is not an expert at back-room structure of files and folders.... have I simply missed it? So far, I have not found a local Python expert to ask for help. I am sure some are in the greater Seattle area where I live- but I don't know how to find even one at this time.

Garry Crane gandkcrane@msn.com

_______________________________________________ Python-Dev mailing list Python-Dev@python.org https://mail.python.org/mailman/listinfo/python-dev Unsubscribe: https://mail.python.org/mailman/options/python-dev/rymg19%40gmail.com

-- Ryan If anybody ever asks me why I prefer C++ to C, my answer will be simple: "It's becauseslejfp23(@#Q*(E*EIdc-SEGFAULT. Wait, I don't think that was nul-terminated." Personal reality distortion fields are immune to contradictory evidence. - srean Check out my website: http://kirbyfan64.github.io/

_______________________________________________ Python-Dev mailing list Python-Dev@python.org https://mail.python.org/mailman/listinfo/python-dev Unsubscribe: https://mail.python.org/mailman/options/python-dev/ncoghlan%40gmail.com

-- Nick Coghlan | ncoghlan@gmail.com | Brisbane, Australia

On 25 February 2015 at 11:43, Ryan Gonzalez <rymg19@gmail.com> wrote:

Ask on python-list. Also check out the FAQ and the Help page. Not sure what your problem is; Python is EXTREMELY well documented.

The core Python docs aren't bad, but getting the full scientific Python stack up and running is still challenging for most folks. Garry, while Ryan is correct that python-list or python-tutor would be a better venue for this question (python-dev is for discussing the development *of* Python, rather than *with* Python), you may also be interested to know that getting the scientific Python stack up and running has its own dedicated section in the Python Packaging User's Guide: https://packaging.python.org/en/latest/science.html In particular, it is likely to be worth your time t to look at adopting one of the downstream Scientific Python distributions, rather than attempting to use upstream Python directly: http://www.scipy.org/install.html Regards, Nick.

On Tue, Feb 24, 2015 at 7:15 PM, GARRY M CRANE <gandkcrane@msn.com> wrote:

...

I am trying to learn Python for use in computational biology. I am using the interesting book: "Computing for Biologists; Python Programming and Principles" (by Ran Libeskind-Hadas and Eliot Bush). It has an interesting and useful set of programming exercises at www.cs.hmc.edu/CFB. I am actually enjoying solving (doing) the example problems. However, I find some of the instructions non-functional for me. For example the import function does not work, nor f=open("filename.txt"). I have saved files per instructions in the programming exercise inside the Python34 folder (I am using Python 3.4 in Windows 7). But use of the f=open() command produces an error message that the requested file does not exist. I assume I have chosen a wrong location for the saved file within that Python34 folder, but trial and error has not led to a successful use of these functions. import simply leaves a blank line .. no suggestion about the problem.

Asking questions in Google and Ask about where to save Python-related files that can be used subsequently have not led to answers - just details about structuring or formatting things to be written/saved/use of the \n at end of each line, etc. Important details, but of no help. I am finding Python to be very handy at many biologic things such as working with DNA strings, etc. but I find the documentation and indexing for finding how to use many Python features exasperating. I am writing to you based on a READ ME file in my Python folder - generated when I installed Python.

FYI, I asked a few questions of one of the authors of the interesting book - who politely replied he was too busy to answer right now - the book and problems were meant for a class ... though neither the book nor problems say so. The professor hopes to get around to issues of use by non-students sometime - but not now.

Another feature I have come across so far that does not work is importation of matplotlib. I copy computed results (that otherwise would go to your plotting routine) then go to Excel and with manipulation produce a usable chart there - but at a cost of time and energy.

Your Python tool has many intriguing features - but some of the most basic functions do not work for me (even though many features do, e.g., import random does work). The failure of these features - so far as I can tell - is because of lack of description (for the general non-expert public) about where/how to install various features. Perhaps I need to reinstall from the ground up??? If so, just what should I do? If there is a less drastic solution, can you tell me about it?

Thank you for any help ... and if you could provide me a lead regarding WHERE to ask subsequent questions I would be most grateful. Sometimes, Google or Ask or a U Tube tutorial does a good job - but if one does not know the 'proper' name or term for something, it often is frustrating or impossible to get an answer. I have not heard about any comprehensive handbook for Python34 aimed at one who wants to use Python for creating programs (functions) that work - and is not an expert at back-room structure of files and folders.... have I simply missed it? So far, I have not found a local Python expert to ask for help. I am sure some are in the greater Seattle area where I live- but I don't know how to find even one at this time.

Garry Crane gandkcrane@msn.com

_______________________________________________ Python-Dev mailing list Python-Dev@python.org https://mail.python.org/mailman/listinfo/python-dev Unsubscribe: https://mail.python.org/mailman/options/python-dev/rymg19%40gmail.com

-- Ryan If anybody ever asks me why I prefer C++ to C, my answer will be simple: "It's becauseslejfp23(@#Q*(E*EIdc-SEGFAULT. Wait, I don't think that was nul-terminated." Personal reality distortion fields are immune to contradictory evidence. - srean Check out my website: http://kirbyfan64.github.io/

_______________________________________________ Python-Dev mailing list Python-Dev@python.org https://mail.python.org/mailman/listinfo/python-dev Unsubscribe: https://mail.python.org/mailman/options/python-dev/ncoghlan%40gmail.com

-- Nick Coghlan | ncoghlan@gmail.com | Brisbane, Australia