Programming course issueshttps://git.lumc.nl/courses/programming-course/-/issues2017-07-18T10:40:44+02:00https://git.lumc.nl/courses/programming-course/-/issues/25Error in NumPy slides2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlError in NumPy slidesJust a formatting error. There's one slide that contains cells from two slides (which doesn't fit).Just a formatting error. There's one slide that contains cells from two slides (which doesn't fit).Martijn Vermaatm.vermaat.hg@lumc.nlMartijn Vermaatm.vermaat.hg@lumc.nlhttps://git.lumc.nl/courses/programming-course/-/issues/21Title for Pandas lesson2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlTitle for Pandas lessonWe should settle on one title for "the Pandas lesson".
Current candidates:
- More on IPython and Python libraries making science peanuts
- Painting Pandas
- Python for data analysis
@wyleung Do you favor one?We should settle on one title for "the Pandas lesson".
Current candidates:
- More on IPython and Python libraries making science peanuts
- Painting Pandas
- Python for data analysis
@wyleung Do you favor one?https://git.lumc.nl/courses/programming-course/-/issues/19Add Bowo and Zuotian to authors?2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlAdd Bowo and Zuotian to authors?I updated some lessons to list the current teachers, but I guess it's better to not remove the original author (in most cases Bowo, Zuotian's Git lesson was removed). Or we list all present and past teachers, that would also include Zuot...I updated some lessons to list the current teachers, but I guess it's better to not remove the original author (in most cases Bowo, Zuotian's Git lesson was removed). Or we list all present and past teachers, that would also include Zuotian.https://git.lumc.nl/courses/programming-course/-/issues/18List of participants - pre course preparations2017-07-18T10:40:44+02:00Wai Yi LeungList of participants - pre course preparationsDo we have a list of participants?
We need to inform them about what to prepare from their side (laptop, readings)
Installation of the virtualenv and such.Do we have a list of participants?
We need to inform them about what to prepare from their side (laptop, readings)
Installation of the virtualenv and such.https://git.lumc.nl/courses/programming-course/-/issues/16Solutions to exercises and assignments2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlSolutions to exercises and assignmentsFrom last year I have some example solutions to NumPy and matplotlib exercises. For some reason I added them to the programming course repository.
So I removed them here and created a new **private** repository for this: [programming-...From last year I have some example solutions to NumPy and matplotlib exercises. For some reason I added them to the programming course repository.
So I removed them here and created a new **private** repository for this: [programming-course-solutions](https://git.lumc.nl/m.vermaat.hg/programming-course-solutions) (had to be outside the humgen group)
If you have any example solutions, please add them there.https://git.lumc.nl/courses/programming-course/-/issues/15Assignments repository2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlAssignments repositoryThere is some material for the assignments in the [programming-course-assignments](https://git.lumc.nl/humgen/programming-course-assignments) repository.
The idea is that students will fork that repository and push solutions to their ...There is some material for the assignments in the [programming-course-assignments](https://git.lumc.nl/humgen/programming-course-assignments) repository.
The idea is that students will fork that repository and push solutions to their fork. We just have to write some documentation on how to do that.
It also needs updating. For example, the sequencer assignment is still in there.
https://git.lumc.nl/courses/programming-course/-/issues/12Show off IPython Notebook2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlShow off IPython NotebookSome people, after asking for suggestions, would like to see the IPython Notebook demonstrated. Perhaps we can take 10 or 15 minutes for this on Friday.Some people, after asking for suggestions, would like to see the IPython Notebook demonstrated. Perhaps we can take 10 or 15 minutes for this on Friday.Martijn Vermaatm.vermaat.hg@lumc.nlMartijn Vermaatm.vermaat.hg@lumc.nlhttps://git.lumc.nl/courses/programming-course/-/issues/11Add files needed for exercises and assignments to assignment repo2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlAdd files needed for exercises and assignments to assignment repohttps://git.lumc.nl/courses/programming-course/-/issues/10Explain virtual environments and pip2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlExplain virtual environments and pipNot sure, but perhaps we should cover this at some point? For now we just have them install it all and activate their virtual environment without explaining what that's all about.Not sure, but perhaps we should cover this at some point? For now we just have them install it all and activate their virtual environment without explaining what that's all about.https://git.lumc.nl/courses/programming-course/-/issues/9Integrate some Rosalind exercises2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlIntegrate some Rosalind exerciseshttp://rosalind.info/problems/locations/http://rosalind.info/problems/locations/https://git.lumc.nl/courses/programming-course/-/issues/8Finish "BioPython" lesson2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlFinish "BioPython" lessonProbably mainly about file parsing.
This can build on the OO lesson before it.
If we have things like DNA transcription and translation as exercises for the first lessons, also show how to properly do it using BioPython.Probably mainly about file parsing.
This can build on the OO lesson before it.
If we have things like DNA transcription and translation as exercises for the first lessons, also show how to properly do it using BioPython.bowbowhttps://git.lumc.nl/courses/programming-course/-/issues/7Finish "More Python" lesson2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlFinish "More Python" lessonAssigned to bowo because he offered to make a start with that. Martijn is also responsible.
I think we discussed something like this:
* Having your code in a file and executing it
* Importing your file as a module
* The `if __nam...Assigned to bowo because he offered to make a start with that. Martijn is also responsible.
I think we discussed something like this:
* Having your code in a file and executing it
* Importing your file as a module
* The `if __name__ == '__main__'` trick
* Some notes on documentation
* Mention PEP8
* Input/output
* Catching exceptions (starting with file not found)
* Raising exceptions
* Reading a stack trace
* Standard library examples: sys, os, argparse, math, random, gzip, datetime, re. (this might be a bit too much)bowbowhttps://git.lumc.nl/courses/programming-course/-/issues/6Finish OO lesson2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlFinish OO lessonLarosLaroshttps://git.lumc.nl/courses/programming-course/-/issues/5Add example exercise solutions to assignments repository2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlAdd example exercise solutions to assignments repositoryShould we only do this later, after they had the chance to do the exercises?Should we only do this later, after they had the chance to do the exercises?Martijn Vermaatm.vermaat.hg@lumc.nlMartijn Vermaatm.vermaat.hg@lumc.nlhttps://git.lumc.nl/courses/programming-course/-/issues/4Finish git lesson2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlFinish git lessonAnything this depends on?Anything this depends on?Zuotian TatumZuotian Tatumhttps://git.lumc.nl/courses/programming-course/-/issues/3Link to Notebook Viewer versions of slides from Trac wiki.2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlLink to Notebook Viewer versions of slides from Trac wiki.Similar to the links I added to this repository's README.md we should have links to the one-page HTML views of the slide notebooks on the Trac wiki for easy access.Similar to the links I added to this repository's README.md we should have links to the one-page HTML views of the slide notebooks on the Trac wiki for easy access.https://git.lumc.nl/courses/programming-course/-/issues/2Remove course contents and course material pages from Trac wiki.2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlRemove course contents and course material pages from Trac wiki.We don't need them any more and they contain outdated info. Just confusion.
We can have everything in the notebooks.
Depends on #3 .We don't need them any more and they contain outdated info. Just confusion.
We can have everything in the notebooks.
Depends on #3 .https://git.lumc.nl/courses/programming-course/-/issues/1Further reading links2017-07-18T10:40:44+02:00Martijn Vermaatm.vermaat.hg@lumc.nlFurther reading linksAdd a final slide with further reading links to each lesson.Add a final slide with further reading links to each lesson.https://git.lumc.nl/courses/programming-course/-/issues/31IPython or jupyter ?2018-04-30T05:44:31+02:00Wai Yi LeungIPython or jupyter ?With the new series of the programming course. Should we convert the IPython notebooks to the new "Jupyter" format? (though, ipynb will work, ipython as cli also)
May be relevant to show some side tracks on using IPython for R/JuliaWith the new series of the programming course. Should we convert the IPython notebooks to the new "Jupyter" format? (though, ipynb will work, ipython as cli also)
May be relevant to show some side tracks on using IPython for R/Juliahttps://git.lumc.nl/courses/programming-course/-/issues/30Post-course evaluation notes2018-04-30T05:44:31+02:00Martijn Vermaatm.vermaat.hg@lumc.nlPost-course evaluation notesPresent:
- Jeroen Laros
- Michiel van Galen
- Wai Yi Leung
- Martijn Vermaat
Boosting participation
----------------------
We want to involve the students more and push them to really do exercises. Afternoons off don't rea...Present:
- Jeroen Laros
- Michiel van Galen
- Wai Yi Leung
- Martijn Vermaat
Boosting participation
----------------------
We want to involve the students more and push them to really do exercises. Afternoons off don't really seem to work for that. Instead, perhaps do 3 full days with some time for supervised exercises.
We have to very careful that it will not get boring for fast students when we wait for the slow ones.
Separate presenting from practice
---------------------------------
Idea is to have more structure here. Ideally have good course material in written narrative, including exercises, which will be the backbone of the course. We introduce concepts in our presentations with separate slides, but these are always based on (or can refer to) the written course material.
This course material can be implemented in IPython notebooks, where the exercises have some empty code cells.
We also do just presentations, and separate this from some time for exercises afterwards. These can be intertwined as 20 or 30 minute sessions.
Object-oriented programming
---------------------------
This lesson can be much sooner, e.g., after *More Python Goodness*.
Mode of operation
-----------------
We introduce different modes of writing code:
1. (I)Python interpreter
2. IPython Notebook
3. Text editor
This makes things more complex. Perhaps we can completely skip the first one?