pythoninchemistry / intro_python_chemists Goto Github PK

Currently there are no #### Exercise in the functions section. It would be nice to include some.

Would this be an interesting thing to include for linear algebra?

Write a section introducing classes:

• class variables
• class methods/functions
• the @property decorator
• docstrings for classes

Before introducing writing documentation (#13), we should have a section on reading documentation (the ? in Jupyter and finding docs online).

@bjmorgan raised the idea that the concept of objects having methods should be introduced immediately after functions, without necessarily explaining classes.

This issue is to chat about that.

@WG150 now that you have contributed can you add yourself to the .zenodo.json so that when the next release is minted you are recognised appropriately!

Write a section showing how custom modules (your own python code in a .py file) can be imported.

Write a section discussing common debugging practices, including how best to read a python traceback. This can link with the testing section.

In #58, @j-m-dean has raised the question "Are model solutions provided for the longer exercises?".

This issue is to get peoples feeling on that.

My preference would be to give answers but not solutions that are only accessible by clicking a link. My rationale is that in programming there are infinite ways to solve a given problem so I don't want to pigeonhole people with one solution, additionally frequently all you want is to know that you got the right answer.

Thoughts?

The circleci falls down with the most recent release of jupyter-book, claiming that it cannot find the toc.

Couldn't find a Table of Contents file. To auto-generate one, run

jupyter-book toc .

But there is a toc. Need to work out why this is, for now jupyter-book==0.6.4 is the the requirements.txt

Should a (permissive) license be added to this repository?

Plan a table of contents to work towards.

Write a section introducing documentation:

• comments
• docstrings (also covered in functions)

This should include the comments from @acnash on issue #5

Write a section introducing:

• for loops
• while loops

This should include some discussion of the range() iterator, the difference between the loops and break/continue.

Update style guide to promote the use of non-gendered pronouns ie the use of they in preference to him/her.

Write ir_spectra section - based on data analysis problem from CH40208

@RMeli now that you have contributed can you add yourself to the .zenodo.json so that when the next release is minted you are recognised appropriately!

@j-m-dean to add orcid ID to .zenodo.json and add Faraday institution to the funders.

What is the project position on LaTeX? LaTeX for chemistry in itself it could easily be (and probably is) the subject another book. However it's very useful when it comes to e.g. axes labels, is it going to be introduced anywhere?

Would it not be an easier learning curve to change the order of the basics section from

• url: /basics/types
  • url: /basics/collections
  • url: /basics/numpy_arrays
  • url: /basics/functions
  • url: /basics/flow_control
  • url: /basics/and_or
  • url: /basics/loops

to

• url: /basics/types
  • url: /basics/collections
  • url: /basics/flow_control
  • url: /basics/and_or
  • url: /basics/loops
  • url: /basics/numpy_arrays
  • url: /basics/functions

Arrays and functions before flow control, loops, and logic seems a bit odd to me. Thoughts?

In the Types section, there is not an discussion of using a variable. For example, in a mathematical operation.

This would help understanding of variables as a whole to include.

@symmy596 needs to be added to the .zenodo.json file.

Write a section introducing testing, discussing it's importance in code reliability. Might also include a discussion about test driven development.

The Types section says that it is preferred to use is and is not instead of == and != in string comparison. This is a lot more nuanced than I first thought so it is probably best to remove it completely.

Write a section that will introduce the pint and uncertainties libraries for working with data.

Depending on exactly what goes in surface_plots I propose covering:

• object oriented plotting, building towards a figure with multiple subplots
• customizing plots, building towards the concept of an .rc file
• brief intro to LaTeX, purely in the context of conveying data in matplotlib

Write a section discussing what OOP is.

Write a section discussing IO:

• python's build in open stuff
• NumPy's np.loadtxt

I (personally) don't think there is scope for pandas here but I am happy to have my mind changed.

Write a section introducing NumPy arrays. Ideally covering, lightly, that these arrays are:

• of fixed type
• make numerical operations faster
• able to perform vectorised operations

When running the and_or.ipynb notebook the following import requires the mendeleev package

from periodic_table_20 import periodic_table_20

but this is not provided in requirements.txt.

The first draft Table of Contents is now online in the _data/toc.yml. However, we want to get more ideas for sections and chapters to include.

Please comment below with potential areas for inclusion (or areas currently included that should be removed).

Any and all ideas are welcome!

Write a section introducing packages:

• discuss pip install of packages
• explain package importing
• explain importing a single module or function from a package

Also discuss the importance of the package infrastructure to the python language.

Write a section to introduce and and or logical, showing it in the context of flow control

Write optimisation section

Write a section covering collections:

• tuples
• lists
• dictionaries

Write a section discussing the raise keyword and how if can be used.

Write a section discussing 2d colourmap style plots.

@symmy596 this one is for you if you want it.

Write a section on 1d plotting:

• plt.plot()
• plt.errorbar()
• multiple lines on a plot

Write a section that will cover:

• if
• else
• elif

As well as introducing why this is useful.

Write a section introduction how numpy and scipy can be used for basic stats

• mean
• std
• percentiles

Write a section about creating python packages:

• sharing them on pypi
• setup.py
• publishing packages

The x-ray scattering length is still included in the dictionaries section of collections. This should be removed outright as it is niche.

Write a section on linear algebra. From @j-m-dean in #5.

@bjmorgan you might enjoy this one 😉