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Tutorials maintenance #3993

Merged
merged 14 commits into from
Nov 16, 2020
Merged

Tutorials maintenance #3993

merged 14 commits into from
Nov 16, 2020

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jngrad
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@jngrad jngrad commented Nov 13, 2020

Description of changes:

  • remove crystallization tutorial (partial fix for Write Tutorial 02 part 2: ELC system with dielectric boundaries #3955, closes Tutorial 02: electrostatics part 2 #3820)
  • remove tutorial numbers and indicate difficulty level (fixes Consistent numbering for tutorials #3959)
  • resolve issues in tutorial LJ (fixes Issue tracker for Tutorial 01 #3934)
  • create a tool to simplify editing exercise2 notebooks by temporarily converting solution markdown cells to executable code cells (fixes Simplify code review of tutorials #3930) and apply pep8 formatting 
    # convert solution cells to code cells
./pypresso doc/tutorials/convert.py exercise2 --to-py doc/tutorials/lennard_jones/lennard_jones.ipynb
# edit the notebook
./ipypresso notebook
# convert solution cells back to markdown cells
./pypresso doc/tutorials/convert.py exercise2 --to-md doc/tutorials/lennard_jones/lennard_jones.ipynb
# apply autopep formatting rules
./pypresso doc/tutorials/convert.py exercise2 --pep8  doc/tutorials/lennard_jones/lennard_jones.ipynb
  • implement an autocorrelation function espressomd.analyze.autocorrelation() to calculate the ACF of 1-dimensional and 2-dimensional data

jngrad added 14 commits November 13, 2020 15:38
@jngrad
docs: Remove tutorial 02 part 2
508a4f2
@jngrad
maintainer: Simplify html_runner.py
23f0cbc
@jngrad
maintainer: Make html_runner.py modular
c2ecd5b 
Move parser to the end of the script and wrap the main logic
into __main__, so that the script can be imported as a module.
The subprocess module is then no longer needed in the testsuite.
@jngrad
maintainer: Add exercise2 converter
f025153 
Use the html_runner.py to convert exercise2 cells from Markdown to
Python and back, while preserving metadata. This is helpful when
editing notebooks, to avoid having to manually copy-paste the
solutions to the empty code cells (to be able to run the notebook)
and then clear these cells.
@jngrad
maintainer: Add autopep8 tool for tutorials
f93a5df
@jngrad
testsuite: Fix edge case in non-deterministic test
28dd7a8
@jngrad
python: Add pylint check W0199 (assert-on-tuple)
c28b24f 
The python `assert` keyword does not behave like a function. Adding
round brackets can lead to subtle bugs: `assert(a == b, "message")`
actually evaluates a tuple and prints "SyntaxWarning: assertion is
always true, perhaps remove parentheses?" without halting the flow
of the program. Warnings cannot be caught by a try/except, instead
one has to rely on the warnings module to convert them to exceptions.
@jngrad
tutorials: Standardize plots, reduce verbosity
e140f8e
@jngrad
tutorials: Formatting with autopep8
6d50bc3
@jngrad
python: Implement autocorrelation function
662202a
@jngrad
tutorials: Re-use autocorrelation function
80ae3fc
@jngrad
docs: Document shape-based constraints pitfalls
5f61cc7
@jngrad
tutorials: Rename tutorials
ae80e5f 
Remove the numbered prefix from all tutorials. Rename html_runner.py
to convert.py to better reflect its new design.
@jngrad
tutorials: Tag difficulty level
71e0350
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@jngrad jngrad added this to the Espresso 4.2 milestone Nov 13, 2020
@jngrad jngrad marked this pull request as ready for review November 13, 2020 22:59
@jngrad jngrad requested a review from RudolfWeeber November 13, 2020 23:06
@RudolfWeeber
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I assume, you ran the html build job locally for this. If not, please do before merging.

@jngrad jngrad added the automerge Merge with kodiak label Nov 16, 2020
@kodiakhq kodiakhq bot merged commit 6f3239e into espressomd:python Nov 16, 2020
@jngrad jngrad deleted the tutorials-maintenance-2 branch December 15, 2020 15:39
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@RudolfWeeber RudolfWeeber RudolfWeeber approved these changes

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