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Improve examples #107

Merged
merged 21 commits into from
Feb 2, 2022
Merged

Improve examples #107

merged 21 commits into from
Feb 2, 2022

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t-young31
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@t-young31 t-young31 commented Jan 21, 2022 •
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Improve the set of examples in the examples folder to provide a better introduction to the API for new users.

  • Enable natural ordering in the folder

@t-young31 t-young31 added the documentation Improvements or additions to documentation label Jan 21, 2022
@t-young31 t-young31 added this to the v 1.2.0 milestone Jan 21, 2022
@t-young31 t-young31 self-assigned this Jan 21, 2022
@t-young31 t-young31 marked this pull request as ready for review January 24, 2022 11:49
@t-young31 t-young31 changed the title [WIP] Improve examples Improve examples Jan 24, 2022
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codecov bot commented Jan 24, 2022 •
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Codecov Report

Merging #107 (c0bcbc6) into v1.2.0 (424bb2a) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           v1.2.0     #107   +/-   ##
=======================================
  Coverage   96.06%   96.07%           
=======================================
  Files          85       85           
  Lines        9311     9329   +18     
=======================================
+ Hits         8945     8963   +18     
  Misses        366      366
Flag Coverage Δ
unittests 96.07% <100.00%> (+<0.01%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
autode/calculation.py 96.67% <ø> (ø)
autode/units.py 100.00% <ø> (ø)
autode/wrappers/QChem.py 97.63% <ø> (ø)
autode/neb/original.py 97.14% <100.00%> (ø)
autode/path/path.py 98.79% <100.00%> (ø)
autode/pes/pes_nd.py 99.30% <100.00%> (+<0.01%) ⬆️
autode/pes/relaxed.py 95.58% <100.00%> (+0.27%) ⬆️
autode/pes/unrelaxed.py 86.79% <100.00%> (+1.07%) ⬆️
autode/plotting.py 94.16% <100.00%> (ø)
autode/species/molecule.py 98.95% <100.00%> (+0.01%) ⬆️
... and 3 more

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josephsilcock
josephsilcock approved these changes Jan 26, 2022
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This file structure of examples seems a but messy to me

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@t-young31
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This file structure of examples seems a but messy to me

I agree – any suggestions? Separate folder for each?

@josephsilcock
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I think separate out the new files from the old examples, then have an xyzs file in that
so...

examples
|
|___addition_elimination.py etc
|
|__tutorials
    |
    |
    |___a_atoms.py etc
    |
    |___xyzs
         |
         |_serine.xyz
         |__DieldAlder
             |
             |_product.xyz

or maybe tutorials should be separate from examples? But something like that is neater imo

tristan-j-wood
tristan-j-wood reviewed Jan 31, 2022
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Nice examples :)

autode/species/species.py Outdated Show resolved Hide resolved
examples/sn2.py Show resolved Hide resolved
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examples/tutorials/a_atoms.py Outdated Show resolved Hide resolved
examples/tutorials/e_molecules.py Outdated Show resolved Hide resolved
examples/tutorials/a_atoms.py Outdated Show resolved Hide resolved
examples/tutorials/e_molecules.py Show resolved Hide resolved
examples/tutorials/l_2d_pes.py Outdated Show resolved Hide resolved
examples/tutorials/o_transition_states.py Show resolved Hide resolved
examples/tutorials/p_reaction_profile1.py Outdated Show resolved Hide resolved
t-young31
t-young31 commented Feb 1, 2022
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examples/tutorials/j_NEB.py Outdated Show resolved Hide resolved
@t-young31 t-young31 merged commit e834c23 into duartegroup:v1.2.0 Feb 2, 2022
@t-young31 t-young31 deleted the improve_examples branch February 2, 2022 20:53
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