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Reorganisation #169

Merged
merged 58 commits into from
Nov 13, 2023
Merged

Reorganisation #169

merged 58 commits into from
Nov 13, 2023

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andrewtarzia
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Major changes internally and in version control, plus docs. But the user interface should be unchanged.

This PR is huge because:

  • moved code into src/_internal
  • added type hints
  • added new functionality
  • removed and rewrote much of the docs

Also should solve:
#165
#116
#121
#134
#153
#158

@andrewtarzia
Modify setup.
a2f2aa4
@andrewtarzia
Move to src dir.
ce6b16d
@andrewtarzia
Update workflows.
6620a10
@andrewtarzia
Ruff fix.
c2815c3
@andrewtarzia
Major docs change.
0af9a18
@andrewtarzia
Change to init organisation.
c100885
@andrewtarzia
Use general exceptions.
d5c7140
@andrewtarzia
Update docs.
1cf07eb
@andrewtarzia
Move utilities.
ce33673
@andrewtarzia
Update examples.
f781c05
@andrewtarzia
Ruff fix.
b3d4869
@andrewtarzia
Add path check.
2bfa6cd
@andrewtarzia
Fix docs.
6900629
@andrewtarzia
Add xtb install.
669bd8b
@andrewtarzia
Add naming comment.
67e4ec4
@andrewtarzia
Clean some docs.
3f52eeb
@andrewtarzia
Handle path checks better.
a94b778
@andrewtarzia
Add types and examples to network.
52ee942
@andrewtarzia
Rm a base class.
c92fb13
@andrewtarzia
Update references, do some typing.
714189c
@andrewtarzia
Add gulp test example, and hopefully fix gulp conformer rounding error.
30d2227
@andrewtarzia
Remove results base class.
e005c5b
@andrewtarzia
Remove Calculator base class.
04e4c38
@andrewtarzia
Update justfile.
87688da
@andrewtarzia
Update setup.
3d8c8cf
@andrewtarzia
Add some examples and new page.
df85e47
@andrewtarzia
Add three site functional groups.
c01fc29
@andrewtarzia
Add first cage analysis class.
c8b50b2
@andrewtarzia
Add docs and examples.
2131636
@andrewtarzia
Add first ditopic analysis methods, plus infrastructure.
e100279
@andrewtarzia
Some typing.
aa035ee
@andrewtarzia
Some typing.
0321ee6
@andrewtarzia
Some typing.
f5d6f58
@andrewtarzia
Some typing.
d8efeb1
@andrewtarzia
Some typing.
fc7b3d3
@andrewtarzia
Trying to get docs to pass, WIP.
bf80776
@andrewtarzia
WIP: get new classes into molecule_analysis module.
5279542
@andrewtarzia
WIP: get new classes into molecule_analysis module.
344a5fd
@andrewtarzia
Redefine vector_angle.
4149d9c
@andrewtarzia
WIP: write three site analysis.
390c1bd
@andrewtarzia
Add constructed analyser.
716c5d9
@andrewtarzia
Add more three site analysis methods.
8605c64
@andrewtarzia
Add pore analysis.
88e59e1
@andrewtarzia
Add geometry analysis. Move pore analysis.
b4c8ce9
@andrewtarzia
Update structures.
788328f
@andrewtarzia
Update structures.
579338b
@andrewtarzia
Update structures.
c824865
@andrewtarzia
Handle misordering of atom ids.
e497891
@andrewtarzia
Minor.
1b62f49
@andrewtarzia
Add moldoc, update docs.
3e15e87
@andrewtarzia
Minor.
fd5a9aa
@andrewtarzia
Add more sub group analysis.
8162348
@andrewtarzia
Move to _internal.
0a7c74a
@andrewtarzia
Merge pull request #3 from andrewtarzia/reorganise
90c9cf2 
Reorganise stko to match stk setup
@andrewtarzia
Use abc, not typing.
ee16c44
@andrewtarzia
Minor.
3fbf139
@andrewtarzia andrewtarzia marked this pull request as ready for review November 13, 2023 11:01
@andrewtarzia andrewtarzia merged commit 8c1b7aa into JelfsMaterialsGroup:master Nov 13, 2023
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@andrewtarzia