scippification and therefore kinisi-2.0.0 - #111

Merged

arm61 merged 385 commits into

Aug 15, 2025

This pull request is big! We're only showing the most recent 250 commits

Commits on Jul 9, 2025

Merge pull request #120 from kinisi-dev/samples
arm61
authored
cad4cdf
Merge branch 'com_new' of github.com:kinisi-dev/kinisi into com_new
Harry-Rich
committed
f09bcf1
Fix dep
arm61
committed
9274a48
Continue on error for now
arm61
committed
0bafb33
Merge pull request #125 from kinisi-dev/dep-fix
arm61
authored
f749a96
Ruff Ruff formatting
Harry-Rich
committed
48841ac
Updated indices size checking

Harry-Rich
and
Copilot
authored
a174489
Update parser.py
jd15489
authored
13bfe42
Merge branch 'scipp' into lint-displacements
arm61
authored
94952ce
Merge pull request #128 from jd15489/MDAnalysisParser
arm61
authored
35c1b39
doc string, updated molecule to atom language
Harry-Rich
committed
4d2f169
Merge pull request #126 from kinisi-dev/centre_of_mass
Harry-Rich
authored
cf2edff
Starting on arrhenius
arm61
committed
cf74dd4
Merge pull request #122 from kinisi-dev/lint-displacements
arm61
authored
2aca4e0
Added test for calc_com
Harry-Rich
committed
4ee7b38
Initial implmentation of arrhenius MCMC sampling
arm61
committed
c2241e2
Merge branch 'scipp' into arrhenius
arm61
authored
8878974

Commits on Jul 10, 2025

Update displacement.py
arm61
authored
8510e9f
small improvements to existing scipp notebooks vasp_msd.ipynb and vasp_d.ipynb
BaerCMI
committed
8eaca0a
first drafts of new scipp notebooks for jump_diffusion and comparison with pymatgen
BaerCMI
committed
922a26e
Merge pull request #134 from kinisi-dev/arm61-patch-1
arm61
authored
3f637c6
linted and formatted
Harry-Rich
committed
9382a24
Merge pull request #131 from kinisi-dev/centre_of_mass
Harry-Rich
authored
d15ef64
Merge pull request #124 from kinisi-dev/remove-docs
Harry-Rich
authored
b864846
fixed struc_coords_latt, reduced distance unit pass
Harry-Rich
committed
5a611b9
linted and removed self.distance_unit
Harry-Rich
committed
10fbb68
nested sampling and tests
arm61
committed
fc749f5
small bug in displacement test
arm61
committed
3a84739
Started adding tests
Harry-Rich
committed
1766b90
Add extrapolation
arm61
committed
19fbdfc
ruff
arm61
committed
e4b8f7b
updated doc strings
Harry-Rich
committed
fc89243
Merge pull request #138 from kinisi-dev/parser_fix
osoulas
authored
6e37f20
msd_da -> da, etc
arm61
committed
53f7cae
Require dynesty
arm61
committed
35b41c0
Add ASE parser
jd15489
committed
40a032c
Update ASE.py
jd15489
committed
9c27936
Added tests for diffusion, added unit to _conductivity jump diffusion
Harry-Rich
committed
c85382a
Update ASE.py
jd15489
committed
45e0872
Update ASE.py
jd15489
committed
93bd205
Merge pull request #139 from kinisi-dev/msd_da
Harry-Rich
authored
dd10c83
Merge pull request #137 from jd15489/ASE
arm61
authored
4685a6c

Commits on Jul 11, 2025

Added test for calc_com

Harry-Rich
authored and
arm61
committed
9f3c33f
linted and formatted

Harry-Rich
authored and
arm61
committed
3308949
Remove bad docs
arm61
committed
31ade84
fixed struc_coords_latt, reduced distance unit pass

Harry-Rich
authored and
arm61
committed
fa56081
linted and removed self.distance_unit

Harry-Rich
authored and
arm61
committed
2f57fbb
updated doc strings

Harry-Rich
authored and
arm61
committed
7dd885b
msd_da -> da, etc
arm61
committed
b8e5828
Add ASE parser

jd15489
authored and
arm61
committed
0ef6d03
Update ASE.py

jd15489
authored and
arm61
committed
94b8766
Update ASE.py

jd15489
authored and
arm61
committed
f287ca6
Update ASE.py

jd15489
authored and
arm61
committed
4c96f27
small improvements to existing scipp notebooks vasp_msd.ipynb and vasp_d.ipynb

BaerCMI
authored and
arm61
committed
11ada4f
first drafts of new scipp notebooks for jump_diffusion and comparison with pymatgen

BaerCMI
authored and
arm61
committed
63bbbfe
Added Triclinic unwrapping
jd15489
committed
8a53af2
Update docstrings
jd15489
committed
583ca98
Update pymatgen.py
jd15489
committed
25e424c
Update parser.py
jd15489
committed
9a5333d
Added test for non-orthorhombic cells
jd15489
committed
33958e5
Created is_orthorhombic
jd15489
committed
6f31510
Added comment
jd15489
committed
9533859
Update parser.py
jd15489
committed
34305e7
Add unit testing for orthorhombic
jd15489
committed
41a86f6
Parser no longer takes Progress as keyword
jd15489
committed
a86ea69
remove keyword
jd15489
committed
921faa9
Fixed orthorhombic tests
jd15489
committed
e5e73d0
Update parser.py
jd15489
committed
30bd54a
Update parser.py
jd15489
committed
7d0da24
Fixing small bugs
arm61
committed
fa51423
Arrhenius docs updatedd
arm61
committed
a71380e
Merge branch 'documentation' of github.com:bjmorgan/kinisi into documentation
arm61
committed
1616576
Merge branch 'scipp' into documentation
arm61
authored
0356aa3
Merge branch 'scipp' into test_diffusion
arm61
authored
9900865
Some more docs updates
arm61
committed
f98dad5
Update docs/source/vasp_dj.ipynb
arm61
authored
9e9bbfc
Update docs/source/vasp_dj.ipynb
arm61
authored
5bef575
Merge
arm61
committed
fd1ff3d
Improved coverage, fixed bug, fixed conductivity_dc
Harry-Rich
committed
5df06ae
Merge branch 'test_diffusion' of github.com:kinisi-dev/kinisi into test_diffusion
Harry-Rich
committed
497179b
More docs
arm61
committed
f038727
Merge pull request #140 from kinisi-dev/test_diffusion
arm61
authored
f6e7f21
Update kinisi/arrhenius.py

arm61
and
Harry-Rich
authored
407523e
Update kinisi/arrhenius.py

arm61
and
Harry-Rich
authored
fb02b8d
Merge pull request #133 from kinisi-dev/arrhenius
arm61
authored
3736a2b
Added Parser interconversion with DataGroups

osoulas
authored and
jd15489
committed
b941eef
Added saving/loading Analyzer to/from HDF5

osoulas
authored and
jd15489
committed
da7ae84
Update kinisi/parser.py

authored and
jd15489
committed
b39f126
Update kinisi/parser.py

authored and
jd15489
committed
47c34f3
WIP saving/loading all Analyzer attributes

osoulas
authored and
jd15489
committed
cc969b3
Fixed saving of unsupported classes

osoulas
authored and
jd15489
committed
b9545c5
Simplification

osoulas
authored and
jd15489
committed
b66372c
Added saving of Diffusion objects

osoulas
authored and
jd15489
committed
bc4a752
Removed unused parameter

osoulas
authored and
jd15489
committed
6a1d1a2
Linting

osoulas
authored and
jd15489
committed
dfe0760
Changed default value

osoulas
authored and
jd15489
committed
ab20e89
Started writing tests

osoulas
authored and
jd15489
committed
1952dbb
parity with scipp

osoulas
authored and
jd15489
committed
8079acc
WIP tests

osoulas
authored and
jd15489
committed
af093e6
fixed msd issues, fixed path issue
Harry-Rich
committed
5dfee28
Removed specie and structure from Parser
jd15489
committed
87289fd
linted and formatted
Harry-Rich
committed
eb84df9
Merge pull request #144 from kinisi-dev/test_diffusion
Harry-Rich
authored
0f3dc0a
Update ASEParser for new parser stucture
jd15489
committed
8141408
Docs readyish
arm61
committed
a512d8a
Merge branch 'scipp' into documentation
arm61
authored
b570818
ruff
arm61
committed
5e8aef4
Update pymatgen.py
jd15489
committed
26e413b
Remove old
arm61
committed
810c6bb
Merge pull request #145 from kinisi-dev/remove_old
arm61
authored
a1fb7e8
Added Triclinic unwrapping
jd15489
committed
3325c3f
Update docstrings
jd15489
committed
bad11e0
Update pymatgen.py
jd15489
committed
87f1027
Update parser.py
jd15489
committed
6b30ba6
Added test for non-orthorhombic cells
jd15489
committed
fea893c
Created is_orthorhombic
jd15489
committed
209a0b6
Added comment
jd15489
committed
c23163e
Update parser.py
jd15489
committed
8f9fae7
Add unit testing for orthorhombic
jd15489
committed
c58daea
Parser no longer takes Progress as keyword
jd15489
committed
26639b9
remove keyword
jd15489
committed
5920d77
Fixed orthorhombic tests
jd15489
committed
e605d0b
Update parser.py
jd15489
committed
2f40f1b
Update parser.py
jd15489
committed
32652c7
Update kinisi/tests/test_parser.py

jd15489
and
arm61
authored
c2b5661
Merge branch 'scipp_triclinic' of https://github.com/jd15489/kinisi into scipp_triclinic
jd15489
committed
01331f3
Removed progress when initialising the Parser superclass
osoulas
committed
0bf77f0
Updated testing
osoulas
committed
5f5e1d0
New tests for saving and loading Analysers
osoulas
committed
c9cec46
fixed msd issues, fixed path issue

Harry-Rich
authored and
osoulas
committed
373dffe
linted and formatted

Harry-Rich
authored and
osoulas
committed
46e9a02
Remove old

arm61
authored and
osoulas
committed
757693d
Changed test name
osoulas
committed
51eaf14
Started adding calc_disps tests
jd15489
committed
11d4bbe
fixed struc_coords_latt, reduced distance unit pass

Harry-Rich
authored and
osoulas
committed
7c29c8e
small improvements to existing scipp notebooks vasp_msd.ipynb and vasp_d.ipynb

BaerCMI
authored and
osoulas
committed
ad6fe6c
first drafts of new scipp notebooks for jump_diffusion and comparison with pymatgen

BaerCMI
authored and
osoulas
committed
aa218b4
Fixing small bugs

arm61
authored and
osoulas
committed
a6625c5
Arrhenius docs updatedd

arm61
authored and
osoulas
committed
6587af0
Some more docs updates

arm61
authored and
osoulas
committed
e89f624
Update docs/source/vasp_dj.ipynb

arm61
authored and
osoulas
committed
3103e54
Update docs/source/vasp_dj.ipynb

arm61
authored and
osoulas
committed
24c799f
More docs

arm61
authored and
osoulas
committed
4639928
Docs readyish

arm61
authored and
osoulas
committed
d13d896
ruff

arm61
authored and
osoulas
committed
fc1e296
Added saving/loading Analyzer to/from HDF5
osoulas
committed
9b505ce
Added saving of Diffusion objects
osoulas
committed
ee90aa5
Updated testing
osoulas
committed
4546d74
Tests and example files for saving and loading of Analyzers
osoulas
committed
f6b3acb
removed duplicate
osoulas
committed
ba300ff
Moved example data to variables
osoulas
committed
91197db
Calc_disps staticmethod and add test
jd15489
committed
29e1b54
Fixed test data not loading
osoulas
committed
9615ae7
Fixed analyzer tests not recognising equal parsers
osoulas
committed
171276d
fixed missing argument in tests
osoulas
committed
d22a8e5
Removed broken test and fixed drift indices test
osoulas
committed
e32268d
Removed incorrect argument for initialising Parser
osoulas
committed
eb47a95
Merge branch 'scipp' into save_and_load
osoulas
authored
332d069

Commits on Jul 14, 2025

Update test_parser.py
jd15489
committed
a94dbd0

Commits on Jul 15, 2025

Merge pull request #135 from kinisi-dev/documentation
arm61
authored
99aef64
Merge branch 'scipp' into save_and_load
arm61
authored
38dacef
Merge pull request #109 from kinisi-dev/save_and_load
arm61
authored
8c40c92
Merge branch 'scipp' into scipp_triclinic
arm61
authored
ea8fcf1
Merge pull request #129 from jd15489/scipp_triclinic
arm61
authored
310c3f2
Fixing post sprint bugs
arm61
committed
e075645
Fixed tests for MDAnalysis parser
jd15489
committed
273b6a9
Remove underscore from the saving/loading methods
arm61
committed
9abf150
Get ASE parser nearly working, still problems with COM
arm61
committed
5cc237b
All linted and formated
arm61
committed
c49dd6a
fix tests
arm61
committed
4f50278
Bringing back more tests
arm61
committed
0551a21
More tests
arm61
committed
bf350d8

Commits on Jul 16, 2025

More tests
arm61
committed
4329f0b
Add save and load with Samples
arm61
committed
a8a603e

Commits on Jul 17, 2025

DJ notebook ready
arm61
committed
4e22394
MDA working
arm61
committed
6bea251
Ruffing
arm61
committed
475f953
Bring back CI ruff
arm61
committed
ecfc4f7
Dont lint docs
arm61
committed
d17d753
Restore
arm61
committed
f576397
Add exception
arm61
committed
7c8e914
More exceptions
arm61
committed
8bc6c1b
Reformat
arm61
committed
366039d

Commits on Jul 23, 2025

Fixed get_molecules indices and updated doc
Harry-Rich
committed
96038d1

Commits on Jul 25, 2025

Notebook fixed
arm61
committed
265191e
Ruff
arm61
committed
b251b49
Updated text
Harry-Rich
committed
2e50e07
Merge branch 'post-sprint' of github.com:kinisi-dev/kinisi into post-sprint
Harry-Rich
committed
b10654d
Change all the names
arm61
committed
27ad532
Tests fixed
arm61
committed
d5b16d8
Ruff
arm61
committed
788ea86

Commits on Jul 28, 2025

Turn off codeclimate
arm61
committed
83687df
Move to docstring
arm61
committed
da21314
Fix non orthorhombic
arm61
committed
39823a8

Commits on Aug 14, 2025

Added get_specie_and_drift_indices
jd15489
committed
a717133
Merge
arm61
committed
90e9aa1
Ruff
arm61
committed
22ba293
Update comment in parser.py
jd15489
committed
a6505d6
Merge pull request #148 from kinisi-dev/post-sprint
arm61
authored
3fe4ac6
Fixed bugs
arm61
committed
9ac1320
Add coverage
arm61
committed
e31b30b
Merge pull request #152 from kinisi-dev/fix
arm61
authored
22432a2
add cov kinisi
arm61
committed
739f88f
equals
arm61
committed
9f73cdd
Permissions
arm61
committed
3f007df
Merge pull request #154 from kinisi-dev/coverage
arm61
authored
8bce570
Quick sort of the existing documentation
arm61
committed
13e2fe7
Badge
arm61
committed
10ee3d2
Mention bounds
arm61
committed
0ab1220
Add duecredit
arm61
committed
12fada8
Remove old tests
arm61
committed
f66e76c
Remove old tests
arm61
committed
0f01b53
ruff
arm61
committed
36b2de4
Lots of docs formatting
arm61
committed
7bc8665
Remove rogue .py files from docs
arm61
committed
c1eaf5f
Mention duecredit
arm61
committed
5fb297c
Remove todo list
arm61
committed
d8e86a1
Update papers.md

arm61
authored and
jd15489
committed
5a32af3
Update papers.md

arm61
authored and
jd15489
committed
8f7105f
Merge branch 'jd_post_sprint' of https://github.com/jd15489/kinisi into jd_post_sprint
jd15489
committed
a5f52e5
Removed generate_indices
jd15489
committed
e0971cb
updated FAQs
jd15489
committed
a40db6a
Add TOR reference
arm61
committed
e49c679

Commits on Aug 15, 2025

Clarification
arm61
committed
8d6e4bb
long to wrong
arm61
committed
afbcbd6
Update papers.md

arm61
authored and
jd15489
committed
39fe2cd
Update papers.md

arm61
authored and
jd15489
committed
6f18966
Update papers.md

arm61
authored and
jd15489
committed
e8139b8
Update papers.md

arm61
authored and
jd15489
committed
e8e6a9b
Removed generate_indices
jd15489
committed
0e69554
updated FAQs
jd15489
committed
2b4cfc0
Merge branch 'jd_post_sprint' of https://github.com/jd15489/kinisi into jd_post_sprint
jd15489
committed
c63bf98
Update parser.py
jd15489
committed
797daf1
Merge pull request #159 from jd15489/jd_post_sprint
arm61
authored
aad7223
Merge branch 'docs' of github.com:bjmorgan/kinisi into docs
arm61
committed
0b1c860
Restore TOR reference
arm61
committed
c546833
Ruff
arm61
committed
13fcca5
Merge pull request #155 from kinisi-dev/docs
arm61
authored
d69c15b
Remove old deps
arm61
committed
c8e0cdd
Remove old deps
arm61
committed
071c34a
Update docs/source/arrhenius_t.ipynb
arm61
authored
a31b8bb
Update docs/source/arrhenius_t.ipynb
arm61
authored
e0ae644
Update docs/source/ase_COG.ipynb
arm61
authored
7d69930
Update docs/source/ase_COG.ipynb
arm61
authored
e49dba9
Update docs/source/ase_COG.ipynb
arm61
authored
7de743a
Update docs/source/condition_number.ipynb
arm61
authored
ac3e2ea
Update docs/source/condition_number.ipynb
arm61
authored
1b8282f
Update docs/source/condition_number.ipynb
arm61
authored
3007650
Typo
arm61
committed
bf39633
Improvements to arrhenius
arm61
committed
b9203d1