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Feat alchemlyb2 #424

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wants to merge 124 commits into from
Closed

Feat alchemlyb2 #424

wants to merge 124 commits into from

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xiki-tempula
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Is this pull request to fix a bug, or to introduce new functionality?

Making BSS compatible with alchemlyb2 as the new MBAR is the AutoMBAR

@lohedges
Blacken.
d29c449
@lohedges
Use interchange to convert OpenFF topology and write to AMBER format.
cd883cb
@lohedges
Use .atoms() for search to avoid segmentation fault.
7fb15d8
@lohedges
Make sure to use absolute paths for working directories.
0e4534c
@lohedges
Update AnteChamber compatibility.
9188c69
@lohedges
Add create_workdir function to avoid code duplication.
5da5bf0
@lohedges
Use absolute path.
566bfbd
@lohedges
Make sure that filebase can include a new directory.
725bd3e
@lohedges
Create unified WorkDir class so that TemporaryDirectory isn't exposed.
f3cf22d
@lohedges
Merge pull request #2 from OpenBioSim/feature_workdir
ac7cee6 
Add create_workdir function to avoid code duplication.
@lohedges
Add isSame method to compare systems given a set of excluded properties.
996f559
@lohedges
Update file caching to use new isSame functionality.
351c32d
@lohedges
Use sets to make cache resilient to duplicate properties and ordering.
276f68b
@lohedges
Refactor file cache into own sub-module.
efddd91
@lohedges
Add test for isSame functionality.
5cbb4ac
@lohedges
Implement fixed-size file cache.
e105bb8
@lohedges
Add missing file cache module in sandpit.
c3038b0
@lohedges
Forgot that popitem returns a key/value pair.
aa8a126
@lohedges
Pass through developer options using **kwargs.
803c08e
@lohedges
Add option to skip water molecules during isSame check.
7ed6d87
@lohedges
Sychronise sandpit.
391dbc2
@lohedges
Fix docstrings.
bc2936e
@lohedges
Expose skip_water option to check_cache function.
19f0270
@lohedges
Add skip_water boolean flag to file cache key.
58ef747
@lohedges
Handle case where 'other' has additional properties.
3bab031
@lohedges
Fix f-string in exception message.
fdeb9d3
@lohedges
Handle exceptions other than SameFileError.
e081fd0
@lohedges
Pass filebase to saveMolecules.
b710eb5
@lohedges
Merge pull request #3 from OpenBioSim/feature_is_same
21c6b73 
Add isSame method to allow file caching based on system/molecule properties [ci skip]
@lohedges
Fix inconsistency with Antechamber version error message. [closes #4]
768a338
lohedges and others added 19 commits March 13, 2023 12:09
@lohedges
Update comment describing unit test. [ci skip]
724ea2e
@lohedges
Set default-valued property to avoid issues with zero values.
ce7e415 
[closes #23]
@lohedges
Pin energy writing to reportInterval for all but Minimisation protocols.
42c18db 
[ref #26]
@lohedges
Make sure stdout dictionary is updated before returning.
f752418 
[ref #26]
@lohedges
No need to swap water topology for RST7 format. [ref #22]
d47bce5
@lohedges
Swap water topology prior to initialising lambda windows. [ref #22]
e879b77
@lohedges
Merge pull request #21 from OpenBioSim/fix_missing_velocities
7403d22 
Remove velocities when not all molecules have the property. [ci skip]
@lohedges
Merge pull request #24 from OpenBioSim/fix_zero_properties
4b6acea 
Set default-valued property to avoid issues with zero values
@lohedges
Remove watchdog to avoid non-deterministic parsing of AMBER output.
de47a6e 
[closes #26]
@lohedges
Remove watchdog from conda requirements.
457e70d
@lohedges
Avoid duplicate records for minimisation protocol.
ef978ea
@lohedges
Fix UnboundLocalError issue.
925aaf7
@lohedges
Still need to parse stdout if duplicate NSTEP entry is found.
47e4c28
@lohedges
Merge pull request #27 from OpenBioSim/fix_remove_watchog
5dc845f 
Remove watchdog to avoid non-deterministic parsing of AMBER output.
@lohedges
Merge branch 'devel' into feature_disulphide
63a0c94
@lohedges
Merge branch 'devel' into feature_lomap_kwargs
bca504a
@lohedges
Merge pull request #29 from OpenBioSim/feature_lomap_kwargs
18f6ac1 
Add ability to pass extra keyword arguments to LOMAP [ci skip]
@lohedges
Merge pull request #28 from OpenBioSim/feature_disulphide
aa94be5 
Improve disulphide handling
@xiki-tempula
update
6c7a673
@xiki-tempula
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Sorry, I guess this is the wrong upstream. For some reason, I cannot make a PR to the new repo.

@lohedges
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Thanks. Did you make any progress with your GitHub ticket? If not, it might be easiest to delete your fork and create a new one, re-pushing your local feature branches to the new remote.

@lohedges
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I'll close this and add your edit to my feature branch on the OpenBioSim repo.

@lohedges lohedges closed this Mar 27, 2023
@xiki-tempula xiki-tempula deleted the feat_alchemlyb2 branch April 9, 2023 10:00
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@xiki-tempula @lohedges