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PyCGTOOL v2.0.0 #52

Merged
merged 280 commits into from
Mar 16, 2022
Merged

PyCGTOOL v2.0.0 #52

merged 280 commits into from
Mar 16, 2022

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jag1g13
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@jag1g13 jag1g13 commented Nov 13, 2021

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js1710 and others added 30 commits October 15, 2018 09:32
@js1710
removed coverage, will add this later
1a28049
@js1710
added documentation for virtual site syntax and other options
1167ec3
@js1710
Fixed formatting
51ebec9
@js1710
typos
6083988
@js1710
fixed bug where all lines after virtual bead definition were set to v…
ca95e70 
…irtual beads. Also added a test to check for this bug
@jag1g13
Fix bug with div 0 in progress bar
9ae76f2
@jag1g13
Merge dev into virtual_sites
2f0f8da
@jag1g13
Remove fixed todo & rearrange imports in bondset
af17a86
@js1710
fixed formatting in multiple places. Also removed outdated TODO state…
6887087 
…ments.
@js1710
Merge pull request #19 from jag1g13/virtual_sites
6dab6ba 
Virtual sites
@js1710
changed dihedral calculation to use atan2. Changed tolerance for one …
f0672a8 
…existing test.
@js1710
fixed bug where the averages and variances angles calculated where no…
2876178 
…t circular. Added some tests to for these new util functions. reduced some tolerances to 0.005 the account for float over/under flow difference between methods
@js1710
removed atan2 dihedral calculation method as previous method worked
350ac49
@js1710
tidied up some lines
d464a6b
@js1710
removed unessary mean calculation
4e42350
@js1710
Merge pull request #20 from jag1g13/dihedrals
b283590 
Dihedrals
@js1710
circular variance function fixed and further tests added to check this
c986209
@js1710
Merge pull request #21 from jag1g13/variance_bug
ada7d2a 
circular variance function fixed and further tests added to check this
@jag1g13
Inject mean / variance dependencies into Boltzmann Inversion
ab91d45
@jag1g13
Add tests for dependency injection into Boltzmann Inversion
2229ccd
@jag1g13
Remove imports which are no longer necessary
b777add
@jag1g13
Remove completed TODO
1b87e2c
@js1710
Merge pull request #22 from jag1g13/refactor-inversions
73601f0 
Refactor Boltzmann Inversion for angles
@js1710
fixed bug where if angles/dihedral were autogenerated then script wou…
98b60f2 
…ld fail
@js1710
beads that are virtual sites are now set to zero
52c47ec
@js1710
now can edit "--advanced" options from the commandline
70b036c
@js1710
raised default contraint threshold
5a5329e
@js1710
removed curses interactive commandline
aa3ba9a
@js1710
print exclusions for each virtual site so that they do not interact w…
32f0c02 
…ith the beads they are contructed from
@js1710
Updated documentation for commandline only version
7907653
jag1g13 and others added 29 commits August 14, 2021 22:02
@jag1g13
build: disallow mdtraj version 1.9.6
d835dff 
A bugfix in this version introduced another bug which prevented reading
GRO files with non-standard residue names
@jag1g13
chore: bump version number
c6798f0
@jag1g13
chore(release): 2.0.0-beta.3
15a22e8
@jag1g13
ci: add CodeQL checks with default template
8a1f6fa
@jag1g13
fix: use correct reference coordinate for virtual bead calc
a0a61f2
@jag1g13
test: add test for using duplicate atoms for weighting
95037df
@jag1g13
Merge remote-tracking branch 'origin/dev' into dev
e973421
@jag1g13
fix(tests): add missing mapping test file
db0be76
@jag1g13
refactor: clean up file backup function
654bfff
@jag1g13
fix: create output directory if it doesn't exist
c4694e8
@jag1g13
fix: backup frame and forcefield output files
626cc3a
@jag1g13
fix: add data files to installable package
a9fdae8 
This allows forcefield directories to be produced using the installed version of PyCGTOOL
@jag1g13
fix: backup forcefield directories instead of overwrite
19b4054
@jag1g13
chore(release): 2.0.0-beta.4
0150172
@jag1g13
build: prevent release body text being overwritten during publish
7c647b2
@jag1g13
refactor: replace float('inf') with math.inf
6402a4a
@jag1g13
refactor: avoid cast to np.ndarray if possible in Boltzmann Inversion
7f792aa
@jag1g13
fix: skip NaNs in bond sample output
ef5a977
@jag1g13
style: reformat util.py with longer line length
222b063
@jag1g13
fix: catch updated exception from MDTraj 1.9.7
b1d1e6d
@jag1g13
build: remove CodeQL job from CI
f394190 
Isn't really doing anything useful here
@jag1g13
Merge remote-tracking branch 'origin/master' into dev
38cc315
@jag1g13
docs: update readme text
d23c2c8 
- Better intro and usage sections
- Conda install

[skip ci]
@jag1g13
feat: add flag to get version number
f3660f7
@jag1g13
build: update dependencies in lockfile
8f6a6ab 
Remove cython as a runtime dependency
@jag1g13
chore(release): 2.0.0-beta.5
dab67d7
@jag1g13
build: update dependencies in lockfile
28ad67f
@jag1g13
feat: add secret flags for output formatting
84eca12
@jag1g13
style: reformat all files with black
fdce365
@jag1g13 jag1g13 merged commit d8b6cd7 into master Mar 16, 2022
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@jag1g13 @js1710