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Merged
dwhswenson merged 75 commits into from
Sep 26, 2020
Merged

Release 1.3 #930

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c633dd7
start adding progress indicators to TIS analysis
dwhswenson Jan 29, 2020
2525525
Add example notebook with progress bars
dwhswenson Jan 30, 2020
7c7de45
Fix pandas Deprepaction and Future Warnings
sroet Feb 1, 2020
ebc4799
Bump master version to 1.3.0.dev0
dwhswenson Feb 3, 2020
f494209
Merge pull request #899 from dwhswenson/bump-1.3.0.dev0
dwhswenson Feb 4, 2020
f38d356
Fix missing newline in the VisitAllStatesEnsemble
dwhswenson Feb 6, 2020
1a42628
undo some style
sroet Feb 7, 2020
1b25cdc
propper spacing
sroet Feb 7, 2020
393beaf
Merge pull request #898 from sroet/fix_pd_depr
dwhswenson Feb 7, 2020
c7f97b9
Merge remote-tracking branch 'upstream/master' into progress_tis_anal…
dwhswenson Feb 7, 2020
27dd3cb
tests should expect the newline
dwhswenson Feb 7, 2020
82460c5
This should have fixed the horrible merge
dwhswenson Feb 7, 2020
412afb8
Merge pull request #900 from dwhswenson/typo_visit_all_ensemble
dwhswenson Feb 7, 2020
c82918b
if ask for tqdm but don't have it, don't get it
dwhswenson Feb 8, 2020
909f77f
tests for progress setters
dwhswenson Feb 8, 2020
79ca42f
Merge pull request #895 from dwhswenson/progress_tis_analysis
dwhswenson Feb 9, 2020
fc1795f
add GMX stuff to docs
dwhswenson Feb 15, 2020
b16205a
Use SimpleProgress in path hist; move summary
dwhswenson Feb 18, 2020
fe10660
block progress indicator output in tests
dwhswenson Feb 18, 2020
8d3768c
fix sphinx issues
dwhswenson Feb 19, 2020
95ae6f2
Merge pull request #902 from dwhswenson/path_hist_progress
dwhswenson Feb 20, 2020
e0f55aa
Merge pull request #901 from dwhswenson/gmx_docs
dwhswenson Feb 21, 2020
4fd5d35
Storage.__init__ docs to class level
dwhswenson Feb 21, 2020
f141e9a
fixed caching_mode='unlimited'
hejung Jun 14, 2018
3caac79
fixed SPA behaviour
hejung Apr 12, 2018
41b1e91
storage.filename is now an absolute path and a read-only property
hejung Feb 23, 2020
7ab3960
Fix up GromacsEngine docs
dwhswenson Feb 23, 2020
991564d
Merge pull request #778 from hejung/fix_caching_mode
dwhswenson Feb 23, 2020
ca3f717
Merge pull request #903 from hejung/storage_abspath
dwhswenson Feb 24, 2020
26997b4
Merge pull request #725 from hejung/fix_SPA
dwhswenson Feb 26, 2020
4815eb9
DirectSimulation should use engine.start/.stop
dwhswenson Mar 4, 2020
b1bc7cc
Add n_frames_since_start=None to ext engine init
dwhswenson Mar 4, 2020
da768f5
stop should be given a trajectory
dwhswenson Mar 4, 2020
647ceb0
Merge pull request #905 from dwhswenson/direct_sim_start_stop
dwhswenson Mar 7, 2020
976df3e
Progress indicator for shooting point analysis
dwhswenson Mar 9, 2020
3dfa58e
minor cleanup
dwhswenson Mar 9, 2020
7a57d14
Fix missing names in ExternalMDSnapshot
dwhswenson Mar 9, 2020
0336f3e
Start improvements to Gromacs Engine
dwhswenson Mar 10, 2020
3e64d75
Merge pull request #906 from dwhswenson/spa_progress
dwhswenson Mar 12, 2020
a535c34
Unformatted gmx cmds are class vars; improve tests
dwhswenson Mar 13, 2020
1c15e90
Add engine_debug.conf
dwhswenson Mar 13, 2020
37a175d
update gmx example notebooks
dwhswenson Mar 13, 2020
73963ef
Merge branch 'sphinx_improvements' into gmx_updates
dwhswenson Mar 13, 2020
085b2da
Merge pull request #909 from dwhswenson/gmx_updates
dwhswenson Mar 15, 2020
799898b
Add tests for external snapshots
dwhswenson Mar 19, 2020
05d72de
remove debugging line
dwhswenson Mar 20, 2020
6e48b62
Merge pull request #908 from dwhswenson/fix_ext_snapshot_missing
dwhswenson Mar 20, 2020
9e5cace
tests, skips, resources, examples, no large files
apdealbao Mar 17, 2020
239da8a
getting box from snapshot
apdealbao Mar 26, 2020
d1a640d
Fix miniconda install
dwhswenson Apr 8, 2020
417b5aa
Merge pull request #912 from dwhswenson/fix_miniconda_install
dwhswenson Apr 8, 2020
1aa6fd3
Merge pull request #910 from apdealbao/ops_with_plumed
dwhswenson May 3, 2020
781e448
make tqdm optional for tests
sroet Jun 3, 2020
642fcde
Merge pull request #916 from sroet/make_tqdm_test_optional
dwhswenson Jun 3, 2020
d5b3be9
set reject_bytes=False for ujson >= 3
sroet Jun 4, 2020
926ffdd
Merge pull request #917 from sroet/support_ujson_ver_3
dwhswenson Jun 4, 2020
9f58b72
use uuid instead of 'is' for selecting ensembles
sroet Jun 9, 2020
049d0d0
support ujson v3
hejung Jun 23, 2020
c6fabe1
Merge pull request #921 from hejung/ujson_v3
dwhswenson Jun 23, 2020
12bc605
Merge pull request #919 from sroet/use_uuid_for_analysis
dwhswenson Jun 30, 2020
965984b
Fix toy_mstis_3 for change in pandas
dwhswenson Sep 15, 2020
f057044
Merge pull request #925 from dwhswenson/fix_nb
dwhswenson Sep 16, 2020
87c47db
Pin ujson<2; nbconvert<6
dwhswenson Sep 16, 2020
71cfa32
Merge pull request #926 from dwhswenson/pins
dwhswenson Sep 16, 2020
6a835c9
Start devtools cleanup
dwhswenson Sep 16, 2020
063d571
More devtools cleanup
dwhswenson Sep 16, 2020
8f01c94
more devtools cleanup
dwhswenson Sep 16, 2020
4b45c0a
and more cleanup
dwhswenson Sep 16, 2020
0a57e91
fix the obvious problem 🙄
dwhswenson Sep 16, 2020
bffabb2
helps if you install the integrations...
dwhswenson Sep 17, 2020
fdeca88
devtools cleanup
dwhswenson Sep 17, 2020
091a949
more py27-related fixes
dwhswenson Sep 17, 2020
da649e6
testing => test
dwhswenson Sep 17, 2020
7b59a7b
Merge pull request #927 from dwhswenson/devtools_cleanup
dwhswenson Sep 22, 2020
1c63186
Release 1.3.0
dwhswenson Sep 26, 2020
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1 change: 1 addition & 0 deletions devtools/conda-recipe/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ requirements:
- ujson
- psutil
- pyemma
- py-plumed

test:
imports:
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100 changes: 100 additions & 0 deletions examples/misc/plumed_wrapper/in_path.pdb
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REMARK ARG=phi,psi phi=-2.498 psi=1.773
END
REMARK ARG=phi,psi phi=-2.480 psi=1.732
END
REMARK ARG=phi,psi phi=-2.461 psi=1.691
END
REMARK ARG=phi,psi phi=-2.443 psi=1.650
END
REMARK ARG=phi,psi phi=-2.424 psi=1.609
END
REMARK ARG=phi,psi phi=-2.406 psi=1.568
END
REMARK ARG=phi,psi phi=-2.388 psi=1.527
END
REMARK ARG=phi,psi phi=-2.369 psi=1.486
END
REMARK ARG=phi,psi phi=-2.351 psi=1.445
END
REMARK ARG=phi,psi phi=-2.332 psi=1.404
END
REMARK ARG=phi,psi phi=-2.314 psi=1.363
END
REMARK ARG=phi,psi phi=-2.296 psi=1.322
END
REMARK ARG=phi,psi phi=-2.277 psi=1.281
END
REMARK ARG=phi,psi phi=-2.259 psi=1.240
END
REMARK ARG=phi,psi phi=-2.240 psi=1.199
END
REMARK ARG=phi,psi phi=-2.222 psi=1.158
END
REMARK ARG=phi,psi phi=-2.203 psi=1.117
END
REMARK ARG=phi,psi phi=-2.185 psi=1.076
END
REMARK ARG=phi,psi phi=-2.167 psi=1.035
END
REMARK ARG=phi,psi phi=-2.148 psi=0.994
END
REMARK ARG=phi,psi phi=-2.130 psi=0.953
END
REMARK ARG=phi,psi phi=-2.111 psi=0.912
END
REMARK ARG=phi,psi phi=-2.093 psi=0.871
END
REMARK ARG=phi,psi phi=-2.075 psi=0.830
END
REMARK ARG=phi,psi phi=-2.056 psi=0.789
END
REMARK ARG=phi,psi phi=-2.038 psi=0.749
END
REMARK ARG=phi,psi phi=-2.019 psi=0.708
END
REMARK ARG=phi,psi phi=-2.001 psi=0.667
END
REMARK ARG=phi,psi phi=-1.983 psi=0.626
END
REMARK ARG=phi,psi phi=-1.964 psi=0.585
END
REMARK ARG=phi,psi phi=-1.946 psi=0.544
END
REMARK ARG=phi,psi phi=-1.927 psi=0.503
END
REMARK ARG=phi,psi phi=-1.909 psi=0.462
END
REMARK ARG=phi,psi phi=-1.891 psi=0.421
END
REMARK ARG=phi,psi phi=-1.872 psi=0.380
END
REMARK ARG=phi,psi phi=-1.854 psi=0.339
END
REMARK ARG=phi,psi phi=-1.835 psi=0.298
END
REMARK ARG=phi,psi phi=-1.817 psi=0.257
END
REMARK ARG=phi,psi phi=-1.798 psi=0.216
END
REMARK ARG=phi,psi phi=-1.780 psi=0.175
END
REMARK ARG=phi,psi phi=-1.762 psi=0.134
END
REMARK ARG=phi,psi phi=-1.743 psi=0.093
END
REMARK ARG=phi,psi phi=-1.725 psi=0.052
END
REMARK ARG=phi,psi phi=-1.706 psi=0.011
END
REMARK ARG=phi,psi phi=-1.688 psi=-0.030
END
REMARK ARG=phi,psi phi=-1.670 psi=-0.071
END
REMARK ARG=phi,psi phi=-1.651 psi=-0.112
END
REMARK ARG=phi,psi phi=-1.633 psi=-0.153
END
REMARK ARG=phi,psi phi=-1.614 psi=-0.194
END
REMARK ARG=phi,psi phi=-1.596 psi=-0.235
END
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