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2f5f033
new branch, initial commit with working rough draft of writer
Mar 17, 2021
a945c15
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
Mar 24, 2021
c064581
writer with all functions
Mar 24, 2021
df690a3
changed create_dataset to require_dataset
Apr 1, 2021
9002dc7
final modifications for now, TODO: tests
May 13, 2021
edfa4c0
updated cobrotoxin.h5md to pass tests
May 13, 2021
e308441
Merge branch 'develop' into issue2866-h5mdwriter
May 14, 2021
f830fc5
Merge branch 'develop' into issue2866-h5mdwriter
May 16, 2021
98b8d34
comitting for Agave testing
May 19, 2021
40d7027
small mistake line 1090
May 19, 2021
d201c6d
cleaned things up
Jun 5, 2021
a75c646
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
Jun 5, 2021
c7f744b
changed how step and time dsets are written
Jun 5, 2021
822b076
typo
Jun 6, 2021
d54e5f5
added unit new unit functionality and pass all tests
Jun 6, 2021
5352e1a
small updates to writer and adding TESTS
Jun 8, 2021
5e7a3c1
comment out valueerror and skipping test to see codecov
Jun 8, 2021
e01a00e
just commiting to kickstart tests
Jun 8, 2021
31702a5
just commiting to kickstart tests
Jun 8, 2021
e5c52e7
fixed bugs and increase codecov
Jun 9, 2021
6076998
small changes + pytest.skip to pass tests
Jun 10, 2021
721d53e
reverting convert units change
Jun 10, 2021
9296b83
Addressed most of the reviews and added ability to write contiguous d…
edisj Jun 12, 2021
3171437
pep changes and skipping test for MIN dependency
edisj Jun 12, 2021
05ae4fc
fixed n_frames+chunk bug, added tests for codecov, made write_next_ti…
edisj Jun 12, 2021
3098293
added RuntimeError to catch different version of h5py... too many err…
edisj Jun 12, 2021
26b73f7
use write_direct() instead
edisj Jun 12, 2021
f7fd452
forgot to uncomment a test
edisj Jun 12, 2021
93a9ed7
updated documentation
edisj Jun 18, 2021
27e3151
merge develop
edisj Jul 30, 2021
4e2716f
addressing comments and updating references
edisj Jul 30, 2021
a03e48f
updated base.py docs with ts.data and updated scipy paper reference
edisj Jul 30, 2021
a26e7b4
removing Timestep autoclass
edisj Jul 31, 2021
b2804b7
adressing final comments plus duecredit
edisj Aug 6, 2021
93228cc
fixed duecredit function and added test for convert_units=False return
edisj Aug 7, 2021
18fdbd6
fix merge
edisj Aug 12, 2021
1885b58
writer api test checks if has h5py
edisj Aug 12, 2021
fbc56ad
remove import
edisj Aug 12, 2021
8348fe7
fix convert_units with h5md
edisj Aug 12, 2021
ac822e9
changed skip comments
edisj Aug 12, 2021
d389b13
addressing review comments
edisj Aug 20, 2021
6cba0f0
adding test to hopefully cover setters
edisj Aug 20, 2021
1ed2917
removed setter
edisj Aug 20, 2021
e00fc61
added match to all error tests and removed chunks from default settings
edisj Aug 20, 2021
e0d621a
double ticks and pep8 fixes
edisj Aug 21, 2021
5a66dc4
added H5MD duecredit test
edisj Aug 21, 2021
4f2f55c
purging excessive double back ticks
edisj Aug 21, 2021
387d562
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
edisj Aug 21, 2021
2f4038c
Update package/MDAnalysis/coordinates/H5MD.py
IAlibay Aug 21, 2021
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9 changes: 5 additions & 4 deletions package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,7 @@ Enhancements
checking if it can be used in parallel analysis. (Issue #2996, PR #2950)
* Improved performance of H5MDReader by using h5py.Dataset.read_direct()
to transfer data from HDF5 file into timestep. (PR #3293)
* Added `H5MDWriter` to coordinate writers (Issue #2866, PR #3189)

Changes
* NCDFWriter now allows for the writing of `scale_factor` attributes for
Expand Down Expand Up @@ -314,10 +315,10 @@ Deprecations
* Deprecated the `bfactors` topology attribute in favour of `tempfactors`.
In 2.0 `bfactors` is simply an alias of `tempfactors`; in 3.0 `bfactors`
will be removed. (Issue #1901, PR #3345)
* The attributes `p_components`, `variance`, `cumulated_variance` and
`mean_atoms` in `analysis.pca.PCA` are now deprecated in favour of
`results.p_components`, `results.variance`, `results.cumulated_variance`
and `results.mean_atoms`. They will be removed in 3.0.0
* The attributes `p_components`, `variance`, `cumulated_variance` and
`mean_atoms` in `analysis.pca.PCA` are now deprecated in favour of
`results.p_components`, `results.variance`, `results.cumulated_variance`
and `results.mean_atoms`. They will be removed in 3.0.0
(Issues #3275 #3285)
* The `bins`, `edges`, `count`, `rdf` attributes for `analysis.rdf.InterRDF`
and `analysis.rdf.InterRDF_s`, and `cdf` attributes for
Expand Down
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