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Merged
merged 132 commits into from
Jun 3, 2021
Merged

Develop ~~> Master #425

merged 132 commits into from
Jun 3, 2021

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@garrettwrong
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@garrettwrong garrettwrong commented Jun 3, 2021

Moving release.

Because we've added the CTF Estimation backend and CLI we discussed categorizing this as a minor release.

Version bumped to 0.7.0.

I'll begin compiling the release notes based on the PRs.

garrettwrong and others added 30 commits March 10, 2021 08:14
@garrettwrong
Move some developer deps to "dev" package extension
bfe7d9c
@garrettwrong
add pytest-cov to tox envs
434e4a0
@garrettwrong
fixup docs tox env
350e79f
@garrettwrong
add some more tests for Rotation class
a28d333 
this is because it crashed when it tried to print itself
@garrettwrong
testRotMatrices should have a dtype based tolerance
80b9dfd
@garrettwrong
Add coveralls job to GitHub Actions by invoking via tox.
61ec674
@garrettwrong
Merge pull request #400 from ComputationalCryoEM/patch_363
22dfbed 
Move some developer deps to "dev" package extension
@garrettwrong
Merge pull request #402 from ComputationalCryoEM/issue_396
904846c 
add some more tests for Rotation class
@garrettwrong
lets try following the codecov docs and see where it goes
e3c8c66
@garrettwrong
Add codecov YAML file for PR integration.
1b33d37
@garrettwrong
Ignore tests directory for coverage.
5687b6b
@garrettwrong
codecov can be a hidden file
f215bcf
@garrettwrong
Update badge to codecov
59ed5d3
@garrettwrong
Merge pull request #404 from ComputationalCryoEM/issue_243
8b920f4 
Add parallel coverage job to GitHub Actions.
@garrettwrong
Fixes corner case where filter eval points outside interp grid.
e33be81 
Odd resolution images could cause omegas outside grid (arithmetic noise 1 vs 0.9999999).  Allow extrapolation in this case instead of zero fill which will crash in later (PowerFilter) computations.

Also implements short circuit optimization for case where transfer function grid is expected to be identical to interpolation grid.  No need to interpolate there.
@garrettwrong
Add unit test and make dimensions consistent
07fea15
@garrettwrong
fix bug in Pandas code supporting startfile IO
b165a88
@garrettwrong
remove short circuit from ArrayFilter eval
92df96a
@garrettwrong
Snake through the evaluate_grid optimization
75f388c
@garrettwrong
Merge pull request #410 from ComputationalCryoEM/patch_pandas
84e5254 
fix bug in Pandas code supporting startfile IO
@garrettwrong
Merge pull request #409 from ComputationalCryoEM/fix_interp_whitening
015992e 
Fixes corner case where filter eval points outside interp grid.
@ayeltg @garrettwrong
Create __init__.py
54640ac
@ayeltg @garrettwrong
Create aspire_ctf.py
9726277
@ayeltg @garrettwrong
Create estimate_ctf.py
c7fa9de
@ayeltg @garrettwrong
remove call for verification
430022c
@ayeltg @garrettwrong
do not save .mat files
738d595
@ayeltg @garrettwrong
update the help
86b306b
@ayeltg @garrettwrong
remove wrong comment
6ff48ab
@ayeltg @garrettwrong
remove print commands
40c3ac1
@ayeltg @garrettwrong
Update environment.yml
a352f8e
garrettwrong and others added 19 commits May 17, 2021 13:37
@garrettwrong
lint style
09a8017
@garrettwrong
replace thon_rings~>amplitude_spectrum
a105c48
@garrettwrong
replace thon_rings~>amplitude_spectrum
67e07fc
@garrettwrong
cleanup 2d background subtraction code a little
868b034
@garrettwrong
Merge branch 'ctf_rebased' of github.com:ComputationalCryoEM/ASPIRE-P…
329618b 
…ython into ctf_rebased
@garrettwrong
remove -1 on dpss and add more color to comment
d73808b
@garrettwrong
slice convex_condition
2640c9f
@garrettwrong
slice convex_condition syntax
04b91a4
@garrettwrong
Merge pull request #380 from ComputationalCryoEM/ctf_rebased
95dff05 
Ctf rebased
@garrettwrong
fix None vs "None" and 0 vs 1
94a8a24 
No longer crashed but estimated result for clean case seems like it is broken
@janden @garrettwrong
Fix shrink_covar behavior when noise_var = 0
029f174
@garrettwrong
get_cwf_coeff identity for noise_var=0
32f99ec 
adjust batched tolerance to relate to dtype
@garrettwrong
get_cwf_coeff needs to invert CTF application in noise_var=0 case.
c4b0cea
@garrettwrong
add test for noise_var=0 case of get_cwf_coeffs
59d27bc
@garrettwrong
add tests for branches in shrinker and noise_var=0
38eb575
@garrettwrong
check cov2d error RuntimeError message is specifically for argument.
1eea1df
@garrettwrong
be more explicit about the shrinker input testing
cbb27f6
@garrettwrong
Merge pull request #421 from ComputationalCryoEM/fix_covar0
0fd9e35 
Fixup covar2d shrinker and get_cwf_coeffs for  noise_var=0
@garrettwrong
Bump version: 0.6.3 → 0.7.0
9314944
@garrettwrong garrettwrong requested a review from janden as a code owner June 3, 2021 11:26
@garrettwrong garrettwrong self-assigned this Jun 3, 2021
@garrettwrong garrettwrong added CI Continuous Integration documentation Improvements or additions to documentation labels Jun 3, 2021
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codecov bot commented Jun 3, 2021 •
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@@            Coverage Diff            @@
##             master     #425   +/-   ##
=========================================
  Coverage          ?   87.60%           
=========================================
  Files             ?       95           
  Lines             ?     6557           
  Branches          ?        0           
=========================================
  Hits              ?     5744           
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  Partials          ?        0

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@garrettwrong
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garrettwrong commented Jun 3, 2021

Draft release notes:

This version adds a core backend component for CTF Estimation along with mating CLI entry point which wraps MRC file IO.

Otherwise this is mostly fixes for issues found during development:

* Bugfix covar2d shrinker and get_cwf_coeffs for clean images (noise_var=0)
* Bugfix Simulation n=1 crashes
* Move some developer deps to "dev" package extension
* Demo Notebook corrections and refresh
* Bugfix in Pandas code supporting Starfile IO
* Bugfix filter eval points outside interp grid
* Add parallel test code coverage job to GitHub Actions (Codecov)
* Add tests for Rotation class

@garrettwrong garrettwrong requested a review from amitsinger June 3, 2021 12:04
@janden
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janden commented Jun 3, 2021

Release notes look good to me.

amitsinger
amitsinger approved these changes Jun 3, 2021
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Looks good to me.

@garrettwrong garrettwrong merged commit 28ebc69 into master Jun 3, 2021
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@janden janden janden approved these changes

@amitsinger amitsinger amitsinger approved these changes

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@garrettwrong @janden @amitsinger @ayeltg