Develop ~~> Master #584

garrettwrong · 2022-02-22T14:22:55Z

Draft Release Notes:

ASPIRE v0.9.0 is a minor release, adding many scientific features and software improvements.

This release provides the following new features:

* Adds simulated and experimental abinitio pipeline gallery experiments
* Adds `ImageSource` subclasses supporting whole-micrograph/particle-coordinate sources
* Refactor and add `Cn` symmetry to Gaussian blob volume generation
* `extract-particles` preprocessing
* Adds Reddy Chetterji based image registration
* Refactors class averaging towards `Averager2D` framework
* `Volume` `.mrc` loading and saving functions
* Adds `Volume` projection gallery tutorial


Bug fixes:

* `FB3D` and `FFB3D` fixes (norm legendre factorial and quadrature points)
* `cov2d` shrinker formula
* Redundant Whitening for Simulation sources
* PolarBasis2D default initialization
* Improve handling empty result sets in APPLE
* Default `cov2d` noise estimation
* `cov2d` denoising matrix normalization
* RelionSource with a single image
* DenoisedImageSource batching
* CTF estimation CLI output_dir


Code Cleanup:

* Standardize use of `Rotation` class
* `PSWF` and `FPSWF` cleanup, minor performance improvements
* Force `finufft` signals to be complex
* Replace CTF estimation log files with STAR
* Refactor and cleanup grid indexing
* Remove APPLE settings from site configuration
* Add APPLE settings as class and command line options
* Removes orientation estimation settings from site configutation
* Replace `importlib_resources` with `importlib.resources`
* Deprecates `ensure`
* Tutorial gallery updates
* Updates code contributors
* Minor logging and documentation improvements


Systems/CI Updates:

* Roll default Python to 3.7
* Deprecates Python 3.6
* Adds Python 3.10
* Update formatting to `Black` 22.1.0
* Roll stable MacOS tests to 10.15 from 10.14

(edited with Chris's suggestion)

…olerance to 0.4%

… Volume instance.

Update authors for this release

Force finufft signals to be complex

…ctor_Reddy_20220207

* Refactor ImageSource <-> RelionSource, and change Simulation accordingly to populate its metadata * typo Co-authored-by: Christopher Langfield <[email protected]>

…or_Reddy Align2D refactor/updates

* take set of mrc sizes (this was the original intention) * add custom number-parsable method * accomodate floats in coordinate files * add tests covering floats in coord files

Deprecate ensure

amitsinger

Looks great!

codecov · 2022-02-22T14:54:07Z

Codecov Report

Merging #584 (0caaaf5) into master (3223d6c) will decrease coverage by 0.67%.
The diff coverage is 82.58%.

@@            Coverage Diff             @@
##           master     #584      +/-   ##
==========================================
- Coverage   87.15%   86.48%   -0.68%     
==========================================
  Files         106      108       +2     
  Lines        7608     8274     +666     
==========================================
+ Hits         6631     7156     +525     
- Misses        977     1118     +141

Impacted Files	Coverage Δ
src/aspire/commands/apple.py	`0.00% <0.00%> (ø)`
src/aspire/commands/preprocess.py	`0.00% <0.00%> (ø)`
src/aspire/nufft/cufinufft.py	`4.68% <0.00%> (+0.07%)`	⬆️
src/aspire/nufft/pynfft.py	`0.00% <0.00%> (ø)`
src/aspire/operators/__init__.py	`100.00% <ø> (ø)`
src/aspire/reconstruction/estimator.py	`92.50% <ø> (-0.10%)`	⬇️
src/aspire/storage/micrograph.py	`82.35% <33.33%> (-0.67%)`	⬇️
src/aspire/abinitio/commonline_base.py	`92.85% <66.66%> (+0.89%)`	⬆️
src/aspire/denoising/denoiser_cov2d.py	`80.00% <66.66%> (-0.77%)`	⬇️
src/aspire/apple/apple.py	`61.53% <70.00%> (-14.22%)`	⬇️
... and 55 more

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chris-langfield · 2022-02-22T15:21:15Z

Addition of CoordinateSource supporting EMAN/Guatomatch/Relion sources
--->
something like
Adds ImageSource subclasses supporting whole-micrograph/particle-coordinate sources?

Everything else looks good!

janden

Looks good. Just one thing:

* Adds`ImageSource` subclasses supporting whole-micrograph/particle-coordinate sources

Missing space after “Adds”.

Merge pull request #584 from ComputationalCryoEM/develop

garrettwrong and others added 30 commits November 5, 2021 08:10

Bump version: 0.8.0 → 0.8.1

993df09

Implement gaussian blob extensions as a functions.

2b08f83

added rotational symmetry to gaussian blob generator.

c7b3bec

Error messages for unsupported symmetries.

3fa2f6d

Added method to rotate volumes. Needs work

ae32957

fixed fft scaling

0c58643

Added 3d gaussian volume generator.

4886aa3

suppress possible bug with fft zero frequency.

946f829

set default for Nyquist frequencies

d45cba6

fixed syntax

bf48679

built unit test for Volume class rotate method.

cc6ad7e

unit test for symmetric volumes

d613164

Adjusted np.allclose tolerance

2f90800

small refactor

f07c5ef

Changed dtype to single. Used grid_3d to mask test points. Adjusted t…

8652eac

…olerance to 0.4%

formatting

208b39b

unit test for symmetryParser error message.

5fafb64

test parseSymmetry directly. Changed test name.

bb8b93b

added test for unsupported C-type symmetry error message.

3f6e975

create initial volume save function. Still need to test.

71bbb3c

Added logger message for dtype. Added Volume.load to load mrc file as…

7d69cef

… Volume instance.

Changed logger type.

220b9e7

Added test for volume save method.

29ab691

Developer packages should include

c3bdf8c

Add new ASPIRE RSE's to contributors list

ecc922d

Add persistant Zenodo DOI and badge

796a8c9

update Joakim affiliation to KTH...

fece27a

added Docstring params

07201e2

added permissive param and dtype logger message

4c326cb

Changed params to tuples to reduce method arguments.

f8bb30a

garrettwrong and others added 19 commits February 16, 2022 10:33

Merge pull request #571 from ComputationalCryoEM/refresh_authors

d5d7747

Update authors for this release

Force finufft signals to be complex

3dcfaeb

Merge pull request #575 from ComputationalCryoEM/nufft_hotfix

5e2d49a

Force finufft signals to be complex

Merge remote-tracking branch 'origin/develop' into cls_avg_align_refa…

6aa0a3e

…ctor_Reddy_20220207

Enable RelionSource to be created with no metadata (#522)

36cc4ec

* Refactor ImageSource <-> RelionSource, and change Simulation accordingly to populate its metadata * typo Co-authored-by: Christopher Langfield <[email protected]>

Remove unused batch_size

53b826e

Docstring and alignment/composite_basis.rotate checks

afd498c

More docstring and note changes

f3f4ec3

source ~~> src

0a917ec

fix __cache of fft in RC methods

2b144d6

Update class2d docstring and add comment about log polar

638776a

update simulated pipeline noise var after whitening change merged in

d51b0ec

Merge pull request #538 from ComputationalCryoEM/cls_avg_align_refact…

11c3dca

…or_Reddy Align2D refactor/updates

convert all multiline ensure to single lines

04c56a4

regex it

5e24858

let the tools do the nasty cleanup

c641207

cleanup straggler ensure and assert formats

0679e86

CoordinateSource patches (#582)

b401824

* take set of mrc sizes (this was the original intention) * add custom number-parsable method * accomodate floats in coordinate files * add tests covering floats in coord files

Merge pull request #583 from ComputationalCryoEM/deprecate_ensure

8ada1e9

Deprecate ensure

garrettwrong requested a review from amitsinger February 22, 2022 14:22

garrettwrong self-assigned this Feb 22, 2022

amitsinger approved these changes Feb 22, 2022

View reviewed changes

Merge branch 'master' into develop

0caaaf5

garrettwrong marked this pull request as ready for review February 22, 2022 14:34

garrettwrong requested a review from janden as a code owner February 22, 2022 14:34

janden approved these changes Feb 23, 2022

View reviewed changes

garrettwrong merged commit 6cb389e into master Feb 23, 2022

garrettwrong added a commit that referenced this pull request Feb 23, 2022

Merge pull request #586 from ComputationalCryoEM/master

b19503c

Merge pull request #584 from ComputationalCryoEM/develop

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