ComputationalCryoEM/ASPIRE-Python issues and pull requests

#965 - Apple bug

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 1 comment
Labels: bug, CI, dependencies

#964 - `test_apple.py` currently failing in CI

Issue - State: closed - Opened by j-c-c over 1 year ago - 14 comments

#963 - Changed Angstrom unit to angstrom

Pull Request - State: closed - Opened by krissowat over 1 year ago - 2 comments
Labels: cleanup

#962 - OSX ARM64 dependency issues

Issue - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: wontfix, extern, support, dependencies

#961 - Cuf13

Pull Request - State: closed - Opened by garrettwrong over 1 year ago
Labels: CI, cleanup, extern, dependencies

#960 - Adopt cufinufft v1.3 final

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: CI, cleanup, extern, dependencies

#959 - Data downloader

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 1 comment
Labels: documentation, enhancement, dependencies

#958 - Sync Develop

Pull Request - State: closed - Opened by garrettwrong over 1 year ago

#957 - Develop

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: documentation, enhancement, cleanup

#956 - Bump version: 0.11.0 → 0.11.1

Pull Request - State: closed - Opened by garrettwrong over 1 year ago

#955 - Python 3.11 and pyproject.toml updates

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 5 comments
Labels: enhancement, CI, cleanup, extern, Python 3.11

#954 - Convert `setup.py` to `pyproject.toml`

Issue - State: closed - Opened by garrettwrong over 1 year ago
Labels: enhancement, CI, cleanup, extern, dependencies

#953 - Add Python 3.11, Drop 3.7

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, CI, extern, dependencies

#952 - BOT Align Algorithm CLI

Issue - State: open - Opened by garrettwrong over 1 year ago
Labels: enhancement, good first issue

#951 - Patch Starfile for change in gemmi 0.6.2 defaults

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: bug, CI, extern

#950 - CI Broken

Issue - State: closed - Opened by garrettwrong over 1 year ago - 5 comments
Labels: bug, CI, extern

#949 - C2 common lines

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 2 comments
Labels: enhancement

#948 - Volume load/save with symmetry

Issue - State: open - Opened by j-c-c over 1 year ago
Labels: enhancement

#947 - Demo updates

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: cleanup

#946 - Docs Search Bar

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 2 comments
Labels: bug, documentation

#945 - intial add of bot align code

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 11 comments
Labels: enhancement

#944 - loosen fc id case tolerance for cufinufft

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: CI

#943 - loosen fc id case tolerance for cufinufft

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, CI, extern

#942 - Skip some problematic FLE gpu tests for now

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: bug, CI

#941 - Add `Volume.project` test with arbitrary rotation

Issue - State: closed - Opened by garrettwrong over 1 year ago - 5 comments
Labels: bug, documentation, enhancement

#940 - FSC `cutoff` `None` plotting option

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, good first issue

#939 - Doc updates

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: documentation, cleanup

#938 - Multi-dimensional Rotations

Issue - State: open - Opened by j-c-c over 1 year ago
Labels: enhancement

#937 - Author updates

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: documentation, cleanup

#936 - Fle ordering

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: cleanup

#935 - Volume project

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 1 comment
Labels: enhancement, cleanup

#934 - Integer metadata fill value

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, cleanup

#933 - Fix metadata fill value for int dtypes

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, cleanup

#932 - Merge pull request #905 from ComputationalCryoEM/develop

Pull Request - State: closed - Opened by garrettwrong over 1 year ago

#931 - Workaround patches

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, invalid, cleanup

#930 - add missing assignment in 10073

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: bug, documentation, cleanup

#928 - Downsample bug for integer offsets

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 3 comments
Labels: bug

#927 - Better Logging for CLSymmetryC*

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 1 comment
Labels: cleanup

#926 - `image.downsample` broken for source with integer `offsets

Issue - State: closed - Opened by j-c-c over 1 year ago - 5 comments
Labels: bug

#925 - Consider `is_iterable` for new `metadata`/`starfile` codes

Issue - State: open - Opened by garrettwrong over 1 year ago

#924 - Check 2D Metadata assignment

Issue - State: open - Opened by garrettwrong over 1 year ago

#923 - `FBBasis3D` NaN values for large resolution

Issue - State: closed - Opened by j-c-c over 1 year ago - 7 comments
Labels: bug

#922 - Remove unneeded threadpool code in `RelionSource`

Issue - State: open - Opened by garrettwrong over 1 year ago - 3 comments

#921 - Potentially simplify _populate_common_metadata

Issue - State: open - Opened by garrettwrong over 1 year ago

#920 - Replace fill values with masked arrays in metadata

Issue - State: open - Opened by garrettwrong over 1 year ago
Labels: enhancement, cleanup

#919 - AsymmetricVolume Patch

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 4 comments
Labels: bug

#918 - Add Contrast Correction to Cov 2D

Issue - State: open - Opened by garrettwrong over 1 year ago - 1 comment

#917 - Volume alignment

Issue - State: open - Opened by janden over 1 year ago - 2 comments
Labels: enhancement

#916 - Basis Reconciliation

Issue - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: enhancement, cleanup

#915 - Expensive Bases Tests

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 2 comments

#914 - `_box_coord_from_center` cleanup

Issue - State: open - Opened by garrettwrong over 1 year ago
Labels: cleanup

#913 - Add seed to flaky class average test

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: bug, CI, cleanup

#912 - Flaky class average unit test

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: CI

#911 - Vb/pdgone

Pull Request - State: closed - Opened by vineetbansal over 1 year ago - 4 comments
Labels: enhancement, cleanup

#910 - test expected to fail - fix

Pull Request - State: closed - Opened by vineetbansal over 1 year ago - 3 comments
Labels: bug, enhancement, cleanup

#909 - test expected to fail

Pull Request - State: closed - Opened by vineetbansal over 1 year ago - 4 comments

#908 - Rm `ImageSource.deepcopy` workaround after FINUFFT Release.

Issue - State: open - Opened by garrettwrong over 1 year ago

#907 - FLEBasis2D rotations incorrect under `match_fb=True`

Issue - State: closed - Opened by garrettwrong over 1 year ago - 4 comments
Labels: bug, cleanup

#906 - correct place to initialize mrc_index_to_particles array

Pull Request - State: closed - Opened by vineetbansal over 1 year ago - 1 comment
Labels: bug, enhancement, cleanup

#905 - `develop` ~~> `master` v0.11.0

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 3 comments

#904 - Migrate sources and preprocessing towards lazy evaluation

Issue - State: open - Opened by garrettwrong over 1 year ago
Labels: enhancement, cleanup

#903 - initial FRC and FSC addition

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 5 comments
Labels: enhancement, question

#902 - Immutable operations

Pull Request - State: closed - Opened by vineetbansal over 1 year ago - 7 comments
Labels: enhancement, cleanup

#901 - Add FRC and FSC

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement

#900 - Remove redundant Image conversion bug in denoised_src (cov2d)

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, cleanup

#899 - denoised source cache bug

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, cleanup

#898 - ManuallyOrientedSource(rotations) and OrientedSource(estimator)

Pull Request - State: closed - Opened by j-c-c over 1 year ago

#897 - Cov2D src should use image accessor

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, good first issue, cleanup

#896 - Default `n_theta` selection

Issue - State: open - Opened by janden over 1 year ago - 1 comment

#895 - LogFilterByCount

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: enhancement, cleanup, Optimization

#894 - Write Class Selection Indices to STAR file

Issue - State: open - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, good first issue, cleanup

#893 - Bump version: 0.10.1 → 0.11.0

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: documentation

#892 - Smarter `overwrite` flag

Issue - State: open - Opened by garrettwrong over 1 year ago - 3 comments
Labels: enhancement, good first issue

#891 - IndexedSource and ImageSource bug fixes

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug

#890 - OrientedSource

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 4 comments
Labels: enhancement

#889 - Multiple resolution/pixel-size data sets

Issue - State: open - Opened by garrettwrong over 1 year ago - 2 comments
Labels: enhancement

#888 - Asnumpy writable

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: enhancement, good first issue, cleanup

#887 - disable writing to `asnumpy()` references

Issue - State: closed - Opened by garrettwrong over 1 year ago
Labels: enhancement, good first issue, cleanup

#886 - Vectorize `Rotation.angle_dist()`

Issue - State: closed - Opened by j-c-c over 1 year ago - 2 comments
Labels: enhancement, Optimization

#885 - Migrate tutorials/experiments away from imshow subplots

Issue - State: open - Opened by garrettwrong over 1 year ago
Labels: documentation, good first issue, cleanup

#884 - Missed img vol return tutorial updates

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: bug, documentation, cleanup

#883 - Simplify Whiten syntax

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, cleanup

#882 - Feature demo breakup

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 7 comments
Labels: documentation, enhancement, cleanup

#881 - add warning and clamp for extremal snr

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: cleanup

#880 - `CnSymmetricVolume`s center mass accumulation

Issue - State: open - Opened by j-c-c over 1 year ago
Labels: Optimization

#879 - Show patch

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: bug

#878 - Allow `whiten(NoiseEstimator)`

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, cleanup

#877 - Initial addition of RemappedSource

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: enhancement, cleanup

#876 - Source slicing/getter

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: enhancement, cleanup

#875 - Orientation and Boosting Sources

Issue - State: closed - Opened by garrettwrong over 1 year ago - 9 comments
Labels: enhancement, cleanup, Optimization

#874 - Demo dry run updates

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: documentation, cleanup

#873 - Simulation `eval_coords` bug

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 3 comments
Labels: bug

#872 - DenoiserCov2D always returns doubles

Issue - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug, cleanup

#871 - RelionSource dtype

Issue - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: enhancement, cleanup

#870 - Minor ctf tweaks

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: bug, documentation, cleanup

#869 - Relative Viewing Direction Estimation for Common-lines (Cn)

Issue - State: open - Opened by j-c-c over 1 year ago
Labels: enhancement, Optimization, theory

#868 - xfail FLE test broken on windows (only on windows).

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 1 comment
Labels: bug

#866 - Class Source

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 3 comments
Labels: enhancement

#865 - Downgrade windows CI from 2022 to 2019 (fixes single test fail in CI)

Pull Request - State: closed - Opened by garrettwrong over 1 year ago - 2 comments
Labels: bug, CI

#864 - Deprecation Warnings

Pull Request - State: closed - Opened by j-c-c over 1 year ago - 1 comment
Labels: CI, cleanup, extern

GitHub / ComputationalCryoEM/ASPIRE-Python issues and pull requests