ComputationalCryoEM/ASPIRE-Python issues and pull requests

#1171 - Cl mask patch

Pull Request - State: closed - Opened by garrettwrong 2 months ago - 2 comments
Labels: bug, cleanup

#1170 - Remove Warnings

Pull Request - State: open - Opened by j-c-c 2 months ago
Labels: CI, cleanup

#1169 - Remove `pyshtools` dependency

Issue - State: open - Opened by garrettwrong 3 months ago
Labels: enhancement, cleanup, dependencies

#1168 - finufft/cufinufft 2.3.0rc1

Pull Request - State: open - Opened by garrettwrong 3 months ago - 20 comments
Labels: extern

#1167 - WIP: CUDA build common lines

Pull Request - State: open - Opened by garrettwrong 3 months ago - 1 comment
Labels: enhancement, Optimization, GPU

#1166 - Fix Fuzzy Mask for small L

Pull Request - State: closed - Opened by garrettwrong 3 months ago - 1 comment
Labels: bug, cleanup

#1165 - Update wemd.py

Pull Request - State: closed - Opened by mosco 3 months ago - 1 comment
Labels: enhancement

#1164 - New Line Class with Back Project Method

Pull Request - State: closed - Opened by certifiedp 3 months ago - 1 comment

#1163 - New Line Class with Back Project Method

Pull Request - State: closed - Opened by certifiedp 3 months ago

#1162 - Downsample Bug

Pull Request - State: closed - Opened by j-c-c 4 months ago - 1 comment
Labels: bug

#1161 - Long running workflow patches

Pull Request - State: closed - Opened by garrettwrong 4 months ago
Labels: bug, CI, cleanup, Optimization, GPU

#1160 - Long Running Workflow patches

Pull Request - State: closed - Opened by garrettwrong 4 months ago - 1 comment
Labels: bug, good first issue, cleanup, GPU

#1159 - Revisit CuPy FFT single precision upcasting

Issue - State: open - Opened by garrettwrong 4 months ago
Labels: good first issue, cleanup, Optimization, GPU

#1158 - Cleanup FFB precomp and preload freq grids to GPU

Issue - State: open - Opened by garrettwrong 4 months ago
Labels: cleanup, Optimization, GPU

#1157 - Pixel Size Attributes

Pull Request - State: closed - Opened by garrettwrong 4 months ago - 4 comments
Labels: enhancement, good first issue

#1156 - Image Downsample Scaling Bug

Issue - State: closed - Opened by j-c-c 4 months ago - 1 comment
Labels: bug

#1155 - Volume Downsample Unexpected Behavior

Issue - State: closed - Opened by j-c-c 4 months ago - 4 comments
Labels: bug

#1154 - Image Offsets Swap

Pull Request - State: closed - Opened by j-c-c 4 months ago - 1 comment
Labels: bug

#1153 - Batched covar test run to run var

Pull Request - State: closed - Opened by garrettwrong 4 months ago - 1 comment
Labels: CI, cleanup

#1152 - Volume pixel size

Issue - State: closed - Opened by j-c-c 4 months ago - 1 comment
Labels: enhancement

#1151 - ClassAvgSource SymmetryGroup Pass-through

Pull Request - State: closed - Opened by j-c-c 4 months ago - 2 comments
Labels: bug, cleanup

#1150 - Class Image line projection method

Pull Request - State: closed - Opened by certifiedp 4 months ago - 3 comments
Labels: enhancement

#1149 - More 10081 fixes

Pull Request - State: closed - Opened by garrettwrong 4 months ago - 3 comments
Labels: bug, documentation, cleanup

#1148 - Check FFB3D Zeros

Issue - State: open - Opened by garrettwrong 4 months ago
Labels: documentation, cleanup, support

#1146 - Relion/ASPIRE projection image offsets

Issue - State: closed - Opened by j-c-c 5 months ago - 1 comment
Labels: bug

#1145 - 10081 Gallery Experiment Patch

Pull Request - State: closed - Opened by garrettwrong 5 months ago - 1 comment
Labels: bug, documentation

#1144 - Remove `sklearn._fit_*` workaround

Issue - State: open - Opened by j-c-c 5 months ago
Labels: good first issue, cleanup

#1143 - Remove `numeric.scipy.cg` workaround

Issue - State: open - Opened by garrettwrong 5 months ago
Labels: good first issue, cleanup

#1142 - Scipy `cg` workaround

Pull Request - State: closed - Opened by garrettwrong 5 months ago
Labels: good first issue, extern, dependencies

#1141 - Develop ~~> Main v0.12.3

Pull Request - State: closed - Opened by garrettwrong 5 months ago - 5 comments

#1140 - Hack24

Pull Request - State: closed - Opened by garrettwrong 5 months ago - 2 comments
Labels: bug, enhancement, CI, cleanup, Optimization, GPU

#1139 - Bumping version

Pull Request - State: closed - Opened by garrettwrong 5 months ago
Labels: documentation, CI

#1138 - 2024 GPU Hackathon Integration

Issue - State: closed - Opened by garrettwrong 5 months ago - 6 comments
Labels: enhancement, CI, cleanup, Optimization, GPU

#1137 - bump stable osx runner image from 11->13

Pull Request - State: closed - Opened by garrettwrong 5 months ago - 2 comments
Labels: good first issue, CI, cleanup, extern, dependencies

#1136 - GHA Mac os 11 removed

Issue - State: closed - Opened by garrettwrong 5 months ago - 1 comment
Labels: good first issue, CI, cleanup, extern, dependencies

#1135 - Cleanup Warnings

Issue - State: open - Opened by garrettwrong 5 months ago - 1 comment
Labels: CI, cleanup

#1134 - support np1 and np2 ComplexWarning

Pull Request - State: closed - Opened by garrettwrong 5 months ago - 1 comment
Labels: CI, extern, dependencies

#1133 - Numpy 2 release

Issue - State: closed - Opened by garrettwrong 5 months ago - 1 comment
Labels: bug, good first issue, CI, extern, dependencies

#1132 - adjust tolerance for m1

Pull Request - State: closed - Opened by certifiedp 5 months ago - 2 comments
Labels: good first issue, CI

#1131 - Testing fast implementations of A* A where A is the projection operator

Issue - State: open - Opened by 09pouchol 5 months ago - 8 comments
Labels: support

#1130 - All the fills

Pull Request - State: closed - Opened by j-c-c 5 months ago

#1129 - Hack24 ffb3d

Pull Request - State: closed - Opened by garrettwrong 5 months ago

#1128 - Move arrays to build

Pull Request - State: closed - Opened by j-c-c 5 months ago

#1127 - FFB2D fix anufft warning

Pull Request - State: closed - Opened by j-c-c 5 months ago

#1126 - ffb_2d gpu

Pull Request - State: closed - Opened by j-c-c 5 months ago

#1125 - Whitening Filter Threshold

Pull Request - State: closed - Opened by j-c-c 5 months ago - 13 comments
Labels: cleanup

#1124 - Hack24 sparse

Pull Request - State: closed - Opened by garrettwrong 5 months ago
Labels: enhancement, cleanup, Optimization, GPU

#1123 - Hack24 nufft updates

Pull Request - State: closed - Opened by garrettwrong 5 months ago
Labels: Optimization, GPU

#1122 - update GHA miniconda setup version to ~v3~ v2.3.0

Pull Request - State: closed - Opened by garrettwrong 5 months ago - 3 comments
Labels: cleanup, extern, dependencies

#1121 - Update GH Actions miniconda setup

Issue - State: closed - Opened by garrettwrong 5 months ago - 1 comment
Labels: CI, extern, dependencies

#1120 - sklearn API change

Pull Request - State: closed - Opened by j-c-c 6 months ago - 2 comments
Labels: bug, CI, extern

#1119 - `sklearn` release breaking API

Issue - State: closed - Opened by j-c-c 6 months ago - 3 comments
Labels: bug, CI, extern

#1118 - Relion now uses `rlnOriginX(Y)Angstrom` instead of `rlnOriginX(Y)`

Issue - State: open - Opened by j-c-c 6 months ago - 1 comment
Labels: bug, extern

#1117 - J-sync Bug

Pull Request - State: closed - Opened by j-c-c 6 months ago
Labels: bug

#1116 - D2 Common-lines Algorithm

Pull Request - State: open - Opened by j-c-c 6 months ago - 3 comments
Labels: enhancement

#1115 - Error when run aspire.cov3d with cupy

Issue - State: closed - Opened by ThinkJanice 6 months ago - 7 comments
Labels: support

#1114 - CUDA/CUPY kernel for building Common Line matrix

Issue - State: open - Opened by garrettwrong 6 months ago - 2 comments
Labels: enhancement, Optimization, GPU

#1113 - CI update

Pull Request - State: closed - Opened by j-c-c 7 months ago - 1 comment
Labels: bug, CI

#1112 - Ampere CI Fix

Pull Request - State: closed - Opened by j-c-c 7 months ago - 2 comments
Labels: bug, CI

#1111 - Non repeatable behavior of Image.backproject

Issue - State: closed - Opened by remy-aber 7 months ago - 5 comments
Labels: extern, support

#1110 - Projection/Backprojection Adjointedness

Pull Request - State: closed - Opened by garrettwrong 7 months ago - 7 comments
Labels: bug, help wanted, support

#1109 - Volume.project and Image.backproject are not adjoint operators

Issue - State: closed - Opened by remy-abergel 7 months ago - 3 comments
Labels: bug, cleanup, support

#1108 - Sync3n Initial Add

Pull Request - State: closed - Opened by garrettwrong 7 months ago - 11 comments
Labels: enhancement, Optimization, GPU

#1107 - Missing CL Features

Issue - State: open - Opened by garrettwrong 8 months ago - 1 comment
Labels: bug, enhancement, cleanup

#1106 - SymmetryGroup Parsing

Pull Request - State: closed - Opened by j-c-c 8 months ago
Labels: cleanup

#1105 - Adding progress bar for CLSync

Pull Request - State: closed - Opened by garrettwrong 8 months ago - 1 comment
Labels: enhancement, good first issue, cleanup

#1104 - FFT swap

Pull Request - State: closed - Opened by garrettwrong 8 months ago - 1 comment
Labels: CI, extern, dependencies

#1103 - Circular Imports

Pull Request - State: closed - Opened by j-c-c 8 months ago
Labels: bug, cleanup

#1102 - MeanEstimator circular dependency

Issue - State: closed - Opened by j-c-c 8 months ago - 1 comment
Labels: bug

#1101 - OrientedSource Lazy Evaluation

Pull Request - State: closed - Opened by j-c-c 8 months ago
Labels: cleanup

#1100 - Use _cached_im when available in IndexedSource

Pull Request - State: closed - Opened by garrettwrong 8 months ago - 1 comment
Labels: bug, cleanup

#1099 - `CLOrient3D` lazy eval

Issue - State: closed - Opened by garrettwrong 8 months ago - 1 comment
Labels: enhancement, cleanup

#1098 - Caching IndexedSource

Issue - State: closed - Opened by garrettwrong 8 months ago
Labels: bug, documentation, cleanup

#1097 - Backprojection Example

Issue - State: open - Opened by garrettwrong 9 months ago - 5 comments
Labels: documentation, enhancement

#1096 - Add `RampFilter`

Issue - State: open - Opened by garrettwrong 9 months ago - 3 comments
Labels: documentation, enhancement, good first issue

#1095 - Add `Sinogram` class

Issue - State: open - Opened by garrettwrong 9 months ago - 2 comments
Labels: enhancement

#1094 - Doc updates 24q1 2

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 1 comment
Labels: documentation, cleanup

#1093 - Update GitHub actions versions

Pull Request - State: closed - Opened by j-c-c 9 months ago - 2 comments
Labels: CI

#1092 - Update ray

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 2 comments

#1091 - Update Github actions `checkout` and `setup-python` versions

Issue - State: closed - Opened by j-c-c 9 months ago - 1 comment
Labels: CI

#1090 - `develop` to `main` v0.12.2

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 1 comment
Labels: documentation, CI, extern, dependencies

#1089 - Gemmi Update

Pull Request - State: closed - Opened by j-c-c 9 months ago - 3 comments
Labels: bug, CI, extern

#1088 - Gemmi Release Bug

Issue - State: closed - Opened by j-c-c 9 months ago - 1 comment
Labels: bug, CI, extern, dependencies

#1087 - cufinufft v2.2.0 migration

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 3 comments
Labels: CI, extern, dependencies, GPU

#1086 - update cufinufft

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 2 comments
Labels: enhancement, CI, cleanup, extern, dependencies

#1085 - Default Estimator 3D basis

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 1 comment
Labels: cleanup

#1084 - SymmetryGroup Pass-through for Volume Transformations

Pull Request - State: closed - Opened by j-c-c 9 months ago - 2 comments
Labels: bug

#1083 - SymmetryGroup Parser

Issue - State: closed - Opened by j-c-c 9 months ago - 1 comment
Labels: cleanup

#1082 - Doc updates 24q1

Pull Request - State: closed - Opened by garrettwrong 9 months ago - 2 comments
Labels: documentation, cleanup

#1081 - Volume transformation removes `symmetry_group`

Issue - State: closed - Opened by j-c-c 9 months ago - 1 comment
Labels: bug

#1080 - Minor doc/tutorial additions.

Issue - State: closed - Opened by garrettwrong 9 months ago - 3 comments
Labels: documentation, enhancement, good first issue, cleanup

#1079 - Allow RelionSource to be double precision

Pull Request - State: closed - Opened by garrettwrong 10 months ago - 4 comments
Labels: bug, enhancement

#1078 - Retry finwin pkg

Pull Request - State: closed - Opened by garrettwrong 10 months ago - 2 comments
Labels: bug, cleanup, extern, dependencies

#1077 - Black updates

Pull Request - State: closed - Opened by garrettwrong 10 months ago - 1 comment
Labels: cleanup, extern, dependencies

#1076 - Bug fix for `evaluate_src_filters_on_grid`

Pull Request - State: closed - Opened by j-c-c 10 months ago - 1 comment
Labels: bug

#1075 - IdentityFilter for Simulation

Pull Request - State: closed - Opened by j-c-c 10 months ago - 2 comments
Labels: bug

#1074 - CUDA 12 Support

Pull Request - State: closed - Opened by garrettwrong 10 months ago - 2 comments
Labels: enhancement, CI, extern, dependencies

#1073 - `finufft` 2.2.0 updates

Pull Request - State: closed - Opened by garrettwrong 10 months ago - 3 comments
Labels: extern, dependencies

#1072 - Symmetry Boosting

Pull Request - State: closed - Opened by j-c-c 10 months ago - 3 comments
Labels: enhancement

#1071 - Incremental Mean Volume Checkpoint

Pull Request - State: closed - Opened by garrettwrong 10 months ago - 3 comments
Labels: enhancement

GitHub / ComputationalCryoEM/ASPIRE-Python issues and pull requests