Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / DiamondLightSource/python-relion issues and pull requests

#204 - Update dependency pydantic to v1.10.13 [SECURITY]

Pull Request - State: open - Opened by renovate[bot] 9 months ago - 1 comment
Labels: dependencies

#203 - Update dependency pillow to v10.3.0 [SECURITY]

Pull Request - State: open - Opened by renovate[bot] 10 months ago - 1 comment
Labels: dependencies

#202 - Update supported python versions

Pull Request - State: closed - Opened by stephen-riggs 10 months ago - 1 comment

#201 - Allow extract_downscale to not be present in ispyb_parameters

Pull Request - State: closed - Opened by d-j-hatton 11 months ago - 1 comment

#200 - Improve the naming and sending of options in the services

Pull Request - State: closed - Opened by stephen-riggs about 1 year ago - 1 comment

#198 - Add tilt quality inserts for tomograms

Pull Request - State: closed - Opened by stephen-riggs about 1 year ago - 1 comment

#197 - Tomogram quality indicator ISPyB insert

Issue - State: closed - Opened by d-j-hatton about 1 year ago

#195 - Remove references to the motion correction drift table

Pull Request - State: closed - Opened by stephen-riggs over 1 year ago - 1 comment

#194 - Subtract plane fit in extract service

Pull Request - State: closed - Opened by d-j-hatton over 1 year ago - 1 comment

#193 - Downscale by Fourier cropping

Pull Request - State: closed - Opened by d-j-hatton over 1 year ago - 1 comment

#192 - Update dependency pillow to v10 [SECURITY]

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#191 - Add service to use Relion's own motion correction

Pull Request - State: closed - Opened by stephen-riggs over 1 year ago - 1 comment

#190 - Add services to run SPA through Kubernetes

Pull Request - State: closed - Opened by stephen-riggs over 1 year ago - 1 comment

#189 - nack iris messages if they have not returned after 20 minutes

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

#188 - Squeeze histograms in tomogram images

Pull Request - State: closed - Opened by d-j-hatton over 1 year ago - 1 comment

#187 - Register 2D classes selected by auto-selection

Pull Request - State: closed - Opened by d-j-hatton over 1 year ago - 1 comment

#186 - Add denoise deployment

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

#185 - Add deployment for denoise

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

#184 - Run a single 3D classification batch

Pull Request - State: closed - Opened by d-j-hatton over 1 year ago - 1 comment

#183 - Changes to fix tests and sqlalchemy version

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

#182 - Locking changes

Pull Request - State: closed - Opened by stephen-riggs almost 2 years ago - 1 comment

#181 - Use cryolo to calculate the particle diameter

Pull Request - State: closed - Opened by stephen-riggs almost 2 years ago - 1 comment

#180 - Add particle diameter option

Pull Request - State: closed - Opened by d-j-hatton almost 2 years ago - 1 comment

#179 - Allow path pattern rather than input file list for tomo_align service

Pull Request - State: closed - Opened by HorstmannA almost 2 years ago - 5 comments

#178 - Add tomo_align_iris service for submission to Iris cluster

Pull Request - State: closed - Opened by HorstmannA almost 2 years ago - 2 comments

#177 - Allow skipping 2D class selection

Pull Request - State: closed - Opened by d-j-hatton almost 2 years ago - 2 comments

#176 - Calculate initial model class number from occupation

Pull Request - State: closed - Opened by d-j-hatton almost 2 years ago - 1 comment

#175 - SPA pipeline class selection

Pull Request - State: closed - Opened by stephen-riggs almost 2 years ago - 1 comment

#174 - Add success and failure outputs for alignment processing status.

Pull Request - State: closed - Opened by HorstmannA almost 2 years ago - 1 comment

#173 - Add a job that can combine any number of star files

Pull Request - State: closed - Opened by stephen-riggs almost 2 years ago - 1 comment

#172 - Use initial model suggested by RELION

Pull Request - State: closed - Opened by d-j-hatton almost 2 years ago - 1 comment

#171 - Allow the use of an externally generated 3D reference for 3D classification

Pull Request - State: closed - Opened by d-j-hatton almost 2 years ago - 1 comment

#170 - Allow the use of a 3D reference for the RELION 4 pipeline

Issue - State: closed - Opened by d-j-hatton almost 2 years ago

#169 - Use RELION suggested initial model

Issue - State: closed - Opened by d-j-hatton almost 2 years ago

#168 - Cryolo picking service

Pull Request - State: closed - Opened by stephen-riggs almost 2 years ago - 1 comment

#167 - Pass dose_per_frame to ISPyB from motioncorr.

Pull Request - State: closed - Opened by HorstmannA almost 2 years ago - 1 comment

#166 - Add command line tool to run refinement followed by post processing

Pull Request - State: closed - Opened by d-j-hatton almost 2 years ago

#165 - Add 2D class selection to pipeline

Issue - State: closed - Opened by d-j-hatton about 2 years ago

#164 - Tomogram table changes

Pull Request - State: closed - Opened by HorstmannA about 2 years ago - 1 comment

#163 - Add method to create APNG movie from tomogram

Pull Request - State: closed - Opened by HorstmannA about 2 years ago - 3 comments

#162 - Images tomo

Pull Request - State: closed - Opened by HorstmannA about 2 years ago - 1 comment

#161 - Update dependency pillow to v9.3.0 [SECURITY]

Pull Request - State: closed - Opened by renovate[bot] about 2 years ago - 1 comment
Labels: dependencies

#160 - Add a command line tool to copy a RELION project structure

Pull Request - State: closed - Opened by d-j-hatton about 2 years ago - 1 comment

#159 - Update dependency pillow to v9.2.0 [SECURITY]

Pull Request - State: closed - Opened by renovate[bot] about 2 years ago - 1 comment
Labels: dependencies

#158 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: closed - Opened by lgtm-com[bot] about 2 years ago

#157 - Tomogram central slice

Pull Request - State: closed - Opened by HorstmannA about 2 years ago - 2 comments

#156 - Images service plugin: ignore the case where no coordinates are given

Pull Request - State: closed - Opened by d-j-hatton about 2 years ago

#155 - Add documentation for running pipelines via command line

Pull Request - State: closed - Opened by d-j-hatton about 2 years ago - 1 comment

#154 - Allow single quotes in job star files and speedup crYOLO data parsing

Pull Request - State: closed - Opened by d-j-hatton about 2 years ago - 1 comment

#153 - Add RELION 4 support to Zocalo wrapper

Pull Request - State: closed - Opened by d-j-hatton over 2 years ago - 1 comment

#152 - Improve mrc to jpeg conversion for cases with outlier pixel values

Pull Request - State: closed - Opened by d-j-hatton over 2 years ago - 1 comment

#151 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] almost 3 years ago - 1 comment
Labels: dependencies

#150 - Allow configuration of cluster qsub templates

Pull Request - State: closed - Opened by d-j-hatton almost 3 years ago - 1 comment

#149 - Add a first attempt Relion 4 pipeline

Pull Request - State: closed - Opened by d-j-hatton almost 3 years ago - 1 comment

#148 - Parsing between pipeline option formats

Pull Request - State: closed - Opened by d-j-hatton almost 3 years ago - 1 comment

#147 - Update dependencies. Drop Python 3.7 support

Pull Request - State: closed - Opened by Anthchirp almost 3 years ago - 2 comments

#146 - Update all dependencies (major)

Pull Request - State: closed - Opened by renovate[bot] almost 3 years ago
Labels: dependencies

#145 - Check preprocessing status if there are no new batches

Pull Request - State: closed - Opened by d-j-hatton about 3 years ago - 1 comment

#144 - Break out of main loop on stop signal

Pull Request - State: closed - Opened by Anthchirp about 3 years ago - 1 comment

#143 - Fully drop python3.6 support

Pull Request - State: closed - Opened by d-j-hatton about 3 years ago - 1 comment

#142 - Look into speeding up particle picking image generation

Issue - State: open - Opened by d-j-hatton about 3 years ago - 2 comments

#141 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] about 3 years ago - 1 comment
Labels: dependencies

#140 - Python 3.10 support

Pull Request - State: closed - Opened by Anthchirp about 3 years ago - 1 comment

#139 - Allow the collection of job run information

Pull Request - State: closed - Opened by d-j-hatton about 3 years ago - 1 comment

#138 - Add custom ORM for storing pipeline/job run information

Pull Request - State: closed - Opened by d-j-hatton about 3 years ago - 1 comment

#137 - Avoid rare motion correction database entry duplication

Pull Request - State: closed - Opened by d-j-hatton about 3 years ago - 1 comment

#135 - Extract motion correction micrograph name from icebreaker five fig paths

Pull Request - State: closed - Opened by d-j-hatton about 3 years ago - 1 comment

#134 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#133 - Ice minor changes

Pull Request - State: closed - Opened by HorstmannA over 3 years ago - 1 comment

#132 - Update dependency pytest-cov to v3

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#131 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#130 - Add movie creation time stamps to ISPyB service message

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#129 - Use file timestamps when inserting images/movies/etc.

Issue - State: closed - Opened by Anthchirp over 3 years ago

#128 - Add external job for the Icebreaker 5 figure script.

Pull Request - State: closed - Opened by HorstmannA over 3 years ago - 1 comment

#127 - Relative ice thickness

Pull Request - State: closed - Opened by HorstmannA over 3 years ago - 1 comment

#126 - Extract industry user check to function

Pull Request - State: closed - Opened by Anthchirp over 3 years ago - 1 comment

#125 - Update dependency sphinx-rtd-theme to v1

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#124 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#123 - Update dependency pillow to v8.3.2 [SECURITY]

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#122 - Add ISPyB package dependency

Pull Request - State: closed - Opened by Anthchirp over 3 years ago - 1 comment

#121 - Update all dependencies (major)

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#120 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#119 - Update precommits

Pull Request - State: closed - Opened by Anthchirp over 3 years ago - 1 comment

#118 - Add image service plugin to make particle picker images

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#117 - Add EER file format support to the pipeline

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#116 - Fix ISPyB messages for classification tables

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#115 - Use a model of the database to collect results from within the wrapper

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#114 - Change Icebreaker group job to run on batches, similar to 2D classification

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#112 - Review comments for Table class PR

Pull Request - State: closed - Opened by Anthchirp over 3 years ago - 2 comments

#111 - Add Table class to support modelling of ISPyB database entries from within the wrapper

Pull Request - State: closed - Opened by d-j-hatton over 3 years ago - 1 comment

#110 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#109 - Update dependency pillow to v8.1.2 [SECURITY]

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies

#108 - Bump pillow from 8.0 to 8.2.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#106 - Add Icebreaker external jobs and histogram

Pull Request - State: closed - Opened by HorstmannA over 3 years ago - 1 comment

#105 - Update all dependencies

Pull Request - State: closed - Opened by renovate[bot] over 3 years ago - 1 comment
Labels: dependencies