cbg-ethz/pyggdrasil issues and pull requests

#202 - README Update - adding thesis link from ETH Collection

Pull Request - State: closed - Opened by gordonkoehn 12 months ago
Labels: 🕮 action: documentation, ⏰ time estimate: S

#201 - Update ETH Collection Link to Thesis

Issue - State: closed - Opened by gordonkoehn 12 months ago
Labels: 🕮 action: documentation

#200 - Fixing Built Typing Issues

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation

#199 - Fix Pyright Version

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation, ❗priority: low, ⏰ time estimate: S

#198 - Fix typos README.md

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation

#197 - Fix typo in ReadMe

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation

#196 - First Release

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation, ❗priority: high, ⏰ time estimate: S

#195 - First Release

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation, ❗priority: medium, ⏰ time estimate: S

#194 - Roadmap to Real-World Data Usage

Issue - State: open - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ⏰ time estimate: L

#193 - Enhance Documentation

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🕮 action: documentation, 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: M

#192 - First Release

Issue - State: closed - Opened by gordonkoehn about 1 year ago - 3 comments
Labels: 🕮 action: documentation, ❗priority: low, ⏰ time estimate: S

#191 - Enhance Documentation

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation, 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: L

#190 - Fixing Paths for Figures in mkdocs/quarto

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🕮 action: documentation, ❗priority: high, ⏰ time estimate: S, 🧪 action: experiment

#189 - Mark02 Summary Convergence Trends

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

#188 - Minor Revision Mark03 Visuals

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: S

#187 - Refine Visuals Mark03

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: S

#186 - Adding Docs Workflow

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation

#185 - Generate Documentation

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation, ❗priority: medium, ⏰ time estimate: M

#184 - Refine Graphics

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago

#183 - Refine Graphics

Issue - State: closed - Opened by gordonkoehn about 1 year ago

#182 - Fixing Pyright False Positive

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug, ❗priority: medium, ⏰ time estimate: S

#181 - Adding Effective Sample Size for MCMC Diagnostics

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 2 comments
Labels: 🦾 action: enhancement

#180 - Fix PyRight issue - built failing.

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: ❗priority: high, ⏰ time estimate: S

#179 - Refine Documentation of Different-Lineage Simialirty

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation, 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: S

#178 - Add True Tree Log-Prob as Horizontal Line to MARK02

Issue - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: M

#177 - Long Chain R-hat memory issues

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🐛 bug

#176 - Fixing node numbers on initial trees MARK02 Long

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago

#175 - Dynamic Memory + Fixing DATADIR in MARK02 long runs

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug, 🦾 action: enhancement

#174 - Refine Mark03 Visuals

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: M

#173 - Refine MARK03 visuals

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: M

#172 - Adding selected 10x long runs for MARK02 experiment

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: ❗priority: high, ⏰ time estimate: S, 🧪 action: experiment

#171 - Make examples usage notebook or script for the next one.

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🕮 action: documentation, 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: M

#170 - Mark02 fix y limits

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug, 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: S

#169 - Mark01 Combined Histogram Minor Fix

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug, 🦾 action: enhancement

#168 - Fix Combined Histogram Issue - Mark01

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug

#167 - MARK01 Rerun with new Error Rates

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: S, 🧪 action: experiment

#166 - Update MARK01

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

#165 - MARK05 - Tree Random and Tree MCMC Distribution under Metrics

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 4 comments
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: M, 🧪 action: experiment

#164 - MARK02 - Up the memory of R-hat computation

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug, 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: S

#163 - Adding Gelman Rubin Statistics to MARK02

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: L

#162 - Add Investigation MARK05 - Tree Distribution DL/AD

Issue - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: L

#161 - Add Gelman-Rubin Statistics

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: M

#160 - Running MARK03 - Post Log Prob Fix

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago

#159 - Fix Position of Legend of MARK02 plots

Issue - State: closed - Opened by gordonkoehn about 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: S

#158 - Running MARK02 - Rerun Post-Log-Prob Fix

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

#157 - Implementing MARK04 - How well does HUNTRESS work for different trees ?

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago - 2 comments

#156 - Consider Blocking HUNTRESS Easy Data

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

#155 - Fix improper random key usage in MCMC kernel

Pull Request - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🐛 bug, ❗priority: high, ⏰ time estimate: S

#154 - Documentation: yg.tree_inference._logprob_validator // test_inspect_logs_of_logprob

Issue - State: closed - Opened by gordonkoehn about 1 year ago
Labels: 🕮 action: documentation

#153 - Documentation: log_probability_validator2

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🕮 action: documentation

#152 - Refine Plots MARK03

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: S

#151 - Remove snakefmt Footprints

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: action: refactor, ❗priority: low, ⏰ time estimate: S

#150 - More Realistic Error Rates

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 4 comments
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: S

#149 - Verify / Add Tests of Log-Probability Calculation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 14 comments
Labels: 🐛 bug, 🦾 action: enhancement, ❗priority: high, ⏰ time estimate: L

#148 - Same Likelihood Investigation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 6 comments

#147 - Update ReadMe and About

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 2 comments
Labels: 🕮 action: documentation, ❗priority: low, ⏰ time estimate: S

#146 - Refinements during Basin Investigation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, 🦾 action: enhancement

#145 - Meeting notes from August 9th

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 4 comments

#144 - Refine Visuals MARK03 - make HUNTRESS line non-transparent.

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: S

#143 - Adding Selected Long MCMC runs

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

#142 - Parallelize distance calculation

Issue - State: open - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: M

#141 - Get SCITE Most-Likely Tree

Issue - State: open - Opened by gordonkoehn over 1 year ago - 10 comments
Labels: 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: M

#140 - Fix of Range of Combined MARK01 plots

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: M

#139 - Clean up MCMC Logging

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: action: refactor, ❗priority: medium, ⏰ time estimate: S

#138 - Clean up MCMC Logging

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#137 - Adding more Tree Similarity Measures

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: M

#136 - Combined Visualizations Error Rates MARK01

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: M

#135 - Remove snakefmt footprints in code

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: action: refactor, ❗priority: low, ⏰ time estimate: S

#134 - Initial Experiments Output Description

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🕮 action: documentation, ⏰ time estimate: S

#133 - Revisie Plots MARK01 - combine to overlapping histograms

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: S

#132 - Make huntress single thread

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

#131 - Revising Mark01: AD Bug + Ploting

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: medium, ⏰ time estimate: S

#130 - Integrate Original HUNTRESS code

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment

#129 - Revision of MARK03 plots

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug

#128 - Update scphylo / fix HUNTRESS implementation

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

#127 - Switch/Update to other HUNTRESS Implementation

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 5 comments
Labels: 🐛 bug, ❗priority: high, ⏰ time estimate: M

#126 - Mark03 Visualization Revision

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: high, ⏰ time estimate: S

#125 - Fixing Mark03 rule error

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: medium, ⏰ time estimate: S

#124 - Fix Analyze Analyze Metric Bug

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: high, ⏰ time estimate: S

#123 - Increase Huntress Resources

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement

#122 - Up the resources for HUNTRESS

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment

#121 - Clean up experimental workflow Mark03 - repeated plotting code block.

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: action: refactor, ❗priority: low, ⏰ time estimate: M

#120 - Revise experiment Mark02

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

#119 - Add different-lineages (DL) accuracy

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: M

#118 - Adding Report Visualisations Workflow

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: S

#117 - Experimental Run: Mark01

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🧪 action: experiment

#116 - Removing tree script dependence of workflows

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, action: refactor, ❗priority: low, ⏰ time estimate: M

#108 - Migrate Tree Inference Snakemake Rules from scripts to run directive

Issue - State: open - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, action: refactor, ❗priority: low, ⏰ time estimate: M

#107 - Implement more Tree Metrics

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🦾 action: enhancement, ❗priority: medium, ⏰ time estimate: S

#100 - Resolving broken `scphylo` ancestor-descendant distance

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: high, 🧩 in sprint, ⏰ time estimate: S

#99 - Run MARK03

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#98 - Test MARK03

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#97 - Implement MAKR03 Worflow

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment

#96 - Run MARK02

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#95 - Test MARK02

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#94 - Implement MARK02 snakemake Workflow

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint, ⏰ time estimate: M

#93 - Run MARK01

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: ❗priority: high, 🧩 in sprint, ⏰ time estimate: S, 🧪 action: experiment

#92 - Test MARK01 Snakemake Workflow

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#91 - Implement MARK01 Snakemake Workflow

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: M, 🧪 action: experiment

#90 - Setting up experiment MARK01

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: ❗priority: high, 🧩 in sprint, ⏰ time estimate: M, 🧪 action: experiment

GitHub / cbg-ethz/pyggdrasil issues and pull requests