Ecosyste.ms: Issues

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

GitHub / segrelab/MiCoNE issues and pull requests

#216 - Chore(deps): Bump urllib3 from 2.0.5 to 2.0.7

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#215 - Chore(deps): Bump urllib3 from 2.0.5 to 2.0.6

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

#214 - update .py scripts

Pull Request - State: closed - Opened by MDHDZ91 about 1 year ago

#213 - Chore(deps-dev): Bump ipython from 7.34.0 to 8.10.0

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

#212 - Chore(deps): Bump certifi from 2022.6.15 to 2022.12.7

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

#211 - Chore(deps): Bump pillow from 9.2.0 to 9.3.0

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

#210 - Chore(deps): Bump pillow from 9.1.0 to 9.1.1

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

#209 - Chore(deps): Bump pillow from 9.0.0 to 9.0.1

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

#207 - Chore(deps-dev): Bump ipython from 7.31.0 to 7.31.1

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

#206 - Use same settings for single and paired end alternatives

Issue - State: closed - Opened by dileep-kishore about 3 years ago
Labels: Type: Maintenance, Priority: Medium

#205 - Fix julia paths for flashweave environment

Issue - State: closed - Opened by dileep-kishore about 3 years ago
Labels: Status: Pending, Type: Bug, Priority: Medium

#204 - Use conda Python api in micone --init

Issue - State: closed - Opened by dileep-kishore about 3 years ago
Labels: Type: Maintenance, Type: Enhancement, Status: Available, Priority: Low

#203 - NetCoMi installation fails

Issue - State: closed - Opened by dileep-kishore about 3 years ago
Labels: Type: Bug, Status: Available, Priority: Low

#202 - Display all errors at end of run (like pytest)

Issue - State: closed - Opened by dileep-kishore over 3 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: High

#201 - Allow support for process aliases in `config.toml` file

Issue - State: closed - Opened by dileep-kishore over 3 years ago - 2 comments
Labels: Type: Enhancement, Status: Available, Priority: Low

#200 - Create a method to add/combine two `NetworkGroup` objects

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#199 - Add module for network inference using FlashWeave.jl

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: High

#198 - Update `make_network` module to support excluding p-values

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 1 comment
Labels: Status: Pending, Type: Bug, Priority: Critical

#197 - Create a `utils` submodule that creates the `config` file programatically

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: Low

#196 - Add module for network inference using SPRING

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 2 comments
Labels: Type: Enhancement, Status: In Progress, Priority: High

#195 - Recreate entry points after migration to pyproject.toml

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#194 - Create a conda recipe for micone

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#193 - Add project description to pypi deployment

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Type: Maintenance, Status: Review Needed, Priority: Low

#192 - Update the README

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Low

#191 - Fix schematics and validate methods

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 1 comment
Labels: Type: Bug, Status: In Progress, Priority: High

#190 - Remove pin on jedi and parso dependencies once ipython issue is fixed

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Type: Maintenance, Status: On Hold, Priority: Low

#189 - Migrate to nextflow DSL 2 workflows

Issue - State: closed - Opened by dileep-kishore almost 4 years ago
Labels: Type: Maintenance, Priority: Medium, Status: In Progress

#188 - Should we draw the pipline workflow without graphviz and pygraphviz [#j7049g]

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 2 comments
Labels: Type: Maintenance, Status: Review Needed, Priority: Critical

#187 - Move to github workflows

Issue - State: closed - Opened by dileep-kishore almost 4 years ago - 1 comment
Labels: Type: Maintenance, Status: Pending, Priority: Medium

#186 - Scheduled monthly dependency update for January

Pull Request - State: closed - Opened by pyup-bot almost 4 years ago

#185 - Scheduled monthly dependency update for December

Pull Request - State: closed - Opened by pyup-bot almost 4 years ago - 1 comment

#184 - Scheduled monthly dependency update for November

Pull Request - State: closed - Opened by pyup-bot about 4 years ago - 1 comment

#183 - Scheduled monthly dependency update for October

Pull Request - State: closed - Opened by pyup-bot about 4 years ago - 1 comment

#182 - Replace `otu_assignment` with `denoise_cluster` in config

Issue - State: closed - Opened by dileep-kishore over 4 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Medium

#181 - Scheduled monthly dependency update for June

Pull Request - State: closed - Opened by pyup-bot over 4 years ago - 1 comment

#180 - Scheduled monthly dependency update for May

Pull Request - State: closed - Opened by pyup-bot over 4 years ago - 1 comment

#179 - Scheduled monthly dependency update for April

Pull Request - State: closed - Opened by pyup-bot over 4 years ago - 1 comment

#178 - UTF-8 bug in qiime2 modules when running in nextflow under qsub

Issue - State: closed - Opened by dileep-kishore over 5 years ago - 1 comment
Labels: Type: Bug, Priority: Critical, Status: In Progress

#177 - Construct module to calculate consensus network

Issue - State: closed - Opened by dileep-kishore over 5 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: Critical

#176 - Switch off spinners for non-interactive runs

Issue - State: closed - Opened by dileep-kishore over 5 years ago
Labels: Type: Enhancement, Status: Pending, Priority: High

#175 - Fix sparcc environment specification

Issue - State: closed - Opened by dileep-kishore over 5 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#174 - Fix mLDM environment

Issue - State: closed - Opened by dileep-kishore over 5 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#173 - Save pipeline

Issue - State: closed - Opened by dileep-kishore over 5 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: High

#172 - Bugs in the pipeline CLI

Issue - State: closed - Opened by dileep-kishore over 5 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical, Priority: High

#171 - Fix bug in pipenv dependency resolution

Issue - State: closed - Opened by dileep-kishore over 5 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#170 - Bug in `NetworkGroup._combine_methods`

Issue - State: closed - Opened by dileep-kishore over 5 years ago - 1 comment
Labels: Type: Bug, Priority: Critical, Status: In Progress

#169 - Current network datastructures do not support multiple edges

Issue - State: closed - Opened by dileep-kishore over 5 years ago - 1 comment
Labels: Type: Enhancement, Status: In Progress, Priority: High

#168 - Make Network load big datasets faster

Issue - State: closed - Opened by dileep-kishore over 5 years ago - 2 comments
Labels: Type: Enhancement, Priority: Critical, Status: In Progress

#167 - Check environment initialization only for processes in current run

Issue - State: closed - Opened by dileep-kishore over 5 years ago
Labels: Type: Enhancement, Status: Review Needed, Priority: Low

#166 - Create a log parser to parse select information from mindpipe log files

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: On Hold, Priority: Low

#165 - Use fdr instead of bh for pvalue correction

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Status: Pending, Type: Bug, Priority: High

#164 - Factor out the resampling and pvalue calculation step out of sparcc pipeline and into separate pipelines

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: In Progress, Priority: High

#163 - Pipeline does not wait after resume

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Bug, Priority: Critical, Status: In Progress

#162 - Support for parameterization of process using 4 level process name

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#161 - Pipeline does not wait for last process

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#160 - Remove "_filtered" suffix from abundance filter pipeline

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Status: Pending, Type: Bug, Priority: High

#159 - Fix the SILVA classifier artifact

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Status: Pending, Type: Bug, Priority: High

#158 - Higher level network file shows full lineage upto species level

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#157 - Attaching inputs to outputs must have > 1 level recursion

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Status: Pending, Type: Bug, Priority: Critical

#156 - Stop all subprocesses when there is an error during a run

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Enhancement, Status: Review Needed, Priority: Low

#155 - Implement `clean` subcommand

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Medium

#154 - Fix the gg qiime2 classifier artifact

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Status: Review Needed, Type: Bug, Priority: Critical

#153 - Script and config files should have unique names

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Bug, Priority: Critical, Status: In Progress

#152 - `Params.copy` does not seem to copy location

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Bug, Priority: Critical, Status: In Progress

#151 - Change output location (name) of process when there are multiple in pipeline

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Bug, Priority: Critical, Status: In Progress

#150 - Add short aliases for each process in their default settings

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: High

#149 - Implement a method to draw the process tree

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#148 - Do not specify base output location in expected "location" for process output

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Bug, Priority: Critical, Status: In Progress

#147 - If inputs for a pipeline process exist then run that without any wait

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Enhancement, Status: Pending, Priority: High

#146 - Add forking support to the pipeline

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: High

#145 - Alternate clustering methods

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Priority: Low

#144 - Add email functionality

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Available, Priority: Low

#143 - CONDA_PREFIX doesn't seem to use self.env

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Bug, Priority: Critical, Status: In Progress

#142 - Testing processes

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Medium

#141 - Add load_data method to NetworkGroup

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: High

#140 - Add abundance to network file

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#139 - Classifier import in naive bayes using qiime2

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Review Needed, Priority: Low

#137 - Module to merge otu_tables and rep_seqs from multiple runs

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Pending, Priority: High

#136 - Change demultiplexing processes to use folder name as ${id}

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Status: Review Needed, Priority: Medium

#135 - Write module for downloading databases and keeping them up to date

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#129 - Unfinished sequence processing modules

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#124 - Add functionality to limit number of edges in network.json

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Pending, Priority: High

#120 - Network inference

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: Critical

#116 - Might want to update `uclust` in post_install script for qiime1 pipeline

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Status: Review Needed, Type: Bug, Priority: High

#115 - Pipeline modules

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Epic

#114 - Taxonomy assignment

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Enhancement, Status: Pending, Priority: Critical

#110 - Use process name for report, timeline and trace filenames

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Enhancement, Status: Pending, Priority: Medium

#109 - Add tests for logger

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Medium

#104 - Tests for NetworkGroup class

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Medium

#103 - Create computational metadata in `Pipeline` class

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Question, Status: Pending, Priority: Medium

#102 - Construct one full sequence to network pipeline

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Enhancement, Status: Pending, Priority: High

#101 - Test pipeline on scc

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Maintenance, Status: Pending, Priority: High

#95 - The NetworkGroup class deletes some node information that can't be merged

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Maintenance, Status: Review Needed, Priority: Low

#93 - Make Travis ignore installed package in coverage

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Status: Pending, Priority: Low

#87 - Module identification

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 1 comment
Labels: Type: Enhancement, Status: Pending, Priority: Low

#86 - Standardize the naming convention in the nextflow scripts

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: Type: Maintenance, Priority: Low, Status: In Progress

#85 - Should we allow each nextflow process in a pipeline process to have it's own env?

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Enhancement, Status: Abandoned, Priority: High

#80 - Can `fastspar` bootstrapping and pvalue calculator be used for other algorithms

Issue - State: closed - Opened by dileep-kishore almost 6 years ago - 2 comments
Labels: Type: Question, Status: Review Needed, Priority: Critical

#74 - Create a proper conda recipe

Issue - State: closed - Opened by dileep-kishore almost 6 years ago
Labels: duplicate