Ecosyste.ms: Issues

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

GitHub / galaxyproject/total-perspective-vortex issues and pull requests

#139 - Proposal: Notification function

Issue - State: open - Opened by mira-miracoli about 2 months ago - 2 comments

#138 - Fix tests

Pull Request - State: closed - Opened by nuwang 2 months ago

#137 - Reformat codebase

Pull Request - State: open - Opened by nuwang 2 months ago - 1 comment

#136 - Add pydantic support

Pull Request - State: open - Opened by nuwang 3 months ago - 2 comments

#135 - Evaluation of params in destination section

Issue - State: closed - Opened by lmfaber 3 months ago - 2 comments

#134 - Alter TagSetManager score function to look at preference only

Pull Request - State: open - Opened by cat-bro 5 months ago - 5 comments

#133 - [WIP] Add get_queue_info helper function

Pull Request - State: open - Opened by cat-bro 5 months ago

#132 - Add test to ensure default inheritance can be overridden

Pull Request - State: open - Opened by nuwang 5 months ago

#131 - Improve linting with automatic type checking

Issue - State: open - Opened by nuwang 5 months ago

#130 - Incorrect handling of default inheritance

Issue - State: open - Opened by nuwang 5 months ago

#129 - Revert "Add optional slow tests"

Pull Request - State: open - Opened by nuwang 7 months ago

#128 - Update shared db short link

Pull Request - State: closed - Opened by nuwang 9 months ago - 1 comment

#127 - TPV config file - documentation should mention the name of the file?

Issue - State: closed - Opened by maikenp 9 months ago - 1 comment

#126 - Improved docs

Pull Request - State: closed - Opened by nuwang 9 months ago - 1 comment

#124 - Add a test that a tool with id kraken2000 will not inherit parameters for kraken2

Pull Request - State: open - Opened by cat-bro 10 months ago - 3 comments

#123 - add a convenient way to get the object_store_id of a input dataset

Issue - State: closed - Opened by bgruening 11 months ago - 1 comment

#122 - Add contributing doc and update readme

Pull Request - State: closed - Opened by afgane 11 months ago - 1 comment

#121 - Add readthedocs configuration

Pull Request - State: closed - Opened by nuwang 12 months ago - 1 comment

#120 - Add support for expressions in context variables

Issue - State: open - Opened by nuwang 12 months ago

#119 - Add to to_dict functions to Destination and TagSetManager classes

Pull Request - State: closed - Opened by pauldg 12 months ago
Labels: enhancement

#118 - Proper method for preventing default inheritance

Issue - State: open - Opened by natefoo 12 months ago - 1 comment

#117 - file size not available for deferred datasets

Issue - State: open - Opened by mvdbeek about 1 year ago

#116 - Fix get_dataset_size for datasets with null file_size column

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

#115 - TPV dry-run: mock tool has `None` as version

Issue - State: open - Opened by kysrpex about 1 year ago - 7 comments

#114 - Add info about cores, mem and gpus to a job in a standard way

Issue - State: closed - Opened by cat-bro about 1 year ago - 1 comment

#113 - Fix E721 for type comparison

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

#103 - Create dependabot.yml

Pull Request - State: open - Opened by nuwang over 1 year ago - 1 comment

#102 - Modify linter to flag regex errors

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

#101 - Swap rule execution order: apply specific rules before general rules

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

#100 - Not correct total input file sizes estimation

Issue - State: closed - Opened by gallardoalba over 1 year ago - 6 comments

#99 - Match cores, mem and gpus whenever they are defined

Pull Request - State: closed - Opened by kysrpex over 1 year ago - 13 comments

#98 - add helper for tool version equal comparision

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

#97 - When regex compilation fails, log what was attempting to be compiled

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

#96 - Add id to `mock_galaxy.User`

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

#95 - Add id to mock_galaxy.User

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

#94 - Fix dry run tool version

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

#93 - Failing test for pulsar user scenario

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

#92 - Fix dry run user

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

#91 - Add helpers for tool version comparison

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

#90 - Fix formatter ordering of inherits field

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

#89 - If a tool has file size rules, a role rule has no access to tool's scheduling tags

Pull Request - State: closed - Opened by cat-bro over 1 year ago - 2 comments

#88 - refactor: remove unnecessary overrides of superclass __init__

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

#87 - Remove condition from tpv packaging

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

#86 - Add helper for checking entity tags within a tpv rule

Pull Request - State: closed - Opened by cat-bro over 1 year ago - 1 comment
Labels: enhancement

#84 - Add initializer to handle empty sequence when reducing

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

#83 - TPV error (version 1.4.1) for jobs with input_size rules but no input datasets

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

#82 - Refactor and fix dryrun

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

#81 - TPV dry-run failing with error

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

#80 - Fix missing app.config.is_set() in mock config for dry-run

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

#79 - Convert env to a list compatible with Galaxy job conf

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

#78 - fix resubmission tests

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

#77 - dry-run stack trace

Issue - State: closed - Opened by bernt-matthias almost 2 years ago - 2 comments

#76 - fix indentation

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

#75 - Automatic Publish to PyPi workflow not working

Issue - State: closed - Opened by nuwang almost 2 years ago - 1 comment

#74 - Create a TPV tutorial on the GTN

Issue - State: closed - Opened by nuwang almost 2 years ago - 11 comments

#73 - Automatically convert envs to string, but make sure params are preserved

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

#72 - TPV should stringify env vars

Issue - State: closed - Opened by neoformit almost 2 years ago - 3 comments

#71 - tpv test results in error

Issue - State: closed - Opened by bgruening almost 2 years ago

#70 - create __init__.py in tpv core test folder

Pull Request - State: closed - Opened by bgruening almost 2 years ago - 4 comments

#69 - Update github actions

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

#68 - Shared rules inheritance test

Pull Request - State: closed - Opened by cat-bro almost 2 years ago - 6 comments

#67 - Add destination min accepted

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

#66 - Add optional slow tests

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

#65 - Resubmission with OOM doesn't seem to be kicked off

Issue - State: open - Opened by pcm32 almost 2 years ago - 7 comments

#64 - Add support for abstract entities

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

#63 - Use only TPV defined destinations, ignoring job_conf

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

#62 - Additional context params

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

#61 - Feature request: abstract destination entities

Issue - State: closed - Opened by cat-bro almost 2 years ago

#60 - Use only TPV defined destinations, ignoring job_conf defined destinations

Issue - State: closed - Opened by nuwang almost 2 years ago
Labels: enhancement

#59 - Enhance linter

Issue - State: open - Opened by nuwang almost 2 years ago - 1 comment
Labels: enhancement

#58 - Simplify TPV by disambiguating terms

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

#57 - Improve formatting of entities and add more tests

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

#56 - Add more helpful initial context variables

Issue - State: closed - Opened by nuwang almost 2 years ago - 1 comment
Labels: enhancement

#55 - Improvements for dry-run cli

Issue - State: open - Opened by natefoo almost 2 years ago - 1 comment
Labels: enhancement

#54 - Avoid deepcopying loader when cloning entities

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

#53 - Exponential runtime and memory usage from deep copy

Issue - State: closed - Opened by natefoo almost 2 years ago - 2 comments
Labels: bug

#52 - Add a `tpv dry-run` subcommand

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

#51 - Use ruamel.yaml in tpv.core.util since PyYAML is not a dependency

Pull Request - State: closed - Opened by natefoo almost 2 years ago - 1 comment
Labels: bug

#50 - replace long-term IDs by default with short-form IDs?

Issue - State: open - Opened by bgruening almost 2 years ago - 1 comment
Labels: enhancement

#49 - tpv lint should lint an entire directory

Issue - State: open - Opened by bgruening almost 2 years ago - 1 comment
Labels: enhancement

#48 - TPV dry-run tool

Issue - State: closed - Opened by mira-miracoli about 2 years ago - 6 comments
Labels: enhancement

#47 - Add support for importing remote files?

Issue - State: open - Opened by nuwang about 2 years ago
Labels: enhancement

#46 - unreadable colours for highlight in docs

Issue - State: open - Opened by hexylena about 2 years ago - 2 comments
Labels: enhancement

#45 - GPUs evaluate to None when set to 0

Issue - State: closed - Opened by bgruening about 2 years ago - 2 comments
Labels: bug

#44 - Add custom capping at destination

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

#43 - add PyPI deploy action from bioblend

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

#42 - Update __init__.py

Pull Request - State: closed - Opened by Slugger70 about 2 years ago - 1 comment

#41 - Make sure execute side effects persist

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

#40 - Given tools requesting "too much" mem/cpu from TPVSDB, allow capping to max(available)

Issue - State: closed - Opened by hexylena about 2 years ago - 9 comments
Labels: enhancement

#39 - Custom user test cases

Issue - State: closed - Opened by hexylena about 2 years ago - 3 comments

#38 - Add link to shared TPV database to readme files

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

#37 - Public rules repository

Issue - State: closed - Opened by bernt-matthias about 2 years ago - 2 comments

#36 - Use coverage to run pytest

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

#35 - Add support for overriding destination name

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

#34 - Add tpv format command

Pull Request - State: closed - Opened by nuwang about 2 years ago - 7 comments

#33 - Only count unique datasets when totalling input dataset sizes

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

#32 - Add context tests for context variables accessed within rules

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