Ecosyste.ms: Issues

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GitHub / fair-workflows/fairworkflows issues and pull requests

#202 - Bump jinja2 from 2.11.3 to 3.1.3

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

#201 - Upgrade `nanopub` to v2.0.0

Pull Request - State: open - Opened by vemonet about 2 years ago

#197 - API reference in documentation is empty

Issue - State: open - Opened by svenvanderburg over 3 years ago

#196 - Add link to user documentation readme

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

#195 - Add docs

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

#194 - Add notebook for workflow building diagram

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

#193 - Integrate manual assistant

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

#192 - Add documentation for prov.py

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

#191 - fw.display() function doesn't show all variables of a workflow

Issue - State: open - Opened by rcelebi almost 4 years ago

#190 - fw.display() function doesn't show inputs/outputs of a workflow

Issue - State: closed - Opened by rcelebi almost 4 years ago - 1 comment

#189 - Allow no type annotation

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

#188 - Allow step without type hints

Issue - State: closed - Opened by svenvanderburg almost 4 years ago

#187 - Add documentation to StepRetroProv & WorkflowRetroProv

Issue - State: closed - Opened by raar1 almost 4 years ago

#186 - Issue185 stepretroprov workflowretroprov

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#185 - Improve StepRetroProv & WorkflowRetroProv

Issue - State: closed - Opened by svenvanderburg almost 4 years ago
Labels: needs refinement

#184 - Fair prov object

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

#183 - Update error message for publish_as_nanopub

Issue - State: closed - Opened by raar1 almost 4 years ago - 1 comment

#182 - Broken dependency rdf2dot in python==3.8.0

Issue - State: open - Opened by svenvanderburg almost 4 years ago

#181 - Fix retrospective logging

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#180 - Check if this (TODO) code can be fixed yet

Issue - State: closed - Opened by raar1 about 4 years ago - 2 comments

#179 - Reintroduce autopublishing of steps

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#178 - Improve display method

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#177 - .execute() should return a FairProv object

Issue - State: closed - Opened by svenvanderburg about 4 years ago

#176 - Use noodles.workflows.from_call for execute method

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#175 - Missing steps bug in is-fairworkflow decorator

Issue - State: closed - Opened by svenvanderburg about 4 years ago
Labels: bug

#174 - Fix missing steps bug in is-fairworkflows decorator

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#173 - Update coveralls badge for new coveralls endpoint

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

#172 - Improve error message when wrongly using is_fairworkflow decorator

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#171 - Retrospective prov should mirror Prospective prov

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment
Labels: blocked

#170 - Issue164 add language to rdf

Pull Request - State: closed - Opened by raar1 about 4 years ago - 1 comment

#168 - Fix retrospective provenance tracking

Issue - State: closed - Opened by svenvanderburg about 4 years ago - 1 comment

#167 - Bind the input arguments to the execute method

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#166 - Issue163 tuple for return semantic types

Pull Request - State: closed - Opened by raar1 about 4 years ago - 1 comment

#165 - publish_as_nanopub() broken by requirement to publish all steps individually

Issue - State: closed - Opened by raar1 about 4 years ago - 3 comments

#164 - Add language/version to Step RDF

Issue - State: closed - Opened by raar1 about 4 years ago - 3 comments

#162 - Map python computational types to e.g. XSD

Issue - State: open - Opened by raar1 about 4 years ago

#161 - Add semantic typing to is_fairworkflow decorator

Issue - State: closed - Opened by raar1 about 4 years ago - 3 comments

#159 - Throw TypeError if workflow does not return a promise

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#158 - Issue143 decorator semantic types

Pull Request - State: closed - Opened by raar1 about 4 years ago - 2 comments

#157 - Update to nanopub 1.2.2

Pull Request - State: closed - Opened by raar1 about 4 years ago

#156 - Adapt execution so that it doesn't require serlialization to database

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#155 - Issue90 generate retroprov nanopubs

Pull Request - State: closed - Opened by raar1 about 4 years ago - 1 comment

#153 - Independent step publications

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#152 - When publishing a workflow, raise error if not all steps are published yet

Issue - State: closed - Opened by svenvanderburg about 4 years ago - 1 comment

#151 - Bug: complex objects cannot be serialized by noodles

Issue - State: closed - Opened by svenvanderburg about 4 years ago - 2 comments

#150 - Restrict fair workflows to only consist of is_fairstep-decorated functions

Issue - State: closed - Opened by svenvanderburg about 4 years ago - 2 comments
Labels: blocked

#149 - Fix bug: #130 Steps without URI are reffered to as <None> in workflow RDF

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

#148 - Add azure devops sync github action

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

#147 - Make coveralls work again

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#146 - Issue141 create plex rdf from noodles workflow

Pull Request - State: closed - Opened by raar1 about 4 years ago

#145 - Bump version, for release with nanopub v1.2.1

Pull Request - State: closed - Opened by raar1 about 4 years ago

#144 - Issue139 implement noodles execution

Pull Request - State: closed - Opened by raar1 about 4 years ago

#143 - Decorator arguments to provide semantic type

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#142 - Provide display() with reduced information density

Issue - State: closed - Opened by raar1 about 4 years ago - 3 comments

#141 - Create Plex RDF from noodles workflow

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#140 - Decorators should not override function call

Issue - State: open - Opened by raar1 about 4 years ago
Labels: low priority

#139 - Implement noodles execution

Issue - State: closed - Opened by raar1 about 4 years ago - 2 comments

#138 - Allow the same step to be reused in a workflow

Issue - State: open - Opened by raar1 about 4 years ago
Labels: low priority

#137 - Allow connection of output of step to (specific) input var of another step

Issue - State: open - Opened by raar1 about 4 years ago - 1 comment
Labels: blocked

#136 - Issue135 noodles fw prototype

Pull Request - State: closed - Opened by raar1 about 4 years ago

#135 - Create FairWorkflows/Noodles prototype

Issue - State: closed - Opened by raar1 about 4 years ago - 2 comments

#134 - Variable RDF triples are wrong, use label instead

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#133 - .execute() method demo

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

#132 - Add derived_from property for RdfWrapper

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#131 - Notebook injection execution demo

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

#130 - Steps without URI are reffered to as <None> in workflow RDF.

Issue - State: closed - Opened by svenvanderburg about 4 years ago - 1 comment
Labels: bug

#129 - Update inputs and outputs of fairstep

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#128 - Fairstep decorator

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#127 - Fix shacl_validate mutating`self._rdf`

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#126 - Fix FileNotFoundError for plex-shapes.ttl in shacl_validate method

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago - 2 comments

#125 - Rename union to onion;

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#124 - How to represent inputs and outputs bound to a workflow?

Issue - State: open - Opened by svenvanderburg about 4 years ago - 3 comments

#123 - Fair data types

Issue - State: closed - Opened by svenvanderburg about 4 years ago - 2 comments

#121 - @fairstep decorator should act as a strict validator of a python function

Issue - State: closed - Opened by raar1 about 4 years ago - 12 comments

#120 - Typo in readme: Onion written as "Union"

Issue - State: closed - Opened by dsmits about 4 years ago - 1 comment

#119 - execute option for a workflow and a step

Issue - State: closed - Opened by rcelebi about 4 years ago - 1 comment

#118 - Add binder badge

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#117 - Investigate workflow.shacl_validate() error

Issue - State: closed - Opened by raar1 about 4 years ago

#116 - Allow user to specify that a FairStep was derived_from something

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#115 - Use nanopub v1

Pull Request - State: closed - Opened by raar1 about 4 years ago

#114 - Update to use nanopub version 1

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#113 - Add kwargs to publish_as_nanopub

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#112 - Bind namespaces to RDF so serialization is nicer

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#111 - Small fixes

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#110 - Bind namespaces to RDF so serialization is nicer

Pull Request - State: closed - Opened by svenvanderburg about 4 years ago

#109 - Update nanopub lib to 0.2.9

Pull Request - State: closed - Opened by raar1 about 4 years ago

#108 - Update fairworkflows to use nanopub v0.2.9

Issue - State: closed - Opened by raar1 about 4 years ago - 1 comment

#107 - Create user documentation

Issue - State: closed - Opened by svenvanderburg over 4 years ago

#106 - Allow control over which steps to publish for FairWorkflow.publish_to_nanopub()

Issue - State: closed - Opened by svenvanderburg over 4 years ago - 9 comments
Labels: low priority, needs refinement

#105 - Add more arguments to publish_as_nanopub method

Issue - State: closed - Opened by svenvanderburg over 4 years ago - 5 comments

#101 - Published workflows and steps have nice namespaces

Issue - State: closed - Opened by svenvanderburg over 4 years ago - 1 comment
Labels: low priority