SynBioDex/pySBOL3 issues and pull requests

#453 - Add Python 3.12 to the active set of Python versions

Pull Request - State: closed - Opened by tcmitchell 8 months ago

#452 - Fix pylint warnings and quite unit test logging

Pull Request - State: closed - Opened by tcmitchell 8 months ago

#451 - Fix dead link to the SBOL spec pdf

Pull Request - State: closed - Opened by PiotrZakrzewski 8 months ago - 2 comments

#450 - New pylint errors

Issue - State: closed - Opened by jakebeal 8 months ago
Labels: bug

#449 - Tutorial on working with SBOL Data Model

Pull Request - State: closed - Opened by PiotrZakrzewski 8 months ago - 6 comments

#448 - Add example of using Range for SubComponent location

Pull Request - State: closed - Opened by PiotrZakrzewski 8 months ago - 2 comments

#447 - updated doc.read to include the appropriate path to simple_library.nt

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

#446 - 'simple_library.nt' not present in the examples directory for it to be accessed by 'getting_started.ipynb' file

Issue - State: closed - Opened by Atishaysjain 10 months ago - 3 comments

#445 - Patch #444 by rolling back Windows/Mac python version

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

#444 - pySHACL fails in Python 3.12 and windows-latest builds

Issue - State: open - Opened by jakebeal about 1 year ago - 1 comment
Labels: bug

#443 - Update compatible python versions

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

#442 - Update supported python versions

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

#441 - Refactor refobj

Pull Request - State: open - Opened by bbartley about 1 year ago - 3 comments

#440 - Fix #437: visitor return values

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

#439 - Update read the docs build

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

#438 - Resolve #436: add wasInformedBy property to Activity

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

#437 - Visitor functions do not actually return values

Issue - State: closed - Opened by jakebeal about 1 year ago
Labels: bug

#436 - Activity missing wasInformedBy property

Issue - State: closed - Opened by jakebeal about 1 year ago
Labels: bug

#435 - Add pylint to GitHub workflow

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

#434 - Bump dependencies

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

#433 - Improve pylint compatibility

Issue - State: open - Opened by tcmitchell over 1 year ago

#432 - Bump version to 1.2

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

#431 - Orientation values need to be updated

Issue - State: open - Opened by jakebeal over 1 year ago - 1 comment
Labels: enhancement

#430 - Support copy of custom classes

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

#429 - Better error message for child objects used before being added to parant object

Pull Request - State: closed - Opened by Omarelsherif010 over 1 year ago - 1 comment

#428 - Problem with python-dateutil requirement

Issue - State: open - Opened by Gonza10V over 1 year ago - 2 comments

#427 - Can `Location` be extended?

Issue - State: open - Opened by tcmitchell over 1 year ago - 1 comment
Labels: question

#426 - Unittest feature class validation update

Pull Request - State: closed - Opened by Omarelsherif010 over 1 year ago - 3 comments

#425 - Fix typo of URL of sbol data model specification

Pull Request - State: closed - Opened by Omarelsherif010 over 1 year ago - 2 comments

#424 - fix typo in URL of SBOL data model specification

Issue - State: closed - Opened by Omarelsherif010 over 1 year ago

#423 - Update Toplevel.copy deprecation warning

Pull Request - State: closed - Opened by Omarelsherif010 over 1 year ago

#422 - Unittest feature class validation

Pull Request - State: closed - Opened by Omarelsherif010 over 1 year ago

#421 - Add support for Python 3.11

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

#420 - Write unit test for feature.py validate function

Issue - State: closed - Opened by Omarelsherif010 almost 2 years ago - 2 comments

#419 - Add files via upload

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

#418 - Adding SHACL for validating extensions

Issue - State: open - Opened by bbartley almost 2 years ago
Labels: question

#417 - Tutorial improvements

Issue - State: open - Opened by jakebeal almost 2 years ago

#416 - Adding an object to more than one parent Document

Issue - State: open - Opened by bbartley about 2 years ago - 3 comments

#415 - Use keyword arguments in Location super init call

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

#414 - Cannot extend `Location` as a `CustomIdentified`

Issue - State: closed - Opened by tcmitchell about 2 years ago - 1 comment

#413 - Update external references in change_object_namespace

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

#412 - if the namespace of an object is changed it should be reflected in the object

Issue - State: open - Opened by JMante1 about 2 years ago - 14 comments

#411 - Namespaces must not end with a slash

Issue - State: open - Opened by jakebeal about 2 years ago

#410 - Error when setting identity for SubComponent

Issue - State: open - Opened by noahsprent over 2 years ago - 4 comments

#409 - Document interface improvements

Pull Request - State: closed - Opened by jakebeal over 2 years ago

#408 - Macro for document create and read

Issue - State: closed - Opened by jakebeal over 2 years ago

#407 - PathLike for Document read/write

Issue - State: closed - Opened by jakebeal over 2 years ago

#406 - Add pySBOL3 paper citation

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#405 - Remove blank line from N-Triples output

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#404 - Eliminate empty lines in .nt serializations

Issue - State: closed - Opened by jakebeal over 2 years ago - 1 comment

#403 - Add CI testing for pypy-3.9

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#402 - Add guidelines for contributors

Issue - State: open - Opened by tcmitchell over 2 years ago

#401 - Fix a typo in the documentation

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#400 - Make CI builds run on Windows and Mac

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#399 - Actions builds for Windows and Mac are running on Ubuntu Linux

Issue - State: closed - Opened by tcmitchell over 2 years ago

#398 - Windows writes SORTED_NTRIPLES with CRLF

Issue - State: closed - Opened by jakebeal over 2 years ago - 7 comments
Labels: bug, invalid

#397 - Add pySBOL3 logo

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#396 - Made Toplevel.copy() deprecation warning more informative

Pull Request - State: closed - Opened by Omarelsherif010 over 2 years ago - 2 comments

#395 - Bump pyshacl dependency

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#394 - Make Toplevel.copy() deprecation warning more informative

Issue - State: closed - Opened by rpgoldman over 2 years ago - 4 comments
Labels: good first issue

#393 - New copy method is far slower than old copy method

Issue - State: open - Opened by jakebeal over 2 years ago

#392 - Bump version to 1.1

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#391 - Bump version to 1.0.1

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#390 - Accelerate loading

Pull Request - State: closed - Opened by tcmitchell over 2 years ago

#389 - Bump version to 1.1

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#388 - Bump version to 1.0

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#387 - Bump version to 1.0rc1

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#386 - Clarify the use of local path in identity

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#385 - Make `extract_display_id` a top level function

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#384 - Add PyPy 3.8 to the CI builds

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#383 - Add test for stable ordering

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago - 1 comment

#382 - Common cases for automatic list wrapping

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#381 - Accelerate loading

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

#380 - Lookup failure exceptions

Issue - State: open - Opened by jakebeal almost 3 years ago - 2 comments
Labels: SBOL-utilities

#379 - Display_name property

Pull Request - State: closed - Opened by mohitdmak almost 3 years ago

#378 - File format to extension function

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

#377 - Add dunder for better representation

Pull Request - State: closed - Opened by mohitdmak almost 3 years ago - 4 comments

#376 - Bump dependencies

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#375 - Bump version to 1.0b13

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#374 - Bump pyshacl version

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#373 - Migrate `TopLevel.copy` and `SBOLObject.copy` to `sbol3.copy`

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#372 - Update copy documentation, change argument names

Pull Request - State: closed - Opened by tcmitchell almost 3 years ago

#343 - Detect / prevent namespaces from ending with slash

Issue - State: closed - Opened by jakebeal about 3 years ago - 11 comments
Labels: question

#328 - Safe construction of identities

Issue - State: closed - Opened by jakebeal about 3 years ago - 4 comments
Labels: SBOL-utilities

#325 - Improve readthedocs formatting

Issue - State: open - Opened by jakebeal about 3 years ago - 3 comments
Labels: documentation, good first issue

#324 - Clean up ReferencedObject typing

Issue - State: open - Opened by jakebeal about 3 years ago - 2 comments

#310 - Unprotect sbol3.Identified._extract_display_id?

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

#304 - Add tutorial code from SynBioDex/Community-Media repo

Issue - State: open - Opened by tcmitchell about 3 years ago - 4 comments
Labels: documentation, good first issue

#303 - Add str method for Identified

Issue - State: closed - Opened by jakebeal about 3 years ago - 1 comment
Labels: good first issue

#301 - Make implicit list wrapping for singleton initial values universal

Issue - State: closed - Opened by jakebeal about 3 years ago - 14 comments

#297 - Append existing subcomponent to Component.features

Issue - State: open - Opened by djross22 about 3 years ago - 1 comment

#295 - Can document.objects contain non-TopLevel objects?

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

#292 - Be careful with automatic (and hidden) online validation and conversion

Issue - State: open - Opened by tcmitchell about 3 years ago - 1 comment

#290 - Object creation assumes that '/' implies a local ID segment. Do we want this?

Issue - State: closed - Opened by jakebeal over 3 years ago - 1 comment
Labels: documentation, question

#288 - Allow default local as well as namespace

Issue - State: closed - Opened by jakebeal over 3 years ago - 1 comment

#244 - Filetype to extension converter

Issue - State: closed - Opened by jakebeal over 3 years ago - 1 comment
Labels: good first issue

#237 - Accelerate lookup()

Issue - State: closed - Opened by jakebeal over 3 years ago - 3 comments
Labels: SBOL-utilities

#236 - Improve error message for setting refobj

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

#235 - Design: copy / clone / rename

Issue - State: closed - Opened by tcmitchell over 3 years ago - 19 comments

#234 - parent property?

Issue - State: open - Opened by jakebeal over 3 years ago - 3 comments

GitHub / SynBioDex/pySBOL3 issues and pull requests