sybila/ebcsgen issues and pull requests

#100 - Robust rate expressions

Pull Request - State: closed - Opened by mopichalova 11 months ago - 3 comments

#100 - Robust rate expressions

Pull Request - State: closed - Opened by mopichalova 11 months ago - 3 comments

#99 - Reverting to BCSL Original Syntax: Implementing "::"

Pull Request - State: closed - Opened by mopichalova 11 months ago - 2 comments

#99 - Reverting to BCSL Original Syntax: Implementing "::"

Pull Request - State: closed - Opened by mopichalova 11 months ago - 2 comments

#98 - Zooming in abstract syntax to original BCSL syntax

Issue - State: closed - Opened by mopichalova 11 months ago

#98 - Zooming in abstract syntax to original BCSL syntax

Issue - State: closed - Opened by mopichalova 11 months ago

#97 - Rule labels in regulations and regular regulations

Pull Request - State: closed - Opened by mopichalova 11 months ago - 4 comments

#97 - Rule labels in regulations and regular regulations

Pull Request - State: closed - Opened by mopichalova 11 months ago - 4 comments

#96 - Bidirectional rules

Pull Request - State: closed - Opened by mopichalova 12 months ago - 6 comments

#96 - Bidirectional rules

Pull Request - State: closed - Opened by mopichalova 12 months ago - 6 comments

#95 - Check that rule labels used in regulations do actually exist

Issue - State: closed - Opened by xtrojak 12 months ago

#95 - Check that rule labels used in regulations do actually exist

Issue - State: closed - Opened by xtrojak 12 months ago

#94 - Improve grammar syntax

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

#94 - Improve grammar syntax

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

#93 - Syntactic grammar improvements

Issue - State: closed - Opened by mopichalova about 1 year ago - 2 comments

#93 - Syntactic grammar improvements

Issue - State: closed - Opened by mopichalova about 1 year ago - 2 comments

#92 - enable direct usage of complexes

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

#92 - enable direct usage of complexes

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

#91 - Insert parsing logic improved

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

#91 - Insert parsing logic improved

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

#90 - 80 testing objects

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

#90 - 80 testing objects

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

#89 - Use complexes directly in `abstract_sequence`

Issue - State: closed - Opened by xtrojak about 1 year ago - 2 comments

#89 - Use complexes directly in `abstract_sequence`

Issue - State: closed - Opened by xtrojak about 1 year ago - 2 comments

#88 - Regular regulation - enable only regular expressions over rule labels

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

#88 - Regular regulation - enable only regular expressions over rule labels

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

#87 - Allow more robust rate expressions

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

#87 - Allow more robust rate expressions

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

#86 - Investigate content of Result.data in parsing tests

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

#86 - Investigate content of Result.data in parsing tests

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

#85 - 79 core tests

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

#85 - 79 core tests

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

#84 - Interactive editor within Galaxy

Issue - State: open - Opened by xtrojak over 1 year ago
Labels: Galaxy

#84 - Interactive editor within Galaxy

Issue - State: open - Opened by xtrojak over 1 year ago
Labels: Galaxy

#83 - Galaxy visualisations

Issue - State: open - Opened by xtrojak over 1 year ago
Labels: Galaxy

#83 - Galaxy visualisations

Issue - State: open - Opened by xtrojak over 1 year ago
Labels: Galaxy

#82 - Create Galaxy training

Issue - State: open - Opened by xtrojak over 1 year ago
Labels: documentation, Galaxy

#82 - Create Galaxy training

Issue - State: open - Opened by xtrojak over 1 year ago
Labels: documentation, Galaxy

#81 - Register to bio.tools

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

#81 - Register to bio.tools

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

#80 - Testing: Clean up creation of objects

Issue - State: closed - Opened by xtrojak over 1 year ago - 3 comments

#80 - Testing: Clean up creation of objects

Issue - State: closed - Opened by xtrojak over 1 year ago - 3 comments

#79 - Write tests for all other classes that are omitted for now

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

#79 - Write tests for all other classes that are omitted for now

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

#78 - Extracting parsing tests

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

#78 - Extracting parsing tests

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

#77 - Created requirements.txt file

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

#77 - Created requirements.txt file

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

#76 - create `requirements.txt` file

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

#76 - create `requirements.txt` file

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

#75 - Separate all parsing tests to a separate file/folder

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

#75 - Separate all parsing tests to a separate file/folder

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

#74 - Added tests for replacing abstract syntax

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

#74 - Added tests for replacing abstract syntax

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

#73 - not supported by macos

Issue - State: open - Opened by xtrojak over 1 year ago - 1 comment

#73 - not supported by macos

Issue - State: open - Opened by xtrojak over 1 year ago - 1 comment

#72 - `insert_atomic_to_complex` and `insert_struct_to_complex` do not check if the replaced agent is unspecified (i.e. atomic has `'_'` feature and structure has no atomics specified)

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

#72 - `insert_atomic_to_complex` and `insert_struct_to_complex` do not check if the replaced agent is unspecified (i.e. atomic has `'_'` feature and structure has no atomics specified)

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

#71 - Write tests targeting parsing issues

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

#71 - Write tests targeting parsing issues

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

#70 - Parsing improvements

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

#70 - Parsing improvements

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

#69 - Update GitHub workflows

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

#69 - Update GitHub workflows

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

#68 - Remove read() from PCTL processing output

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

#68 - Remove read() from PCTL processing output

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

#67 - Static analysis: rule redundancy elimination does not reflect rule labels

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

#67 - Static analysis: rule redundancy elimination does not reflect rule labels

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

#66 - Remove obsolete Galaxy contents

Issue - State: open - Opened by xtrojak over 2 years ago
Labels: Galaxy

#66 - Remove obsolete Galaxy contents

Issue - State: open - Opened by xtrojak over 2 years ago
Labels: Galaxy

#65 - PCTL synthesis output to CSV

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

#65 - PCTL synthesis output to CSV

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

#64 - Update PCTL output to csv

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

#64 - Update PCTL output to csv

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

#63 - Remove remote Storm calls

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

#63 - Remove remote Storm calls

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

#62 - Add dockerfile

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

#62 - Add dockerfile

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

#61 - Fix transforming rules

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

#61 - Fix transforming rules

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

#60 - "Transforming" rules not working

Issue - State: closed - Opened by xtrojak over 2 years ago
Labels: bug

#60 - "Transforming" rules not working

Issue - State: closed - Opened by xtrojak over 2 years ago
Labels: bug

#59 - Add the package on pypi

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

#59 - Add the package on pypi

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

#58 - SBML fix

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

#58 - SBML fix

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

#57 - Update wrappers

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

#57 - Update wrappers

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

#56 - Unify version to single location

Issue - State: open - Opened by xtrojak almost 3 years ago - 1 comment
Labels: enhancement

#56 - Unify version to single location

Issue - State: open - Opened by xtrojak almost 3 years ago - 1 comment
Labels: enhancement

#55 - Galaxy: RegionSampling improvement

Issue - State: open - Opened by xtrojak almost 3 years ago
Labels: Galaxy

#55 - Galaxy: RegionSampling improvement

Issue - State: open - Opened by xtrojak almost 3 years ago
Labels: Galaxy

#54 - Typo in error hadling

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

#54 - Typo in error hadling

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

#53 - Update galaxy wrappers to v2.0.1

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

#52 - SBML export minor bugs

Issue - State: closed - Opened by xtrojak almost 3 years ago - 1 comment
Labels: bug

#52 - SBML export minor bugs

Issue - State: closed - Opened by xtrojak almost 3 years ago - 1 comment
Labels: bug

#51 - Fix replication handling

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

#51 - Fix replication handling

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

#50 - Replication rules incorrect with indirect approach

Issue - State: closed - Opened by xtrojak almost 3 years ago - 1 comment
Labels: bug

GitHub / sybila/ebcsgen issues and pull requests