Recent Releases of PhyloX
PhyloX - v1.1.0
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.1.0] - (Unreleased)
- Improve navigability of docs. (#64)
[1.0.5] - (2024-05-15)
- Rerelease because of failed pypi upload.
[1.0.4] - (2024-05-15)
- Fixed main example from the documentation. (#42)
- Cleaned up Heath network generator. (#48)
- Added more context and description of PhyloX to the JOSS paper. (#52)
- More robust Newick parser: allow empty properties. (#55)
- Add docstrings for LGT generator and for fromcherrypicking_sequence. (#60)
- Fix and test Newick input for HybridizationProblem. (#61)
- Fix bug in HybridizationProblem with lengths due to caching and degree-2 roots. (#62)
[1.0.3] - (2024-01-20)
Changed
- ReadTheDocs requirements, so that it builds again.
[1.0.2] - (2024-01-20)
Changed
- Github action for pypi release
[1.0.1] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] over 1 year ago
PhyloX - v1.0.5
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.0.6] - (Unreleased)
[1.0.5] - (2024-05-15)
- Rerelase because of failed pypi upload.
[1.0.4] - (2024-05-15)
- Fixed main example from the documentation. (#42)
- Cleaned up Heath network generator. (#48)
- Added more context and description of PhyloX to the JOSS paper. (#52)
- More robust Newick parser: allow empty properties. (#55)
- Add docstrings for LGT generator and for fromcherrypicking_sequence. (#60)
- Fix and test Newick input for HybridizationProblem. (#61)
- Fix bug in HybridizationProblem with lengths due to caching and degree-2 roots. (#62)
[1.0.3] - (2024-01-20)
Changed
- ReadTheDocs requirements, so that it builds again.
[1.0.2] - (2024-01-20)
Changed
- Github action for pypi release
[1.0.1] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] over 1 year ago
PhyloX - v1.0.4
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.0.5] - (Unreleased)
[1.0.4] - (2024-05-15)
- Fixed main example from the documentation. (#42)
- Cleaned up Heath network generator. (#48)
- Added more context and description of PhyloX to the JOSS paper. (#52)
- More robust Newick parser: allow empty properties. (#55)
- Add docstrings for LGT generator and for fromcherrypicking_sequence. (#60)
- Fix and test Newick input for HybridizationProblem. (#61)
- Fix bug in HybridizationProblem with lengths due to caching and degree-2 roots. (#62)
[1.0.3] - (2024-01-20)
Changed
- ReadTheDocs requirements, so that it builds again.
[1.0.2] - (2024-01-20)
Changed
- Github action for pypi release
[1.0.1] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] over 1 year ago
PhyloX - v1.0.3
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.0.4] - (Unreleased)
[1.0.3] - (2024-01-20)
Changed
- ReadTheDocs requirements, so that it builds again.
[1.0.2] - (2024-01-20)
Changed
- Github action for pypi release
[1.0.1] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] almost 2 years ago
PhyloX - v1.0.2
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.0.3] - (Unreleased)
[1.0.2] - (2024-01-20)
Changed
- Github action for pypi release
[1.0.1] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] almost 2 years ago
PhyloX - v1.0.1
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.0.2] - (Unreleased)
[1.0.1] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] almost 2 years ago
PhyloX - v1.0.0
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[1.0.1] - (Unreleased)
[1.0.0] - (2024-01-20)
Changed
- Version number, for first official release
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] almost 2 years ago
PhyloX - v0.0.7
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Types of changes: - Added for new features. - Changed for changes in existing functionality. - Deprecated for soon-to-be removed features. - Removed for now removed features. - Fixed for any bug fixes. - Security in case of vulnerabilities.
[0.0.8] - (Unreleased)
[0.0.7] - (2024-01-20)
Added
- Heustics for rearrangement move sequence calculations. (#35)
- Exact methods for rearrangement distance computation. (#37)
- JOSS article. (#39)
Changed
- Release action that also creates a github release, but only when a tag is added to the commit. (#41)
[0.0.6] - (2023-08-09)
Added
- Parsers to and from newick. (#30)
- Random methods with seed. (#34, #16)
Changed
- Licence to BSD-3-Clause to align with networkx. (#32)
[0.0.5] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release FIX.
[0.0.4] - (2023-07-24)
Fixed
- Automatic pypi release when pushing to release.
[0.0.3] - (2023-07-22)
Added
- Network properties methods: b2balance, countcherriesandreticulatedcherries and blobproperties. (#11)
- Tree-child-sequence functions. (#12)
- Usage of NetworkX referenced in README. (#14)
- Cherry picking hybridization workflow works again, including tests. (#15)
- Start documentation using sphinx. (#18)
- ReadtheDocs config. (#21)
- CI/CD release. (#22)
Changed
- Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
- Add lots of docstrings for sphinx autosummary. (#18)
Fixed
- Invalid horizontal moves generated by Move.random_move. (#18)
- Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
- Implementation of applymove for VMIN and VPLU, change the _reticulationnumber, also fixes the mcmc network generator. (#18)
[0.0.2] - (2023-06-19)
Added
- Release and version tag explanation. (#3)
- Automated tests. (#4)
Changed
- Run black and isort. (#4)
[0.0.1] - (2023-06-18)
Changed
- cleaned up DiNetwork class.
- cleaned up basic rearrangement methods.
- cleaned up isomorphism testing.
- cleand up checking for classes, including some cherry-picking methods.
Added
- Migrated messy old code to this repo.
- Automorphism count: count_automorphisms.
- tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
- configuration of pytest with --cov.
Scientific Software - Peer-reviewed
- Python
Published by github-actions[bot] almost 2 years ago