SNPio v1.1.4

Fixed issue with paths in snpio/docs/source/getting_started.rst

Docs would not build on readthedocs without fixing.

v1.1.3.0

moved docs to snpio/docs

SNPio v1.1.3

Version 1.1.3 (2024-10-25)

Features

• Updated tree parsing functionality and added it to the TreeParser class in the analysis/tree_parser.py module to conform to refactor, and added new functionality to parse, modify, draw, and save Newick and NEXUS tree files.
• siterates and qmatrix files now dynamically determine if they are in IQ-TREE format or if they are just in a simple tab-delimited or comma-delimited format.
• site_rates and qmat are now read in as pandas DataFrames with less complex logic.
• Added unit test for tree parsing.
• Added integration test for tree parsing.
• Added documentation for tree parsing.

Bug Fixes

• Fixed bug where the PhylipReader and StructureReader classes did not have the verbose and debug attributes.

Changes

• q property is now called qmat for clarity and easier searching in files.
• Removed redundant siterates_iqtree and qmatrix_iqtree arguments attributes from the GenotypeData, VCFReader, PhylipReader, StructureReader, and TreeParser classes.
• Added error handling for tree parsing.
• Added error handling for siterates and qmatrix files.

SNPio v1.1.2

Version 1.1.1 (2024-10-25)

Features

• Updated tree parsing functionality and added it to the TreeParser class in the analysis/tree_parser.py module to conform to refactor, and added new functionality to parse, modify, draw, and save Newick and NEXUS tree files.
• siterates and qmatrix files now dynamically determine if they are in IQ-TREE format or if they are just in a simple tab-delimited or comma-delimited format.
• site_rates and qmat are now read in as pandas DataFrames with less complex logic.
• Added unit test for tree parsing.
• Added integration test for tree parsing.
• Added documentation for tree parsing.

Bug Fixes

• Fixed bug where the PhylipReader and StructureReader classes did not have the verbose and debug attributes.

Changes

• q property is now called qmat for clarity and easier searching in files.
• Removed redundant siterates_iqtree and qmatrix_iqtree arguments attributes from the GenotypeData, VCFReader, PhylipReader, StructureReader, and TreeParser classes.
• Added error handling for tree parsing.
• Added error handling for siterates and qmatrix files.

SNPio v1.1.1.0

Version 1.1.1 (2024-10-25)

Features

• Updated tree parsing functionality and added it to the TreeParser class in the analysis/tree_parser.py module to conform to refactor, and added new functionality to parse, modify, draw, and save Newick and NEXUS tree files.
• siterates and qmatrix files now dynamically determine if they are in IQ-TREE format or if they are just in a simple tab-delimited or comma-delimited format.
• site_rates and qmat are now read in as pandas DataFrames with less complex logic.
• Added unit test for tree parsing.
• Added integration test for tree parsing.
• Added documentation for tree parsing.

Bug Fixes

• Fixed bug where the PhylipReader and StructureReader classes did not have the verbose and debug attributes.

Changes

• q property is now called qmat for clarity and easier searching in files.
• Removed redundant siterates_iqtree and qmatrix_iqtree arguments attributes from the GenotypeData, VCFReader, PhylipReader, StructureReader, and TreeParser classes.
• Added error handling for tree parsing.
• Added error handling for siterates and qmatrix files.

SNPio v1.1.1

Version 1.1.1 (2024-10-25)

Features

• Updated tree parsing functionality and added it to the TreeParser class in the analysis/tree_parser.py module to conform to refactor, and added new functionality to parse, modify, draw, and save Newick and NEXUS tree files.
• siterates and qmatrix files now dynamically determine if they are in IQ-TREE format or if they are just in a simple tab-delimited or comma-delimited format.
• site_rates and qmat are now read in as pandas DataFrames with less complex logic.
• Added unit test for tree parsing.
• Added integration test for tree parsing.
• Added documentation for tree parsing.

Bug Fixes

• Fixed bug where the PhylipReader and StructureReader classes did not have the verbose and debug attributes.

Changes

• q property is now called qmat for clarity and easier searching in files.
• Removed redundant siterates_iqtree and qmatrix_iqtree arguments attributes from the GenotypeData, VCFReader, PhylipReader, StructureReader, and TreeParser classes.
• Added error handling for tree parsing.
• Added error handling for siterates and qmatrix files.

v1.1.0.1

• Added UserManual.pdf via pandoc
• tidied up API docs

v1.1.0

Version 1.1.0 (2024-10-08)

Features

• Full refactor of the codebase to improve user-friendliness, maintainability and readability.
  • Method chaining: All functions now return the object itself, allowing for method chaining and custom filtering orders with NRemover2.
  • Most objects now just take a GenotypeData object as input, making the code more modular and easier to maintain.
  • Improved documentation and docstrings.
  • Improved error handling.
  • Improved logging. All logging is now done with the Python logging module via the custom LoggerManager class.
  • Improved testing.
  • Improved performance.
    • Reduced memory usage.
    • Reduced disk usage.
    • Reduced CPU usage.
    • Reduced execution time, particularly for reading, loading, filtering, and processing large VCF files.
  • Improved plotting.
  • Improved data handling.
  • Improved file handling. All filenames now use pathlib.Path objects.
  • Code modularity: Many functions are now in separate modules for better organization.
  • Full unit tests for all functions.
  • Full integration tests for all functions.
  • Full documentation for all functions.

Version 1.0.4

Version 1.0.4 (2023-09-10)

Features

• Added functionality to filter out linked SNPs using CHROM and POS fields from VCF file.

Performance

• Made the Sankey plot function more modular and dynamic.

Bug Fixes

• Fix spacing between printed STDOUT.

Version 1.0.3.3

• Fix bug where VCF file CHROM strings were cut off after 10 characters.