Added

• Sequence.L property to get the length of a sequence consistently with HMM.M.
• Matrix.flatten method to get a Vector over the whole C-contiguous buffer of a Matrix.
• allocM property to Profile and OptimizedProfile to get the allocated capacity.
• HMM.emit_sequence, HMM.emit_alignment and Profile.emit_sequence to generate sequences from a model (#102).
• Missing type hints for gap_index, gap_symbol and type properties of Alphabet.

Removed

• Profile.transition_scores due to memory leak.

Fixed

• SequenceFile.__init__ crashing on opening SSI indices for gzip-compressed files.

Added

• Support for Windows AMD64 builds with MinGW (#92, see documentation).
• SequenceBlock.write method to write all sequences from a block to a file.
• SequenceBlock.total_length to compute the sum of lengths of sequences in a block.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.
• VectorI and MatrixI classes to pyhmmer.easel to store C int types (usually 32 bits).
• OptimizedProfile.ssv_filter method for NEON target in addition to SSE.
• msv_filter method to Profile and OptimizedProfile classes.
• Background.null1 to compute the null1 lod score for an arbitrary Sequence.
• HMMFile._file exposing the internal file-like object given to HMMFile constructor, if any (#89).
• SSIReader.primary_keys exposing a read-only sequence of primary keys inside a SSI file.
• SequenceFile.indexed and MSAFile.indexed to access data indexed with a SSI index (#85).

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• Setup distribution to generate a CMake package file to facilitate usage with downstream scikit-build-core dependent packages.
• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.
• Allow passing a buffer-protocol object interpreted as an ASCII string to the TextSequence constructor.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.
• Ensure correct background alphabet in Pipeline constructor when given a Background as argument.
• TopHits.merge potentially recomputing inclusion/reporting flags for hits obtained with bitscore cuttoffs.
• SSIReader missing methods in type stubs (#85).

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• Support for Windows AMD64 builds with MinGW (#92, see documentation).
• SequenceBlock.write method to write all sequences from a block to a file.
• SequenceBlock.total_length to compute the sum of lengths of sequences in a block.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.
• VectorI and MatrixI classes to pyhmmer.easel to store C int types (usually 32 bits).
• OptimizedProfile.ssv_filter method for NEON target in addition to SSE.
• msv_filter method to Profile and OptimizedProfile classes.
• Background.null1 to compute the null1 lod score for an arbitrary Sequence.
• HMMFile._file exposing the internal file-like object given to HMMFile constructor, if any (#89).

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• Setup distribution to generate a CMake package file to facilitate usage with downstream scikit-build-core dependent packages.
• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.
• Allow passing a buffer-protocol object interpreted as an ASCII string to the TextSequence constructor.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.
• Ensure correct background alphabet in Pipeline constructor when given a Background as argument.
• TopHits.merge potentially recomputing inclusion/reporting flags for hits obtained with bitscore cuttoffs.
• SSIReader missing methods in type stubs (#85).

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• Support for Windows AMD64 builds with MinGW (#92, see documentation).
• SequenceBlock.write method to write all sequences from a block to a file.
• SequenceBlock.total_length to compute the sum of lengths of sequences in a block.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.
• VectorI and MatrixI classes to pyhmmer.easel to store C int types (usually 32 bits).
• OptimizedProfile.ssv_filter method for NEON target in addition to SSE.
• msv_filter method to Profile and OptimizedProfile classes.
• Background.null1 to compute the null1 lod score for an arbitrary Sequence.
• HMMFile._file exposing the internal file-like object given to HMMFile constructor, if any (#89).

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• Setup distribution to generate a CMake package file to facilitate usage with downstream scikit-build-core dependent packages.
• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.
• Allow passing a buffer-protocol object interpreted as an ASCII string to the TextSequence constructor.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.
• Ensure correct background alphabet in Pipeline constructor when given a Background as argument.
• TopHits.merge potentially recomputing inclusion/reporting flags for hits obtained with bitscore cuttoffs.
• SSIReader missing methods in type stubs (#85).

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• SequenceBlock.write method to write all sequences from a block to a file.
• SequenceBlock.total_length to compute the sum of lengths of sequences in a block.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.
• VectorI and MatrixI classes to pyhmmer.easel to store C int types (usually 32 bits).
• OptimizedProfile.ssv_filter method for NEON target in addition to SSE.
• msv_filter method to Profile and OptimizedProfile classes.
• Background.null1 to compute the null1 lod score for an arbitrary Sequence.

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• Setup distribution to generate a CMake package file to facilitate usage with downstream scikit-build-core dependent packages.
• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.
• Allow passing a buffer-protocol object interpreted as an ASCII string to the TextSequence constructor.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.
• Ensure correct background alphabet in Pipeline constructor when given a Background as argument.
• TopHits.merge potentially recomputing inclusion/reporting flags for hits obtained with bitscore cuttoffs.
• SSIReader missing methods in type stubs (#85).

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• SequenceBlock.write method to write all sequences from a block to a file.
• SequenceBlock.total_length to compute the sum of lengths of sequences in a block.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.
• VectorI and MatrixI classes to pyhmmer.easel to store C int types (usually 32 bits).
• OptimizedProfile.ssv_filter method for NEON target in addition to SSE.

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.
• Allow passing a buffer-protocol object interpreted as an ASCII string to the TextSequence constructor.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.
• Ensure correct background alphabet in Pipeline constructor when given a Background as argument.

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• SequenceBlock.write method to write all sequences from a block to a file.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• SequenceBlock.write method to write all sequences from a block to a file.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.

Changed

• breaking: Make most textual attributes and properties str rather than bytes (#88).
  • Turn the following properties of Sequence into str instead of bytes: accession, description, name, source.
  • Turn the following properties of MSA into str instead of bytes: accession, description, name, source, author, names, reference, model_mask, secondary_structure, surface_accessibility, posterior_probabilities.
  • Turn the following properties of HMM, Profile and OptimizedProfile into str instead of bytes: name, accession, description.
  • Turn the following properties of Alignment into str instead of bytes: hmm_name, hmm_accession, hmm_sequence, target_name, target_sequence.
  • Make SequenceBlock.indexed and MSA.indexed mapping use str for keys instead of bytes.
  • Make SSIReader and SSIWriter use str for keys and aliases instead of bytes.
• Make DigitalSequence, DigitalSequenceBlock, DigitalMSA, SequenceFile, MSAFile, HMM, Profile, OptimizedProfileBlock, Background, Builder, Pipeline, HMMFile, HMMPressedFile generic over the alphabet type.
• Reorganize setup so that Easel and HMMER libraries, C headers and Cython headers are installed to the Python site path.
• Reorganize tests to skip tests in the absence of data files and remove larger test files from PyPI distributions.
• Enforce detection of invalid buffer sizes in _from_raw_bytes class constructors of various objects.
• Use PyUnicode_DecodeASCII to decode ASCII strings of known length instead of PyUnicode_FromString where applicable.

Fixed

• Remove hmmlogo.c from compiled HMMER sources to avoid an issue with the presence of a main function when linking.
• Avoid using multiprocessing.Value in pyhmmer.hmmer while in single-threaded mode for improved compatibility.
• Memory leak in Matrix caused by outdated allocation logic for zero dimensions.
• Make HMMFile constructor pretend to stream when given a file-like object to prevent HMMER from calling fseek and ftell.
• Incorrect declaration of Cython type declarations in various MSA property setters.

Removed

• Outdated compatibility code for PyPy 3.6.
• Support for positional arguments other than alphabet in TextMSA, DigitalMSA, TextSequence and DigitalSequence constructors.

Added

• Support for multithreading in hmmalign.

Fixed

• Formatting issues in TestMSA.compute_weights documentation (#96).
• Trace.__eq__ exiting the interpreter on inequality (EddyRivasLab/hmmer#344).

Changed

• Make Traces more similar to SequenceBlock and implement list-like interface (append, extend, clear, ...).

Added

• VectorD and MatrixD classes for double-precision data.
• __abs__ implementations for floating-point Vector and Matrix types.
• MSA.sequence_weights to access the sequence weights of an alignment.
• MSA.compute_weights to compute the sequence weights of an alignment like esl-weight (#94)
• MSA.mark_fragments method to identify fragmented sequences in an alignment.
• DigitalMSA.reverse_complement method to reverse-complement a nucleotide alignment.

Fixed

• Erroneous categories in documentation (#95, by @mtrsl).
• TextMSA and DigitalMSA constructors now default-initialize the sequence weights of the Easel alignment.

Changed

• Relax psutil dependency to allow versions as early as 5.0.
• Replace some cases of ValueError exceptions in pyhmmer.easel with more specific InvalidParameter errors.