Release v0.11.0

althonos · Jan 10, 2025 · 04b929b · 04b929b
1 parent 2a95d12
commit 04b929b
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diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
@@ -9,7 +9,7 @@ jobs:
 
   wheel-linux-aarch64:
     name: Build Linux wheels (Aarch64)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
       with:
@@ -20,13 +20,11 @@ jobs:
       with:
         platforms: arm64
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v2.22.0
       env:
         CIBW_ARCHS: aarch64
         CIBW_BUILD: 'cp*-manylinux_aarch64'
-        CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
     - uses: actions/upload-artifact@v4
@@ -36,19 +34,17 @@ jobs:
 
   wheel-linux-x86_64:
     name: Build Linux wheels (x86-64)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: true
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v2.22.0
       env:
         CIBW_ARCHS: x86_64
         CIBW_BUILD: 'cp*-manylinux_x86_64'
-        CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
     - uses: actions/upload-artifact@v4
@@ -58,19 +54,17 @@ jobs:
 
   wheel-macos-x86_64:
     name: Build MacOS wheels (x86-64)
-    runs-on: macOS-12
+    runs-on: macOS-latest
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: true
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v2.22.0
       env:
         CIBW_ARCHS: x86_64
         CIBW_BUILD: 'cp*-macosx_x86_64'
-        CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
     - uses: actions/upload-artifact@v4
@@ -80,19 +74,17 @@ jobs:
 
   wheel-macos-aarch64:
     name: Build MacOS wheels (Aarch64)
-    runs-on: macOS-12
+    runs-on: macOS-latest
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: true
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v2.22.0
       env:
         CIBW_ARCHS: arm64
         CIBW_BUILD: 'cp*-macosx_arm64'
-        CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
     - uses: actions/upload-artifact@v4
@@ -108,10 +100,10 @@ jobs:
       uses: actions/checkout@v4
       with:
         submodules: true
-    - name: Set up Python 3.11
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: 3.11
+        python-version: '3.12'
     - name: Install build requirements
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build wheel distribution
@@ -128,10 +120,10 @@ jobs:
     needs:
     - sdist
     steps:
-    - name: Setup Python 3.11
+    - name: Setup Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Download source distribution
       uses: actions/download-artifact@v4
       with:
@@ -175,8 +167,7 @@ jobs:
       uses: pypa/gh-action-pypi-publish@release/v1
 
   release:
-    permissions:
-      contents: write
+    permissions: write-all
     environment: GitHub Releases
     runs-on: ubuntu-latest
     if: "startsWith(github.ref, 'refs/tags/v')"

diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,8 @@
 .vscode
 *.BAK
 
+src/pyhmmer/_version.py
+
 ### C ###
 # Prerequisites
 *.d

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,7 +6,37 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.10.14...HEAD
+[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.11.0...HEAD
+
+
+## [v0.11.0] - 2025-01-10
+[v0.11.0]: https://github.com/althonos/pyhmmer/compare/v0.10.14...v0.10.15
+
+### Added
+- Missing type annotations to specific options of `LongTargetsPipeline`.
+- `__len__` implementation for `HMMPressedFile` using the entries in the SSI index.
+- Setters for residue-wise annotation properties in `HMM`.
+- Support for process-based parallelism in `pyhmmer.hmmer` in addition to thread-based.
+- Read-only buffer protocol implementation for `TextSequence` and `DigitalSequence` classes.
+
+### Changed
+- Drop support for Python 3.6.
+- Use CMake and `scikit-build-core` to build the package instead of `setuptools`.
+- Use `TypedDict` API to mark allowed keyword arguments in `pyhmmer.hmmer` functions.
+- Reorganize detection and handling of alphabets for arbitrary queries in `pyhmmer.hmmer`.
+- Allow passing a `SequenceFile` to most `pyhmmer.hmmer` functions.
+- Use faster `PyUnicode_FromStringAndSize` function to decode strings of known lengths in several `plan7` classes.
+- Make `SequenceFile` and `MSAFile` generic on the individual sequence and MSA types.
+- Reorganize `pyhmmer.hmmer` into different submodules.
+
+### Fixed
+- Type annotations not using `typing-extensions` for Python3.8 to 3.10.
+- Logic error causing out-of-bounds memory access in `TopHits.__getstate__`.
+- Avoid creating a new `Pipeline` object when running single-threaded searches in `pyhmmer.hmmer`.
+- Detect the appropriate `SequenceFile` type based on the `digital` flag value ([#72](https://github.com/althonos/pyhmmer/issues/72)).
+
+### Removed
+- Deprecated properties of `TopHits` (`query_name`, `query_length`, `query_accession`).
 
 
 ## [v0.10.15] - 2024-10-08

diff --git a/COPYING b/COPYING
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020-2024 Martin Larralde <[email protected]>
+Copyright (c) 2020-2025 Martin Larralde <[email protected]>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1 @@
+related.rst
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "pyhmmer"
-version = "0.10.15"
+version = "0.11.0"
 description = "Cython bindings and Python interface to HMMER3."
 readme = "README.md"
 requires-python = ">=3.7"

diff --git a/src/pyhmmer/__init__.py b/src/pyhmmer/__init__.py
@@ -25,13 +25,12 @@
 from . import easel
 from . import plan7
 from . import daemon
-
+from ._version import __version__
 from .hmmer import hmmalign, hmmsearch, hmmpress, nhmmer, hmmscan, phmmer, jackhmmer
 
 
 __author__ = "Martin Larralde <[email protected]>"
 __license__ = "MIT"
-__version__ = "0.10.15"
 __all__ = [
     "errors",
     "easel",
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,8 @@ @@
     .vscode
     *.BAK
+    src/pyhmmer/_version.py
     ### C ###
     # Prerequisites
     *.d
@@ Expand Down @@