Merge pull request #1049 from pysam-developers/release-0.17.0

Release 0.17.0

.github/workflows/ci.yaml

@@ -1,6 +1,7 @@
 name: CI
 
-on: [push, pull_request]
+# on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   direct:

.github/workflows/release.yaml

@@ -0,0 +1,107 @@
+name: Publish pysam wheels to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-10.15]  # windows-2019, 
+
+    steps:
+      - name: Checkout pysam
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Install prerequisite Python libraries
+        run:  |
+          python -m pip install --upgrade pip        
+          pip install cython pytest pytest-pep8
+
+      - name: Build wheels for linux
+        if:   runner.os == 'Linux'
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
+          CIBW_BEFORE_BUILD: yum install -y libcurl-devel zlib-devel bzip2-devel xz-devel && pip install cython
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux1
+          CIBW_MANYLINUX_I686_IMAGE: manylinux1
+
+      - name: Build wheels for macos
+        if:   runner.os != 'Linux'
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
+          CIBW_BEFORE_BUILD: pip install cython
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        os: [ubuntu, macos]
+        python-version: [3.9]
+
+    steps:
+      - name: Checkout pysam
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install prerequisite Python libraries
+        run:  pip install cython pytest pytest-pep8
+
+      - name: Install build prerequisites
+        if:   runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
+
+      - name: Create source distribution
+        run:  python setup.py sdist
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Get Artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish distribution to Test PyPI
+        if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+
+      - name: Publish distribution to PyPI
+        if: github.event_name == 'release' && github.event.action == 'published'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+

AUTHORS

@@ -1,8 +1,17 @@
+Many people have contributed to pysam. The list of github contributors
+is the best place to get a full list of authors and their contributions.
+The list and summary below is a out-of-date and represents the earlier
+stages of the project.
+
 List of contributors:
 
 Andreas Heger, Tildon Grant Belgard, Florian Finkernagel, Leo
 Goodstadt, Martin Goodson all contributed code to pysam.
 
+John Marshall has been looking after pysam and its community for
+several years, as well as making many code contributions and improving
+the engineering of pysam.
+
 Kevin B. Jacobs implemented a Cython wrapper for the VCF/BCF
 reader/writer in htslib.
 

doc/release.rst

@@ -2,6 +2,48 @@
 Release notes
 =============
 
+Release 0.17.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.13. Corresponding
+to new samtools commands, `pysam.samtools` now has additional functions
+`ampliconclip`, `ampliconstats`, `fqimport`, and `version`.
+
+Bugs fixed:
+
+* [#447] The maximum QNAME length is fully restored to 254
+* [#506, #958, #1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors
+* [#603] count_coverage: ignore reads that have no SEQ field
+* [#928] Fix ``pysam.bcftools.mpileup()`` segmentation fault
+* [#983] Add win32/\*.[ch] to MANIFEST.in
+* [#994] Raise exception in ``get_tid()`` if header could not be parsed
+* [#995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi
+* [#996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases
+* [#1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax
+* [#1035] Improved handling of file iteration errors
+* [#1038] ``tabix_index()`` no longer leaks file descriptors
+* [#1040] ``print(aligned_segment)`` now prints the correct TLEN value
+  (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)
+* *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0
+
+New facilities:
+
+* [PR #963] Additional VCF classes are exposed to pysam programmers
+* [#998, PR #1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion
+* [PR #1012] Running ``python setup.py sdist`` now automatically runs cythonize
+* Running tests with ``pytest`` now automatically runs ``make`` to generate test data
+
+Documentation improvements:
+
+* [#726] Clarify get_forward_sequence/get_forward_qualities documentation
+* [#865] Improved example
+* [#968] ``get_index_statstics`` parameters
+* [#986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open.
+* [#990] Corrected ``PileupColumn.get_query_sequences`` documentation
+* [#999] Fix documentation for ``AlignmentFile.get_reference_length()``
+* [#1002] Document the default min_base_quality for ``pileup()``
+
+
 Release 0.16.0
 ==============
 

pysam/version.py

@@ -1,5 +1,5 @@
 # pysam versioning information
-__version__ = "0.16.0.1"
+__version__ = "0.17.0"
 
 __samtools_version__ = "1.13"
 __bcftools_version__ = "1.13"