chore(main): release 0.13.7

.github/workflows/conventional-prs.yml

@@ -0,0 +1,18 @@
+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

.github/workflows/main.yml

@@ -21,16 +21,22 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Setup black environment
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
         run: |
-          conda create -c conda-forge -y -q --name black black==22.3.0
+            pip install black==22.3.0
+            pip freeze
+
       - name: Check formatting
         run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate black
           black --check --diff -l 100 .
+
       - name: Comment PR
         if: github.event_name == 'pull_request' && failure()
         uses: marocchino/[email protected]
@@ -49,14 +55,12 @@ jobs:
           - '3.10'
     needs: formatting
     steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0 # we need tags for versioneer to work
+      - uses: actions/checkout@v4
 
       - name: Install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "${{ matrix.python-version }}"
 
       - name: Install dependencies
         run: |

.github/workflows/release-please.yml

@@ -0,0 +1,42 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: python
+          package-name: varfish-cli
+          token: ${{ secrets.BOT_TOKEN }}
+
+      - uses: actions/checkout@v2
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          python -m pip install --upgrade pip
+          python setup.py sdist
+
+      - name: Publish to PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

CHANGELOG.md

@@ -0,0 +1,177 @@
+# Changelog
+
+## [0.13.7](https://github.com/bihealth/vcfpy/compare/v0.13.6...v0.13.7) (2024-01-10)
+
+
+### Bug Fixes
+
+* remove versioneer Python 3.12 compatibility ([#160](https://github.com/bihealth/vcfpy/issues/160)) ([5e2860e](https://github.com/bihealth/vcfpy/commit/5e2860e22042aa794304c8805ca716a39c88f24e))
+
+## v0.13.6 (2022-11-28)
+
+-   Fixing bug in `setup.py` that prevented `pysam` dependency to be
+    loaded (#150).
+
+## v0.13.5 (2022-11-13)
+
+-   Treat `.bgz` files the same as `.gz` (#145, \#149)
+
+## v0.13.4 (2022-04-13)
+
+-   Switching to Github Actions for CI
+-   Fix INFO flag raises TypeError (#146)
+
+## v0.13.3 (2020-09-14)
+
+-   Adding `Record.update_calls`.
+-   Making `Record.{format,calls}` use list when empty
+
+## v0.13.2 (2020-08-20)
+
+-   Adding `Call.set_genotype()`.
+
+## v0.13.1 (2020-08-20)
+
+-   Fixed `Call.ploidy`.
+-   Fixed `Call.is_variant`.
+
+## v0.13.0 (2020-07-10)
+
+-   Fixing bug in case `GT` describes only one allele.
+-   Proper escaping of colon and semicolon (or the lack of escaping) in
+    `INFO` and `FORMAT`.
+
+## v0.12.2 (2020-04-29)
+
+-   Fixing bug in case `GT` describes only one allele.
+
+## v0.12.1 (2019-03-08)
+
+-   Not warning on `PASS` filter if not defined in header.
+
+## v0.12.0 (2019-01-29)
+
+-   Fixing tests for Python \>=3.6
+-   Fixing CI, improving tox integration.
+-   Applying `black` formatting.
+-   Replacing Makefile with more minimal one.
+-   Removing some linting errors from flake8.
+-   Adding support for reading VCF without `FORMAT` or any sample
+    column.
+-   Adding support for writing headers and records without `FORMAT` and
+    any sample columns.
+
+## v0.11.2 (2018-04-16)
+
+-   Removing `pip` module from `setup.py` which is not recommended
+    anyway.
+
+## v0.11.1 (2018-03-06)
+
+-   Working around problem in HTSJDK output with incomplete `FORMAT`
+    fields (#127). Writing out `.` instead of keeping trailing empty
+    records empty.
+
+## v0.11.0 (2017-11-22)
+
+-   The field `FORMAT/FT` is now expected to be a semicolon-separated
+    string. Internally, we will handle it as a list.
+-   Switching from warning helper utility code to Python `warnings`
+    module.
+-   Return `str` in case of problems with parsing value.
+
+## v0.10.0 (2017-02-27)
+
+-   Extending API to allow for reading subsets of records. (Writing for
+    sample subsets or reordered samples is possible through using the
+    appropriate `names` list in the `SamplesInfos` for the `Writer`).
+-   Deep-copying header lines and samples infos on `Writer` construction
+-   Using `samples` attribute from `Header` in `Reader` and `Writer`
+    instead of passing explicitely
+
+## 0.9.0 (2017-02-26)
+
+-   Restructuring of requirements.txt files
+-   Fixing parsing of no-call `GT` fields
+
+## 0.8.1 (2017-02-08)
+
+-   PEP8 style adjustments
+-   Using versioneer for versioning
+-   Using `requirements*.txt` files now from setup.py
+-   Fixing dependency on cyordereddict to be for Python \<3.6 instead of
+    \<3.5
+-   Jumping by samtools coordinate string now also allowed
+
+## 0.8.0 (2016-10-31)
+
+-   Adding `Header.has_header_line` for querying existence of header
+    line
+-   `Header.add_*_line` return a `bool` no indicating any conflicts
+-   Construction of Writer uses samples within header and no extra
+    parameter (breaks API)
+
+## 0.7.0 (2016-09-25)
+
+-   Smaller improvements and fixes to documentation
+-   Adding Codacy coverage and static code analysis results to README
+-   Various smaller code cleanup triggered by Codacy results
+-   Adding `__eq__`, `__neq__` and `__hash__` to data types (where
+    applicable)
+
+## 0.6.0 (2016-09-25
+
+-   Refining implementation for breakend and symbolic allele class
+-   Removing `record.SV_CODES`
+-   Refactoring parser module a bit to make the code cleaner
+-   Fixing small typos and problems in documentation
+
+## 0.5.0 (2016-09-24)
+
+-   Deactivating warnings on record parsing by default because of
+    performance
+-   Adding validation for `INFO` and `FORMAT` fields on reading (#8)
+-   Adding predefined `INFO` and `FORMAT` fields to `pyvcf.header` (#32)
+
+## 0.4.1 (2016-09-22)
+
+-   Initially enabling codeclimate
+
+## 0.4.0 (2016-09-22)
+
+-   Exporting constants for encoding variant types
+-   Exporting genotype constants `HOM_REF`, `HOM_ALT`, `HET`
+-   Implementing `Call.is_phased`, `Call.is_het`, `Call.is_variant`,
+    `Call.is_phased`, `Call.is_hom_ref`, `Call.is_hom_alt`
+-   Removing `Call.phased` (breaks API, next release is 0.4.0)
+-   Adding tests, fixing bugs for methods of `Call`
+
+## 0.3.1 (2016-09-21)
+
+-   Work around `FORMAT/FT` being a string; this is done so in the Delly
+    output
+
+## 0.3.0 (2016-09-21)
+
+-   `Reader` and `Writer` can now be used as context manager (with
+    `with`)
+-   Including license in documentation, including Biopython license
+-   Adding support for writing bgzf files (taken from Biopython)
+-   Adding support for parsing arrays in header lines
+-   Removing `example-4.1-bnd.vcf` example file because v4.1 tumor
+    derival lacks `ID` field
+-   Adding `AltAlleleHeaderLine`, `MetaHeaderLine`,
+    `PedigreeHeaderLine`, and `SampleHeaderLine`
+-   Renaming `SimpleHeaderFile` to `SimpleHeaderLine`
+-   Warn on missing `FILTER` entries on parsing
+-   Reordered parameters in `from_stream` and `from_file` (#18)
+-   Renamed `from_file` to `from_stream` (#18)
+-   Renamed `Reader.jump_to` to `Reader.fetch`
+-   Adding `header_without_lines` function
+-   Generally extending API to make it esier to use
+-   Upgrading dependencies, enabling pyup-bot
+-   Greatly extending documentation
+
+## 0.2.1 (2016-09-19)
+
+-   First release on PyPI