Release/0.8.0

.github/workflows/python-package.yml

@@ -1,4 +1,5 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# It will also update the test coverage using coveralls.io
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
 name: Python package
@@ -12,32 +13,44 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
     - name: Install package
       run: |
         python -m pip install .
+
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --statistics
-    - name: Test with pytest
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Test with pytest and output coverage report
       run: |
-        pytest
+        pytest --cov=mavehgvs --cov-report=xml:coverage-${{ matrix.python-version }}.xml --cov-report=term
+
+    - name: Send coverage to coveralls.io
+      # only calculate coverage for the Python version being used by MaveDB
+      if: matrix.python-version == '3.11'
+      uses: coverallsapp/github-action@v2
+      with:
+        file: coverage-${{ matrix.python-version }}.xml

.github/workflows/python-publish.yml

@@ -1,4 +1,4 @@
-# This workflow will upload a Python Package using Twine when a release is created
+# This workflow will upload a Python Package to PyPI when a release is created
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
 
 # This workflow uses actions that are not certified by GitHub.
@@ -16,24 +16,51 @@ permissions:
   contents: read
 
 jobs:
-  deploy:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
 
+      - name: Build release distributions
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install hatch
+          python -m hatch build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
     runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      url: https://pypi.org/p/mavehgvs
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
-    - name: Build package
-      run: hatch build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_MAVEHGVS }}
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 26.5.1
     hooks:
       - id: black
         language_version: python3.11
   - repo: https://github.com/pycqa/flake8
-    rev: 5.0.4
+    rev: 7.3.0
     hooks:
     -   id: flake8

README.md

@@ -1,4 +1,3 @@
-[![Build Status](https://travis-ci.com/VariantEffect/mavehgvs.svg?branch=main)](https://travis-ci.com/VariantEffect/mavehgvs)
 [![Coverage Status](https://coveralls.io/repos/github/VariantEffect/mavehgvs/badge.svg?branch=main)](https://coveralls.io/github/VariantEffect/mavehgvs?branch=main)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 

pyproject.toml

@@ -50,3 +50,7 @@ exclude = [
 
 [tool.setuptools.package-data]
 "mavehgvs" = ["py.typed"]
+
+[tool.black]
+line-length = 88
+target-version = ['py311']

src/mavehgvs/__init__.py

@@ -3,7 +3,7 @@
 from mavehgvs.variant import Variant
 from mavehgvs.util import parse_variant_strings
 
-__version__ = "0.7.0"
+__version__ = "0.8.0"
 
 __all__ = [
     "__version__",

src/mavehgvs/patterns/protein.py

@@ -13,7 +13,9 @@
 """
 
 pro_equal: str = (
-    rf"(?P<pro_equal>(?:(?P<position>{aa_pos})?(?P<equal>=))|(?P<equal_sy>\(=\)))"
+    rf"(?P<pro_equal>(?:(?:(?P<position>{aa_pos})|"
+    + rf"(?:(?P<start>{aa_pos})_(?P<end>{aa_pos})))?(?P<equal>=))|"
+    + rf"(?P<equal_sy>\(=\)))"
 )
 """str: Pattern matching protein equality or synonymous variant.
 """

src/mavehgvs/patterns/util.py

@@ -1,5 +1,4 @@
-"""Utility functions for working with mavehgvs regex pattern strings.
-"""
+"""Utility functions for working with mavehgvs regex pattern strings."""
 
 import re
 from typing import Sequence, Optional

src/mavehgvs/variant.py

@@ -396,19 +396,47 @@ def _variant_dictionary_to_string(  # noqa: max-complexity: 25
             raise MaveHgvsParseError("variant dictionary missing required keys")
 
         if variant_type == "equal":
-            expected_keys = ["variant_type", "prefix"]
-            if prefix == "p":
-                expected_keys.extend(["position", "target"])
-            else:
-                expected_keys.extend(["start_position", "end_position"])
-            if sorted(vdict.keys()) != sorted(expected_keys):
-                raise MaveHgvsParseError("variant dictionary contains invalid keys")
-            if prefix == "p":
-                variant_string = f"{vdict['target']}{vdict['position']}="
-            elif vdict["start_position"] == vdict["end_position"]:
-                variant_string = f"{vdict['start_position']}="
+            # special case for fully-identical variants
+            if sorted(vdict.keys()) == ["prefix", "variant_type"]:
+                variant_string = "="
+            elif (
+                sorted(vdict.keys()) == ["prefix", "synonymous", "variant_type"]
+                and prefix == "p"
+            ):
+                variant_string = "(=)"
             else:
-                variant_string = f"{vdict['start_position']}_{vdict['end_position']}="
+                expected_keys = [
+                    "variant_type",
+                    "prefix",
+                    "start_position",
+                    "end_position",
+                ]
+                if prefix == "p":
+                    expected_keys.extend(["start_target", "end_target"])
+                if sorted(vdict.keys()) != sorted(expected_keys):
+                    raise MaveHgvsParseError("variant dictionary contains invalid keys")
+                if vdict["start_position"] == vdict["end_position"]:
+                    if prefix == "p":
+                        if vdict["start_target"] == vdict["end_target"]:
+                            variant_string = (
+                                f"{vdict['start_target']}{vdict['start_position']}="
+                            )
+                        else:
+                            raise MaveHgvsParseError(
+                                "amino acid mismatch at same position"
+                            )
+                    else:
+                        variant_string = f"{vdict['start_position']}="
+                else:
+                    if prefix == "p":
+                        variant_string = (
+                            f"{vdict['start_target']}{vdict['start_position']}_"
+                            f"{vdict['end_target']}{vdict['end_position']}="
+                        )
+                    else:
+                        variant_string = (
+                            f"{vdict['start_position']}_{vdict['end_position']}="
+                        )
         elif variant_type == "sub":
             if sorted(vdict.keys()) != sorted(
                 ["variant_type", "prefix", "position", "target", "variant"]

tests/test_patterns/test_protein.py

@@ -24,6 +24,7 @@ def setUpClass(cls):
             "=",
             "(=)",
             "Cys22=",
+            "Gly12_Glu14=",
         ]
 
         cls.invalid_strings = ["=22", "Arg18(=)", "Cys-22", "=="]

tests/test_variant.py

@@ -80,6 +80,7 @@ def test_sub(self) -> None:
             "c.12=",
             "g.88_99=",
             "c.43-6_595+12=",
+            "p.Glu12_Gly14=",
         ]
 
         for s in variant_strings:
@@ -229,6 +230,7 @@ def test_creation(self):
         invalid_variant_strings = [
             "p.[Glu27Trp;=;Ter345Lys]",
             "p.[(=);Gly18del;Glu27Trp;Ter345Lys]",
+            "p.[Gln7_Asn19=;Glu27Trp;Ter345Lys]",
             "c.[12T>A;=;78+5_78+10del]",
             "c.[1_3=;12T>A;78+5_78+10del]",
             "p.[Glu27fs;Arg48Lys]",
@@ -296,11 +298,46 @@ def test_equal(self):
                 {
                     "variant_type": "equal",
                     "prefix": "p",
-                    "position": "27",
-                    "target": "Glu",
+                },
+                "p.=",
+            ),
+            (
+                {
+                    "variant_type": "equal",
+                    "prefix": "p",
+                    "synonymous": True,
+                },
+                "p.(=)",
+            ),
+            (
+                {
+                    "variant_type": "equal",
+                    "prefix": "c",
+                },
+                "c.=",
+            ),
+            (
+                {
+                    "variant_type": "equal",
+                    "prefix": "p",
+                    "start_position": "27",
+                    "start_target": "Glu",
+                    "end_position": "27",
+                    "end_target": "Glu",
                 },
                 "p.Glu27=",
             ),
+            (
+                {
+                    "variant_type": "equal",
+                    "prefix": "p",
+                    "start_position": "12",
+                    "start_target": "Glu",
+                    "end_position": "14",
+                    "end_target": "Gly",
+                },
+                "p.Glu12_Gly14=",
+            ),
             (
                 {
                     "variant_type": "equal",
@@ -523,6 +560,14 @@ def test_delins(self):
                 "end_target": "Cys",
                 "variant": "AlaGly",
             },
+            {
+                "variant_type": "equal",
+                "prefix": "p",
+                "start_position": "27",
+                "start_target": "Glu",
+                "end_position": "27",
+                "end_target": "Asp",
+            },
         ]
 
         for d, s in valid_dict_tuples:
@@ -561,6 +606,13 @@ def test_extra_keys(self):
                 "variant": "Ser",
                 "position": "Ala",
             },
+            {
+                "variant_type": "fs",
+                "prefix": "p",
+                "position": 80,
+                "target": "Cys",
+                "start_position": 23,
+            },
         ]
 
         for d in invalid_dicts: