1. Drop support for python 3.6 and 3.7

    * Update versions for most dependencies
    * Update python version matrix in CI workflow
2. Add cgranges as submodule
    * Add build script to compile cgranges
    * Update pyproject.toml to call build script, and include cgranges package
    * Tell mypy to ignore lines that reference cgranges
    * In CI workflow
        * Checkout with submodules
        * Install dev dependencies and build before install
        * Update poetry version
3. Misc
    * Put authors list in correct format, drop Nick, add myself
    * Replace references to `py.path` with `tmp_path` in unit tests

.github/workflows/pythonpackage.yml

@@ -2,16 +2,18 @@ name: Python package
 
 on: [push]
 env:
-  POETRY_VERSION: 1.1.15
+  POETRY_VERSION: 1.6.1
 
 jobs:
   testing:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        PYTHON_VERSION: ["3.6", "3.7", "3.8", "3.9"]
+        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
 
     - name: Set up Python ${{matrix.PYTHON_VERSION}}
       uses: actions/setup-python@v4
@@ -26,8 +28,6 @@ jobs:
     - name: Install poetry
       shell: bash
       run: |
-        # See: https://github.com/python-poetry/poetry/blob/46bf7fd3d1797b75ad9b07adc280039d93414e07/pyproject.toml#L78-L81
-        python -m pip install --upgrade pip urllib3==1.25.10
         pip install poetry==${{env.POETRY_VERSION}}
 
     - name: Configure poetry
@@ -49,6 +49,8 @@ jobs:
     - name: Install deps
       shell: bash
       run: |
+        poetry install --only dev
+        poetry build
         poetry install --extras docs
 
     - name: Run pytest

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "cgranges"]
+	path = cgranges
+	url = https://github.com/lh3/cgranges

README.md

@@ -53,7 +53,7 @@ required.
 
 [rtd-link]:    http://pybedlite.readthedocs.org/en/stable
 
-**Requires python 3.6+**
+**Requires python 3.8+** (for python < 3.8, please use pybedlite <= 0.0.3)
 
 # Getting Setup for Development Work
 
@@ -62,14 +62,14 @@ required.
 A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link].  E.g.:
 
 ```bash
-conda create -n pybedlite python=3.6 poetry
+conda create -n pybedlite python=3.8 poetry
 conda activate pybedlite
 poetry install
 ```
 
 If the methods listed above do not work try the following:
 ```bash
-mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.1.15"
+mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
 mamba activate pybedlite
 poetry install
 ```

build.py

@@ -0,0 +1,26 @@
+from setuptools import Extension
+from Cython.Build import build_ext
+
+ext_modules = [
+    Extension(
+        "cgranges",
+        sources=["cgranges/python/cgranges.pyx", "cgranges/cgranges.c"],
+        depends=[
+            "cgranges/cgranges.h",
+            "cgranges/khash.h",
+            "cgranges/python/cgranges.pyx"
+        ],
+        include_dirs=["cgranges"]
+    )
+]
+
+def build(setup_kwargs):
+    """
+    This function is mandatory in order to build the extensions.
+    """
+    setup_kwargs.update(
+        {
+            "ext_modules": ext_modules,
+            "cmdclass": {"build_ext": build_ext},
+        }
+    )

pybedlite/overlap_detector.py

@@ -116,7 +116,7 @@ class OverlapDetector(Iterable[Interval]):
 
     def __init__(self) -> None:
         # A mapping from the contig/chromosome name to the associated interval tree
-        self._refname_to_tree: Dict[str, cr.cgranges] = {}
+        self._refname_to_tree: Dict[str, cr.cgranges] = {}  # type: ignore
         self._refname_to_indexed: Dict[str, bool] = {}
         self._refname_to_intervals: Dict[str, List[Interval]] = {}
 
@@ -132,7 +132,7 @@ def add(self, interval: Interval) -> None:
         """
         refname = interval.refname
         if refname not in self._refname_to_tree:
-            self._refname_to_tree[refname] = cr.cgranges()
+            self._refname_to_tree[refname] = cr.cgranges()  # type: ignore
             self._refname_to_indexed[refname] = False
             self._refname_to_intervals[refname] = []
 

pybedlite/tests/test_pybedlite.py

@@ -2,7 +2,6 @@
 
 import pytest
 from pathlib import Path
-from py._path.local import LocalPath as TmpDir
 from typing import List
 import pybedlite as pybed
 from pybedlite.bed_writer import MAX_BED_FIELDS
@@ -126,9 +125,8 @@ def compare_bed_records(
         12,
     ],
 )
-def test_bed_parsing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord]) -> None:
-    tmpdir_path = Path(tmpdir)
-    test_bed = tmpdir_path / "test.bed"
+def test_bed_parsing(tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord]) -> None:
+    test_bed = tmp_path / "test.bed"
 
     with BedWriter(test_bed, num_fields=bed_field_number) as test_out:
         test_out.write_all(bed_records, truncate=True, add_missing=True)
@@ -157,10 +155,9 @@ def test_bed_parsing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[Be
     ],
 )
 def test_preopened_bed_parsing(
-    tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord]
+    tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord]
 ) -> None:
-    tmpdir_path = Path(tmpdir)
-    test_bed = tmpdir_path / "test.bed"
+    test_bed = tmp_path / "test.bed"
 
     with BedWriter(test_bed, num_fields=bed_field_number) as test_out:
         test_out.write_all(bed_records, truncate=True, add_missing=True)
@@ -190,10 +187,9 @@ def test_preopened_bed_parsing(
         12,
     ],
 )
-def test_bed_writing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord]) -> None:
-    tmpdir_path = Path(tmpdir)
-    test_written_bed = tmpdir_path / "test_written.bed"
-    test_premade_bed = tmpdir_path / "test_premade.bed"
+def test_bed_writing(tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord]) -> None:
+    test_written_bed = tmp_path / "test_written.bed"
+    test_premade_bed = tmp_path / "test_premade.bed"
 
     with BedWriter(test_written_bed, num_fields=bed_field_number) as test_out:
         test_out.write_all(bed_records, truncate=True, add_missing=True)
@@ -228,11 +224,10 @@ def test_bed_writing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[Be
     ],
 )
 def test_preopened_bed_writing(
-    tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord]
+    tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord]
 ) -> None:
-    tmpdir_path = Path(tmpdir)
-    test_written_bed = tmpdir_path / "test_written.bed"
-    test_premade_bed = tmpdir_path / "test_premade.bed"
+    test_written_bed = tmp_path / "test_written.bed"
+    test_premade_bed = tmp_path / "test_premade.bed"
 
     test_written_bed_fh = test_written_bed.open("w")
 

pyproject.toml

@@ -1,48 +1,51 @@
 [tool.poetry]
 name = "pybedlite"
-version = "0.0.4-dev"
+version = "0.0.4-dev1"
 description = "Python classes for interfacing with bed intervals"
-authors = ["Nils Homer", "Tim Fennell", "Nathan Roach"]
+authors = [
+	"Nils Homer <[email protected]>",
+	"Tim Fennell <[email protected]>",
+	"John Didion <[email protected]>",
+]
 license = "MIT"
 readme = "README.md"
 homepage = "https://github.com/fulcrumgenomics/pybedlite"
 repository = "https://github.com/fulcrumgenomics/pybedlite"
 keywords = ["bioinformatics"]
 classifiers = [
 	"Development Status :: 3 - Alpha",
-    "Environment :: Console",
+	"Environment :: Console",
 	"Intended Audience :: Developers",
 	"Intended Audience :: Science/Research",
 	"License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
+	"Operating System :: OS Independent",
 	"Programming Language :: Python :: 3",
 	"Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Software Development :: Documentation",
-    "Topic :: Software Development :: Libraries :: Python Modules",
-]
-include = [
-    "LICENSE",
+	"Topic :: Software Development :: Documentation",
+	"Topic :: Software Development :: Libraries :: Python Modules",
 ]
+include = ["LICENSE"]
+packages = [{ include = "pybedlite" }, { include = "cgranges" }]
 
 [tool.poetry.dependencies]
-python = ">=3.6.0"
-attrs = ">=19.3.0"
-typing_extensions = { version = ">=3.7.4", python = "<3.8" }  # Literal support
-typing_inspect = { version = ">=0.3.1", python = "<3.8" }  # inspecting types
-sphinx = {version = "4.3.1", optional = true}
-Cython = "^0.29.30"
-cgranges = {git = "https://github.com/lh3/cgranges.git", rev = "v0.1"}
+python = "^3.8.0"
+attrs = "^23.0.0"
+sphinx = { version = "^7.0.0", optional = true }
 
 [tool.poetry.dev-dependencies]
-pytest = ">=5.4.2"
-mypy = ">=0.770"
-flake8 = ">=4.0.1"
-black = ">=19.10b0"
-pytest-cov = ">=2.8.1"
+pytest = "^7.0.0"
+mypy = "^1.5.0"
+flake8 = "^5.0.0"
+black = "^23.0.0"
+pytest-cov = "^4.0.0"
 
 [tool.poetry.extras]
 docs = ["sphinx"]
 
+[tool.poetry.build]
+script = "build.py"
+generate-setup-file = true
+
 [build-system]
-requires = ["poetry>=0.12"]
-build-backend = "poetry.masonry.api"
+requires = ["poetry-core", "setuptools", "cython"]
+build-backend = "poetry.core.masonry.api"