feat: use typeline for IO (#24)

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @clintval

.github/workflows/publish.yml → .github/workflows/publish_bedspec.yml

@@ -2,7 +2,7 @@ name: publish
 
 on:
   push:
-    tags: '\d+.\d+.\d+'
+    tags: '[0-9]+.[0-9]+.[0-9]+'
 
 env:
   POETRY_VERSION: 1.6
@@ -16,27 +16,28 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          submodules: true
 
       - uses: rickstaa/action-contains-tag@v1
         id: contains_tag
         with:
           reference: "main"
           tag: "${{ github.ref_name }}"
 
-  tests:
-    name: tests
+  unit-tests:
+    name: unit-tests
     needs: on-main-branch-check
     if: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
     uses: "./.github/workflows/tests.yml"
 
   build-wheels:
     name: build wheels
-    needs: tests
+    needs: unit-tests
     uses: "./.github/workflows/wheels.yml"
 
   build-sdist:
     name: build source distribution
-    needs: tests
+    needs: unit-tests
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -101,6 +102,7 @@ jobs:
         with:
           fetch-depth: 0
           ref: ${{ github.ref_name }}
+          submodules: true
 
       - name: Generate a Changelog
         uses: orhun/git-cliff-action@v3
@@ -127,6 +129,6 @@ jobs:
         with:
           name: ${{ github.ref_name }}
           body: |
-            ${{ needs.draft-changelog.outputs.release_body }}
+            ${{ needs.make-changelog.outputs.release_body }}
           draft: false
           prerelease: false

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Code checks
+name: unit tests
 
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        PYTHON_VERSION: ["3.11", "3.12"]
+        PYTHON_VERSION: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:

README.md

@@ -2,8 +2,9 @@
 
 [![PyPi Release](https://badge.fury.io/py/bedspec.svg)](https://badge.fury.io/py/bedspec)
 [![CI](https://github.com/clintval/bedspec/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain)
-[![Python Versions](https://img.shields.io/badge/python-3.11_|_3.12-blue)](https://github.com/clintval/bedspec)
-[![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![Python Versions](https://img.shields.io/badge/python-3.10_|_3.11_|_3.12-blue)](https://github.com/clintval/typeline)
+[![basedpyright](https://img.shields.io/badge/basedpyright-checked-42b983)](https://docs.basedpyright.com/latest/)
+[![mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
 [![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/)
 
@@ -21,65 +22,71 @@ pip install bedspec
 
 ### Building a BED Feature
 
-```python
-from bedspec import Bed3
+```pycon
+>>> from bedspec import Bed3
+>>> 
+>>> bed = Bed3("chr1", start=2, end=8)
 
-bed = Bed3("chr1", start=2, end=8)
 ```
 
 ### Writing
 
-```python
-from bedspec import BedWriter
+```pycon
+>>> from bedspec import BedWriter
+>>> from tempfile import NamedTemporaryFile
+>>> 
+>>> temp_file = NamedTemporaryFile(mode="w+t", suffix=".txt")
+>>>
+>>> with BedWriter.from_path(temp_file.name, Bed3) as writer:
+...     writer.write(bed)
 
-with BedWriter.from_path("test.bed") as writer:
-    writer.write(bed)
 ```
 
 ### Reading
 
-```python
-from bedspec import BedReader
+```pycon
+>>> from bedspec import BedReader
+>>> 
+>>> with BedReader.from_path(temp_file.name, Bed3) as reader:
+...     for bed in reader:
+...         print(bed)
+Bed3(refname='chr1', start=2, end=8)
 
-with BedReader.from_path("test.bed", Bed3) as reader:
-    for bed in reader:
-        print(bed)
-```
-```console
-Bed3(refname="chr1", start=2, end=8)
 ```
 
 ### BED Types
 
 This package provides builtin classes for the following BED formats:
 
-```python
-from bedspec import Bed2
-from bedspec import Bed3
-from bedspec import Bed4
-from bedspec import Bed5
-from bedspec import Bed6
-from bedspec import Bed12
-from bedspec import BedGraph
-from bedspec import BedPE
+```pycon
+>>> from bedspec import Bed2
+>>> from bedspec import Bed3
+>>> from bedspec import Bed4
+>>> from bedspec import Bed5
+>>> from bedspec import Bed6
+>>> from bedspec import Bed12
+>>> from bedspec import BedGraph
+>>> from bedspec import BedPE
+
 ```
 
 ### Overlap Detection
 
 Use a fast overlap detector for any collection of interval types, including third-party:
 
-```python
-from bedspec import Bed3, Bed4
-from bedspec.overlap import OverlapDetector
-
-bed1 = Bed3("chr1", start=1, end=4)
-bed2 = Bed3("chr1", start=5, end=9)
+```pycon
+>>> from bedspec import Bed3, Bed4
+>>> from bedspec.overlap import OverlapDetector
+>>>
+>>> bed1 = Bed3("chr1", start=1, end=4)
+>>> bed2 = Bed3("chr1", start=5, end=9)
+>>> 
+>>> detector = OverlapDetector[Bed3]([bed1, bed2])
+>>> 
+>>> my_feature = Bed4("chr1", start=2, end=3, name="hi-mom")
+>>> detector.overlaps(my_feature)
+True
 
-detector = OverlapDetector[Bed3]([bed1, bed2])
-
-my_feature = Bed4("chr1", start=2, end=3, name="hi-mom")
-
-assert detector.overlaps(my_feature) is True
 ```
 
 The overlap detector supports the following operations:
@@ -95,17 +102,18 @@ To create a custom BED record, inherit from the relevant BED-type (`PointBed`, `
 
 For example, to create a custom BED3+1 class:
 
-```python
-from dataclasses import dataclass
-
-from bedspec import SimpleBed
+```pycon
+>>> from dataclasses import dataclass
+>>> 
+>>> from bedspec import SimpleBed
+>>> 
+>>> @dataclass(eq=True)
+... class Bed3Plus1(SimpleBed):
+...     refname: str
+...     start: int
+...     end: int
+...     my_custom_field: float | None
 
-@dataclass(eq=True)
-class Bed3Plus1(SimpleBed):
-    refname: str
-    start: int
-    end: int
-    my_custom_field: float | None
 ```
 
 ## Development and Testing

bedspec/__init__.py

@@ -1,4 +1,3 @@
-# ruff: noqa: F401
 from ._bedspec import Bed2
 from ._bedspec import Bed3
 from ._bedspec import Bed4
@@ -10,11 +9,35 @@
 from ._bedspec import BedLike
 from ._bedspec import BedPE
 from ._bedspec import BedStrand
-from ._bedspec import GenomicSpan
+from ._bedspec import BedType
 from ._bedspec import Named
 from ._bedspec import PairBed
 from ._bedspec import PointBed
+from ._bedspec import ReferenceSpan
 from ._bedspec import SimpleBed
 from ._bedspec import Stranded
-from ._io import BedReader
-from ._io import BedWriter
+from ._reader import BedReader
+from ._writer import BedWriter
+
+__all__ = [
+    "Bed2",
+    "Bed3",
+    "Bed4",
+    "Bed5",
+    "Bed6",
+    "Bed12",
+    "BedColor",
+    "BedGraph",
+    "BedLike",
+    "BedPE",
+    "BedStrand",
+    "BedType",
+    "Named",
+    "PairBed",
+    "PointBed",
+    "ReferenceSpan",
+    "SimpleBed",
+    "Stranded",
+    "BedReader",
+    "BedWriter",
+]