Switch type checker from pyright to ty

check_typing_linting_and_formatting.py

@@ -30,7 +30,7 @@ def main() -> int:
     commands = {
         "ruff format": ["ruff", "format", "--check", "--diff", "pyranges1"],
         "ruff check": ["ruff", "check", "pyranges1"],
-        "pyright": ["pyright", "pyranges1"],
+        "ty": ["ty", "check"],
         "pytest": ["pytest", "--doctest-modules", "pyranges1/", "tests/unit/"],
         # "more doctest": ["python", "tests/run_doctest_tutorial_howto.py"],
     }

pyproject.toml

@@ -58,10 +58,10 @@ add-ons = [
 dev = [
     "tox",
     "ruff == 0.14.1",
-    "pyright",
+    "ty == 0.0.87",
     # Cap to the pandas-2.x stub line: unpinned, pandas-stubs resolves to the
     # 3.0.x series (which targets pandas 3.0 and changed e.g. the Series.map /
-    # astype overloads), producing spurious pyright errors against pandas 2.x.
+    # astype overloads), producing spurious type errors against pandas 2.x.
     "pandas-stubs<3",
     "types-tabulate",
     "pytest-watcher",
@@ -129,7 +129,7 @@ deps =
     pandas-stubs<3
     types-tabulate
     pytest
-    pyright == 1.1.406
+    ty == 0.0.87
     joblib
     gtfreader >= 0.3.0
     ruranges >= 0.1.8
@@ -138,7 +138,7 @@ deps =
     pyarrow
     # fisher
 commands =
-    pyright
+    ty check
     python tests/run_doctest_tutorial_howto.py
     pytest --doctest-modules pyranges1
     pytest tests/unit
@@ -180,18 +180,17 @@ ignore = [
 [tool.pytest-watcher]
 now = true
 
-[tool.pyright]
-include = ["pyranges1"]
-# typeCheckingMode = "strict"
-pythonVersion = "3.12"
+[tool.ty.environment]
+python-version = "3.12"
 
-ignore = ["pyranges1/core/pyranges_groupby.py"]
+[tool.ty.src]
+include = ["pyranges1"]
+exclude = ["pyranges1/core/pyranges_groupby.py"]
 
-# specific rules to disable
-reportUnknownParameterType = false
-reportUnknownMemberType = false
-reportUnknownArgumentType = false
-reportUnknownVariableType = false
+[tool.ty.analysis]
+# optional dependencies that are either compiled without stubs (pyBigWig, gtfreader._parser)
+# or not installed in CI
+allowed-unresolved-imports = ["pyBigWig", "gtfreader._parser", "fisher", "fire"]
 
 [tool.pytest.ini_options]
 markers = [

pyranges1/cli.py

@@ -9,7 +9,7 @@
 from pyranges1.core.pyranges_helpers import ensure_pyranges
 
 try:
-    import fire  # type: ignore[reportMissingImports]
+    import fire
 except ImportError:
     fire = None
 

pyranges1/core/example_data.py

@@ -308,23 +308,23 @@ def aorta(self) -> "pr.PyRanges":
 
         From the epigenomics roadmap.
         """
-        return pr.read_bed(ExampleData.files["aorta.bed"])  # type: ignore[index, misc]
+        return pr.read_bed(ExampleData.files["aorta.bed"])
 
     @property
     def aorta2(self) -> "pr.PyRanges":
         """Example ChIP-seq data.
 
         From the epigenomics roadmap.
         """
-        return pr.read_bed(ExampleData.files["aorta2.bed"])  # type: ignore[index, misc]
+        return pr.read_bed(ExampleData.files["aorta2.bed"])
 
     @property
     def ncbi_gff(self) -> "pr.PyRanges":
         """Example NCBI GFF data.
 
         Subset of the NCBI annotation of D.gyrociliatus assembly GCA_904063045.1.
         """
-        return pr.read_gff3(ExampleData.files["ncbi.gff.gz"])  # type: ignore[index, misc]
+        return pr.read_gff3(ExampleData.files["ncbi.gff.gz"])
 
     @property
     def ncbi_fasta(self) -> "pyfaidx.Fasta":
@@ -336,15 +336,15 @@ def ncbi_fasta(self) -> "pyfaidx.Fasta":
         To retrieve the location of the fasta file, use pyranges.example_data.files['ncbi.fasta']
         """
         try:
-            import pyfaidx  # type: ignore[import]
+            import pyfaidx
         except ImportError:
             LOGGER.exception(
                 "To use this method, pyfaidx must be installed. To get just the fasta file path, use pyranges.example_data.files['ncbi.fasta']. Use `conda install -c bioconda pyfaidx` or `pip install pyfaidx` to install pyfaidx.",
             )
             sys.exit(1)
 
         # note: example data include ncbi.fasta.fai, the pyfaidx index
-        return pyfaidx.Fasta(ExampleData.files["ncbi.fasta"])  # type: ignore[index, misc]
+        return pyfaidx.Fasta(ExampleData.files["ncbi.fasta"])
 
 
 example_data = ExampleData()

pyranges1/core/options.py

@@ -1,10 +1,12 @@
 # below: Class to manage PyRanges options
 # purposedly not using a docstring to avoid it being included in the docs
 
+from typing import Any
+
 
 class PyRangesOptions:
     def __init__(self) -> None:
-        self.options_in_use = {
+        self.options_in_use: dict[str, tuple[Any, str]] = {
             "max_rows_to_show": (8, "the max number of rows to show in PyRanges repr"),
             "max_column_names_to_show": (
                 3,

pyranges1/core/out.py

@@ -5,15 +5,15 @@
 
 import numpy as np
 import pandas as pd
-from natsort import natsorted  # type: ignore[import]
+from natsort import natsorted
 from pandas.core.frame import DataFrame
 
 from pyranges1.core.names import BIGWIG_SCORE_COL, CHROM_COL, END_COL, PANDAS_COMPRESSION_TYPE, START_COL
 from pyranges1.core.pyranges_helpers import ensure_pyranges
 from pyranges1.core.pyranges_main import PyRanges
 
 if TYPE_CHECKING:
-    from runlength import RleBatch  # type: ignore[import-not-found]
+    from runlength import RleBatch
 
 GTF_COLUMNS_TO_PYRANGES = {
     "seqname": "Chromosome",
@@ -199,7 +199,7 @@ def _to_bed_tabix(df: DataFrame, path: str | Path | None, compression: PANDAS_CO
         msg = "tabix=True writes a bgzip-compressed file: give a path ending in .gz or .bgz, and no other compression."
         raise ValueError(msg)
     try:
-        import pysam  # type: ignore[import]
+        import pysam
     except ImportError:
         msg = "pysam must be installed to write a tabix-indexed BED file. Use `pip install pysam`."
         raise ImportError(msg) from None
@@ -238,7 +238,7 @@ def _to_bigwig(
     return_data: bool = False,
 ) -> PyRanges | None:
     try:
-        import pyBigWig  # type: ignore[import]
+        import pyBigWig
     except ModuleNotFoundError:
         msg = "pybigwig must be installed to create bigwigs. Use `conda install -c bioconda pybigwig` or `pip install pybigwig` to install it."
         raise ImportError(msg) from None
@@ -532,7 +532,7 @@ def _to_bigbed(
     autosql: str | None = None,
 ) -> None:
     try:
-        import pybigtools  # type: ignore[import]
+        import pybigtools
     except ImportError:
         msg = "pybigtools must be installed to write BigBed files. Use `pip install pybigtools` to install it."
         raise ImportError(msg) from None
@@ -566,5 +566,5 @@ def _to_bigbed(
         sql = autosql
 
     ordered_sizes = {c: sizes[c] for c in sorted(sizes)}
-    writer = pybigtools.open(str(path), "w")  # type: ignore[attr-defined]
+    writer = pybigtools.open(str(path), "w")
     writer.write(ordered_sizes, iter(vals), autosql=sql)