testing for various python versions, removing .python-version, testing for installation, some mypy fixes, pyproject.toml updates

Author: LinearParadox

.github/workflows/ci.yml

@@ -9,11 +9,14 @@ on:
 jobs:
   lint-and-test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: ${{ matrix.python-version }}
 
       - name: Install uv
         run: pip install uv
@@ -22,13 +25,17 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.cache/uv
-          key: ${{ runner.os }}-uv-${{ hashFiles('pyproject.toml') }}
+          key: ${{ runner.os }}-uv-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-uv-${{ matrix.python-version }}-
 
       - name: Install dependencies
         run: uv pip install --system -e . --group dev
 
       - name: Lint with ruff
+        # Run linting only on one Python version to avoid redundant checks
+        if: matrix.python-version == '3.12'
         run: ruff check .
 
       - name: Run tests with coverage
-        run: pytest --cov=loupepy -vv
+        run: pytest --cov=loupepy -vv

.gitignore

@@ -5,13 +5,15 @@ build/
 dist/
 wheels/
 *.egg-info
+.python-version
 #cache
 *.mypy_cache
 *.pytest_cache
 # Virtual environments
-random_testing*
 .venv/
 .git/
 .idea/
+# internal testing files
+random_testing*
 create_test_file.py
 test.h5ad

.python-version

@@ -1 +1 @@
-3.12
+3.10

pyproject.toml

@@ -1,13 +1,25 @@
 [project]
 name = "loupepy"
 version = "0.1.0"
-description = "Add your description here"
+authors = [
+  { name="Alexei Martsinkovskiy", email="[email protected]" },
+]
+description = "A python package for generating 10x cloupe files from anndata objects"
 readme = "README.md"
-requires-python = ">=3.12"
+requires-python = ">=3.10"
 dependencies = [
     "anndata>=0.11.4",
     "certifi>=2025.4.26",
 ]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+license = "MIT"
+license-files = ["LICEN[CS]E*"]
+[project.urls]
+Homepage = "https://github.com/linearparadox/loupepy"
+Issues = "https://github.com/linearparadox/loupepy/issues"
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
@@ -29,4 +41,4 @@ dev = [
     "ruff>=0.11.5",
     "scanpy>=1.11.1",
     "scipy-stubs>=1.15.2.1",
-]
+]

src/loupepy/convert.py

@@ -1,5 +1,7 @@
 import os
 from os import PathLike
+
+import numpy as np
 from anndata import AnnData # type: ignore
 import pandas as pd
 from scipy.sparse import csc_matrix
@@ -74,7 +76,7 @@ def _write_clusters(f: h5py.File, obs: pd.DataFrame) -> None:
         group.create_dataset(name="score", shape=(1,), data=[0.0])
         _create_string_dataset(group, "clustering_type", "unknown")
 
-def _write_projection(f: h5py.Group, dim: array, name: str) -> None:
+def _write_projection(f: h5py.Group, dim: ndarray, name: str) -> None:
     '''
     Writes the projections to the h5 file
 

src/loupepy/setup.py

@@ -2,7 +2,9 @@
 from urllib.request import urlretrieve
 import hashlib
 from pathlib import Path
+import logging
 import os
+from typing import Union
 OPERATING_SYSTEM = platform.system()
 
 def _get_checksum() -> tuple[str, str]:
@@ -57,37 +59,45 @@ def _download_loupe_converter(path: Path) -> None:
     link = _md5_checksum()
     urlretrieve(link, path)
     path.chmod(0o755)
-    print(path)
+    logging.log(logging.INFO, f"loupe converter binary successfully downloaded to {path}")
 
-def setup(path: Path | None | str = None) -> None:
+def setup(path: Union[os.PathLike[str], Path, None] = None) -> None:
     '''
-    Downloads the loupe converter binary to the specified path.
+    Downloads the loupe converter binary to the specified directory.
     If no path is specified, it will be downloaded to the default location for the operating system.
+    Args:
+        path (Union[os.PathLike[str], Path, None]): The path to download the loupe converter binary to.
+            If None, it will be downloaded to the default location for the operating system.
     '''
     if path is None:
         path = _get_install_path()
     if path is str:
         path = Path(path)
-    eula()
+    eula(path)
     _download_loupe_converter(path) # type: ignore
 
 
 
 
 
-def eula() ->  None:
+def eula(path: Union[os.PathLike[str], Path, None] = None) ->  None:
     '''
     Prompts the user to agree to the EULA, as it is in the R version of the tool
     '''
     print("This tool is independently maintained,"
         " but utilizes 10x genomics tools to perform conversions")
     print("By using this tool, you agree to the 10X Genomics End User License Agreement "
-        "(https://www.10xgenomics.com/legal/end-user-software-license-agreement).")
-    print("Do you agree to the terms of the EULA? (yes/no)")
-    response = input()
-    if response.lower() != 'yes':
+        "(https://www.10xgenomics.com/legal/end-user-software-license-agreement ).")
+    print("Do you agree to the terms of the EULA? (yes/y or no/n)")
+    response = input("Do you agree to the terms of the EULA? (yes/y or no/n)")
+    while response.lower() not in ["yes", "y", "no", "n"]:
+        response = input("Do you agree to the terms of the EULA? (yes/y or no/n)")
+    if response.lower() in  ["no", "n"]:
         raise OSError('You must agree to the EULA to use this tool')
-    path = _get_install_path()
+    if path is None:
+        path = _get_install_path()
+    if not isinstance(path, Path):
+        path = Path(path)
     path.mkdir(parents=False, exist_ok=True)
     path = path / 'eula'
     path.touch(exist_ok=True)
@@ -97,12 +107,16 @@ def eula() ->  None:
 
 
 
-def eula_reset() -> None:
+def eula_reset(path: Union[os.PathLike[str], Path, None] = None) -> None:
     '''
     Resets the EULA agreement
+    "
     '''
-    path = _get_install_path()
-    path = path / 'loupepy' / 'eula'
+    if path is None:
+        path = _get_install_path()
+    if not isinstance(path, Path):
+        path = Path(path)
+    path = path / 'eula'
     path.unlink()
     path=path.parent / 'loupe_converter'
     path.unlink(missing_ok=True)

src/loupepy/utils.py

@@ -101,7 +101,7 @@ def _validate_obs(obs: DataFrame, strict=False) -> DataFrame:
             warnings.warn(f'Column {col} has more than 32768 categories, skipping')
             obs.drop(col, axis=1, inplace=True)
 
-def _validate_obsm(obsm: dict[str, ndarray], obsm_keys: str|None = None, strict: bool = False) -> list[str]:
+def _validate_obsm(obsm: dict[str, ndarray], obsm_keys: list[str]|None = None, strict: bool = False) -> list[str]:
     """
     Validate the obsm dictionary.
     Args:

tests/test_setup.py

@@ -0,0 +1,13 @@
+import pytest
+from loupepy.setup import eula_reset, eula_reset, setup  # type: ignore
+import os
+
+def test_eula_and_reset(monkeypatch, tmp_path_factory):
+    output_dir = tmp_path_factory.mktemp("fake_directory")
+    monkeypatch.setattr('builtins.input', lambda _: "y")
+    setup(output_dir)
+    assert os.path.exists(output_dir / "eula")
+    assert os.path.exists(output_dir / "loupe_converter")
+    eula_reset(output_dir)
+    assert not os.path.exists(output_dir / "eula")
+    assert not os.path.exists(output_dir / "loupe_converter")