ln-ttest 0.1.0__tar.gz

ln_ttest-0.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Oskar Kviman and Pedro F. Ferreira
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ln_ttest-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ln-ttest
+Version: 0.1.0
+Summary: LN's t-test: differential expression testing on an asymptotically unbiased log-fold-change estimator
+Author: Oskar Kviman, Pedro F. Ferreira
+Maintainer-email: "Pedro F. Ferreira" <pedro.miguel.ferreira.pf@gmail.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2026, Oskar Kviman and Pedro F. Ferreira
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/okviman/lntest
+Project-URL: Source, https://github.com/okviman/lntest
+Keywords: single-cell,differential-expression,transcriptomics,scanpy
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.9
+Requires-Dist: statsmodels>=0.13
+Provides-Extra: test
+Requires-Dist: anndata>=0.9; extra == "test"
+Requires-Dist: pandas>=1.5; extra == "test"
+Requires-Dist: scanpy>=1.10; extra == "test"
+Requires-Dist: pytest>=7; extra == "test"
+Provides-Extra: anndata
+Dynamic: license-file
+
+# LN's $t$-test
+
+Differential expression testing on an asymptotically unbiased log-fold-change estimator.
+
+## Installation
+
+```bash
+pip install ln-ttest
+```
+
+From a checkout:
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+```python
+from lntest import rank_genes_groups_ln
+
+rank_genes_groups_ln(adata, groupby="leiden", layer="norm_counts")
+adata.uns["rank_genes_groups"]["logfoldchanges"]
+adata.uns["rank_genes_groups"]["lfc_se"]      # SE of the LFC; lfc ± 1.96·se is the interval
+```
+
+Takes **normalised, not log-transformed** counts.

ln_ttest-0.1.0/README.md

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+# LN's $t$-test
+
+Differential expression testing on an asymptotically unbiased log-fold-change estimator.
+
+## Installation
+
+```bash
+pip install ln-ttest
+```
+
+From a checkout:
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+```python
+from lntest import rank_genes_groups_ln
+
+rank_genes_groups_ln(adata, groupby="leiden", layer="norm_counts")
+adata.uns["rank_genes_groups"]["logfoldchanges"]
+adata.uns["rank_genes_groups"]["lfc_se"]      # SE of the LFC; lfc ± 1.96·se is the interval
+```
+
+Takes **normalised, not log-transformed** counts.

ln_ttest-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+# The PyPI distribution name. It is NOT the import name, which stays `lntest`
+# (see [tool.setuptools] below). PyPI rejected `lntest` as "too similar to an
+# existing project" -- `intest` exists, and PyPI treats l/i/1 as confusable to
+# block typosquatting. So: pip install ln-ttest, then `from lntest import ...`,
+# the way scikit-learn installs and imports as sklearn.
+name = "ln-ttest"
+version = "0.1.0"
+description = "LN's t-test: differential expression testing on an asymptotically unbiased log-fold-change estimator"
+readme = "README.md"
+requires-python = ">=3.10"
+authors = [
+    { name = "Oskar Kviman" },
+    { name = "Pedro F. Ferreira" },
+]
+maintainers = [
+    { name = "Pedro F. Ferreira", email = "pedro.miguel.ferreira.pf@gmail.com" },
+]
+license = { file = "LICENSE" }
+keywords = ["single-cell", "differential-expression", "transcriptomics", "scanpy"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "numpy>=1.23",
+    "scipy>=1.9",
+    # For Benjamini-Hochberg, imported lazily inside the branch that uses it --
+    # the same arrangement scanpy has, which declares statsmodels>=0.14.5 and
+    # imports multipletests inside `_rank_genes_groups.py`. Correcting the same
+    # way scanpy does is worth more than shedding the dependency, and every
+    # scanpy user already has it.
+    "statsmodels>=0.13",
+]
+
+[project.urls]
+# The shared repository, not the fork this happens to be developed on.
+# Renamed from DE-ZILN to lntest on 2026-09-11; the old URL still redirects, but
+# a package's metadata should name the repository as it is.
+Homepage = "https://github.com/okviman/lntest"
+Source = "https://github.com/okviman/lntest"
+
+[project.optional-dependencies]
+# anndata and pandas are needed only to *build* the objects the wrapper is
+# called with. The wrapper is duck-typed and never imports either, so they are
+# test dependencies rather than runtime ones. scanpy is here so the corr_method
+# tests can check we stay interchangeable with scanpy's own correction.
+test = ["anndata>=0.9", "pandas>=1.5", "scanpy>=1.10", "pytest>=7"]
+anndata = []  # kept as an accepted-but-empty alias; the extra is no longer needed
+
+[tool.setuptools]
+packages = ["lntest"]
+package-dir = { "" = "src" }
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

ln_ttest-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

ln_ttest-0.1.0/src/ln_ttest.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: ln-ttest
+Version: 0.1.0
+Summary: LN's t-test: differential expression testing on an asymptotically unbiased log-fold-change estimator
+Author: Oskar Kviman, Pedro F. Ferreira
+Maintainer-email: "Pedro F. Ferreira" <pedro.miguel.ferreira.pf@gmail.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2026, Oskar Kviman and Pedro F. Ferreira
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/okviman/lntest
+Project-URL: Source, https://github.com/okviman/lntest
+Keywords: single-cell,differential-expression,transcriptomics,scanpy
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.9
+Requires-Dist: statsmodels>=0.13
+Provides-Extra: test
+Requires-Dist: anndata>=0.9; extra == "test"
+Requires-Dist: pandas>=1.5; extra == "test"
+Requires-Dist: scanpy>=1.10; extra == "test"
+Requires-Dist: pytest>=7; extra == "test"
+Provides-Extra: anndata
+Dynamic: license-file
+
+# LN's $t$-test
+
+Differential expression testing on an asymptotically unbiased log-fold-change estimator.
+
+## Installation
+
+```bash
+pip install ln-ttest
+```
+
+From a checkout:
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+```python
+from lntest import rank_genes_groups_ln
+
+rank_genes_groups_ln(adata, groupby="leiden", layer="norm_counts")
+adata.uns["rank_genes_groups"]["logfoldchanges"]
+adata.uns["rank_genes_groups"]["lfc_se"]      # SE of the LFC; lfc ± 1.96·se is the interval
+```
+
+Takes **normalised, not log-transformed** counts.

ln_ttest-0.1.0/src/ln_ttest.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+src/ln_ttest.egg-info/PKG-INFO
+src/ln_ttest.egg-info/SOURCES.txt
+src/ln_ttest.egg-info/dependency_links.txt
+src/ln_ttest.egg-info/requires.txt
+src/ln_ttest.egg-info/top_level.txt
+src/lntest/__init__.py
+src/lntest/_ln_test.py
+src/lntest/_rank_genes_groups.py
+tests/test_corr_method.py
+tests/test_lntest.py
+tests/test_scanpy_wrapper.py

ln_ttest-0.1.0/src/ln_ttest.egg-info/dependency_links.txt

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+

ln_ttest-0.1.0/src/ln_ttest.egg-info/requires.txt

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+numpy>=1.23
+scipy>=1.9
+statsmodels>=0.13
+
+[anndata]
+
+[test]
+anndata>=0.9
+pandas>=1.5
+scanpy>=1.10
+pytest>=7

ln_ttest-0.1.0/src/ln_ttest.egg-info/top_level.txt

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+lntest

ln_ttest-0.1.0/src/lntest/__init__.py

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+"""LN's t-test: differential expression on an asymptotically unbiased log-fold-change estimator.
+
+    from lntest import get_LN_lfcs, rank_genes_groups_ln
+
+This module is the whole public surface. The two implementation modules are
+private, following scanpy, which keeps ``rank_genes_groups`` in
+``scanpy/tools/_rank_genes_groups.py`` and exposes only the name.
+
+``_rank_genes_groups`` was called ``scanpy_wrapper`` until 2026-09-10. The name
+was wrong in both directions: the module never imports scanpy, so it wraps
+nothing, and if scanpy ever dispatches to this package then scanpy is the
+wrapper, not us. It is scanpy-*shaped*, which is what its new name says.
+
+Everything here imports eagerly, and can, because the package depends on numpy,
+scipy and statsmodels alone -- and statsmodels only inside the Benjamini-Hochberg
+branch that needs it, which is again what scanpy does.
+"""
+from __future__ import annotations
+
+from ._ln_test import (
+    TRIGAMMA_EXACT,
+    TRIGAMMA_RECOMB25,
+    get_LN_lfcs,
+    get_LN_lfcs_sparse,
+    trigamma_diff_int,
+    trigamma_diff_recomb25,
+)
+from ._rank_genes_groups import CORR_METHODS, rank_genes_groups_ln
+
+def _detect_version() -> str:
+    # Scoped in a function so importlib.metadata's names do not land in the
+    # package namespace; `dir(lntest)` should show the API and nothing else.
+    try:  # pragma: no cover - fails only for a tree with no installed metadata
+        from importlib.metadata import version
+
+        # The distribution name, not this module's name. They differ: PyPI
+        # rejected "lntest" as too close to the existing "intest".
+        return version("ln-ttest")
+    except Exception:
+        return "0.0.0.dev0"
+
+
+__version__ = _detect_version()
+del _detect_version
+
+__all__ = [
+    "CORR_METHODS",
+    "TRIGAMMA_EXACT",
+    "TRIGAMMA_RECOMB25",
+    "get_LN_lfcs",
+    "get_LN_lfcs_sparse",
+    "rank_genes_groups_ln",
+    "trigamma_diff_int",
+    "trigamma_diff_recomb25",
+    "__version__",
+]
+
+
+def __dir__():
+    return sorted(__all__)