Merge pull request #157 from settylab/main

v1.4.0

Author: katosh

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v3
@@ -27,8 +27,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install .[dev]
+        python -m pip install flake8 pytest pytest-cov coverage typing-extensions
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install -e .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -39,6 +40,6 @@ jobs:
       env:
         PYTHONPATH: ./src/
       run: |
-        coverage run --source=src/palantir/ -m pytest tests/*.py
+        python -m pytest --cov=src/palantir
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3

.gitignore

@@ -4,9 +4,9 @@ __pycache__/
 *.h5ad
 build/
 palantir.egg-info/
-.coverage
+.coverage*
 notebooks/testing.ipynb
+.pytest_cache/
 dist/
 .vscode/
 data/
-venv/

README.md

@@ -51,8 +51,7 @@ here: https://palantir.readthedocs.io
 - [Replicate 2 (Rep2)](https://s3.amazonaws.com/dp-lab-data-public/palantir/human_cd34_bm_rep2.h5ad)
 - [Replicate 3 (Rep3)](https://s3.amazonaws.com/dp-lab-data-public/palantir/human_cd34_bm_rep3.h5ad)
 
-This notebook details how to use the data in `Python` and `R`:
-https://github.com/dpeerlab/Palantir/blob/master/notebooks/manuscript_data.ipynb
+This notebook details how to use the data in `Python` and `R`: http://nbviewer.jupyter.org/github/dpeerlab/Palantir/blob/master/notebooks/manuscript_data.ipynb
 
 ## Comparison to trajectory detection algorithms
 Notebooks detailing the generation of results comparing Palantir to trajectory detection algorithms are available [here](https://github.com/dpeerlab/Palantir/blob/master/notebooks/comparisons)
@@ -73,6 +72,24 @@ ____
 
 Release Notes
 -------------
+ ### Version 1.4.0
+ * Made pygam an optional dependency that can be installed with `pip install palantir[gam]` or `pip install palantir[full]`
+ * Added proper conditional imports and improved error handling for pygam
+ * Enhanced `run_magic_imputation` to return appropriate data types for different inputs
+ * Updated code to use direct AnnData imports for newer compatibility
+ * Improved version detection using `importlib.metadata` with graceful fallbacks
+ * Fixed Series indexing deprecation warnings in early cell detection functions
+ * Expanded and standardized documentation with NumPy-style docstrings throughout the codebase
+ * Added comprehensive type hints to improve code quality and IDE support
+ * Remove dependency from `_` methods in scanpy for plotting.
+ 
+ #### Testing and Quality Improvements
+ * Added comprehensive tests for optional pygam dependency
+ * Improved test coverage for run_magic_imputation with various input/output types
+ * Added integration tests against expected results
+ * Enhanced test infrastructure to work with newer library versions
+ * Expanded test coverage to catch edge cases in data processing
+
  ### Version 1.3.6
  * `run_magic_imputation` now has a boolean parameter `sparse` to control output sparsity
  * **bugfix**: `run_local_variability` for dense expression arrays now runs much faster and more accurate
@@ -88,15 +105,15 @@ Release Notes
  * compatibility with `scanpy>=1.10.0`
 
  ### Version 1.3.2
- * require `python>=3.8`
+ * require `python>=3.9`
  * implement CI for testing
- * fixes for edge cases discoverd through extended testing
+ * fixes for edge cases discovered through extended testing
  * implement `plot_trajectory` function to show trajectory on the umap
- * scale pseudotime to unit intervall in anndata
+ * scale pseudotime to unit interval in anndata
 
  ### Version 1.3.1
- * implemented `palantir.plot.plot_stats` to plot arbitray cell-wise statistics as x-/y-positions.
- * reduce memory usgae of `palantir.presults.compute_gene_trends`
+ * implemented `palantir.plot.plot_stats` to plot arbitrary cell-wise statistics as x-/y-positions.
+ * reduce memory usage of `palantir.presults.compute_gene_trends`
  * removed seaborn dependency
  * refactor `run_diffusion_maps` to split out `compute_kernel` and `diffusion_maps_from_kernel`
  * remove unused dependencies `tables`, `Cython`, `cmake`, and `tzlocal`.
@@ -107,49 +124,49 @@ Release Notes
  #### New Features
  * Enable an AnnData-centric workflow for improved usability and interoperability with other single-cell analysis tools.
  * Introduced new utility functions
-     * `palantir.utils.early_cell` To automate fining an early cell based on cell type and diffusion components.
+     * `palantir.utils.early_cell` To automate finding an early cell based on cell type and diffusion components.
      * `palantir.utils.find_terminal_states` To automate finding terminal cell states based on cell type and diffusion components.
      * `palantir.presults.select_branch_cells` To find cells associated to each branch based on fate probability.
      * `palantir.plot.plot_branch_selection` To inspect the cell to branch association.
      * `palantir.utils.run_local_variability` To compute local gene expression variability.
      * `palantir.utils.run_density` A wrapper for [mellon.DensityEstimator](https://mellon.readthedocs.io/en/latest/model.html#mellon.model.DensityEstimator).
      * `palantir.utils.run_density_evaluation` Evaluate computed density on a different dataset.
      * `palantir.utils.run_low_density_variability`. To aggregate local gene expression variability in low density.
-     * `palantir.plot.plot_branch`. To plot branch-selected cells over pseudotime in arbitrary y-postion and coloring.
-     * `palantir.plot.plot_trend`. To plot the gene trend ontop of `palantir.plot.plot_branch`.
+     * `palantir.plot.plot_branch`. To plot branch-selected cells over pseudotime in arbitrary y-position and coloring.
+     * `palantir.plot.plot_trend`. To plot the gene trend on top of `palantir.plot.plot_branch`.
  * Added input validation for better error handling and improved user experience.
  * Expanded documentation within docstrings, providing additional clarity for users and developers.
 
  #### Enhancements
  * Updated tutorial notebook to reflect the new workflow, guiding users through the updated processes.
  * Implemented gene trend computation using [Mellon](https://github.com/settylab/Mellon), providing more robust and efficient gene trend analysis.
- * Enable annotation in `palantir.plot.highight_cells_on_umap`.
+ * Enable annotation in `palantir.plot.highlight_cells_on_umap`.
 
  #### Changes
  * Replaced PhenoGraph dependency with `scanpy.tl.leiden` for gene trend clustering.
- * Deprecated the `run_tsne`, `determine_cell_clusters`, and `plot_cell_clusters` functions. Use corresponding implementations from [Scanpy](https://scanpy.readthedocs.io/en/stable/), widely used single-cell analysis library and direct dependecy of Palantir.
- * Rename `palantir.plot.highight_cells_on_tsne` to `palantir.plot.highight_cells_on_umap`
+ * Deprecated the `run_tsne`, `determine_cell_clusters`, and `plot_cell_clusters` functions. Use corresponding implementations from [Scanpy](https://scanpy.readthedocs.io/en/stable/), widely used single-cell analysis library and direct dependency of Palantir.
+ * Rename `palantir.plot.highlight_cells_on_tsne` to `palantir.plot.highlight_cells_on_umap`
  * Depend on `anndata>=0.8.0` to avoid issues writing dataframes in `ad.obsm`.
 
  #### Fixes
  * Addressed the issue of variability when reproducing results ([issue#64](https://github.com/dpeerlab/Palantir/issues/64)), enhancing the reproducibility and reliability of Palantir.
 
 
 ### Version 1.1.0
- * Replaced rpy2 with pyGAM for computing gene expression trends.
- * Updated tutorial and plotting functions
+ * Replaced rpy2 with pyGAM for computing gene expression trends. 
+ * Updated tutorial and plotting functions 
 
 
 ### Version 1.0.0
 
- * A fix to [issue#41](https://github.com/dpeerlab/Palantir/issues/41)
+ * A fix to [issue#41](https://github.com/dpeerlab/Palantir/issues/41) 
  * A fix to [issue#42](https://github.com/dpeerlab/Palantir/issues/42)
  * Revamped tutorial with support for Anndata and force directed layouts
 
 ### Version 0.2.6
 
  * A fix to [issue#33](https://github.com/dpeerlab/Palantir/issues/33) and [issue#31](https://github.com/dpeerlab/Palantir/issues/31)
-
+ 
 ### Version 0.2.5
 
  * A fix related to [issue#28](https://github.com/dpeerlab/Palantir/issues/28). When identifying terminal states, duplicate values were generated instead of unique ones.

pyproject.toml

@@ -0,0 +1,105 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "palantir"
+version = "1.4.0"
+description = "Palantir for modeling continuous cell state and cell fate choices in single cell data"
+authors = [
+    {name = "Palantir development team", email = "[email protected]"}
+]
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Operating System :: POSIX :: Linux",
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+dependencies = [
+    "numpy>=1.14.2",
+    "pandas>=0.22.0",
+    "scipy>=1.3",
+    "networkx>=2.1",
+    "scikit-learn",
+    "joblib",
+    "fcsparser>=0.1.2",
+    "leidenalg>=0.9.1",
+    "matplotlib>=2.2.2",
+    "anndata>=0.8.0",
+    "scanpy>=1.6.0",
+    "mellon>=1.3.0",
+]
+
+[project.optional-dependencies]
+gam = [
+    "pygam",
+]
+
+full = [
+    "pygam",
+]
+
+test = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "h5py",
+]
+
+[project.urls]
+Homepage = "https://github.com/dpeerlab/palantir"
+"Bug Tracker" = "https://github.com/dpeerlab/palantir/issues"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = "test_*.py"
+
+[tool.black]
+line-length = 100
+target-version = ['py39']
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
+'''
+
+[tool.coverage.run]
+source = ["palantir"]
+omit = [
+    "tests/*",
+    "*/config.py"
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "pass",
+    "raise ImportError",
+    "def _return_cell",
+    "print"
+]

requirements.txt

@@ -1 +1 @@
-.
+-e .

setup.py

@@ -1,56 +1,7 @@
 import sys
 from setuptools import setup
-from warnings import warn
 
-# get version and other attributes
-version_info = {}
-with open("src/palantir/version.py") as f:
-    exec(f.read(), version_info)
-with open("README.md", "r") as fh:
-    long_description = fh.read()
+# For backward compatibility, use setup.py as a proxy to pyproject.toml
+# All configuration is in pyproject.toml
 
-setup(
-    name="palantir",
-    version=version_info['__version__'],
-    author=version_info['__author__'],
-    author_email=version_info['__author_email__'],
-    description="Palantir for modeling continuous cell state and cell fate choices in single cell data",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/dpeerlab/palantir",
-    package_dir={"": "src"},
-    packages=["palantir"],
-    install_requires=[
-        "numpy>=1.14.2",
-        "pandas>=0.22.0",
-        "scipy>=1.3",
-        "networkx>=2.1",
-        "scikit-learn",
-        "joblib",
-        "fcsparser>=0.1.2",
-        "leidenalg>=0.9.1",
-        "matplotlib>=2.2.2",
-        "anndata>=0.8.0",
-        "scanpy>=1.6.0",
-        "mellon>=1.3.0",
-        "pygam",
-    ],
-    extras_require={
-        'dev': [
-            'flake8',
-            'pytest',
-            'coverage',
-            'typing-extensions'
-        ]
-    },
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-        "Operating System :: POSIX :: Linux",
-        "Development Status :: 5 - Production/Stable",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Scientific/Engineering :: Visualization",
-    ],
-    python_requires=">=3.8",
-)
+setup()

src/palantir/__init__.py

@@ -1,11 +1,35 @@
+"""
+Palantir - Modeling continuous cell state and cell fate choices in single cell data.
+
+Palantir is an algorithm to align cells along differentiation trajectories, identify
+differentiation endpoints, and estimate cell-fate probabilities in single-cell data.
+The package provides functions for preprocessing, visualization, trajectory analysis,
+and gene expression modeling along the trajectories.
+
+Modules
+-------
+config : Configuration settings for Palantir
+core : Core functions for running the Palantir algorithm
+presults : Class for storing and accessing Palantir results
+io : Input/output functions for loading and saving data
+preprocess : Preprocessing functions for single-cell data
+utils : Utility functions for analysis
+plot : Visualization functions
+"""
+
+import importlib.metadata
+
 from . import config
-from . import core
+
+# Import modules in a specific order to avoid circular imports
 from . import presults
+from . import core
 from . import io
 from . import preprocess
 from . import utils
 from . import plot
-from .version import __version__
+
+__version__ = importlib.metadata.version("palantir")
 
 __all__ = [
     "config",