dependency update

.github/workflows/pytest.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, windows-2019]
+        os: [ubuntu-22.04, windows-2022]
         python-version: [3.11.9]
     steps:
     - uses: actions/checkout@v3

.readthedocs.yml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 sphinx:
   configuration: docs/source/conf.py
@@ -14,6 +14,7 @@ sphinx:
 python:
   install:
     - requirements: requirements.txt
+    - requirements: requirements_extra.txt
     - requirements: docs/source/requirements.txt
     - method: pip
       path: .

VERSION

@@ -1 +1 @@
-0.28.12
+0.29.0

docs/source/install.md

@@ -2,9 +2,9 @@
 # Installation
 
 ## Installation through PyPi
-If you already have Python version 3.10.0 or greater, then you can install scarf using `pip`
+If you already have Python version 3.11.0 or greater, then you can install scarf using `pip`
 
-    pip install scarf
+    pip install scarf[extra]
 
 
 ````{note}
@@ -54,7 +54,7 @@ Okay, once you have got a terminal window open, type `python --version` and pres
 
 Now you may see one of the following three kinds of output:
 
-- If your output shows you have `Python 3.10.0` or a more recent version.
+- If your output shows you have `Python 3.11.0` or a more recent version.
   In this case, you are good to go, and you can skip Step 3.
 - If you have an earlier version than 3.10, for example 3.5 or 2.7, then see step 3.
 - If you see an error containing words `not found` or `not recognized` then most
@@ -93,7 +93,7 @@ That's it now you have the required build tools.
 
 We recommend that you first create an environment that you then install scarf into. 
 If you have followed the steps above, and you are using conda you create an environment
-by typing ``conda create --name scarf_env python=3.10`` in your terminal (Windows users must use Anaconda Prompt)
+by typing ``conda create --name scarf_env python=3.11`` in your terminal (Windows users must use Anaconda Prompt)
 
 This will also install python 3.10 into that environment. One of the benefits of working with
 environments is that you minimize the risk of some required package that you are using for
@@ -109,7 +109,7 @@ https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.h
 **Step 4:**
 
 Now, in your terminal, type this to install the latest version of Scarf:
-`pip install scarf`
+`pip install scarf[extra]`
 
 **Step 4.5 (Optional)**
 

docs/source/requirements.txt

@@ -1,12 +1,12 @@
 jinja2
-jedi>=0.17.0
-myst-parser>=0.13.7
-myst-nb>=0.12.3
-sphinx>=3.5.4
-sphinx_autodoc_typehints>=1.10.1
-sphinx-book-theme>=0.0.35
-sphinx-copybutton>=0.2.12
-sphinx-external-toc>=0.2.1
-sphinx-tabs>=0.3.1
-topacedo>=0.2.6
-nbclient<0.6
+jedi
+myst-parser
+myst-nb
+sphinx
+sphinx_autodoc_typehints
+sphinx-book-theme
+sphinx-copybutton
+sphinx-external-toc
+sphinx-tabs
+topacedo
+nbclient

requirements.txt

@@ -1,5 +1,4 @@
-# Core dependencies
-numpy>=2.0.1
+numpy
 pandas
 scipy
 scikit-learn
@@ -12,31 +11,10 @@ hnswlib
 zarr
 h5py>=3.3.0
 umap-learn
-scikit-learn
-scikit-network
-scipy==1.11.0
-statsmodels
-seaborn
-tqdm
-matplotlib
-threadpoolctl
-setuptools
-datashader
 leidenalg
-umap-learn
 scikit-network
 tqdm
 loguru
+setuptools
 packaging
 importlib_metadata
-
-# Extra dependencies
-requests
-gensim
-kneed
-matplotlib
-seaborn
-cmocean
-datashader
-ipython-autotime
-ipywidgets

requirements_extra.txt

@@ -0,0 +1,9 @@
+requests
+gensim
+kneed
+matplotlib
+seaborn
+cmocean
+datashader
+ipython-autotime
+ipywidgets

setup.py

@@ -4,8 +4,13 @@
 import glob
 
 
-def read(fname):
-    return open(os.path.join(os.path.dirname(__file__), fname)).read()
+def read(f_name):
+    with open(os.path.join(os.path.dirname(__file__), f_name)) as fp:
+        return fp.read().rstrip("\n")
+
+
+def read_lines(f_name):
+    return read(f_name).split("\n")
 
 
 class PostInstallCommand(install):
@@ -31,34 +36,41 @@ def run(self):
 
 
 if __name__ == "__main__":
-    classifiers = [
-        "Development Status :: 4 - Beta",
-        "License :: OSI Approved :: BSD License",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3",
-    ]
-    keywords = ["store"]
-    version = open("VERSION").readline().rstrip("\n")
+    version = read("VERSION").rstrip("\n")
+    core_requirements = read_lines('requirements.txt')
+    extra_requirements = read_lines('requirements_extra.txt')
+
     install_requires = (
         ["pybind11"]
         + [x.strip() for x in open("requirements.txt")]
         + ["dask[array]", "dask[dataframe]"]
     )
     dependency_links = []
+
     setup(
         name="scarf",
-        description="Scarf",
+        version=version,
+        python_requires='>=3.11',
+        description="Scarf: A scalable tool for single-cell omics data analysis",
         long_description=read("pypi_README.rst"),
+        long_description_content_type="text/x-rst",
         author="Parashar Dhapola",
         author_email="[email protected]",
         url="https://github.com/parashardhapola/scarf",
         license="BSD 3-Clause",
-        classifiers=classifiers,
-        keywords=keywords,
-        install_requires=install_requires,
-        dependency_links=dependency_links,
-        version=version,
-        packages=find_packages(),
+        classifiers=[
+            "Development Status :: 4 - Beta",
+            "License :: OSI Approved :: BSD License",
+            "Natural Language :: English",
+            "Programming Language :: Python :: 3",
+            "Programming Language :: Python :: 3.12",
+        ],
+        keywords=['single-cell'],
+        install_requires=core_requirements,
+        extras_require={
+            'extra': extra_requirements,
+        },
+        packages=find_packages(exclude=['tests*']),
         include_package_data=False,
         cmdclass={"install": PostInstallCommand},
     )