diff --git a/README.md b/README.md index 5d2c576..300a096 100644 --- a/README.md +++ b/README.md @@ -14,10 +14,16 @@ Information of CellTypist can be also found in our CellTypist portal. [![Website # Install CellTypist ### Using pip [![PyPI](https://img.shields.io/pypi/v/celltypist.svg?color=brightgreen&style=flat)](https://pypi.org/project/celltypist) +Install the core package: ```console pip install celltypist ``` +To include additional dependencies for tutorials and documentation, install with the [doc] extras: +```console +pip install celltypist[doc] +``` + ### Using conda [![install with bioconda](https://img.shields.io/conda/vn/bioconda/celltypist.svg?color=brightgreen&style=flat)](https://anaconda.org/bioconda/celltypist) ```console conda install -c bioconda -c conda-forge celltypist diff --git a/requirements-doc.txt b/requirements-doc.txt new file mode 100644 index 0000000..f77b05f --- /dev/null +++ b/requirements-doc.txt @@ -0,0 +1 @@ +leidenalg>=0.9.0 diff --git a/requirements.txt b/requirements.txt index 8a2fbf4..ce7ff6d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,4 +5,3 @@ openpyxl>=3.0.4 click>=7.1.2 requests>=2.23.0 scanpy>=1.7.0 -leidenalg>=0.9.0 diff --git a/setup.py b/setup.py index 63eea14..b577e26 100644 --- a/setup.py +++ b/setup.py @@ -4,8 +4,8 @@ def get_readme(): with open("README.md", "rt", encoding="utf-8") as fh: return fh.read() -def get_requirements(): - with open("requirements.txt", "rt", encoding="utf-8") as fh: +def get_requirements(requirements_file: str): + with open(requirements_file, "rt", encoding="utf-8") as fh: return [line.strip() for line in fh.readlines()] def get_version(): @@ -26,7 +26,10 @@ def get_version(): long_description_content_type="text/markdown", url="https://github.com/Teichlab/celltypist", packages=setuptools.find_packages(), - install_requires=get_requirements(), + install_requires=get_requirements("requirements.txt"), + extras_require={ + "doc": get_requirements("requirements-doc.txt"), + }, include_package_data=True, entry_points={ 'console_scripts': ['celltypist=celltypist.command_line:main'],