diff --git a/server/cli/prepare.py b/server/cli/prepare.py index b0ff3d43..bd8eb286 100644 --- a/server/cli/prepare.py +++ b/server/cli/prepare.py @@ -160,14 +160,7 @@ def prepare( sc.pp.neighbors(adata) def run_louvain(adata): - try: - sc.tl.louvain(adata) - except ModuleNotFoundError: - click.echo( - "\nWarning: louvain module is not installed, no clusters will be calculated. " - "To fix this please install cellxgene with the optional feature louvain enabled: " - "`pip install cellxgene[louvain]`" - ) + sc.tl.louvain(adata) def run_layout(adata): if len(unique(adata.obs["louvain"].values)) < 10: diff --git a/server/requirements-prepare.txt b/server/requirements-prepare.txt index d1b43def..630015df 100644 --- a/server/requirements-prepare.txt +++ b/server/requirements-prepare.txt @@ -1 +1,3 @@ scanpy>=1.3.7 +python-igraph +louvain>=0.6 diff --git a/setup.py b/setup.py index 7987697d..570b4eef 100644 --- a/setup.py +++ b/setup.py @@ -39,5 +39,5 @@ setup( "Topic :: Scientific/Engineering :: Bio-Informatics", ], entry_points={"console_scripts": ["cellxgene = server.cli.cli:cli"]}, - extras_require=dict(prepare=requirements_prepare, louvain=["python-igraph", "louvain>=0.6"], gui=["PySide2>=5.12.3", "cefpython3>=66", "requests"]), + extras_require=dict(prepare=requirements_prepare, gui=["PySide2>=5.12.3", "cefpython3>=66", "requests"]), )