diff --git a/server/app/rest_api/rest.py b/server/app/rest_api/rest.py index f6c60e98..55f0d32d 100644 --- a/server/app/rest_api/rest.py +++ b/server/app/rest_api/rest.py @@ -45,7 +45,7 @@ class ConfigAPI(Resource): }, "links": {"about-dataset": current_app.config["ABOUT_DATASET"]}, "parameters": {**current_app.data.get_config_parameters(uid=cxguid, collection=anno_collection)}, - "library_versions": {"cellxgene": cellxgene_version, "anndata": anndata_version}, + "library_versions": {"cellxgene": cellxgene_version, "anndata": str(anndata_version)}, } } diff --git a/server/app/scanpy_engine/matrix_proxy.py b/server/app/scanpy_engine/matrix_proxy.py index 29e0e4fe..c244d4b6 100644 --- a/server/app/scanpy_engine/matrix_proxy.py +++ b/server/app/scanpy_engine/matrix_proxy.py @@ -38,6 +38,8 @@ class MatrixProxy_anndata_h5py(MatrixProxyView): "anndata.h5py.h5sparse.backed_csc_matrix", "anndata.h5py.h5sparse.backed_csr_matrix", "h5py._hl.dataset.Dataset", + "anndata._core.sparse_dataset.backed_csr_matrix", + "anndata._core.sparse_dataset.backed_csc_matrix", ) @classmethod diff --git a/server/app/util/matrix_proxy.py b/server/app/util/matrix_proxy.py index ad81c43f..988d6f75 100644 --- a/server/app/util/matrix_proxy.py +++ b/server/app/util/matrix_proxy.py @@ -73,6 +73,8 @@ class MatrixProxy(_ArrayProxyBase): "numpy.ndarray": True, "scipy.sparse.csc.csc_matrix": True, "scipy.sparse.csr.csr_matrix": True, + "anndata._core.sparse_dataset.backed_csr_matrix": "MatrixProxy_anndata_h5py", + "anndata._core.sparse_dataset.backed_csc_matrix": "MatrixProxy_anndata_h5py", } proxy_registry = None last_cache_token = None diff --git a/server/requirements.txt b/server/requirements.txt index 0b8abc51..085c1cb1 100644 --- a/server/requirements.txt +++ b/server/requirements.txt @@ -1,18 +1,17 @@ -# TEMP anndata 0.7 breaks cellxgene - workaround -anndata==0.6.22post1 -click>=6.7 -fastobo>=0.6.1 -Flask>=1.0.2 -Flask-Caching>=1.4.0 -Flask-Compress>=1.4.0 -Flask-Cors>=3.0.6 -Flask-RESTful>=0.3.6 -flatbuffers>=1.10.0 -fsspec>=0.4.4 -numpy>=1.15.2 -pandas>=0.24.2 -scipy>=1.3.0 -tables==3.5.1 -# TEMP workaround for https://github.com/theislab/scanpy/issues/832 aka h5py regression -h5py==2.9.0 -requests>=2.22.0 +anndata>=0.6.2 +click>=6.7 +fastobo>=0.6.1 +Flask>=1.0.2 +Flask-Caching>=1.4.0 +Flask-Compress>=1.4.0 +Flask-Cors>=3.0.6 +Flask-RESTful>=0.3.6 +flatbuffers>=1.10.0 +fsspec>=0.4.4 +numpy>=1.15.2 +pandas>=0.24.2 +scipy>=1.3.0 +tables==3.5.1 +# TEMP workaround for https://github.com/theislab/scanpy/issues/832 aka h5py regression +h5py==2.9.0 +requests>=2.22.0