From 9568c4f049f12de794b349afa6cd5aacf87542e1 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Fri, 10 Nov 2023 09:51:15 -0800 Subject: [PATCH 1/4] Fix issues with SE/SCE migration --- setup.cfg | 5 +++-- src/rds2py/interface.py | 10 +++++----- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/setup.cfg b/setup.cfg index b600ef9..878a1c0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -41,7 +41,7 @@ package_dir = =src # Require a min/specific Python version (comma-separated conditions) -# python_requires = >=3.8 +python_requires = >=3.8 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0. # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in @@ -53,7 +53,8 @@ install_requires = numpy pandas scipy - biocpy + singlecellexperiment>=0.3.3 + summarizedexperiment [options.packages.find] where = src diff --git a/src/rds2py/interface.py b/src/rds2py/interface.py index 062674c..580b377 100644 --- a/src/rds2py/interface.py +++ b/src/rds2py/interface.py @@ -243,15 +243,15 @@ def as_summarized_experiment( if _cls == "SummarizedExperiment": return SummarizedExperiment( - assays=robj_asys, rowData=robj_rowdata, colData=robj_coldata + assays=robj_asys, row_data=robj_rowdata, col_data=robj_coldata ) elif _cls == "SingleCellExperiment": return SingleCellExperiment( assays=robj_asys, - rowData=robj_rowdata, - colData=robj_coldata, - alterExps=robj_altExps, - reducedDims=robj_reduced_dims, + row_data=robj_rowdata, + col_data=robj_coldata, + alternative_experiments=robj_altExps, + reduced_dims=robj_reduced_dims, ) else: raise TypeError( From 03dd0c584c3db58c133e26aaf329ec50f2404dea Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Fri, 10 Nov 2023 09:54:33 -0800 Subject: [PATCH 2/4] Add missing anndata package --- setup.cfg | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.cfg b/setup.cfg index 878a1c0..c52944f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -55,6 +55,7 @@ install_requires = scipy singlecellexperiment>=0.3.3 summarizedexperiment + anndata [options.packages.find] where = src From 0a8e38b28514bc1bff36281705d980731699a491 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Fri, 10 Nov 2023 10:41:03 -0800 Subject: [PATCH 3/4] yet another package missing --- setup.cfg | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.cfg b/setup.cfg index c52944f..35d4f5c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -56,6 +56,7 @@ install_requires = singlecellexperiment>=0.3.3 summarizedexperiment anndata + mudata [options.packages.find] where = src From 107dab72022a5a8b824259c6d77c42d103f34373 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Fri, 10 Nov 2023 10:54:59 -0800 Subject: [PATCH 4/4] fix package versions, atleast until all packages are updated --- setup.cfg | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 35d4f5c..80d5076 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,8 +53,9 @@ install_requires = numpy pandas scipy - singlecellexperiment>=0.3.3 - summarizedexperiment + biocframe==0.3.20 + singlecellexperiment==0.3.3 + summarizedexperiment==0.3.7 anndata mudata