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kaizhang · Dec 15, 2024 · d2c317d · d2c317d
1 parent 908524a
commit d2c317d
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Showing 4 changed files with 14 additions and 9 deletions.
diff --git a/.github/workflows/test_python.yml b/.github/workflows/test_python.yml
@@ -52,7 +52,7 @@ jobs:
         merge-multiple: true
 
     - name: Publish to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.8.14
+      uses: pypa/gh-action-pypi-publish@release/v1
 
 #  build-docker:
 #    needs: [build-and-test, build-wheel]

diff --git a/snapatac2-core/Cargo.toml b/snapatac2-core/Cargo.toml
@@ -10,7 +10,8 @@ homepage = "https://github.com/"
 keywords = ["single-cell", "biology"]
 
 [dependencies]
-anndata = "0.6.1"
+#anndata = "0.6.1"
+anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "0d27ac475634ed7703ab1a23e01e6a3031a28541"}
 anyhow = "1.0"
 bstr = "1.0"
 byteorder = "1.0"

diff --git a/snapatac2-python/Cargo.toml b/snapatac2-python/Cargo.toml
@@ -12,10 +12,14 @@ keywords = ["single-cell", "biology"]
 
 [dependencies]
 snapatac2-core = { workspace = true }
-anndata = "0.6.1"
-anndata-hdf5 = "0.5"
-anndata-zarr = "0.1"
-pyanndata = "0.5.1"
+#anndata = "0.6.1"
+anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "0d27ac475634ed7703ab1a23e01e6a3031a28541"}
+#anndata-hdf5 = "0.5"
+anndata-hdf5 = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "0d27ac475634ed7703ab1a23e01e6a3031a28541"}
+#anndata-zarr = "0.1"
+anndata-zarr = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "0d27ac475634ed7703ab1a23e01e6a3031a28541"}
+#pyanndata = "0.5.1"
+pyanndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "0d27ac475634ed7703ab1a23e01e6a3031a28541"}
 anyhow = "1.0"
 bed-utils = "0.7.1"
 flate2 = "1.0"

diff --git a/snapatac2-python/python/snapatac2/_utils.py b/snapatac2-python/python/snapatac2/_utils.py
@@ -27,23 +27,23 @@ def anndata_ipar(inputs, func, n_jobs=4):
         from multiprocess import get_context
 
         def _func(x):
-            adata = internal.read(x[1])
+            adata = internal.read(x[1], backend=x[2])
             result = func((x[0], adata))
             adata.close() 
             return result
 
         # Close the AnnData objects and return the filenames
         files = []
         for i, adata in inputs:
-            files.append((i, adata.filename))
+            files.append((i, adata.filename, adata.backend))
             adata.close()
 
         with get_context("spawn").Pool(n_jobs) as p:
             result = list(tqdm(p.imap(_func, files), total=len(files)))
 
         # Reopen the files if they were closed
         for _, adata in inputs:
-            adata.open()
+            adata.open(mode='r+')
 
         return result