rds2py 0.2.2__tar.gz → 0.2.4__tar.gz

{rds2py-0.2.2 → rds2py-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rds2py
-Version: 0.2.2
+Version: 0.2.4
 Summary: Parse and read RDS files as Python representations
 Home-page: https://github.com/biocpy/rds2py
 Author: jkanche
@@ -58,7 +58,7 @@ sp_mat = as_sparse(rObj)
 sce = as_SCE(rObj)
 ```
 
-For more use cases converting `data.frame`, `dgCMatrix`, `dgRMatrix` to Python, checkout the [documentation](https://biocpy.github.io/rds2py/).
+For more use cases converting `data.frame`, `dgCMatrix`, `dgRMatrix`, `dgTMatrix` to Python, checkout the [documentation](https://biocpy.github.io/rds2py/).
 
 ***If you want to add more representations, feel free to send a PR on this repository!***
 

{rds2py-0.2.2 → rds2py-0.2.4}/README.md

@@ -40,7 +40,7 @@ sp_mat = as_sparse(rObj)
 sce = as_SCE(rObj)
 ```
 
-For more use cases converting `data.frame`, `dgCMatrix`, `dgRMatrix` to Python, checkout the [documentation](https://biocpy.github.io/rds2py/).
+For more use cases converting `data.frame`, `dgCMatrix`, `dgRMatrix`, `dgTMatrix` to Python, checkout the [documentation](https://biocpy.github.io/rds2py/).
 
 ***If you want to add more representations, feel free to send a PR on this repository!***
 

{rds2py-0.2.2 → rds2py-0.2.4}/docs/tutorial.md

@@ -24,7 +24,7 @@ The package provides friendly functions to convert some R representations to use
 
 ### Matrices
 
-Use these methods if the RDS file contains either a sparse matrix (`dgCMatrix` or `dgRMatrix`) or a dense matrix.
+Use these methods if the RDS file contains either a sparse matrix (`dgCMatrix`, `dgRMatrix`, or `dgTMatrix`) or a dense matrix.
 
 
 ***Note: If an R object contains `dims` in the `attributes`, we consider this as a matrix.***

{rds2py-0.2.2/extern/rds2cpp/_deps/byteme-subbuild → rds2py-0.2.4/extern/rds2cpp}/CMakeFiles/3.26.3/CMakeSystem.cmake

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+          arg [-plugin-opt=-fresolution=/tmp/ccVPiZN2.res] ==> ignore
           arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
           arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
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@@ -238,7 +238,7 @@ events:
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           arg [-zrelro] ==> ignore
           arg [-o] ==> ignore
-          arg [cmTC_bbff4] ==> ignore
+          arg [cmTC_9e310] ==> ignore
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@@ -250,7 +250,7 @@ events:
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-          arg [CMakeFiles/cmTC_bbff4.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
+          arg [CMakeFiles/cmTC_9e310.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
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           arg [-lm] ==> lib [m]
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rds2py-0.2.4/extern/rds2cpp/_deps/byteme-src/.git/logs/HEAD

@@ -0,0 +1,2 @@
+0000000000000000000000000000000000000000 c638112d307eb873ec0c719046cf202d061dc4d0 runner <runner@fv-az562-581.uxtbn4doda5ujidlousdb0p40b.cx.internal.cloudapp.net> 1686598504 +0000	clone: from https://github.com/LTLA/byteme
+c638112d307eb873ec0c719046cf202d061dc4d0 52bf754cea80cc079092df2eef96a534876d0300 runner <runner@fv-az562-581.uxtbn4doda5ujidlousdb0p40b.cx.internal.cloudapp.net> 1686598504 +0000	checkout: moving from master to 52bf754cea80cc079092df2eef96a534876d0300

rds2py-0.2.4/extern/rds2cpp/_deps/byteme-src/.git/logs/refs/heads/master

@@ -0,0 +1 @@
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rds2py-0.2.4/extern/rds2cpp/_deps/byteme-src/.git/logs/refs/remotes/origin/HEAD

@@ -0,0 +1 @@
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{rds2py-0.2.2/extern/rds2cpp → rds2py-0.2.4/extern/rds2cpp/_deps/byteme-subbuild}/CMakeFiles/3.26.3/CMakeSystem.cmake

@@ -1,13 +1,13 @@
-set(CMAKE_HOST_SYSTEM "Linux-5.15.0-1036-azure")
+set(CMAKE_HOST_SYSTEM "Linux-5.15.0-1038-azure")
 set(CMAKE_HOST_SYSTEM_NAME "Linux")
-set(CMAKE_HOST_SYSTEM_VERSION "5.15.0-1036-azure")
+set(CMAKE_HOST_SYSTEM_VERSION "5.15.0-1038-azure")
 set(CMAKE_HOST_SYSTEM_PROCESSOR "x86_64")
 
 
 
-set(CMAKE_SYSTEM "Linux-5.15.0-1036-azure")
+set(CMAKE_SYSTEM "Linux-5.15.0-1038-azure")
 set(CMAKE_SYSTEM_NAME "Linux")
-set(CMAKE_SYSTEM_VERSION "5.15.0-1036-azure")
+set(CMAKE_SYSTEM_VERSION "5.15.0-1038-azure")
 set(CMAKE_SYSTEM_PROCESSOR "x86_64")
 
 set(CMAKE_CROSSCOMPILING "FALSE")

{rds2py-0.2.2 → rds2py-0.2.4}/extern/rds2cpp/_deps/byteme-subbuild/CMakeFiles/CMakeConfigureLog.yaml

@@ -7,5 +7,5 @@ events:
       - "/usr/local/share/cmake-3.26/Modules/CMakeDetermineSystem.cmake:204 (message)"
       - "CMakeLists.txt:10 (project)"
     message: |
-      The system is: Linux - 5.15.0-1036-azure - x86_64
+      The system is: Linux - 5.15.0-1038-azure - x86_64
 ...

{rds2py-0.2.2 → rds2py-0.2.4}/src/rds2py/interface.py

@@ -52,9 +52,9 @@ def as_sparse_matrix(robj: MutableMapping) -> sp.spmatrix:
     """
     cls = get_class(robj)
 
-    if cls not in ["dgCMatrix", "dgRMatrix"]:
+    if cls not in ["dgCMatrix", "dgRMatrix", "dgTMatrix"]:
         raise TypeError(
-            f"obj is not a supported sparse matrix format (`dgCMatrix`, `dgRMatrix`) but is `{cls}`"
+            f"obj is not a supported sparse matrix format (`dgCMatrix`, `dgRMatrix`, `dgTMatrix`) but is `{cls}`"
         )
 
     if cls == "dgCMatrix":
@@ -77,6 +77,18 @@ def as_sparse_matrix(robj: MutableMapping) -> sp.spmatrix:
             shape=tuple(robj["attributes"]["Dim"]["data"].tolist()),
         )
 
+    if cls == "dgTMatrix":
+        return sp.csr_matrix(
+            (
+                robj["attributes"]["x"]["data"],
+                (
+                    robj["attributes"]["i"]["data"],
+                    robj["attributes"]["j"]["data"],
+                ),
+            ),
+            shape=tuple(robj["attributes"]["Dim"]["data"].tolist()),
+        )
+
 
 def as_dense_matrix(robj: MutableMapping, order: str = "F") -> np.ndarray:
     """Convert a realized R object to a dense matrix representation
@@ -98,6 +110,7 @@ def as_dense_matrix(robj: MutableMapping, order: str = "F") -> np.ndarray:
 
     return np.ndarray(
         shape=tuple(robj["attributes"]["dim"]["data"].tolist()),
+        dtype=robj["data"].dtype,
         buffer=robj["data"],
         order=order,
     )
@@ -137,7 +150,7 @@ def as_SCE(robj: MutableMapping) -> np.ndarray:
 
         asy_cls = get_class(idx_asy)
 
-        if asy_cls in ["dgCMatrix", "dgRMatrix"]:
+        if asy_cls in ["dgCMatrix", "dgRMatrix", "dgTMatrix"]:
             robj_asys[asy_names[idx]] = as_sparse_matrix(idx_asy)
             if assay_dims is None:
                 assay_dims = robj_asys[asy_names[idx]].shape