From 7a584a74224794fcffc82086483b525531e26596 Mon Sep 17 00:00:00 2001 From: Oren Ben-Kiki Date: Sat, 23 Mar 2024 14:14:57 +0200 Subject: [PATCH] Convert to and from h5ad. --- daf/__init__.py | 2 + daf/anndata_format.py | 56 ++ daf/formats.py | 6 +- daf/generic.py | 21 + daf/julia_import.py | 3 +- docs/API.rst | 4 +- docs/anndata_format.rst | 5 + docs/v0.1.0/html/API.html | 44 +- .../html/_modules/daf/anndata_format.html | 171 ++++ docs/v0.1.0/html/_modules/daf/formats.html | 6 +- .../html/_modules/daf/julia_import.html | 3 +- docs/v0.1.0/html/_modules/index.html | 1 + docs/v0.1.0/html/_sources/API.rst.txt | 4 +- .../html/_sources/anndata_format.rst.txt | 5 + docs/v0.1.0/html/adapters.html | 7 +- docs/v0.1.0/html/anndata_format.html | 917 ++++++++++++++++++ docs/v0.1.0/html/concat.html | 11 +- docs/v0.1.0/html/copies.html | 7 +- docs/v0.1.0/html/data.html | 11 +- docs/v0.1.0/html/formats.html | 47 +- docs/v0.1.0/html/genindex.html | 45 +- docs/v0.1.0/html/julia_import.html | 7 +- docs/v0.1.0/html/objects.inv | Bin 1514 -> 1578 bytes docs/v0.1.0/html/operations.html | 7 +- docs/v0.1.0/html/py-modindex.html | 19 + docs/v0.1.0/html/queries.html | 11 +- docs/v0.1.0/html/searchindex.js | 2 +- docs/v0.1.0/html/storage_types.html | 64 +- docs/v0.1.0/html/views.html | 7 +- juliapkg.json | 3 + tests/test_anndata_format.py | 63 ++ 31 files changed, 1478 insertions(+), 81 deletions(-) create mode 100644 daf/anndata_format.py create mode 100644 daf/generic.py create mode 100644 docs/anndata_format.rst create mode 100644 docs/v0.1.0/html/_modules/daf/anndata_format.html create mode 100644 docs/v0.1.0/html/_sources/anndata_format.rst.txt create mode 100644 docs/v0.1.0/html/anndata_format.html create mode 100644 tests/test_anndata_format.py diff --git a/daf/__init__.py b/daf/__init__.py index 963c9ea..cddf111 100644 --- a/daf/__init__.py +++ b/daf/__init__.py @@ -51,6 +51,7 @@ # pylint: disable=wildcard-import,unused-wildcard-import from .julia_import import * # isort: skip +from .generic import * # isort: skip from .storage_types import * # isort: skip from .operations import * # isort: skip from .queries import * # isort: skip @@ -60,3 +61,4 @@ from .copies import * # isort: skip from .adapters import * # isort: skip from .concat import * # isort: skip +from .anndata_format import * # isort: skip diff --git a/daf/anndata_format.py b/daf/anndata_format.py new file mode 100644 index 0000000..a075b80 --- /dev/null +++ b/daf/anndata_format.py @@ -0,0 +1,56 @@ +""" +Import/export ``Daf`` data from/to ``AnnData``. See the Julia +`documentation `__ for details. +""" + +__all__ = ["h5ad_as_daf", "daf_as_h5ad"] + +from typing import Optional + +from .data import DafReader +from .formats import MemoryDaf +from .generic import JL_ABNORMAL_HANDLER +from .generic import AbnormalHandler +from .julia_import import jl + + +def h5ad_as_daf( + h5ad: str, + *, + name: Optional[str] = None, + obs_is: Optional[str] = None, + var_is: Optional[str] = None, + X_is: Optional[str] = None, + unsupported_handler: AbnormalHandler = "WarnHandler", +) -> MemoryDaf: + """ + View ``AnnData`` as a ``Daf`` data set, specifically using a ``MemoryDaf``. See the Julia + `documentation `__ for details. + + Note that you only pass an ``h5ad`` path, since the Julia ``AnnData`` object comes from the ``Muon.jl`` package and + is not compatible with the Python ``anndata`` object. + """ + return MemoryDaf( + jl.Daf.anndata_as_daf( + h5ad, + name=name, + obs_is=obs_is, + var_is=var_is, + X_is=X_is, + unsupported_handler=JL_ABNORMAL_HANDLER[unsupported_handler], + ) + ) + + +def daf_as_h5ad( + daf: DafReader, *, obs_is: Optional[str] = None, var_is: Optional[str] = None, X_is: Optional[str] = None, h5ad: str +) -> None: + """ + View the ``Daf`` data set as ``AnnData``. See the Julia + `documentation `__ + for details. + + Note this just creates the ``h5ad`` file. We do not return the ``AnnData`` object, because it is a Julia + (``Muon.jl``) ``AnnData`` object, which is **not** a Python ``anndata`` ``AnnData`` object. + """ + jl.daf_as_anndata(daf, obs_is=obs_is, var_is=var_is, X_is=X_is, h5ad=h5ad) diff --git a/daf/formats.py b/daf/formats.py index 2728c15..800053d 100644 --- a/daf/formats.py +++ b/daf/formats.py @@ -20,8 +20,10 @@ class MemoryDaf(DafWriter): `documentation `__ for details. """ - def __init__(self, *, name: str = "memory") -> None: - super().__init__(jl.Daf.MemoryDaf(name=name)) + def __init__(self, jl_obj: Optional[jl.MemoryDaf] = None, *, name: str = "memory") -> None: + if jl_obj is None: + jl_obj = jl.Daf.MemoryDaf(name=name) + super().__init__(jl_obj) class FilesDaf(DafWriter): diff --git a/daf/generic.py b/daf/generic.py new file mode 100644 index 0000000..e08d966 --- /dev/null +++ b/daf/generic.py @@ -0,0 +1,21 @@ +""" +Types that arguably should belong in a more general-purpose package. See the Julia +`documentation `__ for details. +""" + +from typing import Literal + +from .julia_import import jl + +__all__ = ["AbnormalHandler"] + + +#: The action to take when encountering an "abnormal" (but recoverable) operation. See the Julia +#: `documentation `__ for details. +AbnormalHandler = Literal["IgnoreHandler"] | Literal["WarnHandler"] | Literal["ErrorHandler"] + +JL_ABNORMAL_HANDLER = { + "IgnoreHandler": jl.Daf.Generic.IgnoreHandler, + "WarnHandler": jl.Daf.Generic.WarnHandler, + "ErrorHandler": jl.Daf.Generic.ErrorHandler, +} diff --git a/daf/julia_import.py b/daf/julia_import.py index d515e50..174a486 100644 --- a/daf/julia_import.py +++ b/daf/julia_import.py @@ -85,9 +85,10 @@ jl.seval("import DataFrames") jl.seval("import HDF5") jl.seval("import LinearAlgebra") +jl.seval("import Muon") jl.seval("import NamedArrays") -jl.seval("import SparseArrays") jl.seval("import PythonCall") +jl.seval("import SparseArrays") class UndefInitializer: diff --git a/docs/API.rst b/docs/API.rst index fef483d..2b7f3d7 100644 --- a/docs/API.rst +++ b/docs/API.rst @@ -7,6 +7,7 @@ API julia_import data + storage_types queries operations formats @@ -14,4 +15,5 @@ API copies adapters concat - storage_types + anndata_format + generic diff --git a/docs/anndata_format.rst b/docs/anndata_format.rst new file mode 100644 index 0000000..b5e4b47 --- /dev/null +++ b/docs/anndata_format.rst @@ -0,0 +1,5 @@ +anndata_format +============== + +.. automodule:: daf.anndata_format + :Members: diff --git a/docs/v0.1.0/html/API.html b/docs/v0.1.0/html/API.html index 8fa2230..c8c7840 100644 --- a/docs/v0.1.0/html/API.html +++ b/docs/v0.1.0/html/API.html @@ -125,6 +125,11 @@ +
  • +storage_types + +
    • +
  • queries @@ -161,7 +166,7 @@
  • -storage_types +anndata_format
    • @@ -898,6 +903,33 @@

    API +
  • +storage_types + + + +
    • +
  • queries @@ -1565,23 +1597,23 @@

    API

  • -storage_types +anndata_format
    • - + -StorageNumber +h5ad_as_daf()
    • - + -StorageScalar +daf_as_h5ad() diff --git a/docs/v0.1.0/html/_modules/daf/anndata_format.html b/docs/v0.1.0/html/_modules/daf/anndata_format.html new file mode 100644 index 0000000..ad6bf5c --- /dev/null +++ b/docs/v0.1.0/html/_modules/daf/anndata_format.html @@ -0,0 +1,171 @@ + + + + + + daf.anndata_format — Daf 0.1.0 documentation + + + + + + + + + + + + + + + + + +
      + + +
      + +
      +
      +
      + +
      +
      +
      +
      + +

      Source code for daf.anndata_format

      +"""
+Import/export ``Daf`` data from/to ``AnnData``. See the Julia
+`documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html>`__ for details.
+"""
+
+__all__ = ["h5ad_as_daf", "daf_as_h5ad"]
+
+from typing import Optional
+
+from .data import DafReader
+from .formats import MemoryDaf
+from .generic import JL_ABNORMAL_HANDLER
+from .generic import AbnormalHandler
+from .julia_import import jl
+
+
+
      
+[docs]
+def h5ad_as_daf(
+    h5ad: str,
+    *,
+    name: Optional[str] = None,
+    obs_is: Optional[str] = None,
+    var_is: Optional[str] = None,
+    X_is: Optional[str] = None,
+    unsupported_handler: AbnormalHandler = "WarnHandler",
+) -> MemoryDaf:
+    """
+    View ``AnnData`` as a ``Daf`` data set, specifically using a ``MemoryDaf``. See the Julia
+    `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html#anndata_as_daf>`__ for details.
+
+    Note that you only pass an ``h5ad`` path, since the Julia ``AnnData`` object comes from the ``Muon.jl`` package and
+    is not compatible with the Python ``anndata`` object.
+    """
+    return MemoryDaf(
+        jl.Daf.anndata_as_daf(
+            h5ad,
+            name=name,
+            obs_is=obs_is,
+            var_is=var_is,
+            X_is=X_is,
+            unsupported_handler=JL_ABNORMAL_HANDLER[unsupported_handler],
+        )
+    )
      
+
+
+
+
      
+[docs]
+def daf_as_h5ad(
+    daf: DafReader, *, obs_is: Optional[str] = None, var_is: Optional[str] = None, X_is: Optional[str] = None, h5ad: str
+) -> None:
+    """
+    View the ``Daf`` data set as ``AnnData``. See the Julia
+    `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html#Daf.AnnDataFormat.daf_as_anndata>`__
+    for details.
+
+    Note this just creates the ``h5ad`` file. We do not return the ``AnnData`` object, because it is a Julia
+    (``Muon.jl``) ``AnnData`` object, which is **not** a Python ``anndata`` ``AnnData`` object.
+    """
+    jl.daf_as_anndata(daf, obs_is=obs_is, var_is=var_is, X_is=X_is, h5ad=h5ad)
      
+
+
      + +
      +
      +
      + +
      + +
      +

      © Copyright 2023-2024 Weizmann Institute of Science.

      +
      + + Built with Sphinx using a + theme + provided by Read the Docs. + + +
      +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/docs/v0.1.0/html/_modules/daf/formats.html b/docs/v0.1.0/html/_modules/daf/formats.html index 3fe7e52..6584461 100644 --- a/docs/v0.1.0/html/_modules/daf/formats.html +++ b/docs/v0.1.0/html/_modules/daf/formats.html @@ -101,8 +101,10 @@

      Source code for daf.formats

           `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/memory_format.html>`__ for details.
     """
 
-    def __init__(self, *, name: str = "memory") -> None:
-        super().__init__(jl.Daf.MemoryDaf(name=name))
      + def __init__(self, jl_obj: Optional[jl.MemoryDaf] = None, *, name: str = "memory") -> None: + if jl_obj is None: + jl_obj = jl.Daf.MemoryDaf(name=name) + super().__init__(jl_obj) diff --git a/docs/v0.1.0/html/_modules/daf/julia_import.html b/docs/v0.1.0/html/_modules/daf/julia_import.html index 41b6a2b..45e6261 100644 --- a/docs/v0.1.0/html/_modules/daf/julia_import.html +++ b/docs/v0.1.0/html/_modules/daf/julia_import.html @@ -164,9 +164,10 @@

      Source code for daf.julia_import

       jl.seval("import DataFrames")
 jl.seval("import HDF5")
 jl.seval("import LinearAlgebra")
+jl.seval("import Muon")
 jl.seval("import NamedArrays")
-jl.seval("import SparseArrays")
 jl.seval("import PythonCall")
+jl.seval("import SparseArrays")
 
 
 
      
diff --git a/docs/v0.1.0/html/_modules/index.html b/docs/v0.1.0/html/_modules/index.html
index 32c37b8..a9084da 100644
--- a/docs/v0.1.0/html/_modules/index.html
+++ b/docs/v0.1.0/html/_modules/index.html
@@ -77,6 +77,7 @@
              
   
      All modules for which code is available
      
 
      • daf.adapters
        • 
+
      • daf.anndata_format
        • 
 
      • daf.concat
        • 
 
      • daf.copies
        • 
 
      • daf.data
        • 
diff --git a/docs/v0.1.0/html/_sources/API.rst.txt b/docs/v0.1.0/html/_sources/API.rst.txt
index fef483d..2b7f3d7 100644
--- a/docs/v0.1.0/html/_sources/API.rst.txt
+++ b/docs/v0.1.0/html/_sources/API.rst.txt
@@ -7,6 +7,7 @@ API
 
   julia_import
   data
+  storage_types
   queries
   operations
   formats
@@ -14,4 +15,5 @@ API
   copies
   adapters
   concat
-  storage_types
+  anndata_format
+  generic
diff --git a/docs/v0.1.0/html/_sources/anndata_format.rst.txt b/docs/v0.1.0/html/_sources/anndata_format.rst.txt
new file mode 100644
index 0000000..b5e4b47
--- /dev/null
+++ b/docs/v0.1.0/html/_sources/anndata_format.rst.txt
@@ -0,0 +1,5 @@
+anndata_format
+==============
+
+.. automodule:: daf.anndata_format
+    :Members:
diff --git a/docs/v0.1.0/html/adapters.html b/docs/v0.1.0/html/adapters.html
index 999769e..bfd019b 100644
--- a/docs/v0.1.0/html/adapters.html
+++ b/docs/v0.1.0/html/adapters.html
@@ -125,6 +125,11 @@
 
 
 
+
      • 
+storage_types
+
+
        • 
+
 
      • 
 queries
 
@@ -174,7 +179,7 @@
 
        • 
 
 
      • 
-storage_types
+anndata_format
 
 
        • 
 
diff --git a/docs/v0.1.0/html/anndata_format.html b/docs/v0.1.0/html/anndata_format.html
new file mode 100644
index 0000000..9e855ad
--- /dev/null
+++ b/docs/v0.1.0/html/anndata_format.html
@@ -0,0 +1,917 @@
+
+
+
+
+
+
+  
+
+
+
+  
+
+  
+anndata_format — Daf 0.1.0 documentation
+
+      
+
+      
+
+
+  
+  
+
+  
+        
+
+        
+
+        
+
+        
+
+        
+
+    
+
+    
+
+    
+
+    
+ 
+
+
+
+
+ 
+  
+
        
+    
+
+
+    
+
        
+
+
+      
+
        
+        
+
        
+          
+
        
+  
+
+  
+
        
+
+
        
+          
+
        
+           
+
        
+             
+  
+
        
+
+
+
+
        anndata_format
+¶
+
+
        
+
+
        Import/export 
+
+Daf
+
+ data from/to 
+
+AnnData
+
+. See the Julia
+
+documentation
+ for details.
+
        
+
+
        
+
+
        
+
+
+daf.anndata_format.
+
+
+
+h5ad_as_daf
+
+
+(
+
+
+
+h5ad
+
+
+
+:
+
+
+ 
+
+
+str
+
+
+, 
+
+
+*
+
+
+, 
+
+
+name
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+obs_is
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+var_is
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+X_is
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+unsupported_handler
+
+
+
+:
+
+
+ 
+
+
+Literal
+
+
+[
+
+
+
+'IgnoreHandler'
+
+
+
+]
+
+
+ 
+
+
+|
+
+
+ 
+
+Literal
+
+
+[
+
+
+
+'WarnHandler'
+
+
+
+]
+
+
+ 
+
+
+|
+
+
+ 
+
+Literal
+
+
+[
+
+
+
+'ErrorHandler'
+
+
+
+]
+
+
+
+ 
+
+
+=
+
+
+ 
+
+
+'WarnHandler'
+
+
+
+)
+ 
+
+→
+ 
+
+
+MemoryDaf
+
+
+
+
+
+
+[source]
+
+
+
+¶
+
+
        
+
+
        
+
        View 
+
+AnnData
+
+ as a 
+
+Daf
+
+ data set, specifically using a 
+
+MemoryDaf
+
+. See the Julia
+
+documentation
+ for details.
+
        
+
+
        Note that you only pass an 
+
+h5ad
+
+ path, since the Julia 
+
+AnnData
+
+ object comes from the 
+
+Muon.jl
+
+ package and
+is not compatible with the Python 
+
+anndata
+
+ object.
+
        
+
+
        
+
        
+
+
+
        
+
+
        
+
+
+daf.anndata_format.
+
+
+
+daf_as_h5ad
+
+
+(
+
+
+
+daf
+
+
+
+:
+
+
+ 
+
+
+
+DafReader
+
+
+
+, 
+
+
+*
+
+
+, 
+
+
+obs_is
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+var_is
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+X_is
+
+
+
+:
+
+
+ 
+
+
+str
+
+ 
+
+
+|
+
+
+ 
+
+None
+
+
+ 
+
+
+=
+
+
+ 
+
+
+None
+
+
+, 
+
+
+h5ad
+
+
+
+:
+
+
+ 
+
+
+str
+
+
+
+)
+ 
+
+→
+ 
+
+None
+
+
+
+
+
+[source]
+
+
+
+¶
+
+
        
+
+
        
+
        View the 
+
+Daf
+
+ data set as 
+
+AnnData
+
+. See the Julia
+
+documentation
+
+for details.
+
        
+
+
        Note this just creates the 
+
+h5ad
+
+ file. We do not return the 
+
+AnnData
+
+ object, because it is a Julia
+(
+
+Muon.jl
+
+) 
+
+AnnData
+
+ object, which is 
+not
+ a Python 
+
+anndata
+
+ 
+
+AnnData
+
+ object.
+
        
+
+
        
+
        
+
+
+
        
+
+
+           
+
        
+          
+
        
+          
+
+        
+
        
+      
+
        
+    
+
        
+  
+
        
+  
+ 
+
+
+
+
+
\ No newline at end of file
diff --git a/docs/v0.1.0/html/concat.html b/docs/v0.1.0/html/concat.html
index 8911dd2..38ad9bb 100644
--- a/docs/v0.1.0/html/concat.html
+++ b/docs/v0.1.0/html/concat.html
@@ -50,7 +50,7 @@
     
 
     
-
+
     
  
 
@@ -125,6 +125,11 @@
 
 
 
+
      • 
+storage_types
+
+
        • 
+
 
      • 
 queries
 
@@ -174,7 +179,7 @@
 
        • 
 
 
      • 
-storage_types
+anndata_format
 
 
        • 
 
@@ -1144,7 +1149,7 @@ 
        concat
  Previous
 
         
-
diff --git a/docs/v0.1.0/html/copies.html b/docs/v0.1.0/html/copies.html
index 8f356c1..d5843e2 100644
--- a/docs/v0.1.0/html/copies.html
+++ b/docs/v0.1.0/html/copies.html
@@ -125,6 +125,11 @@
 
 
 
+
      • 
+storage_types
+
+
        • 
+
 
      • 
 queries
 
@@ -219,7 +224,7 @@
 
        • 
 
 
      • 
-storage_types
+anndata_format
 
 
        • 
 
diff --git a/docs/v0.1.0/html/data.html b/docs/v0.1.0/html/data.html
index 63f5019..e5c9722 100644
--- a/docs/v0.1.0/html/data.html
+++ b/docs/v0.1.0/html/data.html
@@ -50,7 +50,7 @@
     
 
     
-
+
     
  
 
@@ -501,6 +501,11 @@
 
 
 
+
      • 
+storage_types
+
+
        • 
+
 
      • 
 queries
 
@@ -537,7 +542,7 @@
 
        • 
 
 
      • 
-storage_types
+anndata_format
 
 
        • 
 
@@ -8219,7 +8224,7 @@ 
        data
  Previous
 
         
-
diff --git a/docs/v0.1.0/html/formats.html b/docs/v0.1.0/html/formats.html
index a99c10f..26af5fb 100644
--- a/docs/v0.1.0/html/formats.html
+++ b/docs/v0.1.0/html/formats.html
@@ -125,6 +125,11 @@
 
 
 
+
      • 
+storage_types
+
+
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+
 
      • 
 queries
 
@@ -210,7 +215,7 @@
 
        • 
 
 
      • 
-storage_types
+anndata_format
 
 
        • 
 
@@ -316,35 +321,37 @@ 
        formats
 (
 
 
-
-*
+
+jl_obj:
+ 
+Julia:
+ 
+MemoryDaf
+ 
+|
+ 
+None
+ 
+=
+ 
+None
 
 
 , 
 
 
-name
-
-
-
-:
-
+*
 
- 
 
+, 
+
 
+name:
+ 
 str
-
-
- 
-
-
+ 
 =
-
-
- 
-
-
+ 
 'memory'
 
 
diff --git a/docs/v0.1.0/html/genindex.html b/docs/v0.1.0/html/genindex.html
index 0af9130..9e6c3de 100644
--- a/docs/v0.1.0/html/genindex.html
+++ b/docs/v0.1.0/html/genindex.html
@@ -505,6 +505,21 @@ 
        D
      • +
    • + daf.anndata_format + + + +
      • +
    • daf.concat @@ -579,6 +594,12 @@

      D

    • + + + + + +
    • daf.operations @@ -594,12 +615,6 @@

      D

    - - - - - -
    • daf.queries @@ -646,6 +661,12 @@

      D

    +
  • +daf_as_h5ad() (in module daf.anndata_format) + + +
    • +
  • DafReader (class in daf.data) @@ -896,6 +917,12 @@

    H
      +
    • +h5ad_as_daf() (in module daf.anndata_format) + + +
      • +
    • H5df (class in daf.formats) @@ -1152,6 +1179,12 @@

      M

      • +
    • +daf.anndata_format + + +
      • +
    • daf.concat diff --git a/docs/v0.1.0/html/julia_import.html b/docs/v0.1.0/html/julia_import.html index 245c4ff..46b73aa 100644 --- a/docs/v0.1.0/html/julia_import.html +++ b/docs/v0.1.0/html/julia_import.html @@ -165,6 +165,11 @@
      • +
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    • +storage_types + +
      • +
    • queries @@ -354,7 +359,7 @@
    • -storage_types +anndata_format
      • diff --git a/docs/v0.1.0/html/py-modindex.html b/docs/v0.1.0/html/py-modindex.html index 3901033..e59f20d 100644 --- a/docs/v0.1.0/html/py-modindex.html +++ b/docs/v0.1.0/html/py-modindex.html @@ -250,6 +250,25 @@

      Python Module Index     + +daf.anndata_format + + + + + + + + + + + + + + + +    + daf.concat diff --git a/docs/v0.1.0/html/queries.html b/docs/v0.1.0/html/queries.html index 799a733..086e6a0 100644 --- a/docs/v0.1.0/html/queries.html +++ b/docs/v0.1.0/html/queries.html @@ -52,7 +52,7 @@ - + @@ -125,6 +125,11 @@ +
    • +storage_types + +
      • +
    • queries @@ -399,7 +404,7 @@
    • -storage_types +anndata_format
      • @@ -3642,7 +3647,7 @@

      queries

    - @@ -473,10 +480,15 @@

    storage_types
    diff --git a/docs/v0.1.0/html/views.html b/docs/v0.1.0/html/views.html index 7becff7..44fd935 100644 --- a/docs/v0.1.0/html/views.html +++ b/docs/v0.1.0/html/views.html @@ -125,6 +125,11 @@

    • +
  • +storage_types + +
    • +
  • queries @@ -228,7 +233,7 @@
  • -storage_types +anndata_format
    • diff --git a/juliapkg.json b/juliapkg.json index 4ffbcec..7e95f9a 100644 --- a/juliapkg.json +++ b/juliapkg.json @@ -9,6 +9,9 @@ "HDF5": { "uuid": "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" }, + "Muon": { + "uuid": "446846d7-b4ce-489d-bf74-72da18fe3629" + }, "NamedArrays": { "uuid": "86f7a689-2022-50b4-a561-43c23ac3c673" } diff --git a/tests/test_anndata_format.py b/tests/test_anndata_format.py new file mode 100644 index 0000000..a88be3c --- /dev/null +++ b/tests/test_anndata_format.py @@ -0,0 +1,63 @@ +""" +Test ``Daf`` conversion to and from ``AnnData``. +""" + +# pylint: disable=wildcard-import,unused-wildcard-import,missing-function-docstring +# flake8: noqa: F403,F405 + +from tempfile import TemporaryDirectory +from textwrap import dedent + +import numpy as np + +from daf import * + + +def test_h5ad() -> None: # pylint: disable=too-many-statements + origin = MemoryDaf(name="memory!") + origin.set_scalar("version", 1) + origin.add_axis("cell", ["A", "B"]) + origin.add_axis("gene", ["X", "Y", "Z"]) + origin.set_matrix("gene", "cell", "UMIs", np.array([[0, 1, 2], [3, 4, 5]]).transpose(), relayout=False) + + assert ( + origin.description() + == dedent( + """ + name: memory! + type: MemoryDaf + scalars: + version: 1 (Int64) + axes: + cell: 2 entries + gene: 3 entries + matrices: + gene,cell: + UMIs: 3 x 2 x Int64 in Columns (PyArray{Int64, 2, true, true, Int64} - Dense) + """ + )[1:] + ) + + with TemporaryDirectory() as tmpdir: + daf_as_h5ad(origin, obs_is="cell", var_is="gene", X_is="UMIs", h5ad=f"{tmpdir}/test.h5ad") + back = h5ad_as_daf(f"{tmpdir}/test.h5ad", obs_is="cell", var_is="gene", X_is="UMIs") + assert ( + back.description() + == dedent( + """ + name: anndata + type: MemoryDaf + scalars: + X_is: "UMIs" + obs_is: "cell" + var_is: "gene" + version: 1 (Int64) + axes: + cell: 2 entries + gene: 3 entries + matrices: + gene,cell: + UMIs: 3 x 2 x Int64 in Columns (Dense) + """ + )[1:] + )