removed remaining xarrax references

theislab · Aug 25, 2019 · 1d10086 · 1d10086
1 parent 72d73fc
commit 1d10086
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Showing 6 changed files with 10 additions and 26 deletions.
diff --git a/batchglm/models/base/external.py b/batchglm/models/base/external.py
@@ -1,3 +1,2 @@
 import batchglm.pkg_constants as pkg_constants
 import batchglm.data as data_utils
-from batchglm.xarray_sparse import SparseXArrayDataSet, SparseXArrayDataArray
diff --git a/batchglm/models/glm_nb/model.py b/batchglm/models/glm_nb/model.py
@@ -3,7 +3,6 @@
     import anndata
 except ImportError:
     anndata = None
-import xarray as xr
 import numpy as np
 
 from .external import _ModelGLM
@@ -27,7 +26,7 @@ def inverse_link_scale(self, data):
         return np.exp(data)
 
     @property
-    def eta_loc(self) -> xr.DataArray:
+    def eta_loc(self) -> np.ndarray:
         eta = np.matmul(self.design_loc, self.a)
         if self.size_factors is not None:
             eta += np.expand_dims(self.size_factors, axis=1)
@@ -36,9 +35,9 @@ def eta_loc(self) -> xr.DataArray:
     # Re-parameterizations:
 
     @property
-    def mu(self) -> xr.DataArray:
+    def mu(self) -> np.ndarray:
         return self.location
 
     @property
-    def phi(self) -> xr.DataArray:
+    def phi(self) -> np.ndarray:
         return self.scale
diff --git a/batchglm/train/tf/base_glm/estimator_graph.py b/batchglm/train/tf/base_glm/estimator_graph.py
@@ -4,7 +4,6 @@
 
 import numpy as np
 import tensorflow as tf
-import xarray as xr
 
 try:
     import anndata
@@ -1243,8 +1242,8 @@ def __init__(
             num_scale_params: int,
             graph: tf.Graph,
             batch_size: int,
-            constraints_loc: xr.DataArray,
-            constraints_scale: xr.DataArray,
+            constraints_loc: np.ndarray,
+            constraints_scale: np.ndarray,
             dtype: str
     ):
         """

diff --git a/batchglm/train/tf/base_glm_all/estimator_graph.py b/batchglm/train/tf/base_glm_all/estimator_graph.py
@@ -1,12 +1,9 @@
-from typing import Union
 import logging
-
-import tensorflow as tf
 import numpy as np
-import xarray as xr
+import tensorflow as tf
+from typing import Union
 
 from .external import EstimatorGraphGLM, FullDataModelGraphGLM, BatchedDataModelGraphGLM, ModelVarsGLM
-from .external import op_utils
 from .external import pkg_constants
 
 logger = logging.getLogger(__name__)
@@ -372,8 +369,8 @@ def __init__(
             num_design_scale_params,
             num_loc_params,
             num_scale_params,
-            constraints_loc: xr.DataArray,
-            constraints_scale: xr.DataArray,
+            constraints_loc: np.ndarray,
+            constraints_scale: np.ndarray,
             graph: tf.Graph,
             batch_size: int,
             init_a,

diff --git a/batchglm/train/tf/glm_nb/model.py b/batchglm/train/tf/glm_nb/model.py
@@ -1,8 +1,6 @@
 import logging
-
-import tensorflow as tf
-
 import numpy as np
+import tensorflow as tf
 
 from .external import ProcessModelGLM, ModelVarsGLM, BasicModelGraphGLM
 from .external import pkg_constants

diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -20,14 +20,6 @@ Preprocessing
    :toctree: .
 
    data.design_matrix
-   data.design_matrix_from_xarray
-   data.design_matrix_from_anndata
-   data.sample_description_from_xarray
-   data.sample_description_from_anndata
-   data.load_mtx_to_adata
-   data.load_mtx_to_xarray
-   data.load_recursive_mtx
-   data.xarray_from_data
 
 
 Fitting models