Project import generated by Copybara.

GitOrigin-RevId: 0f86c707eccca096d821b9018110d06e89455665
NKI-CCB · May 12, 2023 · bcbb62a · bcbb62a
1 parent dbb1c3e
commit bcbb62a
Show file tree

Hide file tree

Showing 8 changed files with 34 additions and 41 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -21,13 +21,23 @@ of the Python package would have features that do not exist in version
 0.9 series
 ==========
 
-:Latest Python version:  0.9.4 (July 28, 2021)
+:Latest Python version:  0.9.5 (May 11, 2023)
 :Latest R version:       0.9.4 (July 28, 2021)
 
 
 Python package
 --------------
 
+0.9.5 (May 11, 2023)
+~~~~~~~~~~~~~~~~~~~~
+
+**Fixed**:
+
+- If pandas >= 2.0 was installed, constructing a DiscoverMatrix object
+  gave rise to "AttributeError: 'DataFrame' object has no attribute
+  '__array_wrap__'".
+
+
 0.9.4 (July 28, 2021)
 ~~~~~~~~~~~~~~~~~~~~~
 
@@ -55,7 +65,7 @@ Python package
 **Fixed**:
 
 - If pandas >= 1.0 was installed, subsetting a DiscoverMatrix object
-  gave rise to "AttributeError: 'DataFrame' objects has no attribute
+  gave rise to "AttributeError: 'DataFrame' object has no attribute
   'ix'".
 
 - Fixed the underlying Fortran code to make it compile with GNU

diff --git a/python/.bumpversion.cfg b/python/.bumpversion.cfg
@@ -3,7 +3,7 @@ commit = True
 message = [Python package] Bump version: {current_version} → {new_version}
 tag = True
 tag_name = py_v{new_version}
-current_version = 0.9.4
+current_version = 0.9.5
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+))?
 serialize = 
 	{major}.{minor}.{patch}.{release}

diff --git a/python/conda-recipe/conda_build_config.yaml b/python/conda-recipe/conda_build_config.yaml
@@ -3,10 +3,24 @@ blas_impl:
 #  - openblas                   # [not win]
 
 python:
-  - 3.6
-  - 3.7
   - 3.8
   - 3.9
+  - 3.10
+  - 3.11
 
 numpy:
-  - 1.19
+  # python 3.8-3.9
+  - 1.16    # [not (osx and arm64)]
+  - 1.16    # [not (osx and arm64)]
+  # python 3.8-3.9
+  - 1.19    # [osx and arm64]
+  - 1.19    # [osx and arm64]
+  # python 3.10
+  - 1.21
+  # python 3.11
+  - 1.23
+
+zip_keys:
+  -
+    - python
+    - numpy
diff --git a/python/conda-recipe/meta.yaml b/python/conda-recipe/meta.yaml
@@ -1,14 +1,13 @@
 package:
   name: discover
-  version: 0.9.4
+  version: 0.9.5
 
 source:
   path: ..
   patches:
     - arch-core2.patch
     - no-stack-arrays.patch
     - no-lto.patch                  # [osx]
-    - restore-old-nan-code.patch    # [osx]
 
 build:
   number: 0

diff --git a/python/conda-recipe/restore-old-nan-code.patch b/python/conda-recipe/restore-old-nan-code.patch
diff --git a/python/discover/__init__.py b/python/discover/__init__.py
@@ -3,4 +3,4 @@
 from .pairwise import pairwise_discover_test
 
 
-__version__ = "0.9.4"
+__version__ = "0.9.5"
diff --git a/python/discover/data.py b/python/discover/data.py
@@ -48,7 +48,7 @@ def __init__(self, events, bg=None, strata=None):
         self._events = events.copy(deep=False)
 
         if bg is None:
-            self._bg = events.__array_wrap__(estimate_background(events, strata))
+            self._bg = pandas.DataFrame(estimate_background(events, strata), index=events.index, columns=events.columns)
         else:
             if strata is not None:
                 import warnings

diff --git a/python/setup.py b/python/setup.py
@@ -117,7 +117,7 @@ def get_sorted_source_files(src_dir):
 
 if __name__ == "__main__":
     setup(name="discover",
-          version="0.9.4",
+          version="0.9.5",
           description="DISCOVER mutual exclusivity and co-occurrence analysis",
           author="Sander Canisius",
           author_email="s.canisius@nki.nl",