DataSet patch, numpy method update (#40)

* Patch datset index misbehavior, replace deprecated numpy module

* Bump version: 1.0.0-dev → 1.0.1

* Update bitset representation tests

Author: d-giles

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0-dev
+current_version = 1.0.1
 commit = True
 tag = True
 

docs/conf.py

@@ -86,5 +86,5 @@
 
 
 # rst_epilog = """
-# .. |version| replace:: 1.0.0
+# .. |version| replace:: 1.0.1
 # """

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "lkdata"
-version = "1.0.0"
+version = "1.0.1"
 description = "A friendly package for analysing TESS & Kepler time series data"
 authors = [
     { name = "TESS Science Support Center", email = "tesshelp@bigbang.gsfc.nasa.gov" }]
@@ -19,7 +19,7 @@ dev = [
     "coverage[toml] >=7.4.0",
     "ipykernel >= 6.29.5",
     "IPython >= 8.18.1",
-    "jupyter >= 1.0.0",
+    "jupyter >= 1.0.1",
     "line-profiler >= 4.1.2",
     "mypy >= 1.8.0",
     "nbsphinx >= 0.9.3",
@@ -48,7 +48,7 @@ dev = [
     "coverage[toml] (>=7.10.7,<8.0.0)",
     "ipykernel>=6.29.5",
     "IPython>=8.18.1",
-    "jupyter>=1.0.0",
+    "jupyter>=1.0.1",
     "line-profiler>=4.1.2",
     "mypy>=1.8.0",
     "nbsphinx>=0.9.3",

src/lkdata/dataseries.py

@@ -68,8 +68,8 @@ def __init__(
                 for level in index.levels:
                     common = set(level).intersection(check_index)
                     if len(common) > n_match:
-                        inds_dict = np.where(np.in1d(check_index, list(common)))
-                        inds_index = np.where(np.in1d(level, list(common)))
+                        inds_dict = np.where(np.isin(check_index, list(common)))
+                        inds_index = np.where(np.isin(level, list(common)))
                         n_match = len(common)
                 if n_match > 0:
                     data = np.array([*data.values()])[inds_dict]

src/lkdata/dataset.py

@@ -287,8 +287,9 @@ def __init__(
     ):
         ntime = kwargs.pop("ntime", 0)
         time_indices = kwargs.pop("time_indices", None)
-        index = IndexProcessorMixin.parse_index(index, time_indices, ntime)
-
+        if (index is not None) or (time_indices is not None) or (ntime != 0):
+            index = IndexProcessorMixin.parse_index(index, time_indices, ntime)
+            self.index = index
         self._data_types = dict()
         if input_data is not None:
             input_data = self._unpack_input(input_data)
@@ -446,7 +447,7 @@ def __init__(
         **kwargs,
     ):
         self.kwargs = kwargs
-        super().__init__(data, index)
+        super().__init__(data, index, **kwargs)
 
 
 class BoolProducts(ProductBundle):
@@ -464,7 +465,7 @@ def __init__(
         **kwargs,
     ):
         self.kwargs = kwargs
-        super().__init__(bools, index)
+        super().__init__(bools, index, **kwargs)
 
 
 class BitwiseProducts(ProductBundle):
@@ -482,7 +483,7 @@ def __init__(
         **kwargs,
     ):
         self.kwargs = kwargs
-        super().__init__(bitwise, index)
+        super().__init__(bitwise, index, **kwargs)
 
 
 class AttrsHolder(dict):

src/lkdata/version.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.1"

tests/test_datacube.py

@@ -472,34 +472,38 @@ def strip(string):
     assert (bitcube.array == flags).all()
     # Default repr shows data as given
     bitwise_str = strip(bitcube.styler.to_string())
+    comp = "col0123row00123145672891011312131415"
     assert bitwise_str == "col0123row00123145672891011312131415"
     # bitset repr shows codes individually, without description
     bitcube.values_display = "bitset"
     bitset_str = strip(bitcube.styler.to_string())
-    assert bitset_str == (
+    comp = (
         "col0123row0{}{1}{2}{1,2}1{4}{1,4}{2,4}{1,2,4}"
         "2{8}{1,8}{2,8}{1,2,8}3{4,8}{1,4,8}{2,4,8}{1,2,4,8}"
     )
+    assert bitset_str == comp
     # Detailed repr parses and replaces codes with descriptions in given code_dict
     bitcube.values_display = "detailed"
     detailed_str = strip(bitcube.styler.to_string())
-    assert detailed_str == (
+    comp = (
         "col0123row0{}{1:'C1'}{2:'C2'}{1:'C1',2:'C2'}1{4:'C4'}{1:'C1',4:'C4'}"
         "{2:'C2',4:'C4'}{1:'C1',2:'C2',4:'C4'}2{8:'C8'}{1:'C1',8:'C8'}"
         "{2:'C2',8:'C8'}{1:'C1',2:'C2',8:'C8'}3{4:'C4',8:'C8'}"
         "{1:'C1',4:'C4',8:'C8'}{2:'C2',4:'C4',8:'C8'}"
         "{1:'C1',2:'C2',4:'C4',8:'C8'}"
     )
+    assert detailed_str == comp
     bitcube.codes = {i: f"New{i}" for i in [1, 2, 4, 8, 16]}
     detailed_str = strip(bitcube.styler.to_string())
-    assert detailed_str == (
+    comp = (
         "col0123row0{}{1:'New1'}{2:'New2'}{1:'New1',2:'New2'}"
         "1{4:'New4'}{1:'New1',4:'New4'}{2:'New2',4:'New4'}"
         "{1:'New1',2:'New2',4:'New4'}2{8:'New8'}{1:'New1',8:'New8'}"
         "{2:'New2',8:'New8'}{1:'New1',2:'New2',8:'New8'}"
         "3{4:'New4',8:'New8'}{1:'New1',4:'New4',8:'New8'}{2:'New2',"
         "4:'New4',8:'New8'}{1:'New1',2:'New2',4:'New4',8:'New8'}"
     )
+    assert detailed_str == comp
     # reset codes
     bitcube.codes = code_dict
 
@@ -516,7 +520,7 @@ def strip(string):
     assert bitframe.shape == (2, 16)
     # Ensure codes and values_display transferred to derivative product
     detailed_str = strip(bitframe.styler.to_string())
-    assert detailed_str == (
+    comp = (
         "series0123456789101112131415row0000111122223333"
         "col0123012301230123time_index0{}{1:'C1'}{2:'C2'}{1:'C1',2:'C2'}"
         "{4:'C4'}{1:'C1',4:'C4'}{2:'C2',4:'C4'}{1:'C1',2:'C2',4:'C4'}{8:'C8'}"
@@ -529,18 +533,20 @@ def strip(string):
         "{4:'C4',8:'C8',16:'C16'}{1:'C1',4:'C4',8:'C8',16:'C16'}{2:'C2',4:'C4',"
         "8:'C8',16:'C16'}{1:'C1',2:'C2',4:'C4',8:'C8',16:'C16'}"
     )
+    assert detailed_str == comp
 
     bitframe = BitwiseSeriesCollection(np.arange(0, 32).reshape(2, 16))
     # New bitframe has no codes_dict, detailed display should be the same as bitset
     bitframe.values_display = "bitset"
     bitset_str = strip(bitframe.styler.to_string())
-    assert bitset_str == (
+    comp = (
         "series(0,)(1,)(2,)(3,)(4,)(5,)(6,)(7,)(8,)(9,)(10,)(11,)(12,)(13,)"
         "(14,)(15,)time_index0{}{1}{2}{1,2}{4}{1,4}{2,4}{1,2,4}{8}"
         "{1,8}{2,8}{1,2,8}{4,8}{1,4,8}{2,4,8}{1,2,4,8}1{16}{1,16}{2,16}"
         "{1,2,16}{4,16}{1,4,16}{2,4,16}{1,2,4,16}{8,16}{1,8,16}{2,8,16}"
         "{1,2,8,16}{4,8,16}{1,4,8,16}{2,4,8,16}{1,2,4,8,16}"
     )
+    assert bitset_str == comp
     bitframe.values_display = "detailed"
     detailed_str = strip(bitframe.styler.to_string())
     assert detailed_str == bitset_str
@@ -550,21 +556,24 @@ def strip(string):
     # Series
     assert isinstance(bitcube[:, 0, 0], BitwiseSeries)
     bitseries = BitwiseSeries(np.arange(0, 16), codes=code_dict)
-    bitwise_str = strip(bitseries._repr_html_())[34:-17]
-    assert bitwise_str == "00112233445566778899101011111212131314141515"
+    bitwise_str = strip(bitseries._repr_html_())
+    comp = "00112233445566778899101011111212131314141515"
+    assert comp in bitwise_str
     bitseries.values_display = "bitset"
-    bitset_str = strip(bitseries._repr_html_())[34:-18]
-    assert bitset_str == (
+    bitset_str = strip(bitseries._repr_html_())
+    comp = (
         "0{}1{1}2{2}3{1,2}4{4}5{1,4}6{2,4}7{1,2,4}8{8}9{1,8}"
         "10{2,8}11{1,2,8}12{4,8}13{1,4,8}14{2,4,8}15{1,2,4,8}"
     )
+    assert comp in bitset_str
     bitseries.values_display = "detailed"
-    detailed_str = strip(bitseries._repr_html_())[34:-18]
-    assert detailed_str == (
+    detailed_str = strip(bitseries._repr_html_())
+    comp = (
         "0{}1{1:'C1'}2{2:'C2'}3{1:'C1',2:'C2'}4{4:'C4'}"
         "5{1:'C1',4:'C4'}6{2:'C2',4:'C4'}7{1:'C1',2:'C2',4:'C4'}"
         "8{8:'C8'}9{1:'C1',8:'C8'}10{2:'C2',8:'C8'}"
         "11{1:'C1',2:'C2',8:'C8'}12{4:'C4',8:'C8'}"
         "13{1:'C1',4:'C4',8:'C8'}14{2:'C2',4:'C4',8:'C8'}"
         "15{1:'C1',2:'C2',4:'C4',8:'C8'}"
     )
+    assert comp in detailed_str