phylogenie 1.0.3__py3-none-any.whl → 1.0.4__py3-none-any.whl

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Files changed (8) hide show
  1. phylogenie/skyline/matrix.py +9 -9
  2. phylogenie/skyline/parameter.py +22 -11
  3. phylogenie/skyline/vector.py +10 -10
  4. {phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/METADATA +1 -1
  5. {phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/RECORD +8 -8
  6. {phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/LICENSE.txt +0 -0
  7. {phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/WHEEL +0 -0
  8. {phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/entry_points.txt +0 -0
phylogenie/skyline/matrix.py CHANGED
@@ -80,7 +80,7 @@ class SkylineMatrix:
80
80
  def get_value_at_time(self, time: pgt.Scalar) -> pgt.Vector2D:
81
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  return [param.get_value_at_time(time) for param in self.params]
82
82
 
83
- def operate(
83
+ def _operate(
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  self,
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  other: SkylineMatrixOperand,
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  func: Callable[
@@ -97,28 +97,28 @@ class SkylineMatrix:
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  )
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98
 
99
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  def __add__(self, operand: SkylineMatrixOperand) -> "SkylineMatrix":
100
- return self.operate(operand, lambda x, y: x + y)
100
+ return self._operate(operand, lambda x, y: x + y)
101
101
 
102
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  def __radd__(self, operand: SkylineVectorOperand) -> "SkylineMatrix":
103
- return self.operate(operand, lambda x, y: y + x)
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+ return self._operate(operand, lambda x, y: y + x)
104
104
 
105
105
  def __sub__(self, operand: SkylineMatrixOperand) -> "SkylineMatrix":
106
- return self.operate(operand, lambda x, y: x - y)
106
+ return self._operate(operand, lambda x, y: x - y)
107
107
 
108
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  def __rsub__(self, operand: SkylineVectorOperand) -> "SkylineMatrix":
109
- return self.operate(operand, lambda x, y: y - x)
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+ return self._operate(operand, lambda x, y: y - x)
110
110
 
111
111
  def __mul__(self, operand: SkylineMatrixOperand) -> "SkylineMatrix":
112
- return self.operate(operand, lambda x, y: x * y)
112
+ return self._operate(operand, lambda x, y: x * y)
113
113
 
114
114
  def __rmul__(self, operand: SkylineVectorOperand) -> "SkylineMatrix":
115
- return self.operate(operand, lambda x, y: y * x)
115
+ return self._operate(operand, lambda x, y: y * x)
116
116
 
117
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  def __truediv__(self, operand: SkylineMatrixOperand) -> "SkylineMatrix":
118
- return self.operate(operand, lambda x, y: x / y)
118
+ return self._operate(operand, lambda x, y: x / y)
119
119
 
120
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  def __rtruediv__(self, operand: SkylineVectorOperand) -> "SkylineMatrix":
121
- return self.operate(operand, lambda x, y: y / x)
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+ return self._operate(operand, lambda x, y: y / x)
122
122
 
123
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  @property
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  def T(self) -> "SkylineMatrix":
phylogenie/skyline/parameter.py CHANGED
@@ -23,7 +23,7 @@ class SkylineParameter:
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  self,
24
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  value: pgt.OneOrManyScalars,
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  change_times: pgt.ManyScalars | None = None,
26
- ) -> None:
26
+ ):
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  if isinstance(value, pgt.Scalar):
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  value = [value]
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  elif not tg.is_many_scalars(value):
@@ -42,18 +42,29 @@ class SkylineParameter:
42
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  raise ValueError(
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  f"`value` must have exactly one more element than `change_times` (got value={value} of length {len(value)} and change_times={change_times} of length {len(change_times)})."
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  )
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+ if any(t1 >= t2 for t1, t2 in zip(change_times, change_times[1:])):
46
+ raise ValueError(
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+ f"`change_times` must be sorted in strictly increasing order "
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+ f"(got change_times={change_times})."
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+ )
50
+ if any(t < 0 for t in change_times):
51
+ raise ValueError(
52
+ f"`change_times` must be non-negative (got change_times={change_times})."
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+ )
45
54
 
46
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  self.value = [value[0]]
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  self.change_times: list[pgt.Scalar] = []
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  for i in range(1, len(value)):
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  if value[i] != value[i - 1]:
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  self.value.append(value[i])
51
- self.value.append(change_times[i - 1])
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+ self.change_times.append(change_times[i - 1])
52
61
 
53
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  def get_value_at_time(self, t: pgt.Scalar) -> pgt.Scalar:
63
+ if t < 0:
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+ raise ValueError(f"Time cannot be negative (got t={t}).")
54
65
  return self.value[bisect_right(self.change_times, t)]
55
66
 
56
- def operate(
67
+ def _operate(
57
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  self,
58
69
  other: SkylineParameterLike,
59
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  f: Callable[[pgt.Scalar, pgt.Scalar], pgt.Scalar],
@@ -67,28 +78,28 @@ class SkylineParameter:
67
78
  return SkylineParameter(value, change_times)
68
79
 
69
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  def __add__(self, other: SkylineParameterLike) -> "SkylineParameter":
70
- return self.operate(other, lambda x, y: x + y)
81
+ return self._operate(other, lambda x, y: x + y)
71
82
 
72
83
  def __radd__(self, other: pgt.Scalar) -> "SkylineParameter":
73
- return self.operate(other, lambda x, y: y + x)
84
+ return self._operate(other, lambda x, y: y + x)
74
85
 
75
86
  def __sub__(self, other: SkylineParameterLike) -> "SkylineParameter":
76
- return self.operate(other, lambda x, y: x - y)
87
+ return self._operate(other, lambda x, y: x - y)
77
88
 
78
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  def __rsub__(self, other: pgt.Scalar) -> "SkylineParameter":
79
- return self.operate(other, lambda x, y: y - x)
90
+ return self._operate(other, lambda x, y: y - x)
80
91
 
81
92
  def __mul__(self, other: SkylineParameterLike) -> "SkylineParameter":
82
- return self.operate(other, lambda x, y: x * y)
93
+ return self._operate(other, lambda x, y: x * y)
83
94
 
84
95
  def __rmul__(self, other: pgt.Scalar) -> "SkylineParameter":
85
- return self.operate(other, lambda x, y: y * x)
96
+ return self._operate(other, lambda x, y: y * x)
86
97
 
87
98
  def __truediv__(self, other: SkylineParameterLike) -> "SkylineParameter":
88
- return self.operate(other, lambda x, y: x / y)
99
+ return self._operate(other, lambda x, y: x / y)
89
100
 
90
101
  def __rtruediv__(self, other: pgt.Scalar) -> "SkylineParameter":
91
- return self.operate(other, lambda x, y: y / x)
102
+ return self._operate(other, lambda x, y: y / x)
92
103
 
93
104
  def __bool__(self) -> bool:
94
105
  return any(self.value)
phylogenie/skyline/vector.py CHANGED
@@ -34,7 +34,7 @@ class SkylineVector:
34
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  params: pgt.Many[SkylineParameterLike] | None = None,
35
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  value: pgt.Many2DScalars | None = None,
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  change_times: pgt.ManyScalars | None = None,
37
- ) -> None:
37
+ ):
38
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  if params is not None and value is None and change_times is None:
39
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  if is_many_skyline_parameters_like(params):
40
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  self.params = [skyline_parameter(param) for param in params]
@@ -77,7 +77,7 @@ class SkylineVector:
77
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  def get_value_at_time(self, t: pgt.Scalar) -> pgt.Vector1D:
78
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  return [param.get_value_at_time(t) for param in self.params]
79
79
 
80
- def operate(
80
+ def _operate(
81
81
  self,
82
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  other: SkylineVectorOperand,
83
83
  func: Callable[[SkylineParameter, SkylineParameter], SkylineParameter],
@@ -90,28 +90,28 @@ class SkylineVector:
90
90
  )
91
91
 
92
92
  def __add__(self, operand: SkylineVectorOperand) -> "SkylineVector":
93
- return self.operate(operand, lambda x, y: x + y)
93
+ return self._operate(operand, lambda x, y: x + y)
94
94
 
95
95
  def __radd__(self, operand: SkylineParameterLike) -> "SkylineVector":
96
- return self.operate(operand, lambda x, y: y + x)
96
+ return self._operate(operand, lambda x, y: y + x)
97
97
 
98
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  def __sub__(self, operand: SkylineVectorOperand) -> "SkylineVector":
99
- return self.operate(operand, lambda x, y: x - y)
99
+ return self._operate(operand, lambda x, y: x - y)
100
100
 
101
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  def __rsub__(self, operand: SkylineParameterLike) -> "SkylineVector":
102
- return self.operate(operand, lambda x, y: y - x)
102
+ return self._operate(operand, lambda x, y: y - x)
103
103
 
104
104
  def __mul__(self, operand: SkylineVectorOperand) -> "SkylineVector":
105
- return self.operate(operand, lambda x, y: x * y)
105
+ return self._operate(operand, lambda x, y: x * y)
106
106
 
107
107
  def __rmul__(self, operand: SkylineParameterLike) -> "SkylineVector":
108
- return self.operate(operand, lambda x, y: y * x)
108
+ return self._operate(operand, lambda x, y: y * x)
109
109
 
110
110
  def __truediv__(self, operand: SkylineVectorOperand) -> "SkylineVector":
111
- return self.operate(operand, lambda x, y: x / y)
111
+ return self._operate(operand, lambda x, y: x / y)
112
112
 
113
113
  def __rtruediv__(self, operand: SkylineParameterLike) -> "SkylineVector":
114
- return self.operate(operand, lambda x, y: y / x)
114
+ return self._operate(operand, lambda x, y: y / x)
115
115
 
116
116
  def __len__(self) -> int:
117
117
  return self.N
{phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: phylogenie
3
- Version: 1.0.3
3
+ Version: 1.0.4
4
4
  Summary: Generate phylogenetic datasets with minimal setup effort
5
5
  Author: Gabriele Marino
6
6
  Author-email: gabmarino.8601@gmail.com
{phylogenie-1.0.3.dist-info → phylogenie-1.0.4.dist-info}/RECORD RENAMED
@@ -27,13 +27,13 @@ phylogenie/core/typeguards.py,sha256=yxTdE4G_1gjBFqplyei-GKz4KZo2KFh8qsEsPQ2Z5OQ
27
27
  phylogenie/main.py,sha256=n_joau3dWJIq0ZMHe4a_1_2GigTFagkfzUFuQEMlyRI,1158
28
28
  phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
29
29
  phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
30
- phylogenie/skyline/matrix.py,sha256=WH1aT23hv4QYuH4GDwcJgahrqcgB4mulfzKLGUx3R6M,7091
31
- phylogenie/skyline/parameter.py,sha256=wrtvQDho3OC5tzrMnnFTy95GXaYN20KN8P5Gwyf-rHI,4023
32
- phylogenie/skyline/vector.py,sha256=NgmVbWjWG_itZ9a57q9QqSybvG9-Cr9X264RGPVyp_Q,6399
30
+ phylogenie/skyline/matrix.py,sha256=8C8jFmIFbxYWmmfnPwi6qaew4oErQznvZN8JuvkD8kQ,7100
31
+ phylogenie/skyline/parameter.py,sha256=RXZoaC46FFGTjD8rNb0dkWAZH4Pfxfn2dFGID3l0dMs,4551
32
+ phylogenie/skyline/vector.py,sha256=VuCnIq9aIlKZIiqHWIbrpiOdwSDKXNPuIPunlULaYaQ,6400
33
33
  phylogenie/typeguards.py,sha256=WBOSJSaOC8VDtrYoA2w_AYEXTpyKdCfmsM29KaKXl3A,1350
34
34
  phylogenie/typings.py,sha256=93VRedBxrpzXkT4uaNu_1JiMzsOjp7fUy4kLv_eYxUE,565
35
- phylogenie-1.0.3.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
36
- phylogenie-1.0.3.dist-info/METADATA,sha256=JVGcZNn6O2Wuuek_ZTQp5CBdw5_xoSHzvSyTmENmxNw,6251
37
- phylogenie-1.0.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
38
- phylogenie-1.0.3.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
39
- phylogenie-1.0.3.dist-info/RECORD,,
35
+ phylogenie-1.0.4.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
36
+ phylogenie-1.0.4.dist-info/METADATA,sha256=Ly88IxdRijacsz4-TglRG5GbjjcDkxQxLf5U0kLEj-c,6251
37
+ phylogenie-1.0.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
38
+ phylogenie-1.0.4.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
39
+ phylogenie-1.0.4.dist-info/RECORD,,