Merge pull request #417 from hyanwong/typo

Numpy 2 compatibility

Author: hyanwong

docs/_config.yml

@@ -46,7 +46,7 @@ sphinx:
     config:
       html_theme: sphinx_book_theme
       html_theme_options:
-        pygment_dark_style: monokai
+        pygments_dark_style: monokai
       pygments_style: monokai
       bibtex_reference_style: author_year
       myst_enable_extensions:

docs/requirements.txt

@@ -18,7 +18,7 @@ sphinxcontrib-bibtex
 humanize==4.7.0
 lmdb==1.4.1
 tqdm==4.66.3
-daiquiri==3.2.1
-msprime==1.2.0
+daiquiri
+msprime
 ipywidgets==8.1.0
 sphinx-book-theme #Unpinned to allow easy updating.

tsdate/cli.py

@@ -155,7 +155,7 @@ def tsdate_cli_parser():
         "--rescaling-intervals",
         type=float,
         help=(
-            "The number of time intervals within which to estimate a time scaling"
+            "The number of time intervals within which to estimate a time scaling "
             f"parameter. Default: None treated as {core.DEFAULT_RESCALING_INTERVALS}"
         ),
         default=None,

tsdate/core.py

@@ -409,17 +409,17 @@ class LogLikelihoods(Likelihoods):
     @staticmethod
     @numba.jit(nopython=True)
     def logsumexp(X):
-        alpha = -np.Inf
+        alpha = -np.inf
         r = 0.0
         for x in X:
-            if x != -np.Inf:
+            if x != -np.inf:
                 if x <= alpha:
                     r += np.exp(x - alpha)
                 else:
                     r *= np.exp(alpha - x)
                     r += 1.0
                     alpha = x
-        return -np.Inf if r == 0 else np.log(r) + alpha
+        return -np.inf if r == 0 else np.log(r) + alpha
 
     @staticmethod
     def _lik(muts, span, dt, mutation_rate, standardize=True):