some tweaks to build docs and pass linting

alignparse/consensus.py

@@ -292,7 +292,7 @@ def maxlik_eps(self):
         )
         if not res.success:
             raise RuntimeError(f"optimization failed:\n{res}")
-        return res.x
+        return float(res.x)
 
 
 def empirical_accuracy(

alignparse/cs_tag.py

@@ -532,7 +532,7 @@ def extract_cs(self, start, end):
             == end - start
         ), f"{feature_cs},{clip5},{clip3}"
 
-        return (feature_cs, clip5, clip3)
+        return (feature_cs, int(clip5), int(clip3))
 
 
 @functools.lru_cache(maxsize=16384)

alignparse/utils.py

@@ -221,7 +221,7 @@ def qvals_to_accuracy(qvals, encoding="numbers"):
     elif encoding != "numbers":
         raise ValueError(f"invalid `encoding`: {encoding}")
 
-    return (1 - 10 ** (qvals / -10)).sum() / len(qvals)
+    return ((1 - 10 ** (qvals / -10)).sum() / len(qvals)).astype(object)
 
 
 def sort_mutations(mut_strs):

docs/README.rst

@@ -10,7 +10,11 @@ Build the documentation
 To build the documentation, you need ensure that you have installed the packages in `doc_requirements.txt <doc_requirements.txt>`_.
 If these packages are not installed, you can install them with::
 
-    pip -r doc_requirements.txt
+    pip install -r doc_requirements.txt
+
+You also may need to install ``pandoc``:
+
+    mamba install pandoc
 
 Then simply type::
 

docs/doc_requirements.txt

@@ -1,8 +1,8 @@
-sphinx>=2.0
-sphinx-argparse>=0.2.5
-sphinx_gallery>=0.3.1
-matplotlib>=3.0.2
-nbsphinx>=0.4.2
-nbsphinx-link>=1.2.0
-ipykernel>=5.1.0
-pandoc>=2.7.3
+sphinx
+sphinx-argparse
+sphinx_gallery
+matplotlib
+nbsphinx
+nbsphinx-link
+ipykernel
+pandoc

ruff.toml

@@ -9,6 +9,8 @@ extend-exclude = [
     "dist",
     "docs/_build",
     ".*",
+    "notebooks",
+    "tests",
 ]
 lint.ignore = [
     "D203",