removing BioExt depedency from setup.py

veg · Oct 24, 2023 · 3f239f6 · 3f239f6
1 parent 296383b
commit 3f239f6
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Showing 4 changed files with 57 additions and 10 deletions.
diff --git a/BioExt/tn93/_tn93.c b/BioExt/tn93/_tn93.c
diff --git a/BioExt/tn93/_tn93.html b/BioExt/tn93/_tn93.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by Cython 3.0.3 -->
+<!-- Generated by Cython 3.0.4 -->
 <html>
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
@@ -289,7 +289,7 @@
     </style>
 </head>
 <body class="cython">
-<p><span style="border-bottom: solid 1px grey;">Generated by Cython 3.0.3</span></p>
+<p><span style="border-bottom: solid 1px grey;">Generated by Cython 3.0.4</span></p>
 <p>
     <span style="background-color: #FFFF00">Yellow lines</span> hint at Python interaction.<br />
     Click on a line that starts with a "<code>+</code>" to see the C code that Cython generated for it.

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,4 @@
 [build-system]
-requires = ["setuptools>=42", "wheel", "Cython"]
+requires = ["setuptools>=42", "wheel", "Cython", "numpy"]
 
 build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
@@ -7,7 +7,10 @@
 
 from Cython.Build import cythonize
 from setuptools import Extension, setup
-from BioExt.references._factory import _installrefdirs
+
+from glob import glob
+from os.path import join, abspath, split, basename
+
 
 np_inc = [os.path.join(os.path.dirname(numpy.__file__), 'core', 'include')]
 
@@ -50,10 +53,35 @@
         )
     ] + tn93_extension
 
+_refdir = join(
+    split(
+        split(
+            abspath(__file__)
+        )[0]  # this_directory/
+    )[0],  # this_directory/../
+    'BioExt',
+    'data',
+    'references'
+)
+
+_installrefdirs = []
+
+# Simplified logic to generate _installrefdirs
+for seqdir in glob(join(_refdir, '*')):
+    globber = '*.*'  # Assuming you want all file types, adjust as needed
+    _installrefdirs.append(
+        join(
+            'data',
+            'references',
+            basename(seqdir),
+            globber
+        )
+    )
+
 
 setup(
     name='bioext',
-    version='0.21.3',
+    version='0.21.4',
     description='Misc utilities and definitions not included or hidden in BioPython',
     author='N Lance Hepler',
     author_email='nlhepler@gmail.com',