magenpy==0.0.1 release; Minor bug fixes in GitHub workflow + Cython…

… scripts.

.github/workflows/ci-docs.yml

@@ -1,4 +1,4 @@
-name: ci Docs
+name: Build Docs
 on:
   push:
     branches:
@@ -31,5 +31,5 @@ jobs:
           restore-keys: |
             mkdocs-material-
 
-      - run: python -m pip install -r requirements-docs.txt
+      - run: python -m pip install -v -e .[docs]
       - run: mkdocs gh-deploy --force

.github/workflows/ci-linux.yml

@@ -1,4 +1,4 @@
-name: magenpy Linux-CI
+name: Linux-CI
 
 on: [push, pull_request]
 

.github/workflows/ci-osx.yml

@@ -1,4 +1,4 @@
-name: magenpy OSX-CI
+name: OSX-CI
 
 on: [push, pull_request]
 

.github/workflows/ci-windows.yml

@@ -1,4 +1,4 @@
-name: magenpy OSX-CI
+name: Windows-CI
 
 on: [push, pull_request]
 

.github/workflows/wheels.yml

@@ -1,4 +1,4 @@
-name: Build magenpy and upload to PyPI
+name: Wheels
 
 on:
   workflow_dispatch:

magenpy/stats/ld/c_utils.pyx

@@ -115,8 +115,8 @@ cpdef find_ld_block_boundaries(long[:] pos, long[:, :] block_boundaries):
 
     cdef:
         int i, j, ldb_idx, block_start, block_end, B = block_boundaries.shape[0], M = pos.shape[0]
-        long[:] v_min = np.zeros_like(pos, dtype=np.int64)
-        long[:] v_max = M*np.ones_like(pos, dtype=np.int64)
+        int[:] v_min = np.zeros_like(pos, dtype=np.int32)
+        int[:] v_max = M*np.ones_like(pos, dtype=np.int32)
 
     with nogil:
         for i in range(M):
@@ -156,8 +156,8 @@ cpdef find_windowed_ld_boundaries(double[:] pos, double max_dist):
 
     cdef:
         int i, j, M = pos.shape[0]
-        long[:] v_min = np.zeros_like(pos, dtype=np.int64)
-        long[:] v_max = M*np.ones_like(pos, dtype=np.int64)
+        int[:] v_min = np.zeros_like(pos, dtype=np.int32)
+        int[:] v_max = M*np.ones_like(pos, dtype=np.int32)
 
     with nogil:
         for i in range(M):
@@ -180,9 +180,9 @@ cpdef find_windowed_ld_boundaries(double[:] pos, double max_dist):
 @cython.cdivision(True)
 @cython.exceptval(check=False)
 cpdef find_shrinkage_ld_boundaries(double[:] cm_pos,
-                                   double genmap_ne,
-                                   int genmap_sample_size,
-                                   double cutoff):
+                                  double genmap_ne,
+                                  int genmap_sample_size,
+                                  double cutoff):
     """
     Find the LD boundaries for the shrinkage estimator of Wen and Stephens (2010).
     
@@ -192,9 +192,10 @@ cpdef find_shrinkage_ld_boundaries(double[:] cm_pos,
     :param cutoff: The threshold below which we set the shrinkage factor to zero.
     """
 
-    cdef unsigned int i, j, M = cm_pos.shape[0]
-    cdef long[:] v_min = np.zeros_like(cm_pos, dtype=int)
-    cdef long[:] v_max = M*np.ones_like(cm_pos, dtype=int)
+    cdef:
+        int i, j, M = cm_pos.shape[0]
+        int[:] v_min = np.zeros_like(cm_pos, dtype=np.int32)
+        int[:] v_max = M*np.ones_like(cm_pos, dtype=np.int32)
 
     # The multiplicative term for the shrinkage factor
     # The shrinkage factor is 4 * Ne * (rho_ij/100) / (2*m)

setup.py

@@ -72,6 +72,9 @@ def no_cythonize(extensions, **_ignore):
 with open("requirements-test.txt") as fp:
     test_requires = fp.read().strip().split("\n")
 
+with open("requirements-docs.txt") as fp:
+    docs_requires = fp.read().strip().split("\n")
+
 # ------------------------------------------------------
 
 setup(
@@ -105,7 +108,7 @@ def no_cythonize(extensions, **_ignore):
                               'config/*.ini']},
     scripts=['bin/magenpy_ld', 'bin/magenpy_simulate'],
     install_requires=install_requires,
-    extras_require={'opt': opt_requires, 'test': test_requires},
+    extras_require={'opt': opt_requires, 'test': test_requires, 'docs': docs_requires},
     ext_modules=extensions,
     zip_safe=False
 )