tinygwas 0.2.1__tar.gz → 0.2.3__tar.gz

{tinygwas-0.2.1/tinygwas.egg-info → tinygwas-0.2.3}/PKG-INFO

@@ -1,6 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: tinygwas
-Version: 0.2.1
+Version: 0.2.3
 Summary: Toy C++ implementation with python wrapper for genome-wide association testing
 Author: Kangcheng Hou
 Author-email: kangchenghou@gmail.com
+Requires-Dist: pybind11
+Requires-Dist: numpy
+Dynamic: author
+Dynamic: author-email
+Dynamic: requires-dist
+Dynamic: summary

{tinygwas-0.2.1 → tinygwas-0.2.3}/README.md

@@ -10,5 +10,10 @@ pip install -e .
 ```
 
 
+## Upload to PyPI (for developers)
+```
+python setup.py sdist
+twine upload dist/*
+```
 ## Contact
 Kangcheng Hou (kangchenghou@gmail.com)

{tinygwas-0.2.1 → tinygwas-0.2.3}/setup.py

@@ -40,6 +40,7 @@ class CMakeBuild(build_ext):
         cmake_args = [
             "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir,
             "-DPYTHON_EXECUTABLE=" + sys.executable,
+            "-DPython_EXECUTABLE=" + sys.executable,
         ]
 
         cfg = "Debug" if self.debug else "Release"
@@ -73,7 +74,7 @@ class CMakeBuild(build_ext):
 
 setup(
     name="tinygwas",
-    version="0.2.1",
+    version="0.2.3",
     install_requires=["pybind11", "numpy"],
     author="Kangcheng Hou",
     author_email="kangchenghou@gmail.com",

tinygwas-0.2.3/tests/test_linear.py

@@ -0,0 +1,72 @@
+import statsmodels.api as sm
+import numpy as np
+import tinygwas
+
+# statsmodels implementation
+def linear_ftest(var, cov, pheno, var_size, test_vars):
+    """
+    Same interface with the tinygwas.linear_f_test function.
+    """
+    n_indiv = var.shape[0]
+    n_var = var.shape[1]
+    n_cov = cov.shape[1]
+
+    design = np.zeros((n_indiv, var_size + n_cov))
+    design[:, var_size : var_size + n_cov] = cov
+
+    n_test = int(n_var / var_size)
+    fvalues = np.zeros(n_test)
+
+    f_test_r_matrix = np.zeros((len(test_vars), design.shape[1]))
+    for i, v in enumerate(test_vars):
+        f_test_r_matrix[i, v] = 1
+
+    for i_test in range(n_test):
+        design[:, 0:var_size] = var[:, i_test * var_size : (i_test + 1) * var_size]
+        model = sm.OLS(pheno, design, missing="drop").fit()
+        fvalues[i_test] = model.f_test(f_test_r_matrix).fvalue
+    return fvalues
+
+
+# TODO: also test for logistic regression
+
+
+def test_consistency():
+    np.random.seed(1234)
+    n_indiv = 100
+    n_cov = 3
+    var_size = 3
+    n_snp = 10
+    test_vars = [1, 2]
+    cov = np.random.normal(size=(n_indiv, n_cov))
+    pheno = np.random.normal(size=n_indiv)
+    var = np.random.normal(size=(n_indiv, n_snp * var_size))
+
+    # test consistency without NaN
+    res = np.zeros((n_snp, var_size * 2 + 2))
+    fvalues1 = np.empty(n_snp)
+    nindiv1 = np.empty(n_snp)
+    tinygwas.linear_f_test(var, cov, pheno, var_size, test_vars, res)
+    fvalues1 = res[:, -1]
+    fvalues2 = linear_ftest(var, cov, pheno, var_size, test_vars)
+    print("Without NaN:")
+    print(fvalues1[0:5])
+
+    print("With NaN:")
+
+    # test consistency with NaN
+    n_rand = 10
+    # randomly set two values to NaN
+    for i in range(n_rand):
+        nan_var = var.copy()
+        for _ in range(3):
+            nan_var[
+                np.random.randint(0, nan_var.shape[0]),
+                np.random.randint(0, nan_var.shape[1]),
+            ] = np.nan
+        tinygwas.linear_f_test(nan_var, cov, pheno, var_size, test_vars, res)
+        fvalues1 = res[:, -1]
+        fvalues2 = linear_ftest(nan_var, cov, pheno, var_size, test_vars)
+        print(fvalues1[0:5])
+
+        assert np.allclose(fvalues1, fvalues2)

{tinygwas-0.2.1 → tinygwas-0.2.3}/thirdparty/pybind11/CMakeLists.txt

@@ -5,15 +5,30 @@
 # All rights reserved. Use of this source code is governed by a
 # BSD-style license that can be found in the LICENSE file.
 
-cmake_minimum_required(VERSION 3.4)
+# Propagate this policy (FindPythonInterp removal) so it can be detected later
+if(NOT CMAKE_VERSION VERSION_LESS "3.27")
+  cmake_policy(GET CMP0148 _pybind11_cmp0148)
+endif()
+
+cmake_minimum_required(VERSION 3.5)
 
-# The `cmake_minimum_required(VERSION 3.4...3.18)` syntax does not work with
+# The `cmake_minimum_required(VERSION 3.5...3.29)` syntax does not work with
 # some versions of VS that have a patched CMake 3.11. This forces us to emulate
 # the behavior using the following workaround:
-if(${CMAKE_VERSION} VERSION_LESS 3.18)
+if(${CMAKE_VERSION} VERSION_LESS 3.29)
   cmake_policy(VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION})
 else()
-  cmake_policy(VERSION 3.18)
+  cmake_policy(VERSION 3.29)
+endif()
+
+if(_pybind11_cmp0148)
+  cmake_policy(SET CMP0148 ${_pybind11_cmp0148})
+  unset(_pybind11_cmp0148)
+endif()
+
+# Avoid infinite recursion if tests include this as a subdirectory
+if(DEFINED PYBIND11_MASTER_PROJECT)
+  return()
 endif()
 
 # Extract project version from source
@@ -45,13 +60,8 @@ if(NOT pybind11_FIND_QUIETLY)
   message(STATUS "pybind11 v${pybind11_VERSION} ${pybind11_VERSION_TYPE}")
 endif()
 
-# Avoid infinite recursion if tests include this as a subdirectory
-if(DEFINED PYBIND11_MASTER_PROJECT)
-  set(PYBIND11_TEST OFF)
-endif()
-
 # Check if pybind11 is being used directly or via add_subdirectory
-if(CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR AND NOT DEFINED PYBIND11_MASTER_PROJECT)
+if(CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR)
   ### Warn if not an out-of-source builds
   if(CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
     set(lines
@@ -80,32 +90,73 @@ if(CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR AND NOT DEFINED PYBIND11_MASTER_
   endif()
 
   set(pybind11_system "")
+
+  set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+  if(CMAKE_VERSION VERSION_LESS "3.18")
+    set(_pybind11_findpython_default OFF)
+  else()
+    set(_pybind11_findpython_default ON)
+  endif()
 else()
   set(PYBIND11_MASTER_PROJECT OFF)
   set(pybind11_system SYSTEM)
+  set(_pybind11_findpython_default OFF)
 endif()
 
 # Options
 option(PYBIND11_INSTALL "Install pybind11 header files?" ${PYBIND11_MASTER_PROJECT})
 option(PYBIND11_TEST "Build pybind11 test suite?" ${PYBIND11_MASTER_PROJECT})
 option(PYBIND11_NOPYTHON "Disable search for Python" OFF)
+option(PYBIND11_DISABLE_HANDLE_TYPE_NAME_DEFAULT_IMPLEMENTATION
+       "To enforce that a handle_type_name<> specialization exists" OFF)
+option(PYBIND11_SIMPLE_GIL_MANAGEMENT
+       "Use simpler GIL management logic that does not support disassociation" OFF)
+option(PYBIND11_NUMPY_1_ONLY
+       "Disable NumPy 2 support to avoid changes to previous pybind11 versions." OFF)
+set(PYBIND11_INTERNALS_VERSION
+    ""
+    CACHE STRING "Override the ABI version, may be used to enable the unstable ABI.")
+option(PYBIND11_USE_CROSSCOMPILING "Respect CMAKE_CROSSCOMPILING" OFF)
+
+if(PYBIND11_DISABLE_HANDLE_TYPE_NAME_DEFAULT_IMPLEMENTATION)
+  add_compile_definitions(PYBIND11_DISABLE_HANDLE_TYPE_NAME_DEFAULT_IMPLEMENTATION)
+endif()
+if(PYBIND11_SIMPLE_GIL_MANAGEMENT)
+  add_compile_definitions(PYBIND11_SIMPLE_GIL_MANAGEMENT)
+endif()
+if(PYBIND11_NUMPY_1_ONLY)
+  add_compile_definitions(PYBIND11_NUMPY_1_ONLY)
+endif()
 
 cmake_dependent_option(
   USE_PYTHON_INCLUDE_DIR
   "Install pybind11 headers in Python include directory instead of default installation prefix"
   OFF "PYBIND11_INSTALL" OFF)
 
-cmake_dependent_option(PYBIND11_FINDPYTHON "Force new FindPython" OFF
+cmake_dependent_option(PYBIND11_FINDPYTHON "Force new FindPython" ${_pybind11_findpython_default}
                        "NOT CMAKE_VERSION VERSION_LESS 3.12" OFF)
 
+# Allow PYTHON_EXECUTABLE if in FINDPYTHON mode and building pybind11's tests
+# (makes transition easier while we support both modes).
+if(PYBIND11_MASTER_PROJECT
+   AND PYBIND11_FINDPYTHON
+   AND DEFINED PYTHON_EXECUTABLE
+   AND NOT DEFINED Python_EXECUTABLE)
+  set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+endif()
+
 # NB: when adding a header don't forget to also add it to setup.py
 set(PYBIND11_HEADERS
     include/pybind11/detail/class.h
     include/pybind11/detail/common.h
+    include/pybind11/detail/cpp_conduit.h
     include/pybind11/detail/descr.h
     include/pybind11/detail/init.h
     include/pybind11/detail/internals.h
+    include/pybind11/detail/type_caster_base.h
     include/pybind11/detail/typeid.h
+    include/pybind11/detail/value_and_holder.h
+    include/pybind11/detail/exception_translation.h
     include/pybind11/attr.h
     include/pybind11/buffer_info.h
     include/pybind11/cast.h
@@ -114,8 +165,13 @@ set(PYBIND11_HEADERS
     include/pybind11/complex.h
     include/pybind11/options.h
     include/pybind11/eigen.h
+    include/pybind11/eigen/common.h
+    include/pybind11/eigen/matrix.h
+    include/pybind11/eigen/tensor.h
     include/pybind11/embed.h
     include/pybind11/eval.h
+    include/pybind11/gil.h
+    include/pybind11/gil_safe_call_once.h
     include/pybind11/iostream.h
     include/pybind11/functional.h
     include/pybind11/numpy.h
@@ -123,7 +179,10 @@ set(PYBIND11_HEADERS
     include/pybind11/pybind11.h
     include/pybind11/pytypes.h
     include/pybind11/stl.h
-    include/pybind11/stl_bind.h)
+    include/pybind11/stl_bind.h
+    include/pybind11/stl/filesystem.h
+    include/pybind11/type_caster_pyobject_ptr.h
+    include/pybind11/typing.h)
 
 # Compare with grep and warn if mismatched
 if(PYBIND11_MASTER_PROJECT AND NOT CMAKE_VERSION VERSION_LESS 3.12)
@@ -180,12 +239,19 @@ if(NOT TARGET pybind11_headers)
 
   target_compile_features(pybind11_headers INTERFACE cxx_inheriting_constructors cxx_user_literals
                                                      cxx_right_angle_brackets)
+  if(NOT "${PYBIND11_INTERNALS_VERSION}" STREQUAL "")
+    target_compile_definitions(
+      pybind11_headers INTERFACE "PYBIND11_INTERNALS_VERSION=${PYBIND11_INTERNALS_VERSION}")
+  endif()
 else()
   # It is invalid to install a target twice, too.
   set(PYBIND11_INSTALL OFF)
 endif()
 
 include("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11Common.cmake")
+# https://github.com/jtojnar/cmake-snips/#concatenating-paths-when-building-pkg-config-files
+# TODO: cmake 3.20 adds the cmake_path() function, which obsoletes this snippet
+include("${CMAKE_CURRENT_SOURCE_DIR}/tools/JoinPaths.cmake")
 
 # Relative directory setting
 if(USE_PYTHON_INCLUDE_DIR AND DEFINED Python_INCLUDE_DIRS)
@@ -200,6 +266,12 @@ if(PYBIND11_INSTALL)
       "${CMAKE_INSTALL_DATAROOTDIR}/cmake/${PROJECT_NAME}"
       CACHE STRING "install path for pybind11Config.cmake")
 
+  if(IS_ABSOLUTE "${CMAKE_INSTALL_INCLUDEDIR}")
+    set(pybind11_INCLUDEDIR "${CMAKE_INSTALL_FULL_INCLUDEDIR}")
+  else()
+    set(pybind11_INCLUDEDIR "\$\{PACKAGE_PREFIX_DIR\}/${CMAKE_INSTALL_INCLUDEDIR}")
+  endif()
+
   configure_package_config_file(
     tools/${PROJECT_NAME}Config.cmake.in "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
     INSTALL_DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
@@ -231,6 +303,7 @@ if(PYBIND11_INSTALL)
           tools/pybind11Common.cmake
           tools/pybind11Tools.cmake
           tools/pybind11NewTools.cmake
+          tools/pybind11GuessPythonExtSuffix.cmake
     DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
 
   if(NOT PYBIND11_EXPORT_NAME)
@@ -244,6 +317,30 @@ if(PYBIND11_INSTALL)
     NAMESPACE "pybind11::"
     DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
 
+  # pkg-config support
+  if(NOT prefix_for_pc_file)
+    if(IS_ABSOLUTE "${CMAKE_INSTALL_DATAROOTDIR}")
+      set(prefix_for_pc_file "${CMAKE_INSTALL_PREFIX}")
+    else()
+      set(pc_datarootdir "${CMAKE_INSTALL_DATAROOTDIR}")
+      if(CMAKE_VERSION VERSION_LESS 3.20)
+        set(prefix_for_pc_file "\${pcfiledir}/..")
+        while(pc_datarootdir)
+          get_filename_component(pc_datarootdir "${pc_datarootdir}" DIRECTORY)
+          string(APPEND prefix_for_pc_file "/..")
+        endwhile()
+      else()
+        cmake_path(RELATIVE_PATH CMAKE_INSTALL_PREFIX BASE_DIRECTORY CMAKE_INSTALL_DATAROOTDIR
+                   OUTPUT_VARIABLE prefix_for_pc_file)
+      endif()
+    endif()
+  endif()
+  join_paths(includedir_for_pc_file "\${prefix}" "${CMAKE_INSTALL_INCLUDEDIR}")
+  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11.pc.in"
+                 "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc" @ONLY)
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc"
+          DESTINATION "${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig/")
+
   # Uninstall target
   if(PYBIND11_MASTER_PROJECT)
     configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/cmake_uninstall.cmake.in"