Update versioneer and run cython from CMake (#228)

deeptime-ml · Apr 11, 2022 · fcec08e · fcec08e
1 parent 5397046
commit fcec08e
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Showing 5 changed files with 86 additions and 46 deletions.
diff --git a/deeptime/__init__.py b/deeptime/__init__.py
@@ -1,6 +1,5 @@
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']
 
 from . import util
 from . import numeric

diff --git a/deeptime/_version.py b/deeptime/_version.py
@@ -6,7 +6,7 @@
 # that just contains the computed version number.
 
 # This file is released into the public domain. Generated by
-# versioneer-0.21 (https://github.com/python-versioneer/python-versioneer)
+# versioneer-0.22 (https://github.com/python-versioneer/python-versioneer)
 
 """Git implementation of _version.py."""
 
@@ -16,6 +16,7 @@
 import subprocess
 import sys
 from typing import Callable, Dict
+import functools
 
 
 def get_keywords():
@@ -73,14 +74,22 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
     """Call the given command(s)."""
     assert isinstance(commands, list)
     process = None
+
+    popen_kwargs = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
     for command in commands:
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
             process = subprocess.Popen([command] + args, cwd=cwd, env=env,
                                        stdout=subprocess.PIPE,
                                        stderr=(subprocess.PIPE if hide_stderr
-                                               else None))
+                                               else None), **popen_kwargs)
             break
         except OSError:
             e = sys.exc_info()[1]
@@ -228,10 +237,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     version string, meaning we're inside a checked out source tree.
     """
     GITS = ["git"]
-    TAG_PREFIX_REGEX = "*"
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
-        TAG_PREFIX_REGEX = r"\*"
+
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
 
     _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
                    hide_stderr=True)
@@ -240,12 +254,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
             print("Directory %s not under git control" % root)
         raise NotThisMethod("'git rev-parse --git-dir' returned error")
 
+    MATCH_ARGS = ["--match", "%s*" % tag_prefix] if tag_prefix else []
+
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
     describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
-                                     "--always", "--long",
-                                     "--match",
-                                     "%s%s" % (tag_prefix, TAG_PREFIX_REGEX)],
+                                     "--always", "--long", *MATCH_ARGS],
                               cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:

diff --git a/deeptime/numeric/CMakeLists.txt b/deeptime/numeric/CMakeLists.txt
@@ -2,3 +2,13 @@ project(_numeric_bindings CXX)
 
 set(SRC src/numeric_module.cpp)
 register_pybind_module(${PROJECT_NAME} ${SRC})
+
+find_package(Cython)
+if(Cython_FOUND)
+    find_package(PythonExtensions REQUIRED)
+    add_cython_target(eig_qr eig_qr.pyx)
+    add_library(eig_qr MODULE ${eig_qr})
+    python_extension_module(eig_qr)
+    file(RELATIVE_PATH REL_PATH "${DEEPTIME_ROOT_DIRECTORY}/deeptime" "${CMAKE_CURRENT_LIST_DIR}")
+    install(TARGETS eig_qr DESTINATION ${REL_PATH})
+endif()
diff --git a/setup.py b/setup.py
@@ -1,14 +1,10 @@
 # based on https://github.com/pybind/scikit_build_example/blob/master/setup.py
 
 import os
-import re
-from pathlib import Path
-
 import sys
-import toml
 
-from setuptools import find_packages, Extension
-from Cython.Build import cythonize
+from setuptools import find_packages
+import toml
 
 sys.path.insert(0, os.path.dirname(__file__))
 import versioneer
@@ -25,13 +21,6 @@
 pyproject = toml.load("pyproject.toml")
 
 
-def eig_qr_extension():
-    module_name = 'deeptime.numeric.eig_qr'
-    sources = ["/".join(module_name.split(".")) + '.pyx']
-    return cythonize([Extension(module_name, sources=sources, extra_compile_args=['-std=c99'])],
-                     compiler_directives={'language_level': '3'})[0]
-
-
 def load_long_description():
     with open(pyproject["project"]["readme"], mode='r', encoding="utf-8") as f:
         return f.read()
@@ -61,12 +50,9 @@ def load_long_description():
         cmake_args=cmake_args,
         include_package_data=True,
         python_requires=pyproject["project"]["requires-python"],
-        ext_modules=[eig_qr_extension()]
+        ext_modules=[],
+        cmdclass=versioneer.get_cmdclass()
     )
 
 if __name__ == '__main__':
-    # see issue https://github.com/scikit-build/scikit-build/issues/521
-    # invalidates _skbuild cache
-    for i in (Path(__file__).resolve().parent / "_skbuild").rglob("CMakeCache.txt"):
-        i.write_text(re.sub("^//.*$\n^[^#].*pip-build-env.*$", "", i.read_text(), flags=re.M))
     setup(**metadata)
diff --git a/versioneer.py b/versioneer.py
@@ -1,5 +1,5 @@
 
-# Version: 0.21
+# Version: 0.22
 
 """The Versioneer - like a rocketeer, but for versions.
 
@@ -10,11 +10,11 @@
 * https://github.com/python-versioneer/python-versioneer
 * Brian Warner
 * License: Public Domain
-* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
+* Compatible with: Python 3.6, 3.7, 3.8, 3.9, 3.10 and pypy3
 * [![Latest Version][pypi-image]][pypi-url]
 * [![Build Status][travis-image]][travis-url]
 
-This is a tool for managing a recorded version number in distutils-based
+This is a tool for managing a recorded version number in distutils/setuptools-based
 python projects. The goal is to remove the tedious and error-prone "update
 the embedded version string" step from your release process. Making a new
 release should be as easy as recording a new tag in your version-control
@@ -288,6 +288,7 @@
 import subprocess
 import sys
 from typing import Callable, Dict
+import functools
 
 
 class VersioneerConfig:
@@ -384,14 +385,22 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
     """Call the given command(s)."""
     assert isinstance(commands, list)
     process = None
+
+    popen_kwargs = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
     for command in commands:
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
             process = subprocess.Popen([command] + args, cwd=cwd, env=env,
                                        stdout=subprocess.PIPE,
                                        stderr=(subprocess.PIPE if hide_stderr
-                                               else None))
+                                               else None), **popen_kwargs)
             break
         except OSError:
             e = sys.exc_info()[1]
@@ -422,7 +431,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
 # that just contains the computed version number.
 
 # This file is released into the public domain. Generated by
-# versioneer-0.21 (https://github.com/python-versioneer/python-versioneer)
+# versioneer-0.22 (https://github.com/python-versioneer/python-versioneer)
 
 """Git implementation of _version.py."""
 
@@ -432,6 +441,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
 import subprocess
 import sys
 from typing import Callable, Dict
+import functools
 
 
 def get_keywords():
@@ -489,14 +499,22 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
     """Call the given command(s)."""
     assert isinstance(commands, list)
     process = None
+
+    popen_kwargs = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
     for command in commands:
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
             process = subprocess.Popen([command] + args, cwd=cwd, env=env,
                                        stdout=subprocess.PIPE,
                                        stderr=(subprocess.PIPE if hide_stderr
-                                               else None))
+                                               else None), **popen_kwargs)
             break
         except OSError:
             e = sys.exc_info()[1]
@@ -644,10 +662,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     version string, meaning we're inside a checked out source tree.
     """
     GITS = ["git"]
-    TAG_PREFIX_REGEX = "*"
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
-        TAG_PREFIX_REGEX = r"\*"
+
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
 
     _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
                    hide_stderr=True)
@@ -656,12 +679,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
             print("Directory %%s not under git control" %% root)
         raise NotThisMethod("'git rev-parse --git-dir' returned error")
 
+    MATCH_ARGS = ["--match", "%%s*" %% tag_prefix] if tag_prefix else []
+
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
     describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
-                                     "--always", "--long",
-                                     "--match",
-                                     "%%s%%s" %% (tag_prefix, TAG_PREFIX_REGEX)],
+                                     "--always", "--long", *MATCH_ARGS],
                               cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
@@ -1162,10 +1185,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     version string, meaning we're inside a checked out source tree.
     """
     GITS = ["git"]
-    TAG_PREFIX_REGEX = "*"
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
-        TAG_PREFIX_REGEX = r"\*"
+
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
 
     _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
                    hide_stderr=True)
@@ -1174,12 +1202,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
             print("Directory %s not under git control" % root)
         raise NotThisMethod("'git rev-parse --git-dir' returned error")
 
+    MATCH_ARGS = ["--match", "%s*" % tag_prefix] if tag_prefix else []
+
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
     describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
-                                     "--always", "--long",
-                                     "--match",
-                                     "%s%s" % (tag_prefix, TAG_PREFIX_REGEX)],
+                                     "--always", "--long", *MATCH_ARGS],
                               cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
@@ -1344,7 +1372,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
 
 
 SHORT_VERSION_PY = """
-# This file was generated by 'versioneer.py' (0.21) from
+# This file was generated by 'versioneer.py' (0.22) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -1748,7 +1776,10 @@ def get_cmdclass(cmdclass=None):
     cmds = {} if cmdclass is None else cmdclass.copy()
 
     # we add "version" to both distutils and setuptools
-    from distutils.core import Command
+    try:
+        from setuptools import Command
+    except ImportError:
+        from distutils.core import Command
 
     class cmd_version(Command):
         description = "report generated version string"