setuptools

.github/workflows/build.yml

@@ -25,10 +25,11 @@ jobs:
         python-is-python3
         python3-biopython
         python3-dev
-        python3-distutils
         python3-numpy
         python3-pil
+        python3-pybind11
         python3-pytest
+        python3-setuptools
 
     - name: Install collada2gltf
       run: |

create_shadertext.py

@@ -7,7 +7,7 @@
 from collections import defaultdict
 from os.path import dirname
 from subprocess import Popen, PIPE
-from distutils import dir_util
+from pathlib import Path
 
 def create_all(generated_dir, pymoldir="."):
     '''
@@ -30,7 +30,7 @@ def __init__(self, filename):
             self.out = cStringIO.StringIO()
             self.filename = filename
         else:
-            dir_util.mkpath(os.path.dirname(filename))
+            Path(filename).parent.mkdir(parents=True, exist_ok=True)
             self.out = open(filename, "w")
             self.filename = None
     def close(self):

modules/pymol/plugins/installation.py

@@ -55,9 +55,16 @@ def cmp_version(v1, v2):
     if v2 == '':
         return 1
     try:
-        from distutils.version import StrictVersion as Version
-        return cmp(Version(v1), Version(v2))
-    except:
+        from packaging.version import parse as Version
+        v1 = Version(v1)
+        v2 = Version(v2)
+        if v1 < v2:
+            return -1
+        if v1 > v2:
+            return 1
+        return 0
+    except Exception as ex:
+        print(ex)
         print(' Warning: Version parsing failed for', v1, 'and/or', v2)
         return 0
 

setup.py

@@ -6,9 +6,10 @@
 # It may assume that all of PyMOL's external dependencies are
 # pre-installed into the system.
 
-from distutils.core import setup, Extension
-from distutils.util import change_root
 from glob import glob
+from typing import Iterator, Union, Callable
+import functools
+import shlex
 import shutil
 import sys, os, re
 
@@ -66,7 +67,7 @@ class options:
 if options.help_distutils:
     sys.argv.append("--help")
 
-if True:
+if False:
     import monkeypatch_distutils
     monkeypatch_distutils.set_parallel_jobs(options.jobs)
 
@@ -130,10 +131,74 @@ def guess_msgpackc():
     return 'no'
 
 
+def change_root(new_root: str, pathname: str) -> str:
+    _, pathname = os.path.splitdrive(pathname)
+    pathname = pathname.lstrip("/\\")
+    assert not os.path.isabs(pathname)
+    return os.path.join(new_root, pathname)
+
+
+def test_change_root():
+    if os.path.sep == "\\":
+        assert change_root(r"X:\new\root", r"rel\path") == r"X:\new\root\rel\path"
+        assert change_root(r"X:\new\root", r"\abs\path") == r"X:\new\root\abs\path"
+        assert change_root(r"X:\new\root", r"C:\abs\path") == r"X:\new\root\abs\path"
+    else:
+        assert change_root("/new/root", "rel/path") == "/new/root/rel/path"
+        assert change_root("/new/root", "/abs/path") == "/new/root/abs/path"
+
+
+test_change_root()
+
+cached_getmtime = functools.cache(os.path.getmtime)
+
+
+def get_dot_d_depencendies(obj: str) -> Iterator[str]:
+    """
+    Parse .d file (Makefile syntax)
+
+    Args:
+      obj: Path to object file
+
+    Returns:
+      Iterator over dependency paths
+    """
+    with open(os.path.splitext(obj)[0] + '.d') as handle:
+        contents = handle.read().split(': ', 1)[1]
+    contents = contents.replace('\\\n', ' ')
+    for dep in shlex.split(contents):
+        yield dep
+
+
+def needs_compile_dot_d(obj: str, src: str) -> bool:
+    """
+    Returns true if any source or header dependency changed for the object
+    file.  Parses dependencies from .d files, ignores the `src` argument.
+    """
+    try:
+        obj_mtime = os.path.getmtime(obj)
+        return any(obj_mtime < cached_getmtime(dep)
+                   for dep in get_dot_d_depencendies(obj))
+    except EnvironmentError:
+        return True
+
+
 # Important: import 'distutils.command' modules after monkeypatch_distutils
-from distutils.command.build_ext import build_ext
-from distutils.command.build_py import build_py
-from distutils.command.install import install
+from setuptools import setup
+from setuptools import Extension
+from setuptools.command.build_ext import build_ext
+from setuptools.command.build_py import build_py
+from setuptools.command.install import install
+from pybind11.setup_helpers import ParallelCompile
+
+os.environ["CPPFLAGS"] = os.getenv("CPPFLAGS", "") + " -MMD"
+
+if options.jobs:
+    os.environ["NPY_NUM_BUILD_JOBS"] = str(options.jobs)
+
+ParallelCompile("NPY_NUM_BUILD_JOBS",
+                needs_recompile=needs_compile_dot_d).install()
+
 
 class build_ext_pymol(build_ext):
     def initialize_options(self):