Squashed 'tools/dev_tools/' changes from c4337f5b..3ad5e0d8

3ad5e0d8 Drop testing with Python 2.7, add 3.12
17206759 Switch to argparse
9778d818 Switch to argparse
122d6950 Switch to argparse
69c73496 Use codecov token to avoid rate limits
5ae13679 Stick with older codecov action for now
43582234 Use latest codecov GitHub Action
7e8e4043 Use current year for copyright of autogen files
8164076f Run flake8 separately, not as part of pytest
84af9307 flake8 fix
fb3f9d03 Test with Python 3.11
626e51c1 Use Python 3 by default

git-subtree-dir: tools/dev_tools
git-subtree-split: 3ad5e0d84c668cd06deebfe414d8e16820116335

tools/dev_tools/.github/workflows/build.yml

@@ -9,7 +9,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [2.7, 3.7, 3.8, 3.9, "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -20,8 +20,11 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip install 'pytest-flake8<1.1' pytest-cov
+        pip install pytest flake8 pytest-cov
     - name: Test
       run: |
-        py.test --cov=. --cov-branch --cov-report=xml -v --flake8 .
+        py.test --cov=. --cov-branch --cov-report=xml -v .
+        flake8 --ignore=E402,W503 --exclude python_tools/reindent.py
     - uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

tools/dev_tools/check_standards.py

@@ -18,7 +18,7 @@
     print("Pygments (http://pygments.org/) library: please install.")
     print()
 
-from optparse import OptionParser
+from argparse import ArgumentParser
 
 
 def _check_do_not_commit(line, filename, num, errors):
@@ -187,15 +187,18 @@ def get_all_files():
 
 
 def main():
-    parser = OptionParser()
-    options, args = parser.parse_args()
+    parser = ArgumentParser()
+    parser.add_argument("patterns", metavar="PATTERN", nargs="*",
+                        help="File patterns to check; if unspecified, "
+                             "check all files")
+    args = parser.parse_args()
 
     errors = []
-    if len(args) == 0:
+    if len(args.patterns) == 0:
         modfiles = get_all_files()
         print("usage:", sys.argv[0], "file_patterns")
     else:
-        modfiles = args
+        modfiles = args.patterns
     for pattern in modfiles:
         expanded = glob.glob(pattern)
         # rint pattern, expanded

tools/dev_tools/cleanup_code.py

@@ -4,7 +4,7 @@
    files."""
 
 from __future__ import print_function
-from optparse import OptionParser
+from argparse import ArgumentParser
 import subprocess
 import os
 import sys
@@ -24,8 +24,8 @@
 from python_tools.reindent import Reindenter
 
 
-parser = OptionParser(usage="%prog [options] [FILENAME ...]",
-                      description="""Reformat the given C++ and Python files
+parser = ArgumentParser(
+    description="""Reformat the given C++ and Python files
 (using the clang-format tool if available and
 reindent.py, respectively). If the --all option is given, reformat all such
 files under the current directory.
@@ -34,46 +34,48 @@
 by giving the -a option. autopep8 is much more aggressive than reindent.py
 and will fix other issues, such as use of old-style Python syntax.
 """)
-parser.add_option("-c", "--clang-format", dest="clang_format",
-                  default="auto", metavar="EXE",
-                  help="The clang-format command.")
-parser.add_option("-a", dest="use_ap", action="store_true", default=False,
-                  help="Use autopep8 rather than reindent.py for "
-                       "Python files.")
-parser.add_option("--all", dest="all_files", action="store_true",
-                  default=False,
-                  help="Reformat all files under current directory")
-parser.add_option("--autopep8", dest="autopep8",
-                  default="auto", metavar="EXE",
-                  help="The autopep8 command.")
-parser.add_option("-e", "--exclude", dest="exclude",
-                  default="eigen3:config_templates", metavar="DIRS",
-                  help="Colon-separated list of dirnames to ignore.")
-parser.add_option("-v", "--verbose", dest="verbose", action="store_true",
-                  default=False,
-                  help="Print extra info.")
-(options, args) = parser.parse_args()
-if not args and not options.all_files:
+parser.add_argument("-c", "--clang-format", dest="clang_format",
+                    default="auto", metavar="EXE",
+                    help="The clang-format command.")
+parser.add_argument("-a", dest="use_ap", action="store_true", default=False,
+                    help="Use autopep8 rather than reindent.py for "
+                         "Python files.")
+parser.add_argument("--all", dest="all_files", action="store_true",
+                    default=False,
+                    help="Reformat all files under current directory")
+parser.add_argument("--autopep8", dest="autopep8",
+                    default="auto", metavar="EXE",
+                    help="The autopep8 command.")
+parser.add_argument("-e", "--exclude", dest="exclude",
+                    default="eigen3:config_templates", metavar="DIRS",
+                    help="Colon-separated list of dirnames to ignore.")
+parser.add_argument("-v", "--verbose", dest="verbose", action="store_true",
+                    default=False,
+                    help="Print extra info.")
+parser.add_argument("files", metavar="FILENAME", nargs="*",
+                    help="C++ and Python files to reformat.")
+args = parser.parse_args()
+if not args.files and not args.all_files:
     parser.error("No files selected")
 
 # clang-format-3.4",
 # autopep8
 
 # search for executables
-if options.clang_format == "auto":
-    options.clang_format = None
+if args.clang_format == "auto":
+    args.clang_format = None
     for name in ["clang-format-3.4", "clang-format"]:
         if which(name):
-            options.clang_format = name
+            args.clang_format = name
             break
-if options.autopep8 == "auto":
-    options.autopep8 = None
+if args.autopep8 == "auto":
+    args.autopep8 = None
     for name in ["autopep8"]:
         if which(name):
-            options.autopep8 = name
+            args.autopep8 = name
             break
 
-exclude = options.exclude.split(":")
+exclude = args.exclude.split(":")
 
 error = None
 
@@ -137,10 +139,10 @@ def _do_get_files(glb, cur):
 
 def _get_files(glb):
     match = []
-    if len(args) == 0:
+    if len(args.files) == 0:
         match = _do_get_files(glb, ".")
     else:
-        for a in args:
+        for a in args.files:
             if os.path.isdir(a):
                 match += _do_get_files(glb, a)
             elif a.endswith(glb):
@@ -163,17 +165,17 @@ def clean_cpp(path):
     # skip code that isn't ours
     if "dependency" in path or "/eigen3/" in path:
         return
-    if options.clang_format:
-        contents = _run([options.clang_format, "--style=Google", path])
+    if args.clang_format:
+        contents = _run([args.clang_format, "--style=Google", path])
     else:
         contents = open(path, "r").read()
     contents = contents.replace("% template", "%template")
     python_tools.rewrite(path, contents)
 
 
 def clean_py(path):
-    if options.use_ap and options.autopep8:
-        contents = _run([options.autopep8, "--aggressive", "--aggressive",
+    if args.use_ap and args.autopep8:
+        contents = _run([args.autopep8, "--aggressive", "--aggressive",
                          path])
     else:
         r = Reindenter(open(path))
@@ -185,25 +187,25 @@ def clean_py(path):
 
 
 def main():
-    if options.verbose:
-        if options.autopep8 is None:
+    if args.verbose:
+        if args.autopep8 is None:
             print("autopep8 not found")
         else:
-            print("autopep8 is `%s`" % options.autopep8)
-        if options.clang_format is None:
+            print("autopep8 is `%s`" % args.autopep8)
+        if args.clang_format is None:
             print("clang-format not found")
         else:
-            print("clang-format is `%s`" % options.clang_format)
+            print("clang-format is `%s`" % args.clang_format)
 
     tp = ThreadPool()
 
-    if args:
-        for f in args:
+    if args.files:
+        for f in args.files:
             if f.endswith(".py"):
                 tp.add_task(clean_py, f)
             elif f.endswith(".h") or f.endswith(".cpp"):
                 tp.add_task(clean_cpp, f)
-    elif options.all_files:
+    elif args.all_files:
         for f in _get_files(".py"):
             tp.add_task(clean_py, f)
         for f in _get_files(".h") + _get_files(".cpp"):

tools/dev_tools/git/bootstrap_setup_git.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Update submodules and then call the main setup_git.py. This should be
 copied to the main directory of your project and named setup_git.py."""

tools/dev_tools/git/setup_git.py

@@ -1,24 +1,24 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import os.path
 import subprocess
 import glob
-from optparse import OptionParser
+from argparse import ArgumentParser
 import shutil
 
 dev_tools_path = os.path.join("tools", "dev_tools")
 
 
-opt = OptionParser()
-opt.add_option("-g", "--global",
-               action="store_true", dest="glob", default=False,
-               help="Set global git settings instead of repo "
-                    "settings [default]")
+opt = ArgumentParser()
+opt.add_argument("-g", "--global",
+                 action="store_true", dest="glob", default=False,
+                 help="Set global git settings instead of repo "
+                      "settings [default]")
 
-(options, args) = opt.parse_args()
+args = opt.parse_args()
 
-if options.glob:
+if args.glob:
     git_config = "git config --global --replace-all"
     config_contents = ""
 else:

tools/dev_tools/make_all_header.py

@@ -6,6 +6,7 @@
 
 import sys
 import glob
+import datetime
 import os
 
 sys.path.append(os.path.split(sys.argv[0])[0])
@@ -27,13 +28,14 @@ def _add_includes(headers, output):
 
 includepath = sys.argv[1][sys.argv[1].find("include") + len("include") + 1:]
 
+year = datetime.datetime.now().year
 output = ["""/**
  *  \\file %s
  *  \\brief Include all non-deprecated headers in %s.
  *
- *  Copyright 2007-2022 IMP Inventors. All rights reserved.
+ *  Copyright 2007-%d IMP Inventors. All rights reserved.
  */
-""" % (includepath, includepath[:-2].replace('/', '.'))]
+""" % (includepath, includepath[:-2].replace('/', '.'), year)]
 guard = includepath.replace(
     "/",
     "_").replace("\\",

tools/dev_tools/python_tools/__init__.py

@@ -174,8 +174,8 @@ def get_modules(source):
 
 
 def split(string, sep=":"):
-    return([x.replace("@", ":")
-            for x in string.replace("\\:", "@").split(sep) if x != ""])
+    return ([x.replace("@", ":")
+             for x in string.replace("\\:", "@").split(sep) if x != ""])
 
 
 def get_project_info(path):

tools/dev_tools/test/test_header.py

@@ -1,6 +1,7 @@
 import unittest
 import subprocess
 import os
+import datetime
 import utils
 
 TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
@@ -26,13 +27,14 @@ def test_header(self):
                                   'include/test/subdir'], cwd=tmpdir)
             stdout, stderr = p.communicate()
             self.assertEqual(p.returncode, 0)
+            year = datetime.datetime.now().year
             self.assertEqual(utils.read_file(os.path.join(tmpdir,
                                                           'include/test.h')),
                              """/**
  *  \\file test.h
  *  \\brief Include all non-deprecated headers in test.
  *
- *  Copyright 2007-2022 IMP Inventors. All rights reserved.
+ *  Copyright 2007-%d IMP Inventors. All rights reserved.
  */
 
 #ifndef TEST_H
@@ -43,7 +45,7 @@ def test_header(self):
 #include <bar/deprecated.h>
 #endif
 #endif /* TEST_H */
-""")
+""" % year)
 
 
 if __name__ == '__main__':