Trac #33070: Package upgrades for Python 3.10 support

We add an option `--commit` to `sage --package update` and `sage
--package update-latest` and use it to make the following updates:

- `prometheus-client` -
https://github.com/prometheus/client_python/releases/tag/v0.12.0
- `gmpy2` 2.1.1 - https://github.com/aleaxit/gmpy/commits/master
- `distlib`
 0.3.4 - https://distlib.readthedocs.io/en/stable/overview.html#id1
- `debugpy` 1.5.1 - https://github.com/microsoft/debugpy/releases
- `defusedxml` -
https://github.com/tiran/defusedxml/blob/main/CHANGES.txt
- `decorator` 5.0.9 (not 5.1.0) - https://github.com/micheles/decorator/
blob/master/CHANGES.md#509-2021-05-16
- `jsonschema` 4.3.2 -
https://github.com/Julian/jsonschema/blob/main/CHANGELOG.rst
- `nest_asyncio` 1.5.4 -
https://github.com/erdewit/nest_asyncio/commits/master
- `packaging` 21.3 - https://github.com/pypa/packaging/releases
- `pycparser` 2.21 -
https://github.com/eliben/pycparser/blob/master/CHANGES

Separate tickets:
- #32930 ipython/jupyter
- #32510 igraph

URL: https://trac.sagemath.org/33070
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Michael Orlitzky, Dima Pasechnik

build/pkgs/debugpy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=debugpy-VERSION.zip
-sha1=c0162bd8d68a43702eea2591c67624fd5b4aa87b
-md5=0c1103c7234b1f547eb705aff150ab31
-cksum=676752698
+sha1=169efd648ce0903c30cd300f8040136ec0ee16cc
+md5=7c8ef4f136c9bcf501e80a12b8e21ac1
+cksum=422456395
 upstream_url=https://pypi.io/packages/source/d/debugpy/debugpy-VERSION.zip

build/pkgs/debugpy/package-version.txt

@@ -1 +1 @@
-1.4.1
+1.5.1

build/pkgs/decorator/checksums.ini

@@ -1,4 +1,5 @@
 tarball=decorator-VERSION.tar.gz
-sha1=24d4560ff3e89a6cec068d323383577343c086fb
-md5=d83c624cce93e6bdfab144821b526e1d
-cksum=1324765948
+sha1=4035760ce781a93181eeb3f8a36435eb799ceb76
+md5=a90526e45e7a30cf2710d6467f403e03
+cksum=1796541525
+upstream_url=https://pypi.io/packages/source/d/decorator/decorator-VERSION.tar.gz

build/pkgs/decorator/dependencies

@@ -2,4 +2,3 @@ $(PYTHON) | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.
-It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/decorator/package-version.txt

@@ -1 +1 @@
-4.4.2
+5.0.9

build/pkgs/defusedxml/checksums.ini

@@ -1,4 +1,5 @@
 tarball=defusedxml-VERSION.tar.gz
-sha1=0bba33cc1e6d59f8fc71ceb8d12ad951072ad122
-md5=a59741f675c4cba649de40a99f732897
-cksum=2504737728
+sha1=37667af1dc1357eb96b005c4f408ad5292d77b9f
+md5=a50e7f21aa60a741efe6b1b658dfb3f8
+cksum=3442371004
+upstream_url=https://pypi.io/packages/source/d/defusedxml/defusedxml-VERSION.tar.gz

build/pkgs/defusedxml/dependencies

@@ -2,4 +2,3 @@ $(PYTHON) | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.
-It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/defusedxml/package-version.txt

@@ -1 +1 @@
-0.6.0
+0.7.1

build/pkgs/distlib/checksums.ini

@@ -1,5 +1,5 @@
 tarball=distlib-VERSION.zip
-sha1=47db238631902dbd0fbf730ca303438eaecbb0c8
-md5=442dc114d7e59deec1c727b8a27d7e7c
-cksum=4135782264
+sha1=e7927ebc964676c17d466ed6a345222c34167a85
+md5=c886b7d99b4085c5d960e7435dcbd397
+cksum=10374426
 upstream_url=https://pypi.io/packages/source/d/distlib/distlib-VERSION.zip

build/pkgs/distlib/package-version.txt

@@ -1 +1 @@
-0.3.3
+0.3.4

build/pkgs/gmpy2/checksums.ini

@@ -1,5 +1,5 @@
 tarball=gmpy2-VERSION.tar.gz
-sha1=6564cfd78f552a8db82136c10b19aa7465856865
-md5=a1555e0d7ca28b3a49c9a81aa06e2bb6
-cksum=2826987588
+sha1=fcb929ab9a44d96bfb47b7ed411cc2f048b484b2
+md5=877d324e676b162053772affda5c0de7
+cksum=2408333571
 upstream_url=https://pypi.io/packages/source/g/gmpy2/gmpy2-VERSION.tar.gz

build/pkgs/gmpy2/install-requires.txt

@@ -1,3 +1 @@
-# We would like to write gmpy2 >=2.1.0b5, but pipenv does not accept prereleases in version ranges
-# https://github.com/pypa/pipenv/issues/1760
-gmpy2 ==2.1.0rc1
+gmpy2 >=2.1.0

build/pkgs/gmpy2/package-version.txt

@@ -1 +1 @@
-2.1.0rc1
+2.1.1

build/pkgs/jsonschema/checksums.ini

@@ -1,5 +1,5 @@
 tarball=jsonschema-VERSION.tar.gz
-sha1=fbca135887b3c79e7f08fff6a34fef053746151b
-md5=f1a0b5011f05a02a8dee1070cd10a26d
-cksum=3852093817
+sha1=f804244e37c3f8f1c587ed6aee8f1f6a851f90f5
+md5=87cf45f980c9b48e040c0c5897e574c4
+cksum=1105743845
 upstream_url=https://pypi.io/packages/source/j/jsonschema/jsonschema-VERSION.tar.gz

build/pkgs/jsonschema/package-version.txt

@@ -1 +1 @@
-3.2.0
+4.3.2

build/pkgs/nest_asyncio/checksums.ini

@@ -1,5 +1,5 @@
 tarball=nest_asyncio-VERSION.tar.gz
-sha1=7ef28133a6703242618104a92263a867957b98d8
-md5=6271f5e4181736c2e711657ef1eae915
-cksum=1746231914
+sha1=a139466f747bcd3324b8e080e00fc443603e8fa6
+md5=a97d6622335d35563baeabb87afb758f
+cksum=2526839264
 upstream_url=https://pypi.io/packages/source/n/nest_asyncio/nest_asyncio-VERSION.tar.gz

build/pkgs/nest_asyncio/package-version.txt

@@ -1 +1 @@
-1.5.1
+1.5.4

build/pkgs/packaging/checksums.ini

@@ -1,5 +1,5 @@
 tarball=packaging-VERSION.tar.gz
-sha1=6ba3b8ff3ee43d1d4c0b658241f4fd6036ee7c78
-md5=240ba5823ed31051a1254e74c9d18d55
-cksum=3836397838
+sha1=b8caff3bec760723db6af4092c68075e22bdb769
+md5=e713c1939f294fd729af4a7be40dd141
+cksum=2539089468
 upstream_url=https://pypi.io/packages/source/p/packaging/packaging-VERSION.tar.gz

build/pkgs/packaging/package-version.txt

@@ -1 +1 @@
-21.0
+21.3

build/pkgs/prometheus_client/checksums.ini

@@ -1,5 +1,5 @@
 tarball=prometheus_client-VERSION.tar.gz
-sha1=3d8077107a06a2ec413c64afaf8ca9a7124b283e
-md5=eeb8c4ebac21508e1bb420d6fd90fa95
-cksum=144951026
+sha1=78932e768ad69d5ffe1f12abb41c51554ef12eb8
+md5=4439c954aa7bc68b15915c6360967851
+cksum=4269644267
 upstream_url=https://pypi.io/packages/source/p/prometheus-client/prometheus_client-VERSION.tar.gz

build/pkgs/prometheus_client/package-version.txt

@@ -1 +1 @@
-0.11.0
+0.12.0

build/pkgs/pycparser/checksums.ini

@@ -1,5 +1,5 @@
 tarball=pycparser-VERSION.tar.gz
-sha1=0ae93d89b69fab48af3a407a2f8663bcea270c3d
-md5=b8f88de737db8c346ee8d31c07c7a25a
-cksum=3289554032
+sha1=359c718c6ece361047f61846b9fa4ea0239576dc
+md5=48f7d743bf018f7bb2ffc5fb976d1492
+cksum=1065143416
 upstream_url=https://pypi.io/packages/source/p/pycparser/pycparser-VERSION.tar.gz

build/pkgs/pycparser/package-version.txt

@@ -1 +1 @@
-2.20
+2.21

build/sage_bootstrap/app.py

@@ -114,7 +114,17 @@ def apropos(self, incorrect_name):
             print('There is no package similar to {0}'.format(incorrect_name))
             print('You can find further packages at http://files.sagemath.org/spkg/')
 
-    def update(self, package_name, new_version, url=None):
+    def commit(self, package_name, message=None):
+        """
+        Commit the changes to the Sage source tree for the given package
+        """
+        import os
+        package = Package(package_name)
+        if message is None:
+            message = 'build/pkgs/{0}: Update to {1}'.format(package_name, package.version)
+        os.system('git commit -m "{0}" {1}'.format(message, package.path))
+
+    def update(self, package_name, new_version, url=None, commit=False):
         """
         Update a package. This modifies the Sage sources. 
     
@@ -126,8 +136,10 @@ def update(self, package_name, new_version, url=None):
             log.debug('Downloading %s', url)
             update.download_upstream(url)
         update.fix_checksum()
+        if commit:
+            self.commit(package_name)
 
-    def update_latest(self, package_name):
+    def update_latest(self, package_name, commit=False):
         """
         Update a package to the latest version. This modifies the Sage sources. 
         """
@@ -138,8 +150,10 @@ def update_latest(self, package_name):
             return
         else:
             pypi.update(Package(package_name))
+        if commit:
+            self.commit(package_name)
 
-    def update_latest_cls(self, package_name_or_class):
+    def update_latest_cls(self, package_name_or_class, commit=False):
         exclude = [
             'cypari'   # Name conflict
         ]
@@ -152,7 +166,7 @@ def update_latest_cls(self, package_name_or_class):
                 log.debug('skipping %s because of pypi name collision', package_name)
                 continue
             try:
-                self.update_latest(package_name)
+                self.update_latest(package_name, commit=commit)
             except PyPiError as e:
                 log.warn('updating %s failed: %s', package_name, e)
 

build/sage_bootstrap/cmdline.py

@@ -237,13 +237,19 @@ def make_parser():
         'new_version', type=str, help='New version')
     parser_update.add_argument(
         '--url', type=str, default=None, help='Download URL')
+    parser_update.add_argument(
+        '--commit', action="store_true",
+        help='Whether to run "git commit"')
 
     parser_update_latest = subparsers.add_parser(
         'update-latest', epilog=epilog_update_latest,
         formatter_class=argparse.RawDescriptionHelpFormatter,
         help='Update a package to the latest version. This modifies the Sage sources.')
     parser_update_latest.add_argument(
         'package_name', type=str, help='Package name (:all: for all packages)')
+    parser_update_latest.add_argument(
+        '--commit', action="store_true",
+        help='Whether to run "git commit"')
 
     parser_download = subparsers.add_parser(
         'download', epilog=epilog_download,
@@ -329,9 +335,9 @@ def run():
     elif args.subcommand == 'apropos':
         app.apropos(args.incorrect_name)
     elif args.subcommand == 'update':
-        app.update(args.package_name, args.new_version, url=args.url)
+        app.update(args.package_name, args.new_version, url=args.url, commit=args.commit)
     elif args.subcommand == 'update-latest':
-        app.update_latest_cls(args.package_name)
+        app.update_latest_cls(args.package_name, commit=args.commit)
     elif args.subcommand == 'download':
         app.download_cls(args.package_name,
                          allow_upstream=args.allow_upstream,