`build/pkgs/python3`: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

mkoeppe · 2024-05-01T06:07:14Z

Author: @culler

Split out from:

Remove pointless rpaths on macOS; make sage-env polite when run on systems with no toolchain #37886

📝 Checklist

The title is concise and informative.
The description explains in detail what this PR is about.
I have linked a relevant issue or discussion.
I have created tests covering the changes.
I have updated the documentation and checked the documentation preview.

⌛ Dependencies

…ointless rpaths on macOS

mkoeppe · 2024-05-01T06:11:26Z

Tests on Linux (together with #37906) at https://github.com/mkoeppe/sage/actions/runs/8906088062, on macOS at https://github.com/mkoeppe/sage/actions/runs/8906088065

github-actions · 2024-05-01T06:38:20Z

Documentation preview for this PR (built with commit 9a6c210; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

mkoeppe · 2024-05-02T00:18:17Z

Tests on Linux (37203-37249-37570-37914) at https://github.com/mkoeppe/sage/actions/runs/8917967117 (OK), macOS https://github.com/mkoeppe/sage/actions/runs/8917967115

jhpalmieri · 2024-05-02T22:52:19Z

I did ./configure --with-system-python3=no and I got a lot of doctest failures of the form ld: warning: duplicate -rpath '/Users/jpalmier/Sage/TESTING/sage-10.4.beta3/local/lib' ignored. I believe that I did not get the same failures with #37886.

mkoeppe · 2024-05-02T22:56:44Z

Yes, this PR, split out from #37886, only takes care of one part of the rpaths issue.
I split it out because it is easier to review. I'll need more time to review the other changes in particular because I'm concerned about the effect it may have on packages installed from source using sage -pip install.

jhpalmieri · 2024-05-03T18:56:36Z

Yes, this PR, split out from #37886, only takes care of one part of the rpaths issue. I split it out because it is easier to review. I'll need more time to review the other changes in particular because I'm concerned about the effect it may have on packages installed from source using sage -pip install.

It's hard to give this a positive review when it causes new doctest failures, though.

mkoeppe · 2024-05-03T19:01:52Z

Wait, I missed that the failures that you were talking about are new!

mkoeppe · 2024-05-03T19:02:15Z

I'll try to reproduce this.

jhpalmieri · 2024-05-03T20:01:08Z

Wait, I missed that the failures that you were talking about are new!

I thought that they were, but I'll double-check.

jhpalmieri · 2024-05-03T22:45:39Z

You're right, these seem to be pre-existing failures, at least according to my testing. Feel free to restore the positive review.

mkoeppe · 2024-05-03T22:47:38Z

OK, thanks for checking!

@culler

…in patches, remove pointless rpaths on macOS       Author: @culler Split out from: - sagemath#37886 ### 📝 Checklist  - [x] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37914 Reported by: Matthias Köppe Reviewer(s):

@culler

…in patches, remove pointless rpaths on macOS       Author: @culler Split out from: - sagemath#37886 ### 📝 Checklist  - [x] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37914 Reported by: Matthias Köppe Reviewer(s):

@culler

…in patches, remove pointless rpaths on macOS       Author: @culler Split out from: - sagemath#37886 ### 📝 Checklist  - [x] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37914 Reported by: Matthias Köppe Reviewer(s):

@culler

…in patches, remove pointless rpaths on macOS       Author: @culler Split out from: - sagemath#37886 ### 📝 Checklist  - [x] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37914 Reported by: Matthias Köppe Reviewer(s):

Update cryptographic hashes to use sha256 instead of sha1 due to insecurity of sha1. - Fixes sagemath#37691 - Fixes sagemath#37558, see also sagemath#36677 (comment) ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies    - sagemath#37570 - sagemath#37249 - sagemath#37914 URL: sagemath#37726 Reported by: Faisal Reviewer(s): Matthias Köppe, roed314

…ite when run on systems with no toolchain  This PR does the following (after splitting out the Python upgrade to [sagemath#37914](sagemath#37914)): 1. Fix a comment in the Makefile about how to use the DEBUG flag so it will actually work. 3. Edit sage-env so that it does not print errors to stderr and/or open a dialog whenever it is run on a system which has neither XCode nor command line tools installed. 4. Remove (almost) all uses of rpath on macOS (see below). 5. Fix the primecountpy spkg, which was the only one which actually needed an rpath in its python extension module. **About rpaths on macOS** Sage has been misusing rpaths on macOS for a very long time. As far as I can tell, this was an error based on the incorrect assumption that MACH binaries use rpath in the same way as ELF binaries. The rpath in an ELF binary provides a search path, beyond the default search path, where the loader looks for shared libraries needed by the binary. A MACH binary specifies the dynamic libraries it needs with load commands of type LC_LOAD_DYLIB. The value of a LC_LOAD_DYLIB load command is a path to a specific library. There is one such load command for each library that the binary needs. The path is an absolute path by default. However, the path is allowed to begin with the substring `@rpath`. When the binary is loaded that substring is replaced by the value of each LC_RPATH load command in the binary to produce a list of absolute paths (or relative paths if the value of the LC_RPATH begins with `@loader_path`). Each of the paths on that list is tried as a possible location of the needed dynamic library. An obvious consequence of this design is that if none of the LC_LOAD_DYLIB paths contains the string `@rpath` then there is no need for any LC_RPATH commands, since they won't be used. With one exception (primecountpy) every MACH binary produced when building Sage had absolute paths for its LC_LOAD_DYLIB load commands. Nonetheless Sage was setting the rpath to $SAGE_LOCAL/lib in all of these binaries. In fact, it was doing that multiple times, producing many duplicate rpaths all of which were useless. (And duplicate rpaths are now deprecated by Apple's linker.) This PR removes all of those bogus rpaths. **About xcode-select** The sage-env script was calling gcc to find the names of its linker and archiver in the unlikely case that either of those had a non-standard name, and it was also calling xcode-select as part of a check to see whether the selected XCode toolchain had an ld-classic executable. That executable was added in XCode 15 as a new name for the old linker when a new linker was added. Apple made it possible to use the old linker by passing the linker option -ld_classic to the gcc command. The new linker was buggy in the beginning and was unable to link openblas. So numpy and scipy use the old linker. Sage also wanted to use it. While the new linker is probably working well enough now as a linker, it generates a warning when it encounters duplicate libraries in a link command. It also appears that the new linker, or XCode 15 itself, somehow *creates* duplicate libraries. While the warnings should be innocuous, they were causing Sage doctest failures. So this PR provides code which adds -Wl,-ld_classic to LDFLAGS in sage-env to replace the analogous code which was already there. But the new code is careful to redirect the error messages to /dev/mull so they do not get printed on the users terminal whenever sage starts up on a machine which does not have any XCode toolchain at all. It also avoids calling gcc in that case since doing so posts a dialog on the user's screen asking if they would like to install command line tools. The dialog is a nice touch, but should only appear if the user is actually *using* gcc, not as part of every invocation of Sage, especially since XCode uses the standard names.    ### 📝 Checklist  - [ ] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37886 Reported by: Marc Culler Reviewer(s): John H. Palmieri, Marc Culler, Matthias Köppe, Volker Braun

Update cryptographic hashes to use sha256 instead of sha1 due to insecurity of sha1. - Fixes sagemath#37691 - Fixes sagemath#37558, see also sagemath#36677 (comment) ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies    - sagemath#37570 - sagemath#37249 - sagemath#37914 URL: sagemath#37726 Reported by: Faisal Reviewer(s): Matthias Köppe, roed314

…ite when run on systems with no toolchain  This PR does the following (after splitting out the Python upgrade to [sagemath#37914](sagemath#37914)): 1. Fix a comment in the Makefile about how to use the DEBUG flag so it will actually work. 3. Edit sage-env so that it does not print errors to stderr and/or open a dialog whenever it is run on a system which has neither XCode nor command line tools installed. 4. Remove (almost) all uses of rpath on macOS (see below). 5. Fix the primecountpy spkg, which was the only one which actually needed an rpath in its python extension module. **About rpaths on macOS** Sage has been misusing rpaths on macOS for a very long time. As far as I can tell, this was an error based on the incorrect assumption that MACH binaries use rpath in the same way as ELF binaries. The rpath in an ELF binary provides a search path, beyond the default search path, where the loader looks for shared libraries needed by the binary. A MACH binary specifies the dynamic libraries it needs with load commands of type LC_LOAD_DYLIB. The value of a LC_LOAD_DYLIB load command is a path to a specific library. There is one such load command for each library that the binary needs. The path is an absolute path by default. However, the path is allowed to begin with the substring `@rpath`. When the binary is loaded that substring is replaced by the value of each LC_RPATH load command in the binary to produce a list of absolute paths (or relative paths if the value of the LC_RPATH begins with `@loader_path`). Each of the paths on that list is tried as a possible location of the needed dynamic library. An obvious consequence of this design is that if none of the LC_LOAD_DYLIB paths contains the string `@rpath` then there is no need for any LC_RPATH commands, since they won't be used. With one exception (primecountpy) every MACH binary produced when building Sage had absolute paths for its LC_LOAD_DYLIB load commands. Nonetheless Sage was setting the rpath to $SAGE_LOCAL/lib in all of these binaries. In fact, it was doing that multiple times, producing many duplicate rpaths all of which were useless. (And duplicate rpaths are now deprecated by Apple's linker.) This PR removes all of those bogus rpaths. **About xcode-select** The sage-env script was calling gcc to find the names of its linker and archiver in the unlikely case that either of those had a non-standard name, and it was also calling xcode-select as part of a check to see whether the selected XCode toolchain had an ld-classic executable. That executable was added in XCode 15 as a new name for the old linker when a new linker was added. Apple made it possible to use the old linker by passing the linker option -ld_classic to the gcc command. The new linker was buggy in the beginning and was unable to link openblas. So numpy and scipy use the old linker. Sage also wanted to use it. While the new linker is probably working well enough now as a linker, it generates a warning when it encounters duplicate libraries in a link command. It also appears that the new linker, or XCode 15 itself, somehow *creates* duplicate libraries. While the warnings should be innocuous, they were causing Sage doctest failures. So this PR provides code which adds -Wl,-ld_classic to LDFLAGS in sage-env to replace the analogous code which was already there. But the new code is careful to redirect the error messages to /dev/mull so they do not get printed on the users terminal whenever sage starts up on a machine which does not have any XCode toolchain at all. It also avoids calling gcc in that case since doing so posts a dialog on the user's screen asking if they would like to install command line tools. The dialog is a nice touch, but should only appear if the user is actually *using* gcc, not as part of every invocation of Sage, especially since XCode uses the standard names.    ### 📝 Checklist  - [ ] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37886 Reported by: Marc Culler Reviewer(s): John H. Palmieri, Marc Culler, Matthias Köppe, Volker Braun

Update cryptographic hashes to use sha256 instead of sha1 due to insecurity of sha1. - Fixes sagemath#37691 - Fixes sagemath#37558, see also sagemath#36677 (comment) ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies    - sagemath#37570 - sagemath#37249 - sagemath#37914 URL: sagemath#37726 Reported by: Faisal Reviewer(s): Matthias Köppe, roed314

…ite when run on systems with no toolchain  This PR does the following (after splitting out the Python upgrade to [sagemath#37914](sagemath#37914)): 1. Fix a comment in the Makefile about how to use the DEBUG flag so it will actually work. 3. Edit sage-env so that it does not print errors to stderr and/or open a dialog whenever it is run on a system which has neither XCode nor command line tools installed. 4. Remove (almost) all uses of rpath on macOS (see below). 5. Fix the primecountpy spkg, which was the only one which actually needed an rpath in its python extension module. **About rpaths on macOS** Sage has been misusing rpaths on macOS for a very long time. As far as I can tell, this was an error based on the incorrect assumption that MACH binaries use rpath in the same way as ELF binaries. The rpath in an ELF binary provides a search path, beyond the default search path, where the loader looks for shared libraries needed by the binary. A MACH binary specifies the dynamic libraries it needs with load commands of type LC_LOAD_DYLIB. The value of a LC_LOAD_DYLIB load command is a path to a specific library. There is one such load command for each library that the binary needs. The path is an absolute path by default. However, the path is allowed to begin with the substring `@rpath`. When the binary is loaded that substring is replaced by the value of each LC_RPATH load command in the binary to produce a list of absolute paths (or relative paths if the value of the LC_RPATH begins with `@loader_path`). Each of the paths on that list is tried as a possible location of the needed dynamic library. An obvious consequence of this design is that if none of the LC_LOAD_DYLIB paths contains the string `@rpath` then there is no need for any LC_RPATH commands, since they won't be used. With one exception (primecountpy) every MACH binary produced when building Sage had absolute paths for its LC_LOAD_DYLIB load commands. Nonetheless Sage was setting the rpath to $SAGE_LOCAL/lib in all of these binaries. In fact, it was doing that multiple times, producing many duplicate rpaths all of which were useless. (And duplicate rpaths are now deprecated by Apple's linker.) This PR removes all of those bogus rpaths. **About xcode-select** The sage-env script was calling gcc to find the names of its linker and archiver in the unlikely case that either of those had a non-standard name, and it was also calling xcode-select as part of a check to see whether the selected XCode toolchain had an ld-classic executable. That executable was added in XCode 15 as a new name for the old linker when a new linker was added. Apple made it possible to use the old linker by passing the linker option -ld_classic to the gcc command. The new linker was buggy in the beginning and was unable to link openblas. So numpy and scipy use the old linker. Sage also wanted to use it. While the new linker is probably working well enough now as a linker, it generates a warning when it encounters duplicate libraries in a link command. It also appears that the new linker, or XCode 15 itself, somehow *creates* duplicate libraries. While the warnings should be innocuous, they were causing Sage doctest failures. So this PR provides code which adds -Wl,-ld_classic to LDFLAGS in sage-env to replace the analogous code which was already there. But the new code is careful to redirect the error messages to /dev/mull so they do not get printed on the users terminal whenever sage starts up on a machine which does not have any XCode toolchain at all. It also avoids calling gcc in that case since doing so posts a dialog on the user's screen asking if they would like to install command line tools. The dialog is a nice touch, but should only appear if the user is actually *using* gcc, not as part of every invocation of Sage, especially since XCode uses the standard names.    ### 📝 Checklist  - [ ] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37886 Reported by: Marc Culler Reviewer(s): John H. Palmieri, Marc Culler, Matthias Köppe, Volker Braun

Update cryptographic hashes to use sha256 instead of sha1 due to insecurity of sha1. - Fixes sagemath#37691 - Fixes sagemath#37558, see also sagemath#36677 (comment) ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies    - sagemath#37570 - sagemath#37249 - sagemath#37914 URL: sagemath#37726 Reported by: Faisal Reviewer(s): Matthias Köppe, roed314

…ite when run on systems with no toolchain  This PR does the following (after splitting out the Python upgrade to [sagemath#37914](sagemath#37914)): 1. Fix a comment in the Makefile about how to use the DEBUG flag so it will actually work. 3. Edit sage-env so that it does not print errors to stderr and/or open a dialog whenever it is run on a system which has neither XCode nor command line tools installed. 4. Remove (almost) all uses of rpath on macOS (see below). 5. Fix the primecountpy spkg, which was the only one which actually needed an rpath in its python extension module. **About rpaths on macOS** Sage has been misusing rpaths on macOS for a very long time. As far as I can tell, this was an error based on the incorrect assumption that MACH binaries use rpath in the same way as ELF binaries. The rpath in an ELF binary provides a search path, beyond the default search path, where the loader looks for shared libraries needed by the binary. A MACH binary specifies the dynamic libraries it needs with load commands of type LC_LOAD_DYLIB. The value of a LC_LOAD_DYLIB load command is a path to a specific library. There is one such load command for each library that the binary needs. The path is an absolute path by default. However, the path is allowed to begin with the substring `@rpath`. When the binary is loaded that substring is replaced by the value of each LC_RPATH load command in the binary to produce a list of absolute paths (or relative paths if the value of the LC_RPATH begins with `@loader_path`). Each of the paths on that list is tried as a possible location of the needed dynamic library. An obvious consequence of this design is that if none of the LC_LOAD_DYLIB paths contains the string `@rpath` then there is no need for any LC_RPATH commands, since they won't be used. With one exception (primecountpy) every MACH binary produced when building Sage had absolute paths for its LC_LOAD_DYLIB load commands. Nonetheless Sage was setting the rpath to $SAGE_LOCAL/lib in all of these binaries. In fact, it was doing that multiple times, producing many duplicate rpaths all of which were useless. (And duplicate rpaths are now deprecated by Apple's linker.) This PR removes all of those bogus rpaths. **About xcode-select** The sage-env script was calling gcc to find the names of its linker and archiver in the unlikely case that either of those had a non-standard name, and it was also calling xcode-select as part of a check to see whether the selected XCode toolchain had an ld-classic executable. That executable was added in XCode 15 as a new name for the old linker when a new linker was added. Apple made it possible to use the old linker by passing the linker option -ld_classic to the gcc command. The new linker was buggy in the beginning and was unable to link openblas. So numpy and scipy use the old linker. Sage also wanted to use it. While the new linker is probably working well enough now as a linker, it generates a warning when it encounters duplicate libraries in a link command. It also appears that the new linker, or XCode 15 itself, somehow *creates* duplicate libraries. While the warnings should be innocuous, they were causing Sage doctest failures. So this PR provides code which adds -Wl,-ld_classic to LDFLAGS in sage-env to replace the analogous code which was already there. But the new code is careful to redirect the error messages to /dev/mull so they do not get printed on the users terminal whenever sage starts up on a machine which does not have any XCode toolchain at all. It also avoids calling gcc in that case since doing so posts a dialog on the user's screen asking if they would like to install command line tools. The dialog is a nice touch, but should only appear if the user is actually *using* gcc, not as part of every invocation of Sage, especially since XCode uses the standard names.    ### 📝 Checklist  - [ ] The title is concise and informative. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37886 Reported by: Marc Culler Reviewer(s): John H. Palmieri, Marc Culler, Matthias Köppe, Volker Braun

…port of Python 3.12.x stable       https://docs.python.org/3/whatsnew/changelog.html#python-3-12-4-final - In part cherry-picked from sagemath#36181 ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    - Depends on sagemath#37914 (merged here) - Depends on sagemath#37951 (merged here for sagemath#37026) - Depends on sagemath#38144 (merged here for testing) URL: sagemath#37834 Reported by: Matthias Köppe Reviewer(s):

build/pkgs/python3: Update to 3.11.8, remove Cygwin patches, remove p…

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…ointless rpaths on macOS

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vbraun merged commit f5a724f into sagemath:develop May 12, 2024
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`build/pkgs/python3`: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

`build/pkgs/python3`: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

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build/pkgs/python3: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

build/pkgs/python3: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

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`build/pkgs/python3`: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

`build/pkgs/python3`: Update to 3.11.8, remove Cygwin patches, remove pointless rpaths on macOS #37914

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