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Add GNU Astro #9723
Add GNU Astro #9723
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Hi! This is the friendly automated conda-forge-linting service. I wanted to let you know that I linted all conda-recipes in your PR ( Here's what I've got... For recipes/gnuastro:
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Hi! This is the friendly automated conda-forge-linting service. I just wanted to let you know that I linted all conda-recipes in your PR ( |
Thanks a lot for initiating the Conda recipe for Gnuastro. Just a few comments on
For the macOS builds, I tried pressing "details" in the summary above, but it just says "Bash exited with code '1'." If there is a more detailed error message of what caused the crash, I'd be happy to fix it upstream. |
Thanks, @mohammad-akhlaghi
However, when I commented
For the OSX builds, please have a look at: This time, please click on "Bash exited with code '1'." to see the full error log. |
Great! Thanks for the clarifications.
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Hi, No worries, I will keep pushing changes and we'll ask a conda-forge team to review the final recipe in due course. While I work on the other changes, can I ask a more specific question about the Best regards, |
Good point! Until now, If you can use the most recent version (which is available here until the next stable release: https://akhlaghi.org/src/gnuastro-0.10.32-3fa6.tar.lz ), then the problem will be fixed. Otherwise, you can simply disable BuildProgram in Gnuastro with the |
Many thanks for the acknowledgement upstream! Provided that http://ftp.gnu.org will be the default repository for new releases, I would like to stick to that in the recipe for this version of the package, and I will update it for the next one. You are right, as soon as I added By the way, would you like to be listed as a recipe maintainer for the gnuastro package? |
@conda-forge/help-c-cpp please review |
Great! I also had the same idea about keeping with the stable releases. To stay up to date, you can subscribe to the Gnuastro's announcements mailing list. Traffic on this list is very low by design: once or twice a season ;-). About being listed as a maintainer, yes, no problem, just put me as second maintainer and add a note that I am the upstream developer ;-). I just hope that you'll be around to fix any conda-related problem that comes up, I'll be happy to fix the Gnuastro-releated problems. |
Done. Sure, I will be happy to help maintaining this recipe ;) |
@conda-forge/staged-recipes please review |
recipes/gnuastro/meta.yaml
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build: | ||
number: 0 | ||
skip: True # [win or osx] |
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Looks like the macOS error is due to AT_FDCWD
being added in OSX 10.10 (by default conda-forge targets 10.9). It might be easy to patch in the source? If not can add a file like this to target 10.10.
skip: True # [win or osx] | |
skip: True # [win] |
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I would change the target to 10.10 as a last resort and just patch the source.
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I think neither of us have access and/or experience with OSX, that's why we left it out.
@mohammad-akhlaghi would you be able to patch the source accordingly?
test: | ||
commands: | ||
- test -f ${PREFIX}/lib/libgnuastro${SHLIB_EXT} # [unix] | ||
- test -f ${PREFIX}/lib/libgnuastro.a # [unix] |
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Are there any command line apps you can test? Even if it's just a simple program_name --help
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Thanks! I had it included in 16656e2 but @mohammad-akhlaghi suggested me to remove those and use make check
instead, since the CLI is tested according to the result of the ./configure
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It's nice to check a second time as it tests that the relocation as worked as these tests are ran in a separate environment to the build.
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Thanks, will do.
recipes/gnuastro/meta.yaml
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about: | ||
home: https://www.gnu.org/software/gnuastro | ||
license: GPL-3 |
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license: GPL-3 | |
license: GPL-3.0-or-later |
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source: | ||
url: http://ftp.gnu.org/gnu/{{name}}/{{name}}-{{version}}.tar.gz | ||
sha256: 6d56dc161ecd80c64dbf09808f58114b52ad2ce648c71551b871f5d10d4c07c5 |
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You could download http://git.savannah.gnu.org/cgit/gnuastro.git/patch/?id=3fa6512537ea1905583cf2b7dff45d174260c4c3
and apply it as a patch instead of passing --disable-buildprog
:
sha256: 6d56dc161ecd80c64dbf09808f58114b52ad2ce648c71551b871f5d10d4c07c5 | |
sha256: 6d56dc161ecd80c64dbf09808f58114b52ad2ce648c71551b871f5d10d4c07c5 | |
patches: | |
- remove-hardcoded-gcc.patch |
I tried creating the patch, but there were some complications when trying to apply it to the tarball of Gnuastro 0.10: already more than 30 commits have been made to Gnuastro since the 0.10 release, especially in the part that this commit is applied to the book, the line numbers don't match. Ofcourse, we can technically remove those parts from the patch, but then we'll have a feature that is not documented in Conda! So, I think that until Gnuastro 0.11 is released, |
Many thanks for your feedback. I applied your patch and removed Sorry, could you please confirm what's your opinion on patching Gnuastro-0.10 to get OSX to work? (please see the comment about Best regards, |
About the patch, either option is good ;-)! In any case, some change needs to be made compared to the default Gnuastro 0.10, but now that you have implemented the patch, we can just keep it. The good thing now is that Conda users will have access to About the macOS problem with |
@chrisburr @isuruf should we target OSX 10.10 on this PR or should we wait for the next release of Gnuastro to include OSX? Linux is key for us. OSX not high priority though. |
My preference would be to add OSX 10.10+ support now as I doubt there are many people left running 10.9 but @isuruf knows better than I do. |
I had a fast look at the cases that |
I just removed the use of these macros. The problem on macOS should be fixed after applying this commit. Just remove the change in the |
Ok, so I have now applied the patch but I troubleshooted this same error on Linux by running the tests locally, exec'ing into the container and inspecting the output of |
If it's still not obvious from the log I can take a look |
That's a great addition to the recipe, many thanks @chrisburr Do you understand the |
@chrisburr @isuruf we would like to have this package added to conda-forge for a project we are currently doing, could you please let us know how to move on? |
Thanks a lot @chrisburr and @isuruf. The problem seems to be in the I noticed that this is because until now, BuildProgram was ignoring the Can you please use this commit to patch the Gnuastro build (the patch should be applied after the previous GCC-related patch). Also, don't forget to remove the changes in the |
I think it's there! Thank you @sebastian-luna-valero and @mohammad-akhlaghi for taking the time to package this "correctly", LGTM 🍰 |
Thanks All. FYI: I have intentionally removed the changes in Can we revisit this for the next gnuastro release? |
Indeed, thanks a lot everyone :-D. With two bugs found and some new features added, the Conda packaging was also very productive upstream: I really like how every package manager has different properties that helps highlight different bugs/needs, thus making the software more robust. When Gnuastro 0.11 comes, none of these patches will be necessary any more. Sebastian, the reason the patch failed on these two files is that many different commits (outside the Conda-related commits) have been made on these two files since Gnuastro 0.10 was released: the |
Checklist
url
) rather than a repo (e.g.git_url
) is used in yourrecipe (see
here
for more details)