Fix: add gsl install to macos14 to pass CI.

[stevenhua0320]

@sbillinge ready for review, we should test this whether it would be successful to build CI on macos14.

[codecov]

Welcome to Codecov 🎉

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

Thanks for integrating Codecov - We've got you covered ☂️

[sbillinge]

Is it better to do this or to add gsl to the tests.txt requirements (or the conda requirements)?

[stevenhua0320]

Yes, it might be a better way.

[sbillinge]

We didn't need it in both places. Just tests unless it is needed to run the code itself, in which case, just in conda.txt and pip.txt

[sbillinge]

@stevenhua0320 I looked more into this and it will be a runtime dependency, so we need to add it to the conda.txt and pip.txt files and can then remove it from the tests.txt. We also likely need io add it to the host: and run: section of the meta.yaml in the conda-forge feedstock.

Actually, looking at diffpy.pdffit2 it seems that this was addressed (and tests are passing there) in diffpy/diffpy.pdffit2#144 . There gsl was added to condat.txt requirements in pdffit2. I wonder if the issue is that we didn't add it to the meta.yaml of pdffit2-feedstock so when the dependency installs it from conda-forge it doesn't come with gsl. Is this possible?

tl;dr: Let's try a fix where we see if adding gsl as a dependency to the meta.yaml in pdffit2 fixes the problem over here?

[stevenhua0320]

@sbillinge I have checked the feedstock in diffpy.pdffit2 and I saw @Tieqiong has added gsl into both the requirements in the package and the feedstock. So, the problem does come from diffpy.distanceprinter itself. So, add gsl as an requirement to both this package and the feedstock should solve the problem. I would make the commit shortly.

[sbillinge]

@sbillinge I have checked the feedstock in diffpy.pdffit2 and I saw @Tieqiong has added gsl into both the requirements in the package and the feedstock. So, the problem does come from diffpy.distanceprinter itself. So, add gsl as an requirement to both this package and the feedstock should solve the problem. I would make the commit shortly.

Something is not right here. Gsl is not a requirement of distanceprinter but it is a requirement of pdffit2. It would be good to get to the bottom of why it is not getting loaded as part of the pdffit2 requirements

[stevenhua0320]

It is because in macos14 the homebrew removed many bottles, including the one for gsl. So, if we did not pre-install the gsl bottles, we cannot run the diffpy.pdffit2 on a clean macos14 environment. As diffpy.distanceprinter needs to run diffpy.pdffit2 function, we need gsl install in the env so that it could be run.

[sbillinge]

It is because in macos14 the homebrew removed many bottles, including the one for gsl. So, if we did not pre-install the gsl bottles, we cannot run the diffpy.pdffit2 on a clean macos14 environment. As diffpy.distanceprinter needs to run diffpy.pdffit2 function, we need gsl install in the env so that it could be run.

if gsl is a dependency of pdffit2, then it should be installed already. This is my point.

[stevenhua0320]

I'm afraid it is not defined as a dependency but as build requirement in diffpy.pdffit2? The feedstock looks like this in diffpy.pdffit2

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - {{ stdlib("c") }}
    - gsl
    - python                              # [build_platform != target_platform]
    - cross-python_{{ target_platform }}  # [build_platform != target_platform]
  host:
    - python
    - pip
    - setuptools
    - setuptools-git-versioning >=2.0
    - gsl
  run:
    - python
    - setuptools
    - diffpy.structure

[sbillinge]

Let's try adding it to run and we will see if it allows the tests to pass for distanceprinter

[stevenhua0320]

I think I have added in the feedstock in the diffpy.distanceprinter in the morning. It's ready for review.

[sbillinge]

@stevenhua0320 please can you open a PR on the diffpy.pdffit2-feedstock to bump the build number and add gsl to the run section of the meta.yaml in there.

Let's see if, when we merge that, it fixes this without having to merge this PR.

[sbillinge]

ok, that didn't work. Let's try merging this.

[stevenhua0320]

@sbillinge Seems that the problem persists. Maybe there are other issues on this.

[sbillinge]

@Tieqiong, @bobleesj, any chance you can take a look at the actions on this repo....I think our mac builds may need some tlc.....

[Tieqiong]

@stevenhua0320 @sbillinge The problem is we never released the fixed diffpy.pdffit2 after PR diffpy/diffpy.pdffit2#144 on pypi, so @stevenhua0320's new CF PR is still grabbing the old version that fails for arm Mac. Try testing locally with a Mac by building pdffit2 directly from source.

Didn't expect we all forgot to release it...

[sbillinge]

@stevenhua0320 I made a release issue for pdffit2. Please could you work on that and we can work our way to this release.