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Empty build update for testing #1

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MilesCranmer
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I'm seeing a new issue with PyJulia installs and want to check if the latest conda-forge is failing without changes.

Checklist

  • Used a personal fork of the feedstock to propose changes
  • Bumped the build number (if the version is unchanged)
  • Reset the build number to 0 (if the version changed)
  • Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
  • Ensured the license file is being packaged.

@conda-forge-linter
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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 (recipe) and found it was in an excellent condition.

@MilesCranmer
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@conda-forge-admin, please rerender

@github-actions
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Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

This message was generated by GitHub actions workflow run https://github.com/conda-forge/pyjulia-feedstock/actions/runs/1838006432.

@MilesCranmer
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Yep, something looks to have changed, I'm getting the following error in the conda-forge build, which didn't happen before.

Precompiling PyCall...
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/conda/feedstock_root/build_artifacts/pyjulia_1644787094182/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/site-packages/julia/tools.py", line 125, in install
  File "/home/conda/feedstock_root/build_artifacts/pyjulia_1644787094182/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/subprocess.py", line 345, in call
  File "/home/conda/feedstock_root/build_artifacts/pyjulia_1644787094182/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/subprocess.py", line 966, in __init__
  File "/home/conda/feedstock_root/build_artifacts/pyjulia_1644787094182/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/subprocess.py", line 1842, in _execute_child
FileNotFoundError: [Errno 2] No such file or directory: 'julia'
Tests failed for pyjulia-0.5.7-pyhd8ed1ab_1.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
WARNING:conda_build.build:Tests failed for pyjulia-0.5.7-pyhd8ed1ab_1.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
WARNING conda_build.build:tests_failed(2975): Tests failed for pyjulia-0.5.7-pyhd8ed1ab_1.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
TESTS FAILED: pyjulia-0.5.7-pyhd8ed1ab_1.tar.bz2
##[error]Bash exited with code '1'.
Finishing: Run docker build

@mkitti @ngam do you know if something caused this change in the julia-feedstock?

@ngam
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ngam commented Feb 13, 2022

No idea, but let's try this for now.

@mkitti
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mkitti commented Feb 13, 2022

Umm... we did just release 1.7.2

@ngam
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ngam commented Feb 13, 2022

If you try locally, for some reason, it cannot compile PyCall correctly...

@ngam
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ngam commented Feb 13, 2022

ERROR: LoadError: PyCall not properly installed. Please run Pkg.build("PyCall")
Stacktrace:

@MilesCranmer
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MilesCranmer commented Feb 13, 2022

Indeed it does look like it tried to install 1.7.2. Should I pin to an earlier version?

I tried locally and there is no julia binary showing up in the conda folder anywhere for some reason.
edit: nevermind, not sure what went wrong on my machine, but there is a julia binary now...

@ngam
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ngam commented Feb 13, 2022

I believe the tests now will pass with this addition: e5f351f

What does that tell you @mkitti?

@mkitti
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mkitti commented Feb 13, 2022

That tells me that we tried to build PyCall.jl before our julia-feedstock activate.sh could setup environmental variables:
https://github.com/JuliaPy/PyCall.jl/blob/master/deps/build.jl

@ngam
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ngam commented Feb 13, 2022

Thanks @MilesCranmer

@ngam
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ngam commented Feb 13, 2022

Indeed it does look like it tried to install 1.7.2. Should I pin to an earlier version?

I tried locally and there is no julia binary showing up in the conda folder anywhere for some reason. edit: nevermind, not sure what went wrong on my machine, but there is a julia binary now...

should around here usually, ls $CONDA_PREFIX/bin/julia

@ngam
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ngam commented Feb 13, 2022

@mkitti, maybe we have something wrong with the registry?

No broken requirements found.
+ julia -e 'using Pkg; Pkg.build("PyCall")'
ERROR: The following package names could not be resolved:
 * PyCall (not found in project or manifest)

@mkitti
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mkitti commented Feb 13, 2022

PyCall should be installed by import julia; julia.install(). Perhaps just do Pkg.add("PyCall"), first followed by build.

@ngam
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ngam commented Feb 13, 2022

@MilesCranmer btw.. you were on to something... julia disappeared from my $CONDA_PREFIX/bin...

@ngam
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ngam commented Feb 13, 2022

Okay, I think what's going on is that something is erasing the environments. Try it for yourself. I think the error we are gonna get now is "julia cannot be found". Something to do with stacking maybe?

I do the following locally:

$ mamba create -n pyjl pyjulia
$ mamba activate pyjl
$ mamba list
...
julia 1.7.2
...
$ julia -e 'using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
$ python -c "import julia"
... julia not found ...
$ julia
... no julia ...
$ mamba list
... no julia, no pyjulia

@mkitti
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mkitti commented Feb 13, 2022

By environments, do you mean conda environments?

@ngam
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ngam commented Feb 13, 2022

More loosely, I meant something is erasing the content of the envs. Hence, what happened to @MilesCranmer earlier with julia binary disappearing. Try to reproduce the above steps?

@mkitti
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mkitti commented Feb 13, 2022

We might have added this too soon:
https://github.com/conda-forge/julia-feedstock/blob/master/recipe/scripts/activate.sh#L21-L24

JuliaPy/Conda.jl#216 was merged, but a new version of Conda.jl has not been released.

@ngam
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ngam commented Feb 13, 2022

Does PyCall interact with that?

@mkitti
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mkitti commented Feb 13, 2022

Yes. PyCall.jl uses Conda.jl to locate Python. Conda.jl may be trying to install it's own conda still.

@ngam
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ngam commented Feb 13, 2022

I see now...

@ngam
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ngam commented Feb 13, 2022

🦅 👀 @mkitti, let's revert that CONDA_JL stuff then?

@mkitti
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mkitti commented Feb 13, 2022

Check $CONDA_PREFIX before and after? Confirm location of base conda executable.

@ngam
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ngam commented Feb 13, 2022

@MilesCranmer for future proofing, we may want to always set an upper bound here. What do you think?

Indeed it does look like it tried to install 1.7.2. Should I pin to an earlier version?

I tried locally and there is no julia binary showing up in the conda folder anywhere for some reason. edit: nevermind, not sure what went wrong on my machine, but there is a julia binary now...

@mkitti
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mkitti commented Feb 13, 2022

I think the proper fix would be release a new version of Conda.jl . If that gets stalled for some reason, then perhaps we remove the environmental variables.

@ngam
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ngam commented Feb 13, 2022

also, let's add a test for @MilesCranmer in our julia build from now on.

@ngam
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ngam commented Feb 13, 2022

Check $CONDA_PREFIX before and after? Confirm location of base conda executable.

This is the same before and after, fyi

mkitti referenced this pull request in JuliaPy/Conda.jl Feb 13, 2022
Introduce CONDA_JL_CONDA_EXE environment variable
@ngam
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ngam commented Feb 13, 2022

But, I am now certain that CONDA_JL is installing its own conda. You can tell by inspection.

@MilesCranmer
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we may want to always set an upper bound here. What do you think?

Sounds good. You mean to fix julia version <= 1.7.1 for now right?

also, let's add a test for @MilesCranmer in our julia build from now on.

Yeah an integration test for PyJulia like this would be smart for the julia feedstock itself.

@ngam
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ngam commented Feb 13, 2022

Yes, but this wouldn't fix the current builds. We need repopatch for that. Unless 8f71332 gets registered asap, then we don't have to worry about it

@mkitti
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mkitti commented Feb 13, 2022

I do have the power to register it, but I should give a chance for the other maintainers to weigh in.

@mkitti
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mkitti commented Feb 13, 2022

After running julia.install() in Python, my conda is now lives inside the prefix. This also looks like Conda.jl has installed a new conda mamba:

cat ~/anaconda3/envs/julia172/share/julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/71fd4022ecd0c6d20180e23ff1b3e05a143959c2/build.log
PREFIX=/home/mkitti/anaconda3/envs/julia172
Unpacking payload ...
Extracting "pycosat-0.6.3-py39h3811e60_1009.conda"
Extracting "pycparser-2.21-pyhd8ed1ab_0.conda"
Extracting "ncurses-6.3-h9c3ff4c_0.conda"
Extracting "_libgcc_mutex-0.1-conda_forge.conda"
Extracting "requests-2.27.1-pyhd8ed1ab_0.conda"
Extracting "python_abi-3.9-2_cp39.conda"
Extracting "conda-4.11.0-py39hf3d152e_0.conda"
Extracting "libnsl-2.0.0-h7f98852_0.conda"
Extracting "tqdm-4.62.3-pyhd8ed1ab_0.conda"
Extracting "pip-22.0.3-pyhd8ed1ab_0.conda"
Extracting "ruamel_yaml-0.15.80-py39h3811e60_1006.conda"
Extracting "cryptography-36.0.1-py39h95dcef6_0.conda"
Extracting "ld_impl_linux-64-2.36.1-hea4e1c9_2.conda"
Extracting "pysocks-1.7.1-py39hf3d152e_4.conda"
Extracting "bzip2-1.0.8-h7f98852_4.conda"
Extracting "sqlite-3.37.0-h9cd32fc_0.conda"
Extracting "zlib-1.2.11-h36c2ea0_1013.conda"
Extracting "_openmp_mutex-4.5-1_gnu.conda"
Extracting "cffi-1.15.0-py39h4bc2ebd_0.conda"
Extracting "tk-8.6.11-h27826a3_1.conda"
Extracting "certifi-2021.10.8-py39hf3d152e_1.conda"
Extracting "brotlipy-0.7.0-py39h3811e60_1003.conda"
Extracting "yaml-0.2.5-h7f98852_2.conda"
Extracting "setuptools-60.8.1-py39hf3d152e_0.conda"
Extracting "conda-package-handling-1.7.3-py39h3811e60_1.conda"
Extracting "idna-3.3-pyhd8ed1ab_0.conda"
Extracting "charset-normalizer-2.0.11-pyhd8ed1ab_0.conda"
Extracting "wheel-0.37.1-pyhd8ed1ab_0.conda"
Extracting "libuuid-2.32.1-h7f98852_1000.conda"
Extracting "tzdata-2021e-he74cb21_0.conda"
Extracting "libzlib-1.2.11-h36c2ea0_1013.conda"
Extracting "libffi-3.4.2-h7f98852_5.conda"
Extracting "pyopenssl-22.0.0-pyhd8ed1ab_0.conda"
Extracting "ca-certificates-2021.10.8-ha878542_0.conda"
Extracting "six-1.16.0-pyh6c4a22f_0.conda"
Extracting "xz-5.2.5-h516909a_1.conda"
Extracting "libgcc-ng-11.2.0-h1d223b6_12.conda"
Extracting "urllib3-1.26.8-pyhd8ed1ab_1.conda"
Extracting "readline-8.1-h46c0cb4_0.conda"
Extracting "libgomp-11.2.0-h1d223b6_12.conda"
Extracting "python-3.9.10-h85951f9_2_cpython.conda"
Extracting "colorama-0.4.4-pyh9f0ad1d_0.conda"
Extracting "openssl-1.1.1l-h7f98852_0.conda"

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/linux-64                                         Using cache
conda-forge/noarch                                           Using cache

Transaction

  Prefix: /home/mkitti/anaconda3/envs/julia172

  Updating specs:

   - python==3.9.10=h85951f9_2_cpython
   - _libgcc_mutex==0.1=conda_forge
   - ca-certificates==2021.10.8=ha878542_0
   - ld_impl_linux-64==2.36.1=hea4e1c9_2
   - tzdata==2021e=he74cb21_0
   - libgomp==11.2.0=h1d223b6_12
   - _openmp_mutex==4.5=1_gnu
   - libgcc-ng==11.2.0=h1d223b6_12
   - bzip2==1.0.8=h7f98852_4
   - libffi==3.4.2=h7f98852_5
   - libnsl==2.0.0=h7f98852_0
   - libuuid==2.32.1=h7f98852_1000
   - libzlib==1.2.11=h36c2ea0_1013
   - ncurses==6.3=h9c3ff4c_0
   - openssl==1.1.1l=h7f98852_0
   - xz==5.2.5=h516909a_1
   - yaml==0.2.5=h7f98852_2
   - readline==8.1=h46c0cb4_0
   - zlib==1.2.11=h36c2ea0_1013
   - sqlite==3.37.0=h9cd32fc_0
   - tk==8.6.11=h27826a3_1
   - charset-normalizer==2.0.11=pyhd8ed1ab_0
   - colorama==0.4.4=pyh9f0ad1d_0
   - idna==3.3=pyhd8ed1ab_0
   - pycparser==2.21=pyhd8ed1ab_0
   - python_abi==3.9=2_cp39
   - six==1.16.0=pyh6c4a22f_0
   - wheel==0.37.1=pyhd8ed1ab_0
   - certifi==2021.10.8=py39hf3d152e_1
   - cffi==1.15.0=py39h4bc2ebd_0
   - pycosat==0.6.3=py39h3811e60_1009
   - pysocks==1.7.1=py39hf3d152e_4
   - ruamel_yaml==0.15.80=py39h3811e60_1006
   - setuptools==60.8.1=py39hf3d152e_0
   - tqdm==4.62.3=pyhd8ed1ab_0
   - brotlipy==0.7.0=py39h3811e60_1003
   - conda-package-handling==1.7.3=py39h3811e60_1
   - cryptography==36.0.1=py39h95dcef6_0
   - pip==22.0.3=pyhd8ed1ab_0
   - pyopenssl==22.0.0=pyhd8ed1ab_0
   - urllib3==1.26.8=pyhd8ed1ab_1
   - requests==2.27.1=pyhd8ed1ab_0
   - conda==4.11.0=py39hf3d152e_0


  Package                     Version  Build               Channel                    Size
────────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────────

  + brotlipy                    0.7.0  py39h3811e60_1003   conda-forge/linux-64     Cached
  + certifi                 2021.10.8  py39hf3d152e_1      conda-forge/linux-64     Cached
  + cffi                       1.15.0  py39h4bc2ebd_0      conda-forge/linux-64     Cached
  + charset-normalizer         2.0.11  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + colorama                    0.4.4  pyh9f0ad1d_0        conda-forge/noarch       Cached
  + conda                      4.11.0  py39hf3d152e_0      conda-forge/linux-64     Cached
  + conda-package-handling      1.7.3  py39h3811e60_1      conda-forge/linux-64     Cached
  + cryptography               36.0.1  py39h95dcef6_0      conda-forge/linux-64     Cached
  + idna                          3.3  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + pycosat                     0.6.3  py39h3811e60_1009   conda-forge/linux-64     Cached
  + pycparser                    2.21  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + pyopenssl                  22.0.0  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + pysocks                     1.7.1  py39hf3d152e_4      conda-forge/linux-64     Cached
  + requests                   2.27.1  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + ruamel_yaml               0.15.80  py39h3811e60_1006   conda-forge/linux-64     Cached
  + six                        1.16.0  pyh6c4a22f_0        conda-forge/noarch       Cached
  + tqdm                       4.62.3  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + urllib3                    1.26.8  pyhd8ed1ab_1        conda-forge/noarch       Cached
  + yaml                        0.2.5  h7f98852_2          conda-forge/linux-64     Cached

  Remove:
────────────────────────────────────────────────────────────────────────────────────────────

  - curl                       7.81.0  h494985f_0          conda-forge/linux-64       92kB
  - git                        2.35.0  pl5321hf874766_0    conda-forge/linux-64       14MB
  - julia                       1.7.2  h989b2f6_0          conda-forge/linux-64      109MB
  - krb5                       1.19.2  h48eae69_3          conda-forge/linux-64        2MB
  - libcurl                    7.81.0  h494985f_0          conda-forge/linux-64      348kB
  - libgit2                     1.3.0  haabb1ae_1          conda-forge/linux-64      738kB
  - libnghttp2                 1.46.0  ha19adfc_0          conda-forge/linux-64      820kB
  - libssh2                    1.10.0  ha35d2d1_2          conda-forge/linux-64      238kB
  - pyjulia                     0.5.7  pyhd8ed1ab_0        conda-forge/noarch         51kB

  Downgrade:
────────────────────────────────────────────────────────────────────────────────────────────

  - openssl                     3.0.0  h7f98852_2          conda-forge/linux-64        3MB
  + openssl                    1.1.1l  h7f98852_0          conda-forge/linux-64     Cached
  - python                     3.10.2  hc74c709_3_cpython  conda-forge/linux-64       32MB
  + python                     3.9.10  h85951f9_2_cpython  conda-forge/linux-64     Cached
  - python_abi                   3.10  2_cp310             conda-forge/linux-64        4kB
  + python_abi                    3.9  2_cp39              conda-forge/linux-64     Cached
  - setuptools                 60.8.2  py310hff52083_0     conda-forge/linux-64        1MB
  + setuptools                 60.8.1  py39hf3d152e_0      conda-forge/linux-64     Cached

  Summary:

  Install: 19 packages
  Remove: 9 packages
  Downgrade: 4 packages

  Total download: 0 B

────────────────────────────────────────────────────────────────────────────────────────────


Transaction starting
Unlinking julia-1.7.2-h989b2f6_0
Unlinking git-2.35.0-pl5321hf874766_0
Unlinking libgit2-1.3.0-haabb1ae_1
Unlinking curl-7.81.0-h494985f_0
Unlinking libcurl-7.81.0-h494985f_0
Unlinking krb5-1.19.2-h48eae69_3
Unlinking libssh2-1.10.0-ha35d2d1_2
Unlinking libnghttp2-1.46.0-ha19adfc_0
Linking yaml-0.2.5-h7f98852_2
Changing openssl-3.0.0-h7f98852_2 ==> openssl-1.1.1l-h7f98852_0
Changing python-3.10.2-hc74c709_3_cpython ==> python-3.9.10-h85951f9_2_cpython
Unlinking pyjulia-0.5.7-pyhd8ed1ab_0
Changing python_abi-3.10-2_cp310 ==> python_abi-3.9-2_cp39
Linking ruamel_yaml-0.15.80-py39h3811e60_1006
Linking certifi-2021.10.8-py39hf3d152e_1
Changing setuptools-60.8.2-py310hff52083_0 ==> setuptools-60.8.1-py39hf3d152e_0
Linking pycosat-0.6.3-py39h3811e60_1009
Linking pysocks-1.7.1-py39hf3d152e_4
Linking pycparser-2.21-pyhd8ed1ab_0
Linking charset-normalizer-2.0.11-pyhd8ed1ab_0
Linking colorama-0.4.4-pyh9f0ad1d_0
Linking six-1.16.0-pyh6c4a22f_0
Linking idna-3.3-pyhd8ed1ab_0
Linking tqdm-4.62.3-pyhd8ed1ab_0
Linking cffi-1.15.0-py39h4bc2ebd_0
Linking conda-package-handling-1.7.3-py39h3811e60_1
Linking brotlipy-0.7.0-py39h3811e60_1003
Linking cryptography-36.0.1-py39h95dcef6_0
Linking pyopenssl-22.0.0-pyhd8ed1ab_0
Linking urllib3-1.26.8-pyhd8ed1ab_1
Linking requests-2.27.1-pyhd8ed1ab_0
Linking conda-4.11.0-py39hf3d152e_0
Transaction finished
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/mkitti/anaconda3/envs/julia172

  added / updated specs:
    - numpy


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-1.22.2               |   py39h91f2184_0         6.9 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         6.9 MB

The following NEW packages will be INSTALLED:

  numpy              conda-forge/linux-64::numpy-1.22.2-py39h91f2184_0



Downloading and Extracting Packages
numpy-1.22.2         | 6.9 MB    | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
[ Info: Downloading miniconda installer ...
[ Info: Installing miniconda ...
[ Info: Running `conda install -y numpy` in root environment
[ Info: PyCall is using /home/mkitti/anaconda3/envs/julia172/bin/python (Python 3.9.10) at /home/mkitti/anaconda3/envs/julia172/bin/python, libpython = /home/mkitti/anaconda3/envs/julia172/lib/libpython3.9.so.1.0
[ Info: /home/mkitti/anaconda3/envs/julia172/share/julia/packages/PyCall/L0fLP/deps/deps.jl has been updated
[ Info: /home/mkitti/anaconda3/envs/julia172/share/julia/prefs/PyCall has been updated

@mkitti
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mkitti commented Feb 13, 2022

@mkitti
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mkitti commented Feb 13, 2022

@ngam
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ngam commented Feb 13, 2022

JuliaPy/Conda.jl@8f71332#commitcomment-66609512

Alright, @MilesCranmer, this should fix it. How long do changes take to take effect in the julia registry?

@mkitti
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mkitti commented Feb 13, 2022

Well we need the registry CI to pass first... then it might be an hour to propagate everything through the pkg server mirrors.

@ngam
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ngam commented Feb 13, 2022

Okay, just asking so that we can retest this PR

@MilesCranmer
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Fantastic, thanks for the quick fixing of this!!

Re: registries, it depends on if the julia-feedstock is using the standard registry (up to ~2 hours) or a github-based registry (instant after merging).

@ngam
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ngam commented Feb 13, 2022

I believe we are using the standard one, so we will revisit in ~2 hours

@MilesCranmer
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We could retest this PR quicker if we put the following in the test steps:

rm -rf ~/.julia/registries/General # or wherever the conda one is located
julia -e 'ENV["JULIA_PKG_SERVER"] = ""; import Pkg; Pkg.update()'

this will force Pkg to use the GitHub-based registry which is instantly updated after merging

@mkitti
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mkitti commented Feb 13, 2022

For the purpose of this test, we could just set JULIA_PKG_SERVER to "" in this pull request.

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mkitti commented Feb 13, 2022

@MilesCranmer
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What is the registry directory in the conda folder? I'll add it to the test now

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mkitti commented Feb 13, 2022

It shouldn't matter since the CI is doing a fresh install. It does not install registry by default until you update.

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mkitti commented Feb 13, 2022

phew, it works.

@MilesCranmer
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Amazing. Nice job getting this fix done so quickly! Confirming it works locally too.

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4 participants