conda-incubator / setup-miniconda

Set up your GitHub Actions workflow with conda via miniconda
https://github.com/marketplace/actions/setup-miniconda
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Error on activation of environment on Windows Github Workflow #371

Open langmm opened 6 days ago

langmm commented 6 days ago

I am not sure if this is the right place to report so please redirect me if this error is better reported elsewhere.

I have a workflow that uses setup-miniconda. On 10/9/2024 the windows jobs in this workflow started producing the error below when any mamba command is run after the setup step (in particular the environment activation & mamba info). The error appeared in this run (previous run that did not exhibit the error can be found here). The commit on which the error first occurred did not modify the workflow or environment.yml files. I could not find a difference in the package versions installed in the environment, the version of conda/mamba, or the runner image. I tried using miniforge (previously I was using mambaforge as I was unaware of the deprecation, but the same error occurs with miniforge) and pinning mamba to 1.5.10. Any help would be greatly appreciated.

Error message ``` # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<< Traceback (most recent call last): File "C:\Users\runneradmin\miniconda3\Lib\site-packages\conda\exception_handler.py", line 18, in __call__ return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\runneradmin\miniconda3\Lib\site-packages\conda\cli\main.py", line 98, in main_sourced context.__init__() File "C:\Users\runneradmin\miniconda3\Lib\site-packages\conda\base\context.py", line 497, in __init__ self._set_search_path( File "C:\Users\runneradmin\miniconda3\Lib\site-packages\conda\common\configuration.py", line 1423, in _set_search_path self._search_path = IndexedSet(self._expand_search_path(search_path, **kwargs)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\runneradmin\miniconda3\Lib\site-packages\boltons\setutils.py", line 118, in __init__ self.update(other) File "C:\Users\runneradmin\miniconda3\Lib\site-packages\boltons\setutils.py", line 351, in update for o in other: ^^^^^ File "C:\Users\runneradmin\miniconda3\Lib\site-packages\conda\common\configuration.py", line 1394, in _expand_search_path path = Path(template).expanduser() ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\runneradmin\miniconda3\Lib\pathlib.py", line 1406, in expanduser raise RuntimeError("Could not determine home directory.") RuntimeError: Could not determine home directory. `$ C:\Users\runneradmin\miniconda3\Scripts\conda-script.py shell.cmd.exe activate base` environment variables: CIO_TEST= CONDA_BAT=C:\Users\runneradmin\miniconda3\condabin\conda.bat CONDA_EXE=C:\Users\runneradmin\miniconda3\condabin\..\Scripts\conda.exe CONDA_ROOT=C:\Users\runneradmin\miniconda3 CONDA_SHLVL=0 CURL_CA_BUNDLE= LD_PRELOAD= PATH=C:\Users\runneradmin\miniconda3\condabin;C:\Users\runneradmin\minicond a3\envs\ephoto;C:\Users\runneradmin\miniconda3\envs\ephoto\Library\min gw64\bin;C:\Users\runneradmin\miniconda3\envs\ephoto\Library\mingw- w64\bin;C:\Users\runneradmin\miniconda3\envs\ephoto\Library\usr\bin;C: \Users\runneradmin\miniconda3\envs\ephoto\Library\bin;C:\Users\runnera dmin\miniconda3\envs\ephoto\Scripts;C:\Users\runneradmin\miniconda3\en vs\ephoto\bin;C:\Users\runneradmin\miniconda3\condabin;C:\Users\runner admin\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\local\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Gi t\usr\bin;C:\Users\runneradmin\bin;C:\Users\runneradmin\miniconda3\con dabin;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Tool s\MSVC\14.41.34120\bin\HostX64\x64;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\IDE\VC\VCPackages;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\IDE\CommonExtens ions\Microsoft\TestWindow;C:\Program Files\Microsoft Visual Studio\202 2\Enterprise\Common7\IDE\CommonExtensions\Microsoft\TeamFoundation\Tea m Explorer;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\MSBuild\Current\bin\Roslyn;C:\Program Files (x86)\Microsoft SDKs\Windows\v10.0A\bin\NETFX 4.8 Tools\x64;C:\Program Files (x86)\HTML Help Workshop;C:\Program Files\Microsoft Visual Studi o\2022\Enterprise\Common7\IDE\CommonExtensions\Microsoft\FSharp\Tools; C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Team Tools\DiagnosticsHub\Collector;C:\Program Files\Microsoft Visual Studi o\2022\Enterprise\Common7\IDE\Extensions\Microsoft\CodeCoverage.Consol e;C:\Program Files (x86)\Windows Kits\10\bin\10.0.22621.0\x64;C:\Program Files (x86)\Windows Kits\10\bin\x64;C:\Program Files\Microsoft Visual Studio\2022\Enterpri se\MSBuild\Current\Bin\amd64;C:\Windows\Microsoft.NET\Framework64\v4.0 .30319;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\IDE;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\Tools;C:\Program Files\MongoDB\Server\5.0\bin;C:\aliyun-cli;C:\vcpkg;C:\Program Files (x86)\NSIS;C:\tools\zstd;C:\Program Files\Mercurial;C:\hostedtoolcache \windows\stack\3.1.1\x64;C:\cabal\bin;C:\ghcup\bin;C:\mingw64\bin;C:\P rogram Files\dotnet;C:\Program Files\MySQL\MySQL Server 8.0\bin;C:\Program Files\R\R- 4.4.1\bin\x64;C:\SeleniumWebDrivers\GeckoDriver;C:\SeleniumWebDrivers\ EdgeDriver;C:\SeleniumWebDrivers\ChromeDriver;C:\Program Files (x86)\sbt\bin;C:\Program Files (x86)\GitHub CLI;C:\Program Files\Git\usr\bin;C:\Program Files (x86)\pipx_bin;C:\npm\prefix;C:\hos tedtoolcache\windows\go\1.21.13\x64\bin;C:\hostedtoolcache\windows\Pyt hon\3.9.13\x64\Scripts;C:\hostedtoolcache\windows\Python\3.9.13\x64;C: \hostedtoolcache\windows\Ruby\3.0.7\x64\bin;C:\Program Files\OpenSSL\b in;C:\tools\kotlinc\bin;C:\hostedtoolcache\windows\Java_Temurin- Hotspot_jdk\8.0.422-5\x64\bin;C:\Program Files\ImageMagick-7.1.1-Q16-HDRI;C:\Program Files\Microsoft SDKs\Azure \CLI2\wbin;C:\ProgramData\kind;C:\ProgramData\Chocolatey\bin;C:\Window s\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\Win dowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files\dotnet;C:\Program Files\PowerShell\7;C:\Program Files\Microsoft\Web Platform Installer;C:\Program Files\TortoiseSVN\bin;C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\170\Tools\Binn;C:\Program Files\Microsoft SQL Server\150\Tools\Binn;C:\Program Files (x86)\Windows Kits\10\Windows Performance Toolkit;C:\Program Files (x86)\WiX Toolset v3.14\bin;C:\Program Files\Microsoft SQL Server\130\DTS\Binn;C:\Program Files\Microsoft SQL Server\140\DTS\Binn;C:\Program Files\Microsoft SQL Server\150\DTS\Binn;C:\Program Files\Microsoft SQL Server\1[60](https://github.com/cropsinsilico/ePhotosynthesis_C/actions/runs/11260447218/job/31311685650#step:5:61)\DTS\Binn ;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bi n;C:\ProgramData\chocolatey\lib\pulumi\tools\Pulumi\bin;C:\Program Files\CMake\bin;C:\ProgramData\chocolatey\lib\maven\apache- maven-3.8.7\bin;C:\Program Files\Microsoft Service Fabric\bin\Fabric\Fabric.Code;C:\Program Files\Microsoft SDKs\Service Fabric\Tools\ServiceFabricLocalClusterManager;C:\Program Files\nodejs;C:\Program Files\Git\cmd;C:\Program Files\Git\mingw[64](https://github.com/cropsinsilico/ePhotosynthesis_C/actions/runs/11260447218/job/31311685650#step:5:65)\bin;C:\Program Files\Git\usr\bin;C:\Program Files\GitHub CLI;C:\tools\php;C:\Program Files\Amazon\AWSCLIV2;C:\Program Files\Amazon\SessionManagerPlugin\bin;C:\Program Files\Amazon\AWSSAMCLI\bin;C:\Program Files\Microsoft SQL Server\130\Tools\Binn;C:\Program Files\LLVM\bin;C:\Users\runneradmin\. dotnet\tools;C:\Users\runneradmin\.cargo\bin;C:\Users\runneradmin\AppD ata\Local\Microsoft\WindowsApps;C:\Program Files (x86)\Microsoft Visual Studio\Installer;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Tools\Llvm\x64\bin;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\IDE\CommonExtens ions\Microsoft\CMake\CMake\bin;C:\Program Files\Microsoft Visual Studi o\2022\Enterprise\Common7\IDE\CommonExtensions\Microsoft\CMake\Ninja;C :\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\IDE\VC \Linux\bin\ConnectionManagerExe;C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\vcpkg;C:\Program Files\Git\usr\bin\vendor_perl;C:\Program Files\Git\usr\bin\core_perl REQUESTS_CA_BUNDLE= SSL_CERT_FILE= active environment : None shell level : 0 user config file : D:\a\ePhotosynthesis_C\ePhotosynthesis_C\~\.condarc populated config files : conda version : 24.7.1 conda-build version : not installed python version : 3.12.6.final.0 solver : libmamba (default) virtual packages : __archspec=1=x[86](https://github.com/cropsinsilico/ePhotosynthesis_C/actions/runs/11260447218/job/31311685650#step:5:87)_64_v3 __conda=24.7.1=0 __win=0=0 base environment : C:\Users\runneradmin\miniconda3 (writable) conda av data dir : C:\Users\runneradmin\miniconda3\etc\conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\Users\runneradmin\miniconda3\pkgs D:\a\ePhotosynthesis_C\ePhotosynthesis_C\~\.conda\pkgs C:\Users\runneradmin\AppData\Local\conda\conda\pkgs envs directories : C:\Users\runneradmin\miniconda3\envs D:\a\ePhotosynthesis_C\ePhotosynthesis_C\~\.conda\envs C:\Users\runneradmin\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/24.7.1 requests/2.32.3 CPython/3.12.6 Windows/2022Server Windows/10.0.20348 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.9 administrator : True netrc file : None offline mode : False An unexpected error has occurred. Conda has prepared the above report. If you suspect this error is being caused by a malfunctioning plugin, consider using the --no-plugins option to turn off plugins. Example: conda --no-plugins install Alternatively, you can set the CONDA_NO_PLUGINS environment variable on the command line to run the command without plugins enabled. Example: CONDA_NO_PLUGINS=true conda install No report sent. To permanently opt-out, use $ conda config --set report_errors false ```
jaimergp commented 5 days ago

Hm, it's odd indeed. The error comes all the way from the Python standard library because it can't parse ~ in the passed paths. I wonder if some of the necessary env vars are being shadowed or something. From the docs:

On Windows, USERPROFILE will be used if set, otherwise a combination of HOMEPATH and HOMEDRIVE will be used. An initial ~user is handled by checking that the last directory component of the current user’s home directory matches USERNAME, and replacing it if so.

Maybe you can manually set USERPROFILE=${{ github.workspace }} in that step, or similar?

langmm commented 5 days ago

I just tried setting USERPROFILE=${{ github.workspace }}, but the same error occurred. Based on your comment about the environment variables, I also checked the environment variables that were set before/after the error started occurring, but there was not any difference.