The following popup is shown (everything still works, since as you can see in the logs, eventually it finds the env manager)
2026-05-09 19:13:08.735 [info] Python-envs extension version: 1.30.0
2026-05-09 19:13:08.735 [info]
=== Python Envs Configuration Levels ===
2026-05-09 19:13:08.735 [info] {
"section": "Python Envs Configuration Levels",
"defaultEnvManager": {
"workspaceFolderValue": "undefined",
"workspaceValue": "pypa.hatch:hatch",
"globalValue": "undefined",
"defaultValue": "ms-python.python:venv"
},
"defaultPackageManager": {
"workspaceFolderValue": "undefined",
"workspaceValue": "pypa.hatch:hatch",
"globalValue": "undefined",
"defaultValue": "ms-python.python:pip"
}
}
2026-05-09 19:13:08.735 [debug] TerminalEnvVarInjector: Initializing environment variable injection
2026-05-09 19:13:08.735 [debug] TerminalEnvVarInjector: Updating environment variables for all workspaces
2026-05-09 19:13:08.735 [debug] TerminalEnvVarInjector: Env file injection disabled for workspace: /home/phil/Dev/Python/scverse/scanpy
2026-05-09 19:13:08.735 [debug] TerminalEnvVarInjector: Environment variable injection completed
2026-05-09 19:13:08.735 [info] [pet] Starting Python Locator /home/phil/.vscode/extensions/ms-python.vscode-python-envs-1.30.0-linux-x64/python-env-tools/bin/pet server
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [info] Registering pyenv manager (environments will be discovered lazily)
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [info] Registering pipenv manager (environments will be discovered lazily)
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [info] Registering poetry manager (environments will be discovered lazily)
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [info] Using conda from persistent state: /usr/bin/conda
2026-05-09 19:13:08.735 [info] Conda Sourcing Status:
├─ Conda Path: /usr/bin/conda
├─ Conda Folder: /usr
├─ Active on Launch: true
└─ No Shell-specific Sourcing Scripts Found
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [debug] Using cached extension ID for caller: ms-python.python
2026-05-09 19:13:08.735 [info] [interpreterSelection] Applying initial environment selection for 1 workspace folder(s)
2026-05-09 19:13:08.735 [warning] [priorityChain] /home/phil/Dev/Python/scverse/scanpy defaultEnvManager 'pypa.hatch:hatch' not found, trying next priority
2026-05-09 19:13:08.735 [debug] [Finder] Refreshing all environments
2026-05-09 19:13:08.735 [debug] Environment search directories: 2 paths
2026-05-09 19:13:08.735 [info] [pet] configure: Sending configuration update: {"workspaceDirectories":["/home/phil/Dev/Python/scverse/scanpy"],"environmentDirectories":["/home/phil/Dev/Python/scverse/scanpy/.venv","/home/phil/Dev/Python/scverse/scanpy/*/.venv"],"pipenvExecutable":"pipenv","poetryExecutable":"poetry","cacheDirectory":"/home/phil/.config/Code/User/globalStorage/ms-python.vscode-python-envs/pythonLocator"}
2026-05-09 19:13:08.828 [debug] [venv] Fast path: no persisted path, falling through to slow path
2026-05-09 19:13:08.954 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/anndata2ri/t762Pswd/hatch-test.py3.13/bin/python
2026-05-09 19:13:08.954 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/scverse-tutorials/_YRPCeuX/basic-scrna/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/dask millions of cells/cMqPOBoB/dask millions of cells/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/Dokumente/Diss/dissertation/.venv/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/test.py3.12/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/scanpy-tutorials/vsyQHp6L/notebook/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/test.py3.12/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/scverse-plotting-api/L-p66eTo/scverse-plotting-api/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/session-info2/tMnXjx3R/notebook/bin/python
2026-05-09 19:13:08.955 [debug] Checking Hatch (pypa.hatch:hatch) for /home/phil/.local/share/hatch/env/virtual/hv-anndata/3tS7PuaB/docs/bin/python
2026-05-09 19:13:08.955 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/anndata2ri/t762Pswd/hatch-test.py3.13/bin/python
2026-05-09 19:13:08.955 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/anndata2ri/t762Pswd/hatch-test.py3.13/bin/python
2026-05-09 19:13:08.955 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/scverse-tutorials/_YRPCeuX/basic-scrna/bin/python
2026-05-09 19:13:08.955 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/scverse-tutorials/_YRPCeuX/basic-scrna/bin/python
2026-05-09 19:13:08.955 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/dask millions of cells/cMqPOBoB/dask millions of cells/bin/python
2026-05-09 19:13:08.955 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/dask millions of cells/cMqPOBoB/dask millions of cells/bin/python
2026-05-09 19:13:08.955 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/Dokumente/Diss/dissertation/.venv/bin/python
2026-05-09 19:13:08.955 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/Dokumente/Diss/dissertation/.venv/bin/python
2026-05-09 19:13:08.956 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/test.py3.12/bin/python
2026-05-09 19:13:08.956 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/test.py3.12/bin/python
2026-05-09 19:13:08.956 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/scanpy-tutorials/vsyQHp6L/notebook/bin/python
2026-05-09 19:13:08.956 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/scanpy-tutorials/vsyQHp6L/notebook/bin/python
2026-05-09 19:13:08.956 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/test.py3.12/bin/python
2026-05-09 19:13:08.956 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/test.py3.12/bin/python
2026-05-09 19:13:08.956 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/scverse-plotting-api/L-p66eTo/scverse-plotting-api/bin/python
2026-05-09 19:13:08.956 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/scverse-plotting-api/L-p66eTo/scverse-plotting-api/bin/python
2026-05-09 19:13:08.956 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/session-info2/tMnXjx3R/notebook/bin/python
2026-05-09 19:13:08.956 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/session-info2/tMnXjx3R/notebook/bin/python
2026-05-09 19:13:08.956 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /home/phil/.local/share/hatch/env/virtual/hv-anndata/3tS7PuaB/docs/bin/python
2026-05-09 19:13:08.956 [debug] Checking PyEnv (ms-python.python:pyenv) for /home/phil/.local/share/hatch/env/virtual/hv-anndata/3tS7PuaB/docs/bin/python
2026-05-09 19:13:09.238 [error] [pet] �[2m 0.745144050s�[0m �[33m WARN�[0m �[2mpet_conda::package�[0m�[2m:�[0m Unable to find conda package Python in "/home/phil/.conda/envs/dask3.12", trying slower approach
�[2m 0.745957411s�[0m �[33m WARN�[0m �[2mpet_conda::package�[0m�[2m:�[0m Unable to find conda package Python in "/home/phil/.conda/envs/scanpy-dev", trying slower approach
�[2m 0.745894061s�[0m �[33m WARN�[0m �[2mpet_conda::package�[0m�[2m:�[0m Unable to find conda package Python in "/home/phil/.conda/envs/dask3.11", trying slower approach
�[2m 0.746192301s�[0m �[33m WARN�[0m �[2mpet_conda::package�[0m�[2m:�[0m Unable to find conda package Python in "/home/phil/.conda/envs/anndata", trying slower approach
�[2m 0.746460212s�[0m �[33m WARN�[0m �[2mpet_conda::package�[0m�[2m:�[0m Unable to find conda package Python in "/home/phil/Dev/Python/Jupyter/jupyterlab-deck/.venv", trying slower approach
�[2m 0.748870915s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/pynndescent", executable: Some("/home/phil/.conda/envs/pynndescent/bin/python"), version: Some("3.11.11"), conda_dir: None, arch: None }
�[2m 0.750269826s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/dask3.12", executable: Some("/home/phil/.conda/envs/dask3.12/bin/python"), version: Some("3.12.11"), conda_dir: None, arch: Some(X64) }
�[2m 0.748874855s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/test-flit", executable: Some("/home/phil/.conda/envs/test-flit/bin/python"), version: Some("3.8.5"), conda_dir: None, arch: Some(X64) }
�[2m 0.750727167s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/test", executable: Some("/home/phil/.conda/envs/test/bin/python"), version: Some("3.12.7"), conda_dir: None, arch: None }
�[2m 0.750855087s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/anndata", executable: Some("/home/phil/.conda/envs/anndata/bin/python"), version: Some("3.8.5"), conda_dir: None, arch: Some(X64) }
�[2m 0.751056127s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/Dev/Python/Jupyter/jupyterlab-deck/.venv", executable: Some("/home/phil/Dev/Python/Jupyter/jupyterlab-deck/.venv/bin/python"), version: Some("3.11.14"), conda_dir: None, arch: None }
�[2m 0.750513197s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/dask3.11", executable: Some("/home/phil/.conda/envs/dask3.11/bin/python"), version: Some("3.11.13"), conda_dir: None, arch: Some(X64) }
�[2m 0.752214299s�[0m �[31mERROR�[0m �[2mpet_conda�[0m�[2m:�[0m Unable to find Conda Manager for the Conda env: CondaEnvironment { prefix: "/home/phil/.conda/envs/scanpy-dev", executable: Some("/home/phil/.conda/envs/scanpy-dev/bin/python"), version: Some("3.12.2"), conda_dir: None, arch: Some(X64) }
2026-05-09 19:13:09.238 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.14.0-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.322 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.12.12-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.324 [debug] Checking Hatch (pypa.hatch:hatch) for /bin/python
2026-05-09 19:13:09.324 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /bin/python
2026-05-09 19:13:09.324 [debug] Checking PyEnv (ms-python.python:pyenv) for /bin/python
2026-05-09 19:13:09.326 [debug] Checking Hatch (pypa.hatch:hatch) for /bin/python
2026-05-09 19:13:09.326 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /bin/python
2026-05-09 19:13:09.326 [debug] Checking PyEnv (ms-python.python:pyenv) for /bin/python
2026-05-09 19:13:09.433 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.9.25-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.469 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.8.20-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.476 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.11.14-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.485 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.10.19-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.491 [info] Discovered env: /home/phil/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/bin/python
2026-05-09 19:13:09.526 [info] Discovered manager: (Poetry) /usr/bin/poetry
2026-05-09 19:13:09.588 [info] Discovered env: /home/phil/.conda/envs/pynndescent/bin/python
2026-05-09 19:13:09.702 [info] Discovered env: /home/phil/.conda/envs/dask3.12/bin/python
2026-05-09 19:13:09.811 [info] Discovered env: /home/phil/.conda/envs/test-flit/bin/python
2026-05-09 19:13:09.895 [info] Discovered env: /home/phil/.conda/envs/test/bin/python
2026-05-09 19:13:09.901 [info] Refreshing pyenv environments
2026-05-09 19:13:09.901 [debug] [Finder] Refreshing all environments
2026-05-09 19:13:09.901 [info] Discovered env: /home/phil/.conda/envs/anndata/bin/python
2026-05-09 19:13:09.924 [info] Discovered env: /home/phil/.conda/envs/dask3.11/bin/python
2026-05-09 19:13:09.984 [info] Discovered env: /home/phil/.conda/envs/scanpy-dev/bin/python
2026-05-09 19:13:09.987 [info] Discovered env: /home/phil/Dev/Python/Jupyter/jupyterlab-deck/.venv/bin/python
2026-05-09 19:13:10.031 [info] Discovered env: /bin/python
2026-05-09 19:13:10.036 [debug] Environment search directories: 2 paths
2026-05-09 19:13:10.037 [debug] [pet] configure: No changes detected, skipping configuration update.
2026-05-09 19:13:10.073 [info] [pet] Telemetry: {"event":"RefreshPerformance","data":{"refreshPerformance":{"total":223,"breakdown":{"GlobalVirtualEnvs":1,"Locators":185,"Path":223,"Workspaces":10},"locators":{"Conda":182,"Homebrew":0,"LinuxGlobal":184,"PipEnv":1,"Pixi":0,"Poetry":24,"PyEnv":0,"Uv":22,"Venv":0,"VirtualEnv":0,"VirtualEnvWrapper":0}}}}
2026-05-09 19:13:10.099 [debug] Checking Hatch (pypa.hatch:hatch) for /bin/python
2026-05-09 19:13:10.099 [debug] Checking Hatch (pypa.hatch:hatch) for /bin/python
2026-05-09 19:13:10.100 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /bin/python
2026-05-09 19:13:10.100 [debug] Checking PyEnv (ms-python.python:pyenv) for /bin/python
2026-05-09 19:13:10.100 [debug] Manager Hatch (pypa.hatch:hatch) cannot handle /bin/python
2026-05-09 19:13:10.100 [debug] Checking PyEnv (ms-python.python:pyenv) for /bin/python
2026-05-09 19:13:10.179 [info] Python API: Changed environment from undefined to hatch-test.stable for: /home/phil/Dev/Python/scverse/scanpy
2026-05-09 19:13:10.179 [info] Internal: Changed environment from undefined to hatch-test.stable for: /home/phil/Dev/Python/scverse/scanpy
Environment data
ms-python.python) version: 2026.4.0venv/conda/pyenv/poetry/pipenv/system/uv/ other):pypa.hatch:hatchRepro Steps
ext install PyPA.hatch"python-envs.defaultEnvManager": "pypa.hatch:hatch"setExpected behavior
The env manager is used, no warning popup
Actual behavior
The following popup is shown (everything still works, since as you can see in the logs, eventually it finds the env manager)
Logs
Additional context