From 2cbe32b6706b79d72a79a3b09182cb9142b0e85d Mon Sep 17 00:00:00 2001 From: Renan Rodrigues dos Santos Date: Thu, 28 Nov 2024 20:38:10 -0300 Subject: [PATCH 1/7] Update project dependencies --- .github/workflows/ci.yml | 6 +- .github/workflows/release.yml | 2 +- pyproject.toml | 6 +- tests/integration/ipykernel/pixi.lock | 1702 ++++---- tests/integration/r-irkernel/pixi.lock | 3877 +++++++++---------- tests/unit/data/pixi_project/pixi.lock | 1293 ++++--- tests/unit/data/pyproject_project/pixi.lock | 825 ++-- uv.lock | 781 ++-- 8 files changed, 4315 insertions(+), 4177 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 72d9039..361dc25 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -12,7 +12,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-latest, windows-latest] - pixi-version: ["0.30.0", "0.34.0"] + pixi-version: ["0.30.0", "0.38.0"] runs-on: ${{ matrix.os }} steps: - name: Checkout repo @@ -25,13 +25,13 @@ jobs: run-install: false - name: Install uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@v4 - name: Test, lint and typecheck run: uv run tox - name: Upload coverage to Codecov - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: fail_ci_if_error: true token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 48e9f2a..42baa46 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -17,7 +17,7 @@ jobs: uses: actions/checkout@v4 - name: Install uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@v4 - name: Build release run: uv build diff --git a/pyproject.toml b/pyproject.toml index 71c8891..07aea81 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "pixi-kernel" -version = "0.5.1" +version = "0.5.2" description = "Jupyter kernels using Pixi for reproducible notebooks" license = { text = "MIT" } authors = [ @@ -43,8 +43,8 @@ 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0000000..327f848 --- /dev/null +++ b/tests/unit/data/pixi_on_pixi/good_project/pixi.toml @@ -0,0 +1,9 @@ +[project] +name = "pixi_project" +version = "0.1.0" +channels = ["conda-forge"] +platforms = ["linux-64", "osx-64", "win-64"] + +[dependencies] +python = "*" +ipykernel = "*" diff --git a/tests/unit/data/pixi_on_pixi/pixi.lock b/tests/unit/data/pixi_on_pixi/pixi.lock new file mode 100644 index 0000000..12036fe --- /dev/null +++ b/tests/unit/data/pixi_on_pixi/pixi.lock @@ -0,0 +1,7 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + packages: {} +packages: [] diff --git a/tests/unit/data/pixi_on_pixi/pixi.toml b/tests/unit/data/pixi_on_pixi/pixi.toml new file mode 100644 index 0000000..3ff03ce --- /dev/null +++ b/tests/unit/data/pixi_on_pixi/pixi.toml @@ -0,0 +1,7 @@ +[project] +name = "empty_project" +version = "0.1.0" +channels = ["conda-forge"] +platforms = ["linux-64", "osx-64", "win-64"] + +[dependencies] diff --git a/tests/unit/test_pixi.py b/tests/unit/test_pixi.py index 18eef48..7be7c8d 100644 --- a/tests/unit/test_pixi.py +++ b/tests/unit/test_pixi.py @@ -1,5 +1,8 @@ import logging +import os import re +import subprocess +import sys from pathlib import Path import pytest @@ -140,3 +143,43 @@ def test_pyproject_project(): kernel_name=kernel_name, ) assert Path(environment.prefix).parts[-2:] == ("envs", "default") + + +@pytest.fixture +def update_env_for_pixi_on_pixi(): + result = subprocess.run( + ["pixi", "run", "env"], + cwd=data_dir / "pixi_on_pixi", + capture_output=True, + text=True, + ) + assert result.returncode == 0, result.stderr + + # Update the current environment where the tests are running to merge all the env vars returned + # by `pixi run env` + original_env = dict(os.environ) + for line in result.stdout.splitlines(): + key, value = line.split("=", 1) + os.environ[key] = value + + yield + + # Restore the original environment + os.environ.clear() + os.environ.update(original_env) + + +# https://github.com/renan-r-santos/pixi-kernel/issues/35 +@pytest.mark.skipif(sys.platform == "win32", reason="No need to write Windows-specific code here") +@pytest.mark.usefixtures("update_env_for_pixi_on_pixi") +def test_pixi_on_pixi(): + cwd = data_dir / "pixi_on_pixi" / "good_project" + required_package = "ipykernel" + kernel_name = "Python (Pixi)" + + environment = ensure_readiness( + cwd=cwd, + required_package=required_package, + kernel_name=kernel_name, + ) + assert Path(environment.prefix).parts[-2:] == ("envs", "default") From b6c809781063bd3f4115e0106992d914ccb595ae Mon Sep 17 00:00:00 2001 From: Renan Rodrigues dos Santos Date: Thu, 28 Nov 2024 21:05:56 -0300 Subject: [PATCH 3/7] Remove `PIXI_IN_SHELL` env var before calling `pixi` https://github.com/renan-r-santos/pixi-kernel/issues/35 --- src/pixi_kernel/pixi.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/pixi_kernel/pixi.py b/src/pixi_kernel/pixi.py index e3e6ed6..2ead5f6 100644 --- a/src/pixi_kernel/pixi.py +++ b/src/pixi_kernel/pixi.py @@ -1,5 +1,6 @@ from __future__ import annotations +import os import shutil import subprocess from pathlib import Path @@ -63,6 +64,10 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E PIXI_OUTDATED.format(kernel_name=kernel_name, minimum_version=MINIMUM_PIXI_VERSION) ) + # Remove PIXI_IN_SHELL for when JupyterLab was started from a Pixi shell + # https://github.com/renan-r-santos/pixi-kernel/issues/35 + os.environ.pop("PIXI_IN_SHELL", None) + # Ensure there is a Pixi project in the current working directory or any of its parents result = subprocess.run( ["pixi", "info", "--json"], From d9f3418abb01fd871e2ef07526583b62065e6a3b Mon Sep 17 00:00:00 2001 From: Renan Rodrigues dos Santos Date: Thu, 28 Nov 2024 21:13:08 -0300 Subject: [PATCH 4/7] Improve logging and error messages --- CONTRIBUTING.md | 2 +- src/pixi_kernel/__init__.py | 3 +++ src/pixi_kernel/errors.py | 4 +++- src/pixi_kernel/pixi.py | 9 ++++++++- src/pixi_kernel/provisioner.py | 6 ++++-- tests/unit/test_pixi.py | 1 + 6 files changed, 20 insertions(+), 5 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b5972a8..fce84ff 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -56,7 +56,7 @@ uv run tox run -e type_check 1. Bump 1. Increment version in `pyproject.toml` - 2. Update all Pixi lock files by running `uv sync` + 2. Update all lock files by running `uv sync -U` and `pixi update` 3. Commit with message "chore: Bump version number to X.Y.Z" 4. Push commit to GitHub 5. Check [CI](https://github.com/renan-r-santos/pixi-kernel/actions/workflows/ci.yml) to ensure diff --git a/src/pixi_kernel/__init__.py b/src/pixi_kernel/__init__.py index e69de29..bc2230c 100644 --- a/src/pixi_kernel/__init__.py +++ b/src/pixi_kernel/__init__.py @@ -0,0 +1,3 @@ +import logging + +logging.basicConfig(level=logging.INFO, format="pixi-kernel %(levelname)s: %(message)s") diff --git a/src/pixi_kernel/errors.py b/src/pixi_kernel/errors.py index def307a..324a206 100644 --- a/src/pixi_kernel/errors.py +++ b/src/pixi_kernel/errors.py @@ -31,7 +31,9 @@ PIXI_KERNEL_NOT_FOUND = """ To run the {kernel_name} kernel, you need to add the {required_package} package to your project dependencies. You can do this by running 'pixi add {required_package}' -in your project directory and restarting your kernel. +in your project directory and restarting your kernel. Make sure the prefix +{prefix} +points to the correct Pixi environment. If you continue to face issues, report them at https://github.com/renan-r-santos/pixi-kernel/issues """ diff --git a/src/pixi_kernel/pixi.py b/src/pixi_kernel/pixi.py index 2ead5f6..c21dcfb 100644 --- a/src/pixi_kernel/pixi.py +++ b/src/pixi_kernel/pixi.py @@ -1,5 +1,6 @@ from __future__ import annotations +import logging import os import shutil import subprocess @@ -12,6 +13,8 @@ MINIMUM_PIXI_VERSION = "0.30.0" +logger = logging.getLogger(__name__) + class PixiInfo(BaseModel): environments: list[Environment] = Field(alias="environments_info") @@ -75,6 +78,8 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E capture_output=True, text=True, ) + logger.info(f"pixi info stderr: {result.stderr}") + logger.info(f"pixi info stdout: {result.stdout}") if result.returncode != 0: raise RuntimeError(f"Failed to run 'pixi info': {result.stderr}") @@ -108,7 +113,9 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E if required_package not in dependencies: raise RuntimeError( PIXI_KERNEL_NOT_FOUND.format( - kernel_name=kernel_name, required_package=required_package + kernel_name=kernel_name, + required_package=required_package, + prefix=default_environment.prefix, ) ) diff --git a/src/pixi_kernel/provisioner.py b/src/pixi_kernel/provisioner.py index 0d462b7..1b5ef4e 100644 --- a/src/pixi_kernel/provisioner.py +++ b/src/pixi_kernel/provisioner.py @@ -1,4 +1,4 @@ -from logging import Logger +import logging from pathlib import Path from typing import Any, Optional, cast @@ -7,6 +7,8 @@ from .pixi import ensure_readiness +logger = logging.getLogger(__name__) + class PixiKernelProvisioner(LocalProvisioner): # type: ignore async def pre_launch(self, **kwargs: Any) -> dict[str, Any]: @@ -14,7 +16,6 @@ async def pre_launch(self, **kwargs: Any) -> dict[str, Any]: This includes ensuring Pixi is installed and that a Pixi project is available. """ - logger = cast(Logger, self.log) kernel_spec = cast(KernelSpec, self.kernel_spec) kernel_metadata: Optional[dict[str, str]] = kernel_spec.metadata.get("pixi-kernel") @@ -29,6 +30,7 @@ async def pre_launch(self, **kwargs: Any) -> dict[str, Any]: raise ValueError("Pixi Kernel metadata is missing the 'required-package' key") cwd = Path(kwargs.get("cwd", Path.cwd())) + logger.info(f"JupyterLab provided current working directory: {kwargs.get("cwd", None)}") logger.info(f"The current working directory is {cwd}") environment = ensure_readiness( diff --git a/tests/unit/test_pixi.py b/tests/unit/test_pixi.py index 7be7c8d..479de76 100644 --- a/tests/unit/test_pixi.py +++ b/tests/unit/test_pixi.py @@ -103,6 +103,7 @@ def test_missing_ipykernel(): PIXI_KERNEL_NOT_FOUND.format( required_package=required_package, kernel_name=kernel_name, + prefix=str(cwd / ".pixi" / "envs" / "default"), ) ) with pytest.raises(RuntimeError, match=message): From 70f1259cb19bc462d5843e9aedf709286206d9ea Mon Sep 17 00:00:00 2001 From: Renan Rodrigues dos Santos Date: Thu, 28 Nov 2024 22:06:52 -0300 Subject: [PATCH 5/7] Remove `PIXI_IN_SHELL` from kernel `env` and use that for running `pixi` verifications --- src/pixi_kernel/pixi.py | 24 ++++++++------- src/pixi_kernel/provisioner.py | 9 +++++- tests/unit/test_pixi.py | 55 +++++++++++++++++++++++----------- 3 files changed, 60 insertions(+), 28 deletions(-) diff --git a/src/pixi_kernel/pixi.py b/src/pixi_kernel/pixi.py index c21dcfb..3c43440 100644 --- a/src/pixi_kernel/pixi.py +++ b/src/pixi_kernel/pixi.py @@ -1,7 +1,6 @@ from __future__ import annotations import logging -import os import shutil import subprocess from pathlib import Path @@ -32,7 +31,13 @@ class Project(BaseModel): manifest_path: str -def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> Environment: +def ensure_readiness( + *, + cwd: Path, + env: dict[str, str], + required_package: str, + kernel_name: str, +) -> Environment: """Ensure the Pixi environment is ready to run the kernel. This function checks the following: @@ -52,7 +57,7 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E raise RuntimeError(PIXI_NOT_FOUND.format(kernel_name=kernel_name)) # Ensure a supported Pixi version is installed - result = subprocess.run(["pixi", "--version"], capture_output=True, text=True) + result = subprocess.run(["pixi", "--version"], capture_output=True, env=env, text=True) if result.returncode != 0 or not result.stdout.startswith("pixi "): raise RuntimeError(PIXI_VERSION_ERROR.format(kernel_name=kernel_name)) @@ -67,15 +72,12 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E PIXI_OUTDATED.format(kernel_name=kernel_name, minimum_version=MINIMUM_PIXI_VERSION) ) - # Remove PIXI_IN_SHELL for when JupyterLab was started from a Pixi shell - # https://github.com/renan-r-santos/pixi-kernel/issues/35 - os.environ.pop("PIXI_IN_SHELL", None) - # Ensure there is a Pixi project in the current working directory or any of its parents result = subprocess.run( ["pixi", "info", "--json"], cwd=str(cwd.absolute()), capture_output=True, + env=env, text=True, ) logger.info(f"pixi info stderr: {result.stderr}") @@ -97,14 +99,15 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E ["pixi", "project", "version", "get"], cwd=str(cwd.absolute()), capture_output=True, + env=env, text=True, ) raise RuntimeError(result.stderr) # Find the default environment and check if the required kernel package is a dependency - for env in pixi_info.environments: - if env.name == "default": - default_environment = env + for pixi_env in pixi_info.environments: + if pixi_env.name == "default": + default_environment = pixi_env break else: raise RuntimeError("Default Pixi environment not found.") @@ -124,6 +127,7 @@ def ensure_readiness(*, cwd: Path, required_package: str, kernel_name: str) -> E ["pixi", "install"], cwd=str(cwd.absolute()), capture_output=True, + env=env, text=True, ) if result.returncode != 0: diff --git a/src/pixi_kernel/provisioner.py b/src/pixi_kernel/provisioner.py index 1b5ef4e..690b722 100644 --- a/src/pixi_kernel/provisioner.py +++ b/src/pixi_kernel/provisioner.py @@ -1,4 +1,5 @@ import logging +import os from pathlib import Path from typing import Any, Optional, cast @@ -30,11 +31,17 @@ async def pre_launch(self, **kwargs: Any) -> dict[str, Any]: raise ValueError("Pixi Kernel metadata is missing the 'required-package' key") cwd = Path(kwargs.get("cwd", Path.cwd())) - logger.info(f"JupyterLab provided current working directory: {kwargs.get("cwd", None)}") + logger.info(f"JupyterLab provided this value for cwd: {kwargs.get('cwd', None)}") logger.info(f"The current working directory is {cwd}") + # Remove PIXI_IN_SHELL for when JupyterLab is started from a Pixi shell + # https://github.com/renan-r-santos/pixi-kernel/issues/35 + env: dict[str, str] = kwargs.get("env", os.environ) + env.pop("PIXI_IN_SHELL", None) + environment = ensure_readiness( cwd=cwd, + env=env, required_package=required_package, kernel_name=kernel_spec.display_name, ) diff --git a/tests/unit/test_pixi.py b/tests/unit/test_pixi.py index 479de76..a14d1a6 100644 --- a/tests/unit/test_pixi.py +++ b/tests/unit/test_pixi.py @@ -23,21 +23,27 @@ def test_pixi_not_installed(): message = re.escape(PIXI_NOT_FOUND.format(kernel_name="Pixi")) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) @pytest.mark.usefixtures("_patch_pixi_version_exit_code") def test_pixi_version_bad_exit_code(): message = re.escape(PIXI_VERSION_ERROR.format(kernel_name="Pixi")) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) @pytest.mark.usefixtures("_patch_pixi_version_stdout") def test_pixi_version_bad_stdout(): message = re.escape(PIXI_VERSION_ERROR.format(kernel_name="Pixi")) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) @pytest.mark.usefixtures("_patch_pixi_version") @@ -49,14 +55,18 @@ def test_outdated_pixi(): ) ) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) @pytest.mark.usefixtures("_patch_pixi_info_exit_code") def test_pixi_info_bad_exit_code(): message = re.escape("Failed to run 'pixi info': error") with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) @pytest.mark.usefixtures("_patch_pixi_info_stdout") @@ -65,7 +75,9 @@ def test_pixi_info_bad_stdout(): ("Failed to parse 'pixi info' output: not JSON\n1 validation error for PixiInfo") ) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) def test_empty_project(): @@ -77,21 +89,23 @@ def test_empty_project(): "could not find pixi.toml or pyproject.toml which is configured to use pixi" ) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=cwd, required_package="pixi", kernel_name="Pixi") + ensure_readiness(cwd=cwd, env=os.environ, required_package="pixi", kernel_name="Pixi") def test_bad_pixi_toml(): cwd = data_dir / "bad_pixi_toml" message = re.escape("failed to parse project manifest") with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=cwd, required_package="pixi", kernel_name="Pixi") + ensure_readiness(cwd=cwd, env=os.environ, required_package="pixi", kernel_name="Pixi") @pytest.mark.usefixtures("_patch_pixi_info_no_default_env") def test_missing_default_environment(): message = re.escape("Default Pixi environment not found.") with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=Path.cwd(), required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + ) def test_missing_ipykernel(): @@ -107,7 +121,9 @@ def test_missing_ipykernel(): ) ) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=cwd, required_package=required_package, kernel_name=kernel_name) + ensure_readiness( + cwd=cwd, env=os.environ, required_package=required_package, kernel_name=kernel_name + ) def test_non_existing_dependency(): @@ -117,7 +133,9 @@ def test_non_existing_dependency(): message = re.escape("Failed to run 'pixi install':") with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=cwd, required_package=required_package, kernel_name=kernel_name) + ensure_readiness( + cwd=cwd, env=os.environ, required_package=required_package, kernel_name=kernel_name + ) def test_pixi_project(): @@ -127,6 +145,7 @@ def test_pixi_project(): environment = ensure_readiness( cwd=cwd, + env=os.environ, required_package=required_package, kernel_name=kernel_name, ) @@ -140,6 +159,7 @@ def test_pyproject_project(): environment = ensure_readiness( cwd=cwd, + env=os.environ, required_package=required_package, kernel_name=kernel_name, ) @@ -147,7 +167,7 @@ def test_pyproject_project(): @pytest.fixture -def update_env_for_pixi_on_pixi(): +def env_for_pixi_on_pixi(): result = subprocess.run( ["pixi", "run", "env"], cwd=data_dir / "pixi_on_pixi", @@ -157,13 +177,14 @@ def update_env_for_pixi_on_pixi(): assert result.returncode == 0, result.stderr # Update the current environment where the tests are running to merge all the env vars returned - # by `pixi run env` + # by `pixi run env` except for PIXI_IN_SHELL original_env = dict(os.environ) for line in result.stdout.splitlines(): key, value = line.split("=", 1) - os.environ[key] = value + if key != "PIXI_IN_SHELL": + os.environ[key] = value - yield + yield os.environ # Restore the original environment os.environ.clear() @@ -172,14 +193,14 @@ def update_env_for_pixi_on_pixi(): # https://github.com/renan-r-santos/pixi-kernel/issues/35 @pytest.mark.skipif(sys.platform == "win32", reason="No need to write Windows-specific code here") -@pytest.mark.usefixtures("update_env_for_pixi_on_pixi") -def test_pixi_on_pixi(): +def test_pixi_on_pixi(env_for_pixi_on_pixi: dict[str, str]): cwd = data_dir / "pixi_on_pixi" / "good_project" required_package = "ipykernel" kernel_name = "Python (Pixi)" environment = ensure_readiness( cwd=cwd, + env=env_for_pixi_on_pixi, required_package=required_package, kernel_name=kernel_name, ) From cc215d2bd3ff70d66aae422d0eff46ca2b764baa Mon Sep 17 00:00:00 2001 From: Renan Rodrigues dos Santos Date: Fri, 29 Nov 2024 09:02:01 -0300 Subject: [PATCH 6/7] Better location for removing PIXI_IN_SHELL Rename pixi_on_pixi to pixi_in_pixi Remove str() on subprocess.run calls Use cwd.resolve instead ot csd.absolute --- src/pixi_kernel/pixi.py | 16 +++++++--------- src/pixi_kernel/provisioner.py | 10 +++------- .../good_project/pixi.lock | 0 .../good_project/pixi.toml | 0 .../{pixi_on_pixi => pixi_in_pixi}/pixi.lock | 0 .../{pixi_on_pixi => pixi_in_pixi}/pixi.toml | 0 tests/unit/test_pixi.py | 15 +++++++-------- 7 files changed, 17 insertions(+), 24 deletions(-) rename tests/unit/data/{pixi_on_pixi => pixi_in_pixi}/good_project/pixi.lock (100%) rename tests/unit/data/{pixi_on_pixi => pixi_in_pixi}/good_project/pixi.toml (100%) rename tests/unit/data/{pixi_on_pixi => pixi_in_pixi}/pixi.lock (100%) rename tests/unit/data/{pixi_on_pixi => pixi_in_pixi}/pixi.toml (100%) diff --git a/src/pixi_kernel/pixi.py b/src/pixi_kernel/pixi.py index 3c43440..f82aa63 100644 --- a/src/pixi_kernel/pixi.py +++ b/src/pixi_kernel/pixi.py @@ -52,6 +52,10 @@ def ensure_readiness( Returns the path to the Pixi environment prefix. """ + # Remove PIXI_IN_SHELL for when JupyterLab is started from a Pixi shell + # https://github.com/renan-r-santos/pixi-kernel/issues/35 + env.pop("PIXI_IN_SHELL", None) + # Ensure Pixi is in PATH if shutil.which("pixi") is None: raise RuntimeError(PIXI_NOT_FOUND.format(kernel_name=kernel_name)) @@ -75,7 +79,7 @@ def ensure_readiness( # Ensure there is a Pixi project in the current working directory or any of its parents result = subprocess.run( ["pixi", "info", "--json"], - cwd=str(cwd.absolute()), + cwd=cwd, capture_output=True, env=env, text=True, @@ -97,7 +101,7 @@ def ensure_readiness( # a typo in the toml file (parsing error) or there is no project at all. result = subprocess.run( ["pixi", "project", "version", "get"], - cwd=str(cwd.absolute()), + cwd=cwd, capture_output=True, env=env, text=True, @@ -123,13 +127,7 @@ def ensure_readiness( ) # Make sure the environment can be solved and is up-to-date - result = subprocess.run( - ["pixi", "install"], - cwd=str(cwd.absolute()), - capture_output=True, - env=env, - text=True, - ) + result = subprocess.run(["pixi", "install"], cwd=cwd, capture_output=True, env=env, text=True) if result.returncode != 0: raise RuntimeError(f"Failed to run 'pixi install': {result.stderr}") diff --git a/src/pixi_kernel/provisioner.py b/src/pixi_kernel/provisioner.py index 690b722..c28d2f9 100644 --- a/src/pixi_kernel/provisioner.py +++ b/src/pixi_kernel/provisioner.py @@ -34,13 +34,9 @@ async def pre_launch(self, **kwargs: Any) -> dict[str, Any]: logger.info(f"JupyterLab provided this value for cwd: {kwargs.get('cwd', None)}") logger.info(f"The current working directory is {cwd}") - # Remove PIXI_IN_SHELL for when JupyterLab is started from a Pixi shell - # https://github.com/renan-r-santos/pixi-kernel/issues/35 env: dict[str, str] = kwargs.get("env", os.environ) - env.pop("PIXI_IN_SHELL", None) - - environment = ensure_readiness( - cwd=cwd, + pixi_environment = ensure_readiness( + cwd=cwd.resolve(), env=env, required_package=required_package, kernel_name=kernel_spec.display_name, @@ -49,7 +45,7 @@ async def pre_launch(self, **kwargs: Any) -> dict[str, Any]: # R kernel needs special treatment # https://github.com/renan-r-santos/pixi-kernel/issues/15 if required_package == "r-irkernel": - r_libs_path = str(Path(environment.prefix) / "lib" / "R" / "library") + r_libs_path = str(Path(pixi_environment.prefix) / "lib" / "R" / "library") kernel_spec.env["R_LIBS"] = r_libs_path kernel_spec.env["R_LIBS_SITE"] = r_libs_path kernel_spec.env["R_LIBS_USER"] = r_libs_path diff --git a/tests/unit/data/pixi_on_pixi/good_project/pixi.lock b/tests/unit/data/pixi_in_pixi/good_project/pixi.lock similarity index 100% rename from tests/unit/data/pixi_on_pixi/good_project/pixi.lock rename to tests/unit/data/pixi_in_pixi/good_project/pixi.lock diff --git a/tests/unit/data/pixi_on_pixi/good_project/pixi.toml b/tests/unit/data/pixi_in_pixi/good_project/pixi.toml similarity index 100% rename from tests/unit/data/pixi_on_pixi/good_project/pixi.toml rename to tests/unit/data/pixi_in_pixi/good_project/pixi.toml diff --git a/tests/unit/data/pixi_on_pixi/pixi.lock b/tests/unit/data/pixi_in_pixi/pixi.lock similarity index 100% rename from tests/unit/data/pixi_on_pixi/pixi.lock rename to tests/unit/data/pixi_in_pixi/pixi.lock diff --git a/tests/unit/data/pixi_on_pixi/pixi.toml b/tests/unit/data/pixi_in_pixi/pixi.toml similarity index 100% rename from tests/unit/data/pixi_on_pixi/pixi.toml rename to tests/unit/data/pixi_in_pixi/pixi.toml diff --git a/tests/unit/test_pixi.py b/tests/unit/test_pixi.py index a14d1a6..573ee67 100644 --- a/tests/unit/test_pixi.py +++ b/tests/unit/test_pixi.py @@ -167,22 +167,21 @@ def test_pyproject_project(): @pytest.fixture -def env_for_pixi_on_pixi(): +def env_for_pixi_in_pixi(): result = subprocess.run( ["pixi", "run", "env"], - cwd=data_dir / "pixi_on_pixi", + cwd=data_dir / "pixi_in_pixi", capture_output=True, text=True, ) assert result.returncode == 0, result.stderr # Update the current environment where the tests are running to merge all the env vars returned - # by `pixi run env` except for PIXI_IN_SHELL + # by `pixi run env` original_env = dict(os.environ) for line in result.stdout.splitlines(): key, value = line.split("=", 1) - if key != "PIXI_IN_SHELL": - os.environ[key] = value + os.environ[key] = value yield os.environ @@ -193,14 +192,14 @@ def env_for_pixi_on_pixi(): # https://github.com/renan-r-santos/pixi-kernel/issues/35 @pytest.mark.skipif(sys.platform == "win32", reason="No need to write Windows-specific code here") -def test_pixi_on_pixi(env_for_pixi_on_pixi: dict[str, str]): - cwd = data_dir / "pixi_on_pixi" / "good_project" +def test_pixi_in_pixi(env_for_pixi_in_pixi: dict[str, str]): + cwd = data_dir / "pixi_in_pixi" / "good_project" required_package = "ipykernel" kernel_name = "Python (Pixi)" environment = ensure_readiness( cwd=cwd, - env=env_for_pixi_on_pixi, + env=env_for_pixi_in_pixi, required_package=required_package, kernel_name=kernel_name, ) From 9c40656b1991092eddb40715b9295bde2e7dc740 Mon Sep 17 00:00:00 2001 From: Renan Rodrigues dos Santos Date: Fri, 29 Nov 2024 09:08:57 -0300 Subject: [PATCH 7/7] Copy os.environ in tests --- tests/unit/test_pixi.py | 36 +++++++++++++++++++++++------------- 1 file changed, 23 insertions(+), 13 deletions(-) diff --git a/tests/unit/test_pixi.py b/tests/unit/test_pixi.py index 573ee67..5b56fad 100644 --- a/tests/unit/test_pixi.py +++ b/tests/unit/test_pixi.py @@ -24,7 +24,7 @@ def test_pixi_not_installed(): message = re.escape(PIXI_NOT_FOUND.format(kernel_name="Pixi")) with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -33,7 +33,7 @@ def test_pixi_version_bad_exit_code(): message = re.escape(PIXI_VERSION_ERROR.format(kernel_name="Pixi")) with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -42,7 +42,7 @@ def test_pixi_version_bad_stdout(): message = re.escape(PIXI_VERSION_ERROR.format(kernel_name="Pixi")) with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -56,7 +56,7 @@ def test_outdated_pixi(): ) with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -65,7 +65,7 @@ def test_pixi_info_bad_exit_code(): message = re.escape("Failed to run 'pixi info': error") with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -76,7 +76,7 @@ def test_pixi_info_bad_stdout(): ) with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -89,14 +89,18 @@ def test_empty_project(): "could not find pixi.toml or pyproject.toml which is configured to use pixi" ) with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=cwd, env=os.environ, required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=cwd, env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" + ) def test_bad_pixi_toml(): cwd = data_dir / "bad_pixi_toml" message = re.escape("failed to parse project manifest") with pytest.raises(RuntimeError, match=message): - ensure_readiness(cwd=cwd, env=os.environ, required_package="pixi", kernel_name="Pixi") + ensure_readiness( + cwd=cwd, env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" + ) @pytest.mark.usefixtures("_patch_pixi_info_no_default_env") @@ -104,7 +108,7 @@ def test_missing_default_environment(): message = re.escape("Default Pixi environment not found.") with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=Path.cwd(), env=os.environ, required_package="pixi", kernel_name="Pixi" + cwd=Path.cwd(), env=os.environ.copy(), required_package="pixi", kernel_name="Pixi" ) @@ -122,7 +126,10 @@ def test_missing_ipykernel(): ) with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=cwd, env=os.environ, required_package=required_package, kernel_name=kernel_name + cwd=cwd, + env=os.environ.copy(), + required_package=required_package, + kernel_name=kernel_name, ) @@ -134,7 +141,10 @@ def test_non_existing_dependency(): message = re.escape("Failed to run 'pixi install':") with pytest.raises(RuntimeError, match=message): ensure_readiness( - cwd=cwd, env=os.environ, required_package=required_package, kernel_name=kernel_name + cwd=cwd, + env=os.environ.copy(), + required_package=required_package, + kernel_name=kernel_name, ) @@ -145,7 +155,7 @@ def test_pixi_project(): environment = ensure_readiness( cwd=cwd, - env=os.environ, + env=os.environ.copy(), required_package=required_package, kernel_name=kernel_name, ) @@ -159,7 +169,7 @@ def test_pyproject_project(): environment = ensure_readiness( cwd=cwd, - env=os.environ, + env=os.environ.copy(), required_package=required_package, kernel_name=kernel_name, )