Extend test and make sure that python isn't added to pyproject.toml

crates/pixi_manifest/src/lib.rs

@@ -35,7 +35,7 @@ pub use features_ext::FeaturesExt;
 pub use has_features_iter::HasFeaturesIter;
 pub use has_manifest_ref::HasManifestRef;
 use itertools::Itertools;
-pub use manifests::{Manifest, ManifestKind, WorkspaceManifest};
+pub use manifests::{Manifest, ManifestKind, ManifestSource, WorkspaceManifest};
 use miette::Diagnostic;
 pub use preview::{KnownPreviewFeature, Preview, PreviewFeature};
 pub use pypi::pypi_requirement::PyPiRequirement;

src/cli/upgrade.rs

@@ -195,6 +195,22 @@ fn parse_specs(
                 None
             }
         })
+        // Only upgrade in pyproject.toml if it is explicitly mentioned in `tool.pixi.dependencies.python`
+        .filter(|(name, _)| {
+            if name.as_normalized() == "python" {
+                if let pixi_manifest::ManifestSource::PyProjectToml(document) =
+                    project.manifest.document.clone()
+                {
+                    if document
+                        .get_nested_table("[tool.pixi.dependencies.python]")
+                        .is_err()
+                    {
+                        return false;
+                    }
+                }
+            }
+            true
+        })
         .collect();
     let pypi_deps = pypi_deps_iter
         // Don't upgrade excluded packages

tests/integration_python/common.py

@@ -7,6 +7,16 @@
 PIXI_VERSION = "0.38.0"
 
 
+ALL_PLATFORMS = '["linux-64", "osx-64", "win-64", "linux-ppc64le", "linux-aarch64"]'
+
+EMPTY_BOILERPLATE_PROJECT = f"""
+[project]
+name = "test"
+channels = []
+platforms = {ALL_PLATFORMS}
+"""
+
+
 class ExitCode(IntEnum):
     SUCCESS = 0
     FAILURE = 1

tests/integration_python/test_main_cli.py

@@ -1,6 +1,7 @@
 import os
 from pathlib import Path
-from .common import verify_cli_command, ExitCode, PIXI_VERSION
+
+from .common import verify_cli_command, ExitCode, PIXI_VERSION, ALL_PLATFORMS
 import tomllib
 import json
 import pytest
@@ -529,19 +530,19 @@ def test_upgrade_pypi_and_conda_package(pixi: Path, tmp_path: Path) -> None:
 
 
 @pytest.mark.slow
-def test_upgrade_dependency_location(pixi: Path, tmp_path: Path) -> None:
+def test_upgrade_dependency_location_pixi(pixi: Path, tmp_path: Path) -> None:
     # Test based on https://github.com/prefix-dev/pixi/issues/2470
     # Making sure pixi places the upgraded package in the correct location
     manifest_path = tmp_path / "pyproject.toml"
-    pyproject = """
+    pyproject = f"""
 [project]
-dependencies = []
 name = "test-upgrade"
-requires-python = ">= 3.11"
+dependencies = ["numpy==1.*"]
+requires-python = ">3.10"
 
 [tool.pixi.project]
 channels = ["conda-forge"]
-platforms = ["linux-64"]
+platforms = {ALL_PLATFORMS}
 
 [tool.pixi.pypi-dependencies]
 polars = "==0.*"
@@ -555,21 +556,24 @@ def test_upgrade_dependency_location(pixi: Path, tmp_path: Path) -> None:
         stderr_contains=["polars"],
     )
     parsed_manifest = tomllib.loads(manifest_path.read_text())
-    # Check that the requires-python is modified
-    requires_python = parsed_manifest["project"]["requires-python"]
-    assert "3.11" not in requires_python
 
-    # Check that `tool.pixi.dependencies.python` doesn't exist
+    # Check that `tool.pixi.dependencies.python` isn't added
     assert "python" not in parsed_manifest.get("tool", {}).get("pixi", {}).get("dependencies", {})
 
-    # Check that the pypi-dependency is upgraded
+    # Check that the pypi-dependencies are upgraded
     polars_pypi = parsed_manifest["tool"]["pixi"]["pypi-dependencies"]["polars"]
-    assert polars_pypi
     assert polars_pypi != "==0.*"
 
-    # Check that the pypi-dependency doesn't exist in the project dependencies
+    # Check that project.dependencies are upgraded
+    numpy_pypi = parsed_manifest["project"]["dependencies"][0]
+    assert numpy_pypi != "==1.*"
+
+    # Check that the polars doesn't exist in the project dependencies
     assert "polars" not in parsed_manifest["project"]["dependencies"]
 
+    # Check that numpy doesn't exist in the pypi-dependencies
+    assert "numpy" not in parsed_manifest["tool"]["pixi"]["pypi-dependencies"]
+
 
 def test_upgrade_keep_info(pixi: Path, tmp_path: Path, multiple_versions_channel_1: str) -> None:
     manifest_path = tmp_path / "pixi.toml"

tests/integration_python/test_run_cli.py

@@ -1,18 +1,9 @@
 import json
 from pathlib import Path
-from .common import verify_cli_command, ExitCode, default_env_path
+from .common import EMPTY_BOILERPLATE_PROJECT, verify_cli_command, ExitCode, default_env_path
 import tempfile
 import os
 
-ALL_PLATFORMS = '["linux-64", "osx-64", "win-64", "linux-ppc64le", "linux-aarch64"]'
-
-EMPTY_BOILERPLATE_PROJECT = f"""
-[project]
-name = "test"
-channels = []
-platforms = {ALL_PLATFORMS}
-"""
-
 
 def test_run_in_shell_environment(pixi: Path, tmp_path: Path) -> None:
     manifest = tmp_path.joinpath("pixi.toml")