feat: pypi-options.dependency-overrides

crates/pixi_manifest/src/manifests/snapshots/pixi_manifest__manifests__workspace__tests__pypi_options_default_feature.snap

@@ -11,4 +11,5 @@ find-links:
 no-build-isolation: []
 index-strategy: ~
 no-build: ~
+dependency-overrides: ~
 no-binary: ~

crates/pixi_manifest/src/manifests/snapshots/pixi_manifest__manifests__workspace__tests__pypy_options_project_and_default_feature.snap

@@ -9,4 +9,5 @@ find-links: ~
 no-build-isolation: []
 index-strategy: ~
 no-build: ~
+dependency-overrides: ~
 no-binary: ~

crates/pixi_manifest/src/pypi/pypi_options.rs

@@ -1,7 +1,9 @@
 use std::{hash::Hash, path::PathBuf};
 
+use indexmap::IndexMap;
 use indexmap::IndexSet;
 use pep508_rs::PackageName;
+use pixi_pypi_spec::{PixiPypiSpec, PypiPackageName};
 use serde::{Serialize, Serializer, ser::SerializeSeq};
 use thiserror::Error;
 use url::Url;
@@ -133,6 +135,8 @@ pub struct PypiOptions {
     pub index_strategy: Option<IndexStrategy>,
     /// Don't build sdist for all or certain packages
     pub no_build: Option<NoBuild>,
+    /// Dependency overrides
+    pub dependency_overrides: Option<IndexMap<PypiPackageName, PixiPypiSpec>>,
     /// Don't use pre-built wheels all or certain packages
     pub no_binary: Option<NoBinary>,
 }
@@ -151,13 +155,15 @@ fn clone_and_deduplicate<'a, I: Iterator<Item = &'a T>, T: Clone + Eq + Hash + '
 }
 
 impl PypiOptions {
+    #[allow(clippy::too_many_arguments)]
     pub fn new(
         index: Option<Url>,
         extra_indexes: Option<Vec<Url>>,
         flat_indexes: Option<Vec<FindLinksUrlOrPath>>,
         no_build_isolation: NoBuildIsolation,
         index_strategy: Option<IndexStrategy>,
         no_build: Option<NoBuild>,
+        dependency_overrides: Option<IndexMap<PypiPackageName, PixiPypiSpec>>,
         no_binary: Option<NoBinary>,
     ) -> Self {
         Self {
@@ -167,6 +173,7 @@ impl PypiOptions {
             no_build_isolation,
             index_strategy,
             no_build,
+            dependency_overrides,
             no_binary,
         }
     }
@@ -271,6 +278,21 @@ impl PypiOptions {
             (None, Some(b)) => Some(b.clone()),
             (None, None) => None,
         };
+        // Set the dependency overrides
+        // notice that default feature comes last in the feature_ext
+        // so we want self overwriting the other
+        // i.e. if same key exists in both, we want the value from `self` to be used
+        // so we extend b with a (a overrides b)
+        let dependency_overrides = match (&self.dependency_overrides, &other.dependency_overrides) {
+            (Some(a), Some(b)) => {
+                let mut overrides = b.clone();
+                overrides.extend(a.into_iter().map(|(k, v)| (k.clone(), v.clone())));
+                Some(overrides)
+            }
+            (Some(a), None) => Some(a.clone()),
+            (None, Some(b)) => Some(b.clone()),
+            (None, None) => None,
+        };
 
         // Set the no-binary option
         let no_binary = match (self.no_binary.as_ref(), other.no_binary.as_ref()) {
@@ -287,6 +309,7 @@ impl PypiOptions {
             no_build_isolation,
             index_strategy,
             no_build,
+            dependency_overrides,
             no_binary,
         })
     }
@@ -441,6 +464,16 @@ mod tests {
             ]),
             index_strategy: None,
             no_build: None,
+            dependency_overrides:Some(IndexMap::from_iter([
+                (
+                    "pkg1".parse().unwrap(),
+                    PixiPypiSpec::RawVersion("==1.0.0".parse().unwrap()),
+                ),
+                (
+                    "pkg2".parse().unwrap(),
+                    PixiPypiSpec::RawVersion("==2.0.0".parse().unwrap()),
+                ),
+            ])),
             no_binary: Default::default(),
         };
 
@@ -455,6 +488,17 @@ mod tests {
             no_build_isolation: NoBuildIsolation::from_iter(["foo".parse().unwrap()]),
             index_strategy: None,
             no_build: Some(NoBuild::All),
+            dependency_overrides: Some(IndexMap::from_iter([
+                (
+                    "pkg1".parse().unwrap(),
+                    PixiPypiSpec::RawVersion("==1.2.0".parse().unwrap()),
+                ),
+                (
+                    "pkg3".parse().unwrap(),
+                    PixiPypiSpec::RawVersion("==3.2.0".parse().unwrap()),
+                ),
+            ])),
+
             no_binary: Default::default(),
         };
 
@@ -550,6 +594,7 @@ mod tests {
             no_build_isolation: NoBuildIsolation::default(),
             index_strategy: None,
             no_build: Default::default(),
+            dependency_overrides: None,
             no_binary: Default::default(),
         };
 
@@ -561,6 +606,7 @@ mod tests {
             no_build_isolation: NoBuildIsolation::default(),
             index_strategy: None,
             no_build: Default::default(),
+            dependency_overrides: None,
             no_binary: Default::default(),
         };
 
@@ -580,6 +626,7 @@ mod tests {
             no_build_isolation: NoBuildIsolation::default(),
             index_strategy: Some(IndexStrategy::FirstIndex),
             no_build: Default::default(),
+            dependency_overrides: None,
             no_binary: Default::default(),
         };
 
@@ -591,6 +638,7 @@ mod tests {
             no_build_isolation: NoBuildIsolation::default(),
             index_strategy: Some(IndexStrategy::UnsafeBestMatch),
             no_build: Default::default(),
+            dependency_overrides: None,
             no_binary: Default::default(),
         };
 

crates/pixi_manifest/src/pypi/snapshots/pixi_manifest__pypi__pypi_options__tests__merge_pypi_options.snap

@@ -16,4 +16,8 @@ no-build-isolation:
   - bar
 index-strategy: ~
 no-build: all
+dependency-overrides:
+  pkg1: "==1.0.0"
+  pkg3: "==3.2.0"
+  pkg2: "==2.0.0"
 no-binary: ~

crates/pixi_manifest/src/toml/pypi_options.rs

@@ -1,7 +1,7 @@
 use std::{path::PathBuf, str::FromStr};
 
 use indexmap::IndexSet;
-use pixi_toml::{TomlEnum, TomlFromStr, TomlWith};
+use pixi_toml::{TomlEnum, TomlFromStr, TomlIndexMap, TomlWith};
 use toml_span::{
     DeserError, ErrorKind, Value,
     de_helpers::{TableHelper, expected},
@@ -124,6 +124,9 @@ impl<'de> toml_span::Deserialize<'de> for PypiOptions {
             .map(TomlEnum::into_inner);
 
         let no_build = th.optional::<NoBuild>("no-build");
+        let dependency_overrides = th
+            .optional::<TomlIndexMap<_, _>>("dependency-overrides")
+            .map(TomlIndexMap::into_inner);
 
         let no_binary = th.optional::<NoBinary>("no-binary");
 
@@ -136,6 +139,7 @@ impl<'de> toml_span::Deserialize<'de> for PypiOptions {
             no_build_isolation,
             index_strategy,
             no_build,
+            dependency_overrides,
             no_binary,
         })
     }
@@ -238,6 +242,7 @@ impl<'de> toml_span::Deserialize<'de> for NoBuildIsolation {
 #[cfg(test)]
 mod test {
     use insta::{assert_debug_snapshot, assert_snapshot};
+    use pixi_pypi_spec::PypiPackageName;
     use pixi_test_utils::format_parse_error;
 
     use super::*;
@@ -262,6 +267,9 @@ mod test {
 
                  [[find-links]]
                  url = "https://flat.index"
+
+                 [dependency-overrides]
+                 numpy = ">=2.0.0"
              "#;
         let deserialized_options: PypiOptions = PypiOptions::from_toml_str(toml_str).unwrap();
         assert_eq!(
@@ -279,6 +287,12 @@ mod test {
                 ]),
                 index_strategy: None,
                 no_build: Default::default(),
+                dependency_overrides: Some(indexmap::IndexMap::from_iter([(
+                    PypiPackageName::from_str("numpy").unwrap(),
+                    pixi_pypi_spec::PixiPypiSpec::RawVersion(
+                        pixi_pypi_spec::VersionOrStar::from_str(">=2.0.0").unwrap()
+                    )
+                )]),),
                 no_binary: Default::default(),
             },
         );

crates/pixi_manifest/src/toml/snapshots/pixi_manifest__toml__pypi_options__test__full.snap

@@ -1,6 +1,5 @@
 ---
 source: crates/pixi_manifest/src/toml/pypi_options.rs
-assertion_line: 299
 expression: options
 ---
 PypiOptions {
@@ -88,6 +87,7 @@ PypiOptions {
     no_build: Some(
         All,
     ),
+    dependency_overrides: None,
     no_binary: Some(
         Packages(
             {

crates/pixi_manifest/src/toml/snapshots/pixi_manifest__toml__pypi_options__test__no_binary_packages.snap

@@ -1,6 +1,5 @@
 ---
 source: crates/pixi_manifest/src/toml/pypi_options.rs
-assertion_line: 317
 expression: options
 ---
 PypiOptions {
@@ -12,6 +11,7 @@ PypiOptions {
     ),
     index_strategy: None,
     no_build: None,
+    dependency_overrides: None,
     no_binary: Some(
         Packages(
             {

crates/pixi_manifest/src/toml/snapshots/pixi_manifest__toml__pypi_options__test__no_build_isolation_boolean.snap

@@ -9,5 +9,6 @@ PypiOptions {
     no_build_isolation: All,
     index_strategy: None,
     no_build: None,
+    dependency_overrides: None,
     no_binary: None,
 }

crates/pixi_manifest/src/toml/snapshots/pixi_manifest__toml__pypi_options__test__no_build_packages.snap

@@ -19,5 +19,6 @@ PypiOptions {
             },
         ),
     ),
+    dependency_overrides: None,
     no_binary: None,
 }

crates/pixi_pypi_spec/src/name.rs

@@ -1,4 +1,5 @@
 use pep508_rs::{InvalidNameError, PackageName};
+use serde::{Serialize, Serializer};
 use std::{borrow::Borrow, str::FromStr};
 
 /// A package name for Pypi that also stores the source version of the name.
@@ -39,6 +40,15 @@ impl FromStr for PypiPackageName {
     }
 }
 
+impl Serialize for PypiPackageName {
+    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
+    where
+        S: Serializer,
+    {
+        self.as_source().serialize(serializer)
+    }
+}
+
 impl PypiPackageName {
     pub fn from_normalized(normalized: PackageName) -> Self {
         Self {

docs/overrides/override.md

@@ -0,0 +1,66 @@
+## Overview
+
+Sometimes our direct dependency declares outdated intermediate dependency or is too tight to solve with other direct dependencies. In this case, we can override the intermediate dependency in our `pyproject.toml`or `pixi.toml` file.
+
+> [!Note] This option is not recommended unless you know what you are doing, as uv will ignore all the version constraints of the dependency and use the version you specified.
+
+## Example
+### Override a dependency version
+```toml
+# pyproject.toml
+[tool.pixi.pypi-options.dependency-overrides]
+numpy = ">=2.0.0"
+```
+or in `pixi.toml`:
+
+```toml
+# pixi.toml
+[pypi-options.dependency-overrides]
+numpy = ">=2.0.0"
+```
+This will override the version of `numpy` used by all dependencies to be at least `2.0.0`, regardless of what the dependencies specify.
+This is useful if you need a specific version of a library that is not compatible with the versions specified by your dependencies.
+
+### Override a dependency version in a specific feature
+it can also be specified in feature level,
+```toml
+[features.dev.pypi-options.dependency-overrides]
+numpy = ">=2.0.0"
+```
+This will override the version of `numpy` used by all dependencies in the `dev` feature to be at least `2.0.0`, regardless of what the dependencies specify when the `dev` feature is enabled.
+
+### Interact with other overrides
+For a specific environment, all the `dependency-overrides` defined in different features will be combined in the order they were when defining the environment.
+
+If the same dependency is overridden multiple times, we'll use the override from the **prior** feature in that environment.
+
+Also, the default feature will always come, and come last in the list of all overrides.
+
+```toml
+# pixi.toml
+[pypi-options]
+dependency-overrides = { numpy = ">=2.1.0" }
+
+[pypi-dependencies]
+numpy = ">=1.25.0"
+
+[feature.dev.pypi-options.dependency-overrides]
+numpy = "==2.0.0"
+
+[feature.outdated.pypi-options.dependency-overrides]
+numpy = "==1.21.0"
+
+[environments]
+dev = ["dev"]
+outdated = ["outdated"]
+conflict_a=["outdated", "dev"]
+conflict_b=["dev","outdated"]
+```
+the following constrains are merged out:
+default: `numpy >= 2.1.0`
+dev: `numpy == 2.0.0`
+outdated: `numpy == 1.21.0`
+conflict_a: `numpy == 1.21.0` (from `outdated`)
+conflict_b: `numpy == 2.0.0` (from `dev`)
+
+This may contrast with the intuition that all overrides are applied and combined to a result, but it is done this way to avoid conflicts and confusion. Since users are granted fully control over the overrides, it is up to ourselves to choose the right overrides for the environment.

mkdocs.yml

@@ -172,6 +172,7 @@ nav:
   - Advanced:
       - Channel Logic: advanced/channel_logic.md
       - Info Command: advanced/explain_info_command.md
+      - Dependency Overrides: overrides/override.md
       - Shebang: advanced/shebang.md
       - Shell: advanced/pixi_shell.md
   - Reference:

schema/examples/valid/full.toml

@@ -19,6 +19,8 @@ version = "0.1.0"
 
 [project.pypi-options]
 no-build = false
+[project.pypi-options.dependency-overrides]
+numpy = { version = ">=1.21.0" }
 
 [package]
 # Inherit the name and version the workspace
@@ -125,6 +127,7 @@ test = "*"
 test = "*"
 
 [feature.yes-build.pypi-options]
+dependency-overrides = { numpy = ">=2.0.0" }
 no-build = true
 
 [feature.prod]

schema/model.py

@@ -605,6 +605,13 @@ class PyPIOptions(StrictBaseModel):
         description="Packages that should NOT be built",
         examples=["true", "false"],
     )
+    dependency_overrides: dict[PyPIPackageName, PyPIRequirement] | None = Field(
+        None,
+        description="A list of PyPI dependencies that override the resolved dependencies",
+        examples=[
+            {"numpy": ">=1.21.0"},
+        ],
+    )
     no_binary: bool | list[PyPIPackageName] | None = Field(
         None,
         description="Don't use pre-built wheels for these packages",