Preliminary support for Pixi projects using pyproject.toml

README.md

@@ -124,7 +124,7 @@ The `--deps` option tells FawltyDeps where to look for your project's declared
 dependencies. A number of file formats are supported:
 
 - `*requirements*.txt` and `*requirements*.in`
-- `pyproject.toml` (following PEP 621 or Poetry conventions)
+- `pyproject.toml` (following PEP 621, Poetry, or Pixi conventions)
 - `setup.py` (only limited support for simple files with a single `setup()`
   call and no computation involved for setting the `install_requires` and
   `extras_require` arguments)

fawltydeps/extract_declared_dependencies.py

@@ -2,6 +2,7 @@
 
 import ast
 import configparser
+import contextlib
 import logging
 import re
 import sys
@@ -57,10 +58,15 @@ def parse_requirements_txt(path: Path) -> Iterator[DeclaredDependency]:
     https://pip.pypa.io/en/stable/reference/requirements-file-format/.
     """
     source = Location(path)
-    for dep in RequirementsFile.from_file(path).requirements:
+    parsed = RequirementsFile.from_file(path)
+    for dep in parsed.requirements:
         if dep.name:
             yield DeclaredDependency(dep.name, source)
 
+    if parsed.invalid_lines and logger.isEnabledFor(logging.DEBUG):
+        error_messages = "\n".join(line.dumps() for line in parsed.invalid_lines)
+        logger.debug(f"Invalid lines found in {source}:\n{error_messages}")
+
 
 def parse_setup_py(path: Path) -> Iterator[DeclaredDependency]:  # noqa: C901
     """Extract dependencies (package names) from setup.py.
@@ -239,6 +245,60 @@ def parse_extra(contents: TomlData, src: Location) -> NamedLocations:
     yield from parse_pyproject_elements(poetry_config, source, "Poetry", fields_parsers)
 
 
+def parse_pixi_pyproject_dependencies(
+    pixi_config: TomlData, source: Location
+) -> Iterator[DeclaredDependency]:
+    """Extract dependencies from `tool.pixi` fields in a pyproject.toml.
+
+    - [tool.pixi.dependencies] contains mandatory Conda deps
+    - [tool.pixi.pypi-dependencies] contains mandatory PyPI deps
+    - [tool.pixi.feature.<NAME>.dependencies] contains optional Conda deps
+    - [tool.pixi.feature.<NAME>.pypi-dependencies] contains optional PyPI deps
+
+    NOTE: We do not currently differentiate between Conda dependencies and PyPI
+    dependencies, meaning that we assume that a Conda dependency named FOO will
+    map one-to-one to a Python package named FOO. This is certainly not true for
+    Conda dependencies that are not Python packages, and it probably isn't even
+    true for all Conda dependencies that do indeed include Python packages.
+    """
+
+    def parse_main(contents: TomlData, src: Location) -> NamedLocations:
+        return (
+            (req, src)
+            for req in contents["dependencies"].keys()  # noqa: SIM118
+            if req != "python"
+        )
+
+    def parse_pypi(contents: TomlData, src: Location) -> NamedLocations:
+        return (
+            (req, src)
+            for req in contents["pypi-dependencies"].keys()  # noqa: SIM118
+        )
+
+    def parse_feature(contents: TomlData, src: Location) -> NamedLocations:
+        return (
+            (req, src)
+            for feature in contents["feature"].values()
+            for req in feature.get("dependencies", {}).keys()  # noqa: SIM118
+            if req != "python"
+        )
+
+    def parse_feature_pypi(contents: TomlData, src: Location) -> NamedLocations:
+        return (
+            (req, src)
+            for feature in contents["feature"].values()
+            for req in feature.get("pypi-dependencies", {}).keys()  # noqa: SIM118
+        )
+
+    fields_parsers = [
+        ("main", parse_main),
+        ("pypi", parse_pypi),
+        ("feature", parse_feature),
+        ("feature pypi", parse_feature_pypi),
+    ]
+    yield from parse_pyproject_elements(pixi_config, source, "Pixi", fields_parsers)
+
+
 def parse_pep621_pyproject_contents(  # noqa: C901
     parsed_contents: TomlData, source: Location
 ) -> Iterator[DeclaredDependency]:
@@ -351,12 +411,35 @@ def parse_pyproject_toml(path: Path) -> Iterator[DeclaredDependency]:
     We currently handle:
     - PEP 621 core and dynamic metadata fields.
     - Poetry-specific metadata in `tool.poetry` sections.
+    - Pixi-specific metadata in `tool.pixi` sections.
     """
     source = Location(path)
     with path.open("rb") as tomlfile:
         parsed_contents = tomllib.load(tomlfile)
 
-    yield from parse_pep621_pyproject_contents(parsed_contents, source)
+    skip = set()
+
+    # Skip dependencies onto self (such as Pixi's "editable mode" hack)
+    with contextlib.suppress(KeyError):
+        skip.add(parsed_contents["project"]["name"])
+
+    # In Pixi, dependencies from [tool.pixi.dependencies] _override_
+    # dependencies from PEP621 dependencies with the same name.
+    # Therefore, parse the Pixi sections first, and skip dependencies with the
+    # same name in the PEP621 section below.
+    if "pixi" in parsed_contents.get("tool", {}):
+        for dep in parse_pixi_pyproject_dependencies(
+            parsed_contents["tool"]["pixi"], source
+        ):
+            if dep.name not in skip:
+                skip.add(dep.name)
+                yield dep
+    else:
+        logger.debug("%s does not contain [tool.pixi].", source)
+
+    for dep in parse_pep621_pyproject_contents(parsed_contents, source):
+        if dep.name not in skip:
+            yield dep
 
     if "poetry" in parsed_contents.get("tool", {}):
         yield from parse_poetry_pyproject_dependencies(

fawltydeps/main.py

@@ -4,10 +4,10 @@
 notebooks (*.ipynb).
 
 Supports finding dependency declarations in *requirements*.txt (and .in) files,
-pyproject.toml (following PEP 621 or Poetry conventions), setup.cfg, as well as
-limited support for setup.py files with a single, simple setup() call and
-minimal computation involved in setting the install_requires and extras_require
-arguments.
+pyproject.toml (following PEP 621, Poetry, or Pixi conventions), setup.cfg, as
+well as limited support for setup.py files with a single, simple setup() call
+and minimal computation involved in setting the install_requires and
+extras_require arguments.
 """
 
 from __future__ import annotations

tests/sample_projects/pixi_pyproject_example/.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

tests/sample_projects/pixi_pyproject_example/.gitignore

@@ -0,0 +1,3 @@
+# pixi environments
+.pixi
+*.egg-info

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/bin/python

@@ -0,0 +1 @@
+python3.12

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/bin/python3

@@ -0,0 +1 @@
+python3.12

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/bin/python3-config

@@ -0,0 +1 @@
+python3.12-config

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/bin/python3.1

@@ -0,0 +1 @@
+python3.12

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/conda-meta/history

@@ -0,0 +1 @@
+// not relevant for pixi but for `conda run -p`

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/conda-meta/pixi

@@ -0,0 +1,5 @@
+{
+  "manifest_path": "/home/jherland/code/fawltydeps/tests/sample_projects/pixi_pyproject_example/pyproject.toml",
+  "environment_name": "default",
+  "pixi_version": "0.27.1"
+}

tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/conda-meta/pixi_env_prefix

@@ -0,0 +1 @@
+/home/jherland/code/fawltydeps/tests/sample_projects/pixi_pyproject_example/.pixi/envs/default/conda-meta