Trace dependencies in Spec (PR 2)

example/README.md

@@ -67,7 +67,13 @@ This would be the same as running `unidep merge --name myenv --verbose`:
 📄 Parsing `setup_py_project/requirements.yaml`
 📄 Parsing `../setuptools_project` from `local_dependencies`
 📄 Parsing `setup_py_project/../setuptools_project/requirements.yaml`
+📄 Parsing `../hatch_project[test]` from `local_dependencies`
+📄 Parsing `setup_py_project/../setuptools_project/../hatch_project/requirements.yaml[test]`
+📄 Moving `test` optional dependencies to main dependencies for `setup_py_project/../setuptools_project/../hatch_project/requirements.yaml[test]`
 📄 Parsing `setuptools_project/requirements.yaml`
+📄 Parsing `../hatch_project[test]` from `local_dependencies`
+📄 Parsing `setuptools_project/../hatch_project/requirements.yaml[test]`
+📄 Moving `test` optional dependencies to main dependencies for `setuptools_project/../hatch_project/requirements.yaml[test]`
 📝 Generating environment file at `environment.yaml`
 📝 Environment file generated successfully.
 ✅ Generated environment file at `environment.yaml` from `hatch2_project/pyproject.toml`, `hatch_project/requirements.yaml`, `pyproject_toml_project/pyproject.toml`, `setup_py_project/requirements.yaml`, `setuptools_project/requirements.yaml`
@@ -110,11 +116,11 @@ Using `unidep` for installation offers a more comprehensive approach. It handles
 $ unidep install --dry-run -e ./setup_py_project
 📦 Installing conda dependencies with `conda install --yes --override-channels --channel conda-forge pandas">=1,<3" adaptive">=0.15.0, <2.0.0" pfapack packaging adaptive-scheduler numpy">=1.21" hpc05 pexpect pytest pytest-cov`
 
-📦 Installing pip dependencies with `/opt/hostedtoolcache/Python/3.13.1/x64/bin/python -m pip install yaml2bib rsync-time-machine slurm-usage pyyaml aiokef markdown-code-runner numthreads unidep`
+📦 Installing pip dependencies with `/opt/hostedtoolcache/Python/3.13.2/x64/bin/python -m pip install yaml2bib rsync-time-machine slurm-usage pyyaml aiokef markdown-code-runner numthreads unidep`
 
 📝 Found local dependencies: {'setup_py_project': ['hatch_project', 'setuptools_project']}
 
-📦 Installing project with `/opt/hostedtoolcache/Python/3.13.1/x64/bin/python -m pip install --no-deps -e /home/runner/work/unidep/unidep/example/hatch_project -e /home/runner/work/unidep/unidep/example/setuptools_project -e ./setup_py_project`
+📦 Installing project with `/opt/hostedtoolcache/Python/3.13.2/x64/bin/python -m pip install --no-deps -e /home/runner/work/unidep/unidep/example/hatch_project -e /home/runner/work/unidep/unidep/example/setuptools_project -e ./setup_py_project`
 
 ```
 
@@ -157,11 +163,11 @@ unidep install-all -e
 $ unidep install-all -e --dry-run
 📦 Installing conda dependencies with `conda install --yes --override-channels --channel conda-forge adaptive-scheduler numpy">=1.21" hpc05 pandas">=1,<3" pexpect adaptive">=0.15.0, <2.0.0" pfapack packaging pytest pytest-cov`
 
-📦 Installing pip dependencies with `/opt/hostedtoolcache/Python/3.13.1/x64/bin/python -m pip install unidep markdown-code-runner numthreads yaml2bib rsync-time-machine slurm-usage pyyaml aiokef`
+📦 Installing pip dependencies with `/opt/hostedtoolcache/Python/3.13.2/x64/bin/python -m pip install unidep markdown-code-runner numthreads yaml2bib rsync-time-machine slurm-usage pyyaml aiokef`
 
 📝 Found local dependencies: {'pyproject_toml_project': ['hatch_project'], 'setup_py_project': ['hatch_project', 'setuptools_project'], 'setuptools_project': ['hatch_project']}
 
-📦 Installing project with `/opt/hostedtoolcache/Python/3.13.1/x64/bin/python -m pip install --no-deps -e ./hatch2_project -e ./hatch_project -e ./pyproject_toml_project -e ./setup_py_project -e ./setuptools_project`
+📦 Installing project with `/opt/hostedtoolcache/Python/3.13.2/x64/bin/python -m pip install --no-deps -e ./hatch2_project -e ./hatch_project -e ./pyproject_toml_project -e ./setup_py_project -e ./setuptools_project`
 
 ```
 

tests/test_parse_yaml_local_dependencies.py

@@ -81,6 +81,66 @@ def test_circular_local_dependencies(
     assert len(resolved["adaptive-scheduler"][None]) == 2
 
 
+@pytest.mark.parametrize("toml_or_yaml", ["toml", "yaml"])
+def test_circular_local_dependencies_with_common(
+    toml_or_yaml: Literal["toml", "yaml"],
+    tmp_path: Path,
+) -> None:
+    project1 = tmp_path / "project1"
+    project1.mkdir(exist_ok=True, parents=True)
+    project2 = tmp_path / "project2"
+    project2.mkdir(exist_ok=True, parents=True)
+
+    r1 = project1 / "requirements.yaml"
+    r2 = project2 / "requirements.yaml"
+    r1.write_text(
+        textwrap.dedent(
+            """\
+            dependencies:
+                - adaptive-scheduler
+            local_dependencies:
+                - ../project2
+                - ../project2  # duplicate include (shouldn't affect the result)
+            """,
+        ),
+    )
+    # Test with old `includes` name
+    r2.write_text(
+        textwrap.dedent(
+            """\
+            dependencies:
+                - adaptive
+            includes:  # `local_dependencies` was called `includes` in <=0.41.0
+                - ../project1
+                - ../common-requirements.yaml
+            """,
+        ),
+    )
+
+    # Add a common requirements file
+    common_requirements = tmp_path / "common-requirements.yaml"
+    common_requirements.write_text("dependencies: [unidep]")
+
+    r1 = maybe_as_toml(toml_or_yaml, r1)
+    # Only convert r1 to toml, not r2, because we want to test that
+    with pytest.warns(DeprecationWarning, match="is deprecated since 0.42.0"):
+        requirements = parse_requirements(r1, r2, verbose=False)
+    # Both will be duplicated because of the circular dependency
+    # but `resolve_conflicts` will remove the duplicates
+    assert len(requirements.requirements["adaptive"]) == 4
+    assert len(requirements.requirements["adaptive-scheduler"]) == 2
+    unidep = requirements.requirements["unidep"]
+    assert len(unidep) == 4
+    resolved = resolve_conflicts(requirements.requirements, requirements.platforms)
+    assert len(resolved["adaptive"]) == 1
+    assert len(resolved["adaptive"][None]) == 2
+    assert len(resolved["adaptive-scheduler"]) == 1
+    assert len(resolved["adaptive-scheduler"][None]) == 2
+    unidep_origin = resolved["unidep"][None]["conda"].origin
+    # Should have all 3 files in its origin
+    assert len(unidep_origin) == 3
+
+
 @pytest.mark.parametrize("toml_or_yaml", ["toml", "yaml"])
 def test_parse_local_dependencies(
     toml_or_yaml: Literal["toml", "yaml"],

tests/test_project_dependency_handling.py

@@ -12,6 +12,7 @@
     parse_requirements,
 )
 from unidep.platform_definitions import Spec
+from unidep.utils import PathWithExtras
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -100,33 +101,72 @@ def test_project_dependency_handling_in_pyproject_toml(
     )
 
     requirements = parse_requirements(p)
-
+    ori = (PathWithExtras(p, []),)
     expected = {
         "python-graphviz": [
-            Spec(name="python-graphviz", which="conda", identifier="17e5d607"),
+            Spec(
+                name="python-graphviz",
+                which="conda",
+                identifier="17e5d607",
+                origin=ori,
+            ),
         ],
         "graphviz": [
-            Spec(name="graphviz", which="pip", identifier="17e5d607"),
-            Spec(name="graphviz", which="conda", identifier="5eb93b8c"),
+            Spec(name="graphviz", which="pip", identifier="17e5d607", origin=ori),
+            Spec(name="graphviz", which="conda", identifier="5eb93b8c", origin=ori),
         ],
     }
     if project_dependency_handling == "pip-only":
         expected.update(
             {
-                "requests": [Spec(name="requests", which="pip", identifier="08fd8713")],
-                "pandas": [Spec(name="pandas", which="pip", identifier="9e467fa1")],
+                "requests": [
+                    Spec(
+                        name="requests",
+                        which="pip",
+                        identifier="08fd8713",
+                        origin=ori,
+                    ),
+                ],
+                "pandas": [
+                    Spec(
+                        name="pandas",
+                        which="pip",
+                        identifier="9e467fa1",
+                        origin=ori,
+                    ),
+                ],
             },
         )
     elif project_dependency_handling == "same-name":
         expected.update(
             {
                 "requests": [
-                    Spec(name="requests", which="conda", identifier="08fd8713"),
-                    Spec(name="requests", which="pip", identifier="08fd8713"),
+                    Spec(
+                        name="requests",
+                        which="conda",
+                        identifier="08fd8713",
+                        origin=ori,
+                    ),
+                    Spec(
+                        name="requests",
+                        which="pip",
+                        identifier="08fd8713",
+                        origin=ori,
+                    ),
                 ],
                 "pandas": [
-                    Spec(name="pandas", which="conda", identifier="9e467fa1"),
-                    Spec(name="pandas", which="pip", identifier="9e467fa1"),
+                    Spec(
+                        name="pandas",
+                        which="conda",
+                        identifier="9e467fa1",
+                        origin=ori,
+                    ),
+                    Spec(
+                        name="pandas",
+                        which="pip",
+                        identifier="9e467fa1",
+                        origin=ori,
+                    ),
                 ],
             },
         )