Fix install_command ignored from TOML config (#3724)

## Summary

Fixes #3574 — custom `install_command` was silently ignored when
specified in `tox.toml` or `pyproject.toml`, always falling back to the
default pip install command.

### Root cause

Two bugs conspired to produce this behavior:

1. **`get_base_sections` placed base sections under the `env`
namespace.** It used `test_env(b)` which wraps the section name under
`env.*`, but `env_run_base` and `env_pkg_base` are top-level sections —
`[env_run_base]` in `tox.toml` and `[tool.tox.env_run_base]` in
`pyproject.toml`. This caused the loader to navigate to
`env.env_run_base` (which doesn't exist) and return `None`, so no
settings from `env_run_base` were applied.

2. **The TOML replacement engine raised on unknown `{...}`
placeholders.** When `Unroll` processed strings like `{packages}` inside
an `install_command` array, `TomlReplaceLoader` tried to resolve
`packages` as a config key, failed with `KeyError`, and raised — causing
the config loader to fall through to the default. The INI loader's
equivalent (`ReplaceReferenceIni`) returns `None` for unresolvable
references (keeping the original text), matching the documented contract
of `ReplaceReference.__call__`.

### Changes

- **`toml_pyproject.py`**: `get_base_sections` now constructs sections
with the core prefix (or `None`), correctly placing
`env_run_base`/`env_pkg_base` at the top level rather than under `env`.
- **`_replace.py`**: `TomlReplaceLoader.__call__` returns `None`
(instead of raising) when a `KeyError` occurs with no default,
consistent with the INI loader and the `ReplaceReference` protocol.
- **Test**: Parameterized test verifying `install_command` is respected
from both `tox.toml` and `pyproject.toml`.
- **Changelog**: Added `docs/changelog/3574.bugfix.rst`.

### Test plan

- [x] New parameterized test (`tox.toml` and `pyproject.toml` variants)
- [x] All 27 show_config tests pass
- [x] All 143 config/loader/source tests pass
- [x] All 49 pip install tests pass

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

docs/changelog/3574.bugfix.rst

@@ -0,0 +1,2 @@
+Fix custom ``install_command`` being ignored when specified in TOML configuration (``tox.toml``/``pyproject.toml``) - by
+:user:`Fridayai700`.

src/tox/config/loader/toml/_replace.py

@@ -123,6 +123,7 @@ def __call__(self, value: str, conf_args: ConfigLoadArgs) -> str | None:
                     default = settings["default"]
                     if default is not None:
                         return default
+                    return None  # keep original text, consistent with ini loader behavior
                 raise exception
         return value
 

src/tox/config/source/toml_pyproject.py

@@ -55,26 +55,16 @@ def run_env_base(cls) -> str:
 
     @property
     def keys(self) -> Iterable[str]:
-        # Build keys from prefix and name components directly, rather than
-        # splitting the joined key on SEP.  This preserves dots that are part
-        # of the name (e.g. environment name "py3.11") instead of treating
-        # them as path separators.
-        prefix = self._prefix
-        name = self._name
+        # Build keys from prefix + name directly, preserving dots in names (e.g. env "py3.11").
+        prefix, name = self._prefix, self._name
         if prefix is None and not name:
             return []
-        prefix_parts: list[str] = prefix.split(self.SEP) if prefix else []
-        # Strip the global PREFIX (e.g. ("tool", "tox")) from the front
-        if (
-            self.PREFIX
-            and len(prefix_parts) >= len(self.PREFIX)
-            and tuple(prefix_parts[: len(self.PREFIX)]) == self.PREFIX
-        ):
-            prefix_parts = prefix_parts[len(self.PREFIX) :]
-        result = prefix_parts
+        parts: list[str] = prefix.split(self.SEP) if prefix else []
+        if self.PREFIX and len(parts) >= len(self.PREFIX) and tuple(parts[: len(self.PREFIX)]) == self.PREFIX:
+            parts = parts[len(self.PREFIX) :]  # strip global PREFIX (e.g. ("tool", "tox"))
         if name:
-            result.append(name)
-        return result
+            parts.append(name)
+        return parts
 
 
 class TomlPyProjectSection(TomlSection):
@@ -128,7 +118,7 @@ def get_loader(self, section: Section, override_map: OverrideMap) -> Loader[Any]
 
     def envs(self, core_conf: CoreConfigSet) -> Iterator[str]:
         yield from core_conf["env_list"]
-        yield from [i.name for i in self.sections()]
+        yield from [section.name for section in self.sections()]
 
     def sections(self) -> Iterator[Section]:
         for env_name in self._our_content.get(self._Section.ENV, {}):
@@ -138,7 +128,10 @@ def sections(self) -> Iterator[Section]:
             yield self._Section.test_env(env_name)
 
     def get_base_sections(self, base: list[str], in_section: Section) -> Iterator[Section]:  # noqa: ARG002
-        yield from [self._Section.test_env(b) for b in base]
+        core_prefix = self._Section.core_prefix()
+        strip = f"{core_prefix}{self._Section.SEP}" if core_prefix else ""
+        for entry in base:
+            yield self._Section(prefix=core_prefix or None, name=entry.removeprefix(strip))
 
     def get_tox_env_section(self, item: str) -> tuple[Section, list[str], list[str]]:
         return self._Section.test_env(item), [self._Section.run_env_base()], [self._Section.package_env_base()]

tests/session/cmd/test_show_config.py

@@ -9,6 +9,7 @@
 import pytest
 
 from tox.config.types import Command
+from tox.execute.request import shell_cmd
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -112,6 +113,41 @@ def test_show_config_empty_install_command_exception(tox_project: ToxProjectCrea
     assert txt in outcome.out
 
 
+@pytest.mark.parametrize(
+    ("filename", "content"),
+    [
+        pytest.param(
+            "tox.toml",
+            """
+            [env_run_base]
+            package = "skip"
+            install_command = ["echo", "CUSTOM", "{packages}"]
+            commands = [["python", "-c", "pass"]]
+            """,
+            id="tox.toml",
+        ),
+        pytest.param(
+            "pyproject.toml",
+            """
+            [tool.tox]
+            env_list = ["py"]
+            [tool.tox.env_run_base]
+            package = "skip"
+            install_command = ["echo", "CUSTOM", "{packages}"]
+            commands = [["python", "-c", "pass"]]
+            """,
+            id="pyproject.toml",
+        ),
+    ],
+)
+def test_show_config_install_command_toml(tox_project: ToxProjectCreator, filename: str, content: str) -> None:
+    project = tox_project({filename: content})
+    outcome = project.run("c", "-k", "install_command")
+    outcome.assert_success()
+    expected_cmd = shell_cmd(["echo", "CUSTOM", "{packages}"])
+    assert f"install_command = {expected_cmd}" in outcome.out
+
+
 def test_show_config_invalid_python_exit_code(tox_project: ToxProjectCreator) -> None:
     project = tox_project(
         {