From 967e2cf164d1dfc1687034858c5db0b94bdddccd Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 29 Mar 2025 06:31:36 +0530
Subject: [PATCH 01/32] Support building without isolation

---
 pyodide_build/cli/build.py         |  73 ++++++++++++++++++--
 pyodide_build/out_of_tree/build.py |  11 ++-
 pyodide_build/pypabuild.py         | 106 ++++++++++++++++++++++++++---
 3 files changed, 172 insertions(+), 18 deletions(-)

diff --git a/pyodide_build/cli/build.py b/pyodide_build/cli/build.py
index 10a3cb69..a312cc9a 100644
--- a/pyodide_build/cli/build.py
+++ b/pyodide_build/cli/build.py
@@ -46,6 +46,8 @@ def pypi(
     output_directory: Path,
     exports: str,
     config_settings: ConfigSettingsType,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
 ) -> Path:
     """Fetch a wheel from pypi, or build from source if none available."""
     with tempfile.TemporaryDirectory() as tmpdir:
@@ -65,6 +67,8 @@ def pypi(
             output_directory,
             convert_exports(exports),
             config_settings,
+            isolation=isolation,
+            skip_dependency_check=skip_dependency_check,
         )
         return built_wheel
 
@@ -86,6 +90,8 @@ def url(
     output_directory: Path,
     exports: str,
     config_settings: ConfigSettingsType,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
 ) -> Path:
     """Fetch a wheel or build sdist from url."""
     with tempfile.TemporaryDirectory() as tmpdir:
@@ -102,7 +108,12 @@ def url(
             # unzipped into subfolder
             builddir = files[0]
         wheel_path = build.run(
-            builddir, output_directory, convert_exports(exports), config_settings
+            builddir,
+            output_directory,
+            convert_exports(exports),
+            config_settings,
+            isolation=isolation,
+            skip_dependency_check=skip_dependency_check,
         )
         return wheel_path
 
@@ -112,10 +123,17 @@ def source(
     output_directory: Path,
     exports: str,
     config_settings: ConfigSettingsType,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
 ) -> Path:
     """Use pypa/build to build a Python package from source"""
     built_wheel = build.run(
-        source_location, output_directory, convert_exports(exports), config_settings
+        source_location,
+        output_directory,
+        convert_exports(exports),
+        config_settings,
+        isolation=isolation,
+        skip_dependency_check=skip_dependency_check,
     )
     return built_wheel
 
@@ -164,6 +182,19 @@ def main(
     compression_level: int = typer.Option(
         6, help="Compression level to use for the created zip file"
     ),
+    no_isolation: bool = typer.Option(
+        False,
+        "--no-isolation",
+        "-n",
+        help="Disable building the project in an isolated virtual environment. "
+        "Build dependencies must be installed separately when this option is used",
+    ),
+    skip_dependency_check: bool = typer.Option(
+        False,
+        "--skip-dependency-check",
+        "-x",
+        help="Do not check that build dependencies are installed",
+    ),
     config_setting: Optional[list[str]] = typer.Option(  # noqa: UP007 typer does not accept list[str] | None yet.
         None,
         "--config-setting",
@@ -232,6 +263,8 @@ def main(
                 # dependencies? Not sure this makes sense...
                 convert_exports(exports),
                 config_settings,
+                isolation=not no_isolation,
+                skip_dependency_check=skip_dependency_check,
                 output_lockfile=output_lockfile,
             )
         except BaseException as e:
@@ -247,17 +280,43 @@ def main(
             source_location = source_location[0 : source_location.find("[")]
     if not source_location:
         # build the current folder
-        wheel = source(Path.cwd(), outpath, exports, config_settings)
+        wheel = source(
+            Path.cwd(),
+            outpath,
+            exports,
+            config_settings,
+            isolation=not no_isolation,
+            skip_dependency_check=skip_dependency_check,
+        )
     elif source_location.find("://") != -1:
-        wheel = url(source_location, outpath, exports, config_settings)
+        wheel = url(
+            source_location,
+            outpath,
+            exports,
+            config_settings,
+            isolation=not no_isolation,
+            skip_dependency_check=skip_dependency_check,
+        )
     elif Path(source_location).is_dir():
         # a folder, build it
         wheel = source(
-            Path(source_location).resolve(), outpath, exports, config_settings
+            Path(source_location).resolve(),
+            outpath,
+            exports,
+            config_settings,
+            isolation=not no_isolation,
+            skip_dependency_check=skip_dependency_check,
         )
     elif source_location.find("/") == -1:
         # try fetch or build from pypi
-        wheel = pypi(source_location, outpath, exports, config_settings)
+        wheel = pypi(
+            source_location,
+            outpath,
+            exports,
+            config_settings,
+            isolation=not no_isolation,
+            skip_dependency_check=skip_dependency_check,
+        )
     else:
         raise RuntimeError(f"Couldn't determine source type for {source_location}")
     # now build deps for wheel
@@ -271,6 +330,8 @@ def main(
                 # dependencies? Not sure this makes sense...
                 convert_exports(exports),
                 config_settings,
+                isolation=not no_isolation,
+                skip_dependency_check=skip_dependency_check,
                 output_lockfile=output_lockfile,
                 compression_level=compression_level,
             )
diff --git a/pyodide_build/out_of_tree/build.py b/pyodide_build/out_of_tree/build.py
index 6d450849..951111ef 100644
--- a/pyodide_build/out_of_tree/build.py
+++ b/pyodide_build/out_of_tree/build.py
@@ -13,6 +13,8 @@ def run(
     outdir: Path,
     exports: _BuildSpecExports,
     config_settings: ConfigSettingsType,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
 ) -> Path:
     outdir = outdir.resolve()
     cflags = build_env.get_build_flag("SIDE_MODULE_CFLAGS")
@@ -39,7 +41,14 @@ def run(
     )
 
     with build_env_ctx as env:
-        built_wheel = pypabuild.build(srcdir, outdir, env, config_settings)
+        built_wheel = pypabuild.build(
+            srcdir,
+            outdir,
+            env,
+            config_settings,
+            isolation=isolation,
+            skip_dependency_check=skip_dependency_check,
+        )
 
     wheel_path = Path(built_wheel)
     if "emscripten" in wheel_path.name:
diff --git a/pyodide_build/pypabuild.py b/pyodide_build/pypabuild.py
index 392b0c09..a43f071a 100644
--- a/pyodide_build/pypabuild.py
+++ b/pyodide_build/pypabuild.py
@@ -5,6 +5,16 @@
 import sys
 import traceback
 from collections.abc import Callable, Iterator, Mapping, Sequence
+
+
+# A helper function from pypa/build/__main__.py since
+# it's not in the vendorized code we have
+# TODO: we should move this to a new file. it's out of place
+# between the other imports ;-)
+def _format_dep_chain(dep_chain: Sequence[str]) -> str:
+    return " -> ".join(dep.partition(";")[0].strip() for dep in dep_chain)
+
+
 from contextlib import contextmanager
 from itertools import chain
 from pathlib import Path
@@ -54,7 +64,7 @@
 
 def _gen_runner(
     cross_build_env: Mapping[str, str],
-    isolated_build_env: _DefaultIsolatedEnv,
+    isolated_build_env: _DefaultIsolatedEnv = None,
 ) -> Callable[[Sequence[str], str | None, Mapping[str, str] | None], None]:
     """
     This returns a slightly modified version of default subprocess runner that pypa/build uses.
@@ -79,7 +89,15 @@ def _runner(cmd, cwd=None, extra_environ=None):
 
         # Some build dependencies like cmake, meson installs binaries to this directory
         # and we should add it to the PATH so that they can be found.
-        env["BUILD_ENV_SCRIPTS_DIR"] = isolated_build_env.scripts_dir
+        if isolated_build_env:
+            env["BUILD_ENV_SCRIPTS_DIR"] = isolated_build_env.scripts_dir
+        else:
+            # For non-isolated builds, set a fallback path or use the current Python path
+            import sysconfig
+
+            scripts_dir = sysconfig.get_path("scripts")
+            env["BUILD_ENV_SCRIPTS_DIR"] = scripts_dir
+
         env["PATH"] = f"{cross_build_env['COMPILER_WRAPPER_DIR']}:{env['PATH']}"
         # For debugging: Uncomment the following line to print the build command
         # print("Build backend call:", " ".join(str(x) for x in cmd), file=sys.stderr)
@@ -191,6 +209,45 @@ def _build_in_isolated_env(
             )
 
 
+def _build_in_current_env(
+    build_env: Mapping[str, str],
+    srcdir: Path,
+    outdir: str,
+    distribution: Literal["sdist", "wheel"],
+    config_settings: ConfigSettingsType,
+    skip_dependency_check: bool = False,
+) -> str:
+    with common.replace_env(build_env):
+        # Setup sysconfigdata path in environment
+        sysconfigdata_name = get_build_flag("SYSCONFIG_NAME")
+        sysconfig_dir = Path(get_build_flag("TARGETINSTALLDIR")) / "sysconfigdata"
+        env = os.environ.copy()
+        env["_PYTHON_SYSCONFIGDATA_NAME"] = sysconfigdata_name
+        env["PYTHONPATH"] = f"{str(sysconfig_dir)}:{env.get('PYTHONPATH', '')}"
+
+        with common.replace_env(env):
+            builder = _ProjectBuilder(srcdir, runner=_gen_runner(build_env))
+
+            if not skip_dependency_check:
+                missing = builder.check_dependencies(
+                    distribution, config_settings or {}
+                )
+                if missing:
+                    dependencies = "".join(
+                        "\n\t" + dep
+                        for deps in missing
+                        for dep in (deps[0], _format_dep_chain(deps[1:]))
+                        if dep
+                    )
+                    _error(f"Missing dependencies:{dependencies}")
+
+            return builder.build(
+                distribution,
+                outdir,
+                config_settings,
+            )
+
+
 def parse_backend_flags(backend_flags: str | list[str]) -> ConfigSettingsType:
     config_settings: dict[str, str | list[str]] = {}
 
@@ -254,7 +311,9 @@ def make_command_wrapper_symlinks(symlink_dir: Path) -> dict[str, str]:
 
 
 @contextmanager
-def _create_symlink_dir(env: dict[str, str], build_dir: Path | None):
+def _create_symlink_dir(
+    env: dict[str, str], build_dir: Path | None, no_isolation: bool = False
+):
     if build_dir:
         # If we're running under build-recipes, leave the symlinks in
         # the build directory. This helps with reproducing.
@@ -264,10 +323,22 @@ def _create_symlink_dir(env: dict[str, str], build_dir: Path | None):
         yield symlink_dir
         return
 
-    # Running from "pyodide build". Put symlinks in a temporary directory.
-    # TODO: Add a debug option to save the symlinks.
-    with TemporaryDirectory() as symlink_dir_str:
-        yield Path(symlink_dir_str)
+    # TODO: FIXME: compiler wrappers are still ending up in a temporary
+    # directory, which breaks persistent builds. This is not ideal, but
+    # it is better than nothing so this is non-blocking for now. It has
+    # to be investigated further.
+
+    if no_isolation:
+        # For non-isolated builds, create a persistent directory in the current working directory
+        # or in a well-known location like ~/.pyodide/compiler_wrappers
+        symlink_dir = Path.cwd() / ".pyodide_compiler_wrappers"
+        symlink_dir.mkdir(exist_ok=True)
+        yield symlink_dir
+    else:
+        # Running from "pyodide build". Put symlinks in a temporary directory.
+        # TODO: Add a debug option to save the symlinks.
+        with TemporaryDirectory() as symlink_dir_str:
+            yield Path(symlink_dir_str)
 
 
 @contextmanager
@@ -281,6 +352,7 @@ def get_build_env(
     target_install_dir: str,
     exports: _BuildSpecExports,
     build_dir: Path | None = None,
+    no_isolation: bool = False,
 ) -> Iterator[dict[str, str]]:
     """
     Returns a dict of environment variables that should be used when building
@@ -299,7 +371,7 @@ def get_build_env(
     args["exports"] = exports
     env = env.copy()
 
-    with _create_symlink_dir(env, build_dir) as symlink_dir:
+    with _create_symlink_dir(env, build_dir, no_isolation) as symlink_dir:
         env.update(make_command_wrapper_symlinks(symlink_dir))
         sysconfig_dir = Path(get_build_flag("TARGETINSTALLDIR")) / "sysconfigdata"
         args["PYTHONPATH"] = sys.path + [str(symlink_dir), str(sysconfig_dir)]
@@ -328,12 +400,24 @@ def build(
     outdir: Path,
     build_env: Mapping[str, str],
     config_settings: ConfigSettingsType,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
 ) -> str:
     try:
         with _handle_build_error():
-            built = _build_in_isolated_env(
-                build_env, srcdir, str(outdir), "wheel", config_settings
-            )
+            if isolation:
+                built = _build_in_isolated_env(
+                    build_env, srcdir, str(outdir), "wheel", config_settings
+                )
+            else:
+                built = _build_in_current_env(
+                    build_env,
+                    srcdir,
+                    str(outdir),
+                    "wheel",
+                    config_settings,
+                    skip_dependency_check,
+                )
             print("{bold}{green}Successfully built {}{reset}".format(built, **_STYLES))
             return built
     except Exception as e:  # pragma: no cover

From f7968106b0e30c3b0f06c55dd46e753d9f3eea84 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sun, 30 Mar 2025 05:46:08 +0530
Subject: [PATCH 02/32] Pass along extra args, fix tests [integration]

---
 pyodide_build/out_of_tree/pypi.py | 34 +++++++++++++++++++++++--------
 pyodide_build/tests/test_cli.py   | 27 +++++++++++++++++++++---
 2 files changed, 50 insertions(+), 11 deletions(-)

diff --git a/pyodide_build/out_of_tree/pypi.py b/pyodide_build/out_of_tree/pypi.py
index a5750b1d..a4c58153 100644
--- a/pyodide_build/out_of_tree/pypi.py
+++ b/pyodide_build/out_of_tree/pypi.py
@@ -70,12 +70,12 @@ def stream_redirected(to=os.devnull, stream=None):
             to = None
 
 
-def get_built_wheel(url):
-    return _get_built_wheel_internal(url)["path"]
+def get_built_wheel(url, isolation=True, skip_dependency_check=False):
+    return _get_built_wheel_internal(url, isolation, skip_dependency_check)["path"]
 
 
 @cache
-def _get_built_wheel_internal(url):
+def _get_built_wheel_internal(url, isolation=True, skip_dependency_check=False):
     parsed_url = urlparse(url)
     gz_name = Path(parsed_url.path).name
 
@@ -107,6 +107,8 @@ def _get_built_wheel_internal(url):
                 build_path / "dist",
                 PyPIProvider.BUILD_EXPORTS,
                 PyPIProvider.BUILD_FLAGS,
+                isolation=isolation,
+                skip_dependency_check=skip_dependency_check,
             )
         except BaseException as e:
             logger.error(" Failed\n Error is:")
@@ -199,11 +201,15 @@ def get_project_from_pypi(package_name, extras):
 
 
 def download_or_build_wheel(
-    url: str, target_directory: Path, compression_level: int = 6
+    url: str,
+    target_directory: Path,
+    compression_level: int = 6,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
 ) -> None:
     parsed_url = urlparse(url)
     if parsed_url.path.endswith("gz"):
-        wheel_file = get_built_wheel(url)
+        wheel_file = get_built_wheel(url, isolation, skip_dependency_check)
         shutil.copy(wheel_file, target_directory)
         wheel_path = target_directory / wheel_file.name
     elif parsed_url.path.endswith(".whl"):
@@ -333,6 +339,8 @@ def _resolve_and_build(
     build_dependencies: bool,
     extras: list[str],
     output_lockfile: str | None,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
     compression_level: int = 6,
 ) -> None:
     requirements = []
@@ -362,7 +370,7 @@ def _resolve_and_build(
     if output_lockfile is not None and len(output_lockfile) > 0:
         version_file = open(output_lockfile, "w")
     for x in result.mapping.values():
-        download_or_build_wheel(x.url, target_folder)
+        download_or_build_wheel(x.url, target_folder, compression_level)
         if len(x.extras) > 0:
             extratxt = "[" + ",".join(x.extras) + "]"
         else:
@@ -380,7 +388,10 @@ def build_wheels_from_pypi_requirements(
     skip_dependency: list[str],
     exports: _BuildSpecExports,
     config_settings: ConfigSettingsType,
-    output_lockfile: str | None,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
+    output_lockfile: str | None = None,
+    compression_level: int = 6,
 ) -> None:
     """
     Given a list of package requirements, build or fetch them. If build_dependencies is true, then
@@ -395,6 +406,9 @@ def build_wheels_from_pypi_requirements(
         build_dependencies,
         extras=[],
         output_lockfile=output_lockfile,
+        isolation=isolation,
+        skip_dependency_check=skip_dependency_check,
+        compression_level=compression_level,
     )
 
 
@@ -404,7 +418,9 @@ def build_dependencies_for_wheel(
     skip_dependency: list[str],
     exports: _BuildSpecExports,
     config_settings: ConfigSettingsType,
-    output_lockfile: str | None,
+    isolation: bool = True,
+    skip_dependency_check: bool = False,
+    output_lockfile: str | None = None,
     compression_level: int = 6,
 ) -> None:
     """Extract dependencies from this wheel and build pypi dependencies
@@ -435,6 +451,8 @@ def build_dependencies_for_wheel(
         build_dependencies=True,
         extras=extras,
         output_lockfile=output_lockfile,
+        isolation=isolation,
+        skip_dependency_check=skip_dependency_check,
         compression_level=compression_level,
     )
     # add the current wheel to the package-versions.txt
diff --git a/pyodide_build/tests/test_cli.py b/pyodide_build/tests/test_cli.py
index 09e534a1..f3f527cd 100644
--- a/pyodide_build/tests/test_cli.py
+++ b/pyodide_build/tests/test_cli.py
@@ -355,7 +355,14 @@ def test_py_compile(tmp_path, target, compression_level):
 def test_build1(tmp_path, monkeypatch, dummy_xbuildenv, mock_emscripten):
     from pyodide_build import pypabuild
 
-    def mocked_build(srcdir: Path, outdir: Path, env: Any, backend_flags: Any) -> str:
+    def mocked_build(
+        srcdir: Path,
+        outdir: Path,
+        env: Any,
+        backend_flags: Any,
+        isolation=True,
+        skip_dependency_check=False,
+    ) -> str:
         results["srcdir"] = srcdir
         results["outdir"] = outdir
         results["backend_flags"] = backend_flags
@@ -431,7 +438,14 @@ def unpack_archive_shim(*args):
 
     exports_ = None
 
-    def run_shim(builddir, output_directory, exports, backend_flags):
+    def run_shim(
+        builddir,
+        output_directory,
+        exports,
+        backend_flags,
+        isolation=True,
+        skip_dependency_check=False,
+    ):
         nonlocal exports_
         exports_ = exports
 
@@ -491,7 +505,14 @@ def test_build_config_settings(monkeypatch, dummy_xbuildenv):
 
     config_settings_passed = None
 
-    def run(srcdir, outdir, exports, config_settings):
+    def run(
+        srcdir,
+        outdir,
+        exports,
+        config_settings,
+        isolation=True,
+        skip_dependency_check=False,
+    ):
         nonlocal config_settings_passed
         config_settings_passed = config_settings
 

From c2ae4af21d2f4cf68d6140a8852870206489b19a Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sun, 30 Mar 2025 06:26:08 +0530
Subject: [PATCH 03/32] Add a few stub tests

---
 pyodide_build/tests/test_cli.py | 198 ++++++++++++++++++++++++++++++++
 1 file changed, 198 insertions(+)

diff --git a/pyodide_build/tests/test_cli.py b/pyodide_build/tests/test_cli.py
index f3f527cd..b3a86873 100644
--- a/pyodide_build/tests/test_cli.py
+++ b/pyodide_build/tests/test_cli.py
@@ -678,3 +678,201 @@ def test_build_constraint(tmp_path, dummy_xbuildenv, mock_emscripten, capsys):
     build_dir = RECIPE_DIR / pkg / "build"
     assert (build_dir / "setuptools.version").read_text() == "74.1.3"
     assert (build_dir / "pytest.version").read_text() == "7.0.0"
+
+
+@pytest.mark.parametrize(
+    "isolation_flag",
+    [
+        None,
+        "--no-isolation",
+    ],
+)
+def test_build_isolation_flags(
+    tmp_path, monkeypatch, dummy_xbuildenv, mock_emscripten, isolation_flag
+):
+    """Test that build works with different isolation flags."""
+    from pyodide_build import pypabuild
+
+    build_calls = []
+
+    def mocked_build(
+        srcdir,
+        outdir,
+        env,
+        config_settings,
+        isolation=True,
+        skip_dependency_check=False,
+    ):
+        build_calls.append(
+            {
+                "srcdir": srcdir,
+                "isolation": isolation,
+                "skip_dependency_check": skip_dependency_check,
+            }
+        )
+        dummy_wheel = outdir / "package-1.0.0-py3-none-any.whl"
+        return str(dummy_wheel)
+
+    monkeypatch.setattr(pypabuild, "build", mocked_build)
+    monkeypatch.setattr(build_env, "check_emscripten_version", lambda: None)
+    monkeypatch.setattr(build_env, "replace_so_abi_tags", lambda whl: None)
+    monkeypatch.setattr(
+        common, "retag_wheel", lambda wheel_path, platform: Path(wheel_path)
+    )
+
+    from contextlib import nullcontext
+
+    monkeypatch.setattr(common, "modify_wheel", lambda whl: nullcontext())
+
+    app = typer.Typer()
+    app.command(**build.main.typer_kwargs)(build.main)  # type:ignore[attr-defined]
+
+    srcdir = tmp_path / "in"
+    outdir = tmp_path / "out"
+    srcdir.mkdir()
+
+    args = [str(srcdir), "--outdir", str(outdir)]
+    if isolation_flag:
+        args.append(isolation_flag)
+
+    result = runner.invoke(app, args)
+
+    assert result.exit_code == 0, result.stdout
+    assert len(build_calls) == 1
+
+    # Check that isolation was properly passed
+    expected_isolation = isolation_flag is None
+    assert build_calls[0]["isolation"] == expected_isolation
+
+
+@pytest.mark.parametrize(
+    "skip_check_flag",
+    [
+        None,  # Default: with dependency check
+        "--skip-dependency-check",
+        "-x",
+    ],
+)
+def test_build_skip_dependency_check(
+    tmp_path, monkeypatch, dummy_xbuildenv, mock_emscripten, skip_check_flag
+):
+    """Test that build works with different skip dependency check flags."""
+    from pyodide_build import pypabuild
+
+    build_calls = []
+
+    def mocked_build(
+        srcdir,
+        outdir,
+        env,
+        config_settings,
+        isolation=True,
+        skip_dependency_check=False,
+    ):
+        build_calls.append(
+            {
+                "srcdir": srcdir,
+                "isolation": isolation,
+                "skip_dependency_check": skip_dependency_check,
+            }
+        )
+        dummy_wheel = outdir / "package-1.0.0-py3-none-any.whl"
+        return str(dummy_wheel)
+
+    monkeypatch.setattr(pypabuild, "build", mocked_build)
+    monkeypatch.setattr(build_env, "check_emscripten_version", lambda: None)
+    monkeypatch.setattr(build_env, "replace_so_abi_tags", lambda whl: None)
+    monkeypatch.setattr(
+        common, "retag_wheel", lambda wheel_path, platform: Path(wheel_path)
+    )
+
+    from contextlib import nullcontext
+
+    monkeypatch.setattr(common, "modify_wheel", lambda whl: nullcontext())
+
+    app = typer.Typer()
+    app.command(**build.main.typer_kwargs)(build.main)  # type:ignore[attr-defined]
+
+    srcdir = tmp_path / "in"
+    outdir = tmp_path / "out"
+    srcdir.mkdir()
+
+    args = [str(srcdir), "--outdir", str(outdir)]
+    if skip_check_flag:
+        args.append(skip_check_flag)
+
+    result = runner.invoke(app, args)
+
+    assert result.exit_code == 0, result.stdout
+    assert len(build_calls) == 1
+
+    # Check that skip_dependency_check was properly passed
+    expected_skip = skip_check_flag is not None
+    assert build_calls[0]["skip_dependency_check"] == expected_skip
+
+
+@pytest.mark.parametrize(
+    "isolation,skip_check",
+    [
+        (True, False),  # default: with isolation, without skipping dependency checking
+        (False, False),
+        (True, True),
+        (False, True),
+    ],
+)
+def test_build_combined_flags(
+    tmp_path, monkeypatch, dummy_xbuildenv, mock_emscripten, isolation, skip_check
+):
+    """Test combinations of isolation and skip dependency check flags."""
+    from pyodide_build import pypabuild
+
+    build_calls = []
+
+    def mocked_build(
+        srcdir,
+        outdir,
+        env,
+        config_settings,
+        isolation=True,
+        skip_dependency_check=False,
+    ):
+        build_calls.append(
+            {
+                "srcdir": srcdir,
+                "isolation": isolation,
+                "skip_dependency_check": skip_dependency_check,
+            }
+        )
+        dummy_wheel = outdir / "package-1.0.0-py3-none-any.whl"
+        return str(dummy_wheel)
+
+    monkeypatch.setattr(pypabuild, "build", mocked_build)
+    monkeypatch.setattr(build_env, "check_emscripten_version", lambda: None)
+    monkeypatch.setattr(build_env, "replace_so_abi_tags", lambda whl: None)
+    monkeypatch.setattr(
+        common, "retag_wheel", lambda wheel_path, platform: Path(wheel_path)
+    )
+
+    from contextlib import nullcontext
+
+    monkeypatch.setattr(common, "modify_wheel", lambda whl: nullcontext())
+
+    app = typer.Typer()
+    app.command(**build.main.typer_kwargs)(build.main)  # type:ignore[attr-defined]
+
+    srcdir = tmp_path / "in"
+    outdir = tmp_path / "out"
+    srcdir.mkdir()
+
+    args = [str(srcdir), "--outdir", str(outdir)]
+    if not isolation:
+        args.append("--no-isolation")
+    if skip_check:
+        args.append("--skip-dependency-check")
+
+    result = runner.invoke(app, args)
+
+    assert result.exit_code == 0, result.stdout
+    assert len(build_calls) == 1
+    assert build_calls[0]["isolation"] == isolation
+    assert build_calls[0]["skip_dependency_check"] == skip_check

From b52ea77b0df33e7653906148b98f9d5013f4c91b Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sun, 30 Mar 2025 06:39:41 +0530
Subject: [PATCH 04/32] Add [integration] test to build NumPy with `-nx`

---
 .github/workflows/main.yml     |  1 +
 integration_tests/Makefile     | 13 +++++++++++++
 integration_tests/src/numpy.sh | 13 ++++++++++++-
 3 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index dca6d7e6..5b3a5d2b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -98,6 +98,7 @@ jobs:
           {name: test-recipe, installer: uv},
           {name: test-src, installer: uv},
           {name: test-integration-marker, installer: pip},  # installer doesn't matter
+          {name: test-src-no-isolation, installer: pip}, # installer doesn't matter
         ]
         os: [ubuntu-latest, macos-latest]
     if: needs.check-integration-test-trigger.outputs.run-integration-test
diff --git a/integration_tests/Makefile b/integration_tests/Makefile
index d50dc9be..68c3a503 100644
--- a/integration_tests/Makefile
+++ b/integration_tests/Makefile
@@ -23,6 +23,19 @@ test-src: check
 
 	@echo "... Passed"
 
+.PHONY: test-src-no-isolation
+test-src-no-isolation: check
+	@echo "... Running integration tests for building src with --no-isolation --skip-dependency-check"
+
+	# Ensure the necessary build dependencies are installed in the
+	# host environment as we need to do so ourselves.
+
+	pip install meson-python meson cython
+
+	./src/numpy.sh --no-isolation --skip-dependency-check
+
+	@echo "... Passed"
+
 .PHONY: check
 check:
 	@echo "... Checking dependencies"
diff --git a/integration_tests/src/numpy.sh b/integration_tests/src/numpy.sh
index 1abe6b44..8c790a8f 100755
--- a/integration_tests/src/numpy.sh
+++ b/integration_tests/src/numpy.sh
@@ -2,6 +2,17 @@
 
 set -e
 
+NO_ISOLATION=""
+SKIP_DEPS=""
+
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        --no-isolation) NO_ISOLATION="--no-isolation"; shift ;;
+        --skip-dependency-check) SKIP_DEPS="--skip-dependency-check"; shift ;;
+        *) echo "Unknown parameter: $1"; exit 1 ;;
+    esac
+done
+
 VERSION="2.0.2"
 URL="https://files.pythonhosted.org/packages/source/n/numpy/numpy-${VERSION}.tar.gz"
 
@@ -10,4 +21,4 @@ tar -xf numpy-${VERSION}.tar.gz
 cd numpy-${VERSION}
 
 MESON_CROSS_FILE=$(pyodide config get meson_cross_file)
-${UV_RUN_PREFIX} pyodide build -Csetup-args=-Dallow-noblas=true -Csetup-args=--cross-file="${MESON_CROSS_FILE}"
+${UV_RUN_PREFIX} pyodide build -Csetup-args=-Dallow-noblas=true -Csetup-args=--cross-file="${MESON_CROSS_FILE}" $NO_ISOLATION $SKIP_DEPS

From 4515ef7d4ce49de490eb8da50bba7252c6f0f7a1 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sun, 30 Mar 2025 06:41:33 +0530
Subject: [PATCH 05/32] Don't run tests on pushes with PRs

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5b3a5d2b..629319bc 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -2,6 +2,8 @@ name: CI
 
 on:
   push:
+    branches:
+      - main
   pull_request:
 
 concurrency:

From 523e3d31de4e622de6e52008c915a8e18780d26c Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sun, 30 Mar 2025 06:41:49 +0530
Subject: [PATCH 06/32] Trigger [integration] tests


From ed6175995cedc839ee4b8ff95928b95c45132534 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sun, 30 Mar 2025 06:42:56 +0530
Subject: [PATCH 07/32] Drop [integration] no-isolation test on macOS

---
 .github/workflows/main.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 629319bc..991dfd90 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -100,9 +100,11 @@ jobs:
           {name: test-recipe, installer: uv},
           {name: test-src, installer: uv},
           {name: test-integration-marker, installer: pip},  # installer doesn't matter
-          {name: test-src-no-isolation, installer: pip}, # installer doesn't matter
         ]
         os: [ubuntu-latest, macos-latest]
+        include:
+          - task: {name: test-src-no-isolation, installer: pip} # installer doesn't matter
+            os: ubuntu-latest
     if: needs.check-integration-test-trigger.outputs.run-integration-test
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2

From 8530171ac2f30bbb18099089382cffb89ca7c51d Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:00:05 +0530
Subject: [PATCH 08/32] No need to determine `sysconfigdata` again

---
 pyodide_build/pypabuild.py | 51 +++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 28 deletions(-)

diff --git a/pyodide_build/pypabuild.py b/pyodide_build/pypabuild.py
index a43f071a..e400c466 100644
--- a/pyodide_build/pypabuild.py
+++ b/pyodide_build/pypabuild.py
@@ -209,6 +209,16 @@ def _build_in_isolated_env(
             )
 
 
+# TODO: move to common.py
+def _format_missing_dependencies(missing) -> str:
+    return "".join(
+        "\n\t" + dep
+        for deps in missing
+        for dep in (deps[0], _format_dep_chain(deps[1:]))
+        if dep
+    )
+
+
 def _build_in_current_env(
     build_env: Mapping[str, str],
     srcdir: Path,
@@ -218,34 +228,19 @@ def _build_in_current_env(
     skip_dependency_check: bool = False,
 ) -> str:
     with common.replace_env(build_env):
-        # Setup sysconfigdata path in environment
-        sysconfigdata_name = get_build_flag("SYSCONFIG_NAME")
-        sysconfig_dir = Path(get_build_flag("TARGETINSTALLDIR")) / "sysconfigdata"
-        env = os.environ.copy()
-        env["_PYTHON_SYSCONFIGDATA_NAME"] = sysconfigdata_name
-        env["PYTHONPATH"] = f"{str(sysconfig_dir)}:{env.get('PYTHONPATH', '')}"
-
-        with common.replace_env(env):
-            builder = _ProjectBuilder(srcdir, runner=_gen_runner(build_env))
-
-            if not skip_dependency_check:
-                missing = builder.check_dependencies(
-                    distribution, config_settings or {}
-                )
-                if missing:
-                    dependencies = "".join(
-                        "\n\t" + dep
-                        for deps in missing
-                        for dep in (deps[0], _format_dep_chain(deps[1:]))
-                        if dep
-                    )
-                    _error(f"Missing dependencies:{dependencies}")
-
-            return builder.build(
-                distribution,
-                outdir,
-                config_settings,
-            )
+        builder = _ProjectBuilder(srcdir, runner=_gen_runner(build_env))
+
+        if not skip_dependency_check:
+            missing = builder.check_dependencies(distribution, config_settings or {})
+            if missing:
+                dependencies = _format_missing_dependencies(missing)
+                _error(f"Missing dependencies: {dependencies}")
+
+        return builder.build(
+            distribution,
+            outdir,
+            config_settings,
+        )
 
 
 def parse_backend_flags(backend_flags: str | list[str]) -> ConfigSettingsType:

From e38a704953522fcdc7366f612d52b4c4e77e798b Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:03:30 +0530
Subject: [PATCH 09/32] Accept any args to `numpy.sh`

---
 integration_tests/src/numpy.sh | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/integration_tests/src/numpy.sh b/integration_tests/src/numpy.sh
index 8c790a8f..465052b8 100755
--- a/integration_tests/src/numpy.sh
+++ b/integration_tests/src/numpy.sh
@@ -2,17 +2,6 @@
 
 set -e
 
-NO_ISOLATION=""
-SKIP_DEPS=""
-
-while [[ "$#" -gt 0 ]]; do
-    case $1 in
-        --no-isolation) NO_ISOLATION="--no-isolation"; shift ;;
-        --skip-dependency-check) SKIP_DEPS="--skip-dependency-check"; shift ;;
-        *) echo "Unknown parameter: $1"; exit 1 ;;
-    esac
-done
-
 VERSION="2.0.2"
 URL="https://files.pythonhosted.org/packages/source/n/numpy/numpy-${VERSION}.tar.gz"
 
@@ -21,4 +10,4 @@ tar -xf numpy-${VERSION}.tar.gz
 cd numpy-${VERSION}
 
 MESON_CROSS_FILE=$(pyodide config get meson_cross_file)
-${UV_RUN_PREFIX} pyodide build -Csetup-args=-Dallow-noblas=true -Csetup-args=--cross-file="${MESON_CROSS_FILE}" $NO_ISOLATION $SKIP_DEPS
+${UV_RUN_PREFIX} pyodide build -Csetup-args=-Dallow-noblas=true -Csetup-args=--cross-file="${MESON_CROSS_FILE}" "$@"

From 0aed06b6b02ba02dd08d9686a7c00d4e54437129 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:03:58 +0530
Subject: [PATCH 10/32] Move helper functions to `pyodide_build.common`

---
 pyodide_build/common.py    | 13 +++++++++++++
 pyodide_build/pypabuild.py | 22 +---------------------
 2 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/pyodide_build/common.py b/pyodide_build/common.py
index fa0448b0..357655c6 100644
--- a/pyodide_build/common.py
+++ b/pyodide_build/common.py
@@ -315,6 +315,19 @@ def _get_sha256_checksum(archive: Path) -> str:
     return h.hexdigest()
 
 
+def _format_dep_chain(dep_chain: Sequence[str]) -> str:
+    return " -> ".join(dep.partition(";")[0].strip() for dep in dep_chain)
+
+
+def _format_missing_dependencies(missing) -> str:
+    return "".join(
+        "\n\t" + dep
+        for deps in missing
+        for dep in (deps[0], _format_dep_chain(deps[1:]))
+        if dep
+    )
+
+
 def unpack_wheel(wheel_path: Path, target_dir: Path | None = None) -> None:
     if target_dir is None:
         target_dir = wheel_path.parent
diff --git a/pyodide_build/pypabuild.py b/pyodide_build/pypabuild.py
index e400c466..6450cb46 100644
--- a/pyodide_build/pypabuild.py
+++ b/pyodide_build/pypabuild.py
@@ -5,16 +5,6 @@
 import sys
 import traceback
 from collections.abc import Callable, Iterator, Mapping, Sequence
-
-
-# A helper function from pypa/build/__main__.py since
-# it's not in the vendorized code we have
-# TODO: we should move this to a new file. it's out of place
-# between the other imports ;-)
-def _format_dep_chain(dep_chain: Sequence[str]) -> str:
-    return " -> ".join(dep.partition(";")[0].strip() for dep in dep_chain)
-
-
 from contextlib import contextmanager
 from itertools import chain
 from pathlib import Path
@@ -209,16 +199,6 @@ def _build_in_isolated_env(
             )
 
 
-# TODO: move to common.py
-def _format_missing_dependencies(missing) -> str:
-    return "".join(
-        "\n\t" + dep
-        for deps in missing
-        for dep in (deps[0], _format_dep_chain(deps[1:]))
-        if dep
-    )
-
-
 def _build_in_current_env(
     build_env: Mapping[str, str],
     srcdir: Path,
@@ -233,7 +213,7 @@ def _build_in_current_env(
         if not skip_dependency_check:
             missing = builder.check_dependencies(distribution, config_settings or {})
             if missing:
-                dependencies = _format_missing_dependencies(missing)
+                dependencies = common._format_missing_dependencies(missing)
                 _error(f"Missing dependencies: {dependencies}")
 
         return builder.build(

From 6c5da50434a00862e3e7d732504d62780fc6c3f8 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:05:17 +0530
Subject: [PATCH 11/32] Mention effect of `--skip-dependency-check`

---
 pyodide_build/cli/build.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyodide_build/cli/build.py b/pyodide_build/cli/build.py
index a312cc9a..b55e610c 100644
--- a/pyodide_build/cli/build.py
+++ b/pyodide_build/cli/build.py
@@ -193,7 +193,8 @@ def main(
         False,
         "--skip-dependency-check",
         "-x",
-        help="Do not check that build dependencies are installed",
+        help="Do not check that the build dependencies are installed. This option "
+        "is only useful when used with --no-isolation.",
     ),
     config_setting: Optional[list[str]] = typer.Option(  # noqa: UP007 typer does not accept list[str] | None yet.
         None,

From 8325e803d78cc3e3833edceeb652aee2e7974891 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:45:27 +0530
Subject: [PATCH 12/32] Save symlinks in the build directory

Co-Authored-By: Gyeongjae Choi <def6488@gmail.com>
---
 pyodide_build/out_of_tree/build.py |  4 ++++
 pyodide_build/pypabuild.py         | 33 ++++++------------------------
 2 files changed, 10 insertions(+), 27 deletions(-)

diff --git a/pyodide_build/out_of_tree/build.py b/pyodide_build/out_of_tree/build.py
index 951111ef..400432a1 100644
--- a/pyodide_build/out_of_tree/build.py
+++ b/pyodide_build/out_of_tree/build.py
@@ -30,6 +30,9 @@ def run(
     env = os.environ.copy()
     env.update(build_env.get_build_environment_vars(get_pyodide_root()))
 
+    # create a persistent build dir in the source dir
+    build_dir = srcdir / ".pyodide_build"
+    build_dir.mkdir(exist_ok=True)
     build_env_ctx = pypabuild.get_build_env(
         env=env,
         pkgname="",
@@ -38,6 +41,7 @@ def run(
         ldflags=ldflags,
         target_install_dir=target_install_dir,
         exports=exports,
+        build_dir=build_dir,
     )
 
     with build_env_ctx as env:
diff --git a/pyodide_build/pypabuild.py b/pyodide_build/pypabuild.py
index 6450cb46..77eff0de 100644
--- a/pyodide_build/pypabuild.py
+++ b/pyodide_build/pypabuild.py
@@ -8,7 +8,6 @@
 from contextlib import contextmanager
 from itertools import chain
 from pathlib import Path
-from tempfile import TemporaryDirectory
 from typing import Literal, cast
 
 from build import BuildBackendException, ConfigSettingsType
@@ -287,33 +286,13 @@ def make_command_wrapper_symlinks(symlink_dir: Path) -> dict[str, str]:
 
 @contextmanager
 def _create_symlink_dir(
-    env: dict[str, str], build_dir: Path | None, no_isolation: bool = False
+    env: dict[str, str], build_dir: Path, no_isolation: bool = False
 ):
-    if build_dir:
-        # If we're running under build-recipes, leave the symlinks in
-        # the build directory. This helps with reproducing.
-        symlink_dir = build_dir / "pywasmcross_symlinks"
-        shutil.rmtree(symlink_dir, ignore_errors=True)
-        symlink_dir.mkdir()
-        yield symlink_dir
-        return
-
-    # TODO: FIXME: compiler wrappers are still ending up in a temporary
-    # directory, which breaks persistent builds. This is not ideal, but
-    # it is better than nothing so this is non-blocking for now. It has
-    # to be investigated further.
-
-    if no_isolation:
-        # For non-isolated builds, create a persistent directory in the current working directory
-        # or in a well-known location like ~/.pyodide/compiler_wrappers
-        symlink_dir = Path.cwd() / ".pyodide_compiler_wrappers"
-        symlink_dir.mkdir(exist_ok=True)
-        yield symlink_dir
-    else:
-        # Running from "pyodide build". Put symlinks in a temporary directory.
-        # TODO: Add a debug option to save the symlinks.
-        with TemporaryDirectory() as symlink_dir_str:
-            yield Path(symlink_dir_str)
+    # Leave the symlinks in the build directory. This helps with reproducing.
+    symlink_dir = build_dir / "pywasmcross_symlinks"
+    shutil.rmtree(symlink_dir, ignore_errors=True)
+    symlink_dir.mkdir()
+    yield symlink_dir
 
 
 @contextmanager

From efee932d5404f1939d46f15578eb8581f7461578 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:46:57 +0530
Subject: [PATCH 13/32] Git-ignore the created symlinks directory

---
 pyodide_build/out_of_tree/build.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/pyodide_build/out_of_tree/build.py b/pyodide_build/out_of_tree/build.py
index 400432a1..ca6f2e4d 100644
--- a/pyodide_build/out_of_tree/build.py
+++ b/pyodide_build/out_of_tree/build.py
@@ -1,5 +1,6 @@
 import os
 from pathlib import Path
+from textwrap import dedent
 
 from build import ConfigSettingsType
 
@@ -33,6 +34,16 @@ def run(
     # create a persistent build dir in the source dir
     build_dir = srcdir / ".pyodide_build"
     build_dir.mkdir(exist_ok=True)
+    # don't track the build dir (helps if building in a git repo)
+    gitignore_path = build_dir / ".gitignore"
+    if not gitignore_path.exists():
+        with gitignore_path.open("w") as f:
+            f.write(
+                dedent("""\
+                    # Created by pyodide-build
+                    *""")
+            )
+
     build_env_ctx = pypabuild.get_build_env(
         env=env,
         pkgname="",

From 8d17f99aa5098f24f876676c8c4e556a05ed64d8 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 05:47:27 +0530
Subject: [PATCH 14/32] Trigger [integration] tests


From 97e41b693c3b29a487fc8419b662dfd3bd2fde34 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 06:16:50 +0530
Subject: [PATCH 15/32] Trigger [integration] tests


From 47d458bb82640be852fa7acc0b20d8ef9149428c Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 06:38:55 +0530
Subject: [PATCH 16/32] Fix test

---
 pyodide_build/tests/test_pypabuild.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyodide_build/tests/test_pypabuild.py b/pyodide_build/tests/test_pypabuild.py
index 02bab233..5c6af469 100644
--- a/pyodide_build/tests/test_pypabuild.py
+++ b/pyodide_build/tests/test_pypabuild.py
@@ -77,6 +77,7 @@ def test_get_build_env(tmp_path, dummy_xbuildenv):
         ldflags="",
         target_install_dir=str(tmp_path),
         exports="pyinit",
+        build_dir=tmp_path,
     )
 
     with build_env_ctx as env:

From 4f793fdb6bac38cbf6613fbe4708d0b3e6d42b25 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 07:26:51 +0530
Subject: [PATCH 17/32] Add better "no isolation" [integration] test

---
 integration_tests/Makefile                  | 24 ++++++++++-----
 integration_tests/src/numpy_no_isolation.sh | 33 +++++++++++++++++++++
 2 files changed, 50 insertions(+), 7 deletions(-)
 create mode 100755 integration_tests/src/numpy_no_isolation.sh

diff --git a/integration_tests/Makefile b/integration_tests/Makefile
index 68c3a503..f77e859c 100644
--- a/integration_tests/Makefile
+++ b/integration_tests/Makefile
@@ -27,15 +27,21 @@ test-src: check
 test-src-no-isolation: check
 	@echo "... Running integration tests for building src with --no-isolation --skip-dependency-check"
 
-	# Ensure the necessary build dependencies are installed in the
-	# host environment as we need to do so ourselves.
-
-	pip install meson-python meson cython
-
-	./src/numpy.sh --no-isolation --skip-dependency-check
+	# Some virtualenv workarounds from https://stackoverflow.com/a/24736236
+	# to make sure that we are using the right environment
+	@( \
+        set -e; \
+		python -m venv ./test_venv; \
+		source ./test_venv/bin/activate; \
+		pip install meson-python meson cython; \
+		pip install -e ../; \
+		./src/numpy_no_isolation.sh; \
+		deactivate; \
+	)
+
+	@rm -rf ./test_venv
 
 	@echo "... Passed"
-
 .PHONY: check
 check:
 	@echo "... Checking dependencies"
@@ -49,5 +55,9 @@ check:
 clean:
 	rm -rf .pyodide-xbuildenv*
 	rm -rf recipes/*/build
+	rm -rf test_venv
 	rm -rf src/numpy-*
+	rm -rf src/numpy-*.tar.gz
+	rm -rf numpy-*
+	rm -rf numpy-*.tar.gz
 	rm -rf dist
diff --git a/integration_tests/src/numpy_no_isolation.sh b/integration_tests/src/numpy_no_isolation.sh
new file mode 100755
index 00000000..8fc2b69b
--- /dev/null
+++ b/integration_tests/src/numpy_no_isolation.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# The same as "numpy.sh", but without the isolation.
+
+set -e
+
+VERSION="2.0.2"
+URL="https://files.pythonhosted.org/packages/source/n/numpy/numpy-${VERSION}.tar.gz"
+
+wget $URL
+tar -xf numpy-${VERSION}.tar.gz
+cd numpy-${VERSION}
+
+MESON_CROSS_FILE=$(pyodide config get meson_cross_file)
+
+# Build in a persistent build directory
+${UV_RUN_PREFIX} pyodide build \
+    -Csetup-args=-Dallow-noblas=true \
+    -Csetup-args=--cross-file="${MESON_CROSS_FILE}" \
+    -Cinstall-args=--tags=runtime,python-runtime,devel \
+    -Cbuild-dir="build" \
+    --no-isolation --skip-dependency-check
+
+sed -i 's/numpy/numpy-tests/g' pyproject.toml
+
+${UV_RUN_PREFIX} pyodide build \
+    -Csetup-args=-Dallow-noblas=true \
+    -Csetup-args=--cross-file="${MESON_CROSS_FILE}" \
+    -Cinstall-args=--tags=tests \
+    -Cbuild-dir="build" \
+    --no-isolation --skip-dependency-check
+
+echo "Successfully built wheels for numpy-${VERSION} and numpy-tests-${VERSION}."

From abad178406cc9b276963c3299a380c932e99dafd Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 07:35:10 +0530
Subject: [PATCH 18/32] Use bash shell for [integration] tests

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 991dfd90..5b9223f9 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -154,6 +154,7 @@ jobs:
 
       - name: Run the recipe integration tests (${{ matrix.task }})
         if: matrix.task.name != 'test-integration-marker'
+        shell: bash
         env:
           PYODIDE_JOBS: ${{ steps.get-cores.outputs.CORES }}
         working-directory: integration_tests

From d586dc49d0ebf411d5ea2fd07f7eed526da69151 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 07:45:56 +0530
Subject: [PATCH 19/32] Revert "Use bash shell for [integration] tests"

This reverts commit abad178406cc9b276963c3299a380c932e99dafd.
---
 .github/workflows/main.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5b9223f9..991dfd90 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -154,7 +154,6 @@ jobs:
 
       - name: Run the recipe integration tests (${{ matrix.task }})
         if: matrix.task.name != 'test-integration-marker'
-        shell: bash
         env:
           PYODIDE_JOBS: ${{ steps.get-cores.outputs.CORES }}
         working-directory: integration_tests

From b81e52538e13bcd4b7555d81478038730b6d7720 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 07:46:13 +0530
Subject: [PATCH 20/32] `source` doesn't work for some reason [integration]

---
 integration_tests/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/integration_tests/Makefile b/integration_tests/Makefile
index f77e859c..05dd79b4 100644
--- a/integration_tests/Makefile
+++ b/integration_tests/Makefile
@@ -32,7 +32,7 @@ test-src-no-isolation: check
 	@( \
         set -e; \
 		python -m venv ./test_venv; \
-		source ./test_venv/bin/activate; \
+		. ./test_venv/bin/activate; \
 		pip install meson-python meson cython; \
 		pip install -e ../; \
 		./src/numpy_no_isolation.sh; \

From 2c5ce4bab31c11e9dd2d4c989c68f2b8461a2c6c Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 08:04:48 +0530
Subject: [PATCH 21/32] Miscellaneous edits

---
 integration_tests/src/numpy.sh              | 2 +-
 integration_tests/src/numpy_no_isolation.sh | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/integration_tests/src/numpy.sh b/integration_tests/src/numpy.sh
index 465052b8..1abe6b44 100755
--- a/integration_tests/src/numpy.sh
+++ b/integration_tests/src/numpy.sh
@@ -10,4 +10,4 @@ tar -xf numpy-${VERSION}.tar.gz
 cd numpy-${VERSION}
 
 MESON_CROSS_FILE=$(pyodide config get meson_cross_file)
-${UV_RUN_PREFIX} pyodide build -Csetup-args=-Dallow-noblas=true -Csetup-args=--cross-file="${MESON_CROSS_FILE}" "$@"
+${UV_RUN_PREFIX} pyodide build -Csetup-args=-Dallow-noblas=true -Csetup-args=--cross-file="${MESON_CROSS_FILE}"
diff --git a/integration_tests/src/numpy_no_isolation.sh b/integration_tests/src/numpy_no_isolation.sh
index 8fc2b69b..82379d8c 100755
--- a/integration_tests/src/numpy_no_isolation.sh
+++ b/integration_tests/src/numpy_no_isolation.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 
-# The same as "numpy.sh", but without the isolation.
+# The same as "numpy.sh", but without the isolation, and
+# builds both NumPy and numpy-tests from a persistent
+# build directory.
 
 set -e
 

From f654818f8bbfe90be9a21c502364e857343afdcc Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 08:17:28 +0530
Subject: [PATCH 22/32] Add a CHANGELOG entry for #152

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4d587b3c..b13c4d92 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added basic support for uv. `uv tool install pyodide-cli --with pyodide-build`, or `uvx --from pyodide-cli --with pyodide-build pyodide --help`, or using `pyodide-build` in `uv`-managed virtual environments will now work.
   [#132](https://github.com/pyodide/pyodide-build/pull/132)
 
+- Added support for building without a wheel without build isolation: `pyodide build` no accepts
+  the `--no-isolation`/`-n` and/or `--skip-dependency-check`/`-x` flags to customise the wheel
+  building behaviour, similar to `pypa/build`.
+
 ### Changed
 
 - The Rust toolchain version has been updated to `nightly-2025-01-18`.

From 1b879bdfd891b82036ecebb5389570cf25b65e73 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Mon, 31 Mar 2025 08:17:58 +0530
Subject: [PATCH 23/32] Trigger [integration] tests


From 689c284e1dcf2b27bfa5513a6aaf42be528b425a Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Tue, 1 Apr 2025 22:33:28 +0530
Subject: [PATCH 24/32] Trigger [integration] tests


From 21562ecffd466901f201e291ebd0c2ec3a571648 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Tue, 1 Apr 2025 23:13:27 +0530
Subject: [PATCH 25/32] Try to fix geos recipe [integration]

---
 integration_tests/recipes/geos/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/integration_tests/recipes/geos/meta.yaml b/integration_tests/recipes/geos/meta.yaml
index 77d763dc..187062d6 100644
--- a/integration_tests/recipes/geos/meta.yaml
+++ b/integration_tests/recipes/geos/meta.yaml
@@ -1,11 +1,11 @@
 package:
   name: geos
-  version: 3.12.1
+  version: 3.13.1
   tag:
     - library
 source:
-  url: https://github.com/libgeos/geos/releases/download/3.12.1/geos-3.12.1.tar.bz2
-  sha256: d6ea7e492224b51193e8244fe3ec17c4d44d0777f3c32ca4fb171140549a0d03
+  url: https://github.com/libgeos/geos/releases/download/3.13.1/geos-3.13.1.tar.bz2
+  sha256: df2c50503295f325e7c8d7b783aca8ba4773919cde984193850cf9e361dfd28c
 
 build:
   type: shared_library

From 6088abac8fa777155f1f8dc606063e26271944d5 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Tue, 1 Apr 2025 23:26:25 +0530
Subject: [PATCH 26/32] `--fresh` is no longer needed [integration]

---
 pyodide_build/pywasmcross.py            | 4 ----
 pyodide_build/tests/test_pywasmcross.py | 1 -
 2 files changed, 5 deletions(-)

diff --git a/pyodide_build/pywasmcross.py b/pyodide_build/pywasmcross.py
index a766b15d..13b2ee64 100755
--- a/pyodide_build/pywasmcross.py
+++ b/pyodide_build/pywasmcross.py
@@ -521,10 +521,6 @@ def handle_command_generate_args(  # noqa: C901
             "emcmake",
             "cmake",
             *flags,
-            # Since we create a temporary directory and install compiler symlinks every time,
-            # CMakeCache.txt will contain invalid paths to the compiler when re-running,
-            # so we need to tell CMake to ignore the existing cache and build from scratch.
-            "--fresh",
         ]
         return line
     elif cmd == "meson":
diff --git a/pyodide_build/tests/test_pywasmcross.py b/pyodide_build/tests/test_pywasmcross.py
index 6b7381c2..f6bf9a90 100644
--- a/pyodide_build/tests/test_pywasmcross.py
+++ b/pyodide_build/tests/test_pywasmcross.py
@@ -257,7 +257,6 @@ def test_get_cmake_compiler_flags():
 
 def test_handle_command_cmake(build_args):
     args = build_args
-    assert "--fresh" in handle_command_generate_args(["cmake", "./"], args)
 
     build_cmd = ["cmake", "--build", "." "--target", "target"]
     assert handle_command_generate_args(build_cmd, args) == build_cmd

From 206a28e68c8b731827e7876048beb90f16179607 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Apr 2025 15:51:34 +0530
Subject: [PATCH 27/32] Add type annotation for `_format_missing_dependencies`

---
 pyodide_build/common.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyodide_build/common.py b/pyodide_build/common.py
index 65b11a69..f75d7b73 100644
--- a/pyodide_build/common.py
+++ b/pyodide_build/common.py
@@ -387,7 +387,7 @@ def _format_dep_chain(dep_chain: Sequence[str]) -> str:
     return " -> ".join(dep.partition(";")[0].strip() for dep in dep_chain)
 
 
-def _format_missing_dependencies(missing) -> str:
+def _format_missing_dependencies(missing: set[tuple[str, ...]]) -> str:
     return "".join(
         "\n\t" + dep
         for deps in missing

From de93d2b62c6119ea245dbeeb674d0b0301f20bca Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Apr 2025 16:10:23 +0530
Subject: [PATCH 28/32] Extract away directory building logic

---
 pyodide_build/out_of_tree/build.py | 35 ++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/pyodide_build/out_of_tree/build.py b/pyodide_build/out_of_tree/build.py
index ca6f2e4d..5016f089 100644
--- a/pyodide_build/out_of_tree/build.py
+++ b/pyodide_build/out_of_tree/build.py
@@ -9,6 +9,29 @@
 from pyodide_build.spec import _BuildSpecExports
 
 
+def prepare_build_dir(build_dir: Path) -> None:
+    # create a persistent build dir in the source dir
+    # don't track the build dir in git (helps if building in a git/mercurial repo)
+    build_dir.mkdir(exist_ok=True)
+    gitignore_path = build_dir / ".gitignore"
+    if not gitignore_path.exists():
+        with gitignore_path.open("w") as f:
+            f.write(
+                dedent("""\
+                    # Created by pyodide-build
+                    *""")
+            )
+    hgignore_path = build_dir / ".hgignore"
+    if not hgignore_path.exists():
+        with hgignore_path.open("w") as f:
+            f.write(
+                dedent("""\
+                    # Created by pyodide-build
+                    syntax: glob
+                    **/*""")
+            )
+
+
 def run(
     srcdir: Path,
     outdir: Path,
@@ -31,18 +54,8 @@ def run(
     env = os.environ.copy()
     env.update(build_env.get_build_environment_vars(get_pyodide_root()))
 
-    # create a persistent build dir in the source dir
     build_dir = srcdir / ".pyodide_build"
-    build_dir.mkdir(exist_ok=True)
-    # don't track the build dir (helps if building in a git repo)
-    gitignore_path = build_dir / ".gitignore"
-    if not gitignore_path.exists():
-        with gitignore_path.open("w") as f:
-            f.write(
-                dedent("""\
-                    # Created by pyodide-build
-                    *""")
-            )
+    prepare_build_dir(build_dir)
 
     build_env_ctx = pypabuild.get_build_env(
         env=env,

From 6ef79be4e11702e9139af8001b989859548ea2d8 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Apr 2025 16:19:42 +0530
Subject: [PATCH 29/32] Extract away version control ignore even more

---
 pyodide_build/out_of_tree/build.py | 44 ++++++++++++++++--------------
 1 file changed, 24 insertions(+), 20 deletions(-)

diff --git a/pyodide_build/out_of_tree/build.py b/pyodide_build/out_of_tree/build.py
index 5016f089..8b1935e4 100644
--- a/pyodide_build/out_of_tree/build.py
+++ b/pyodide_build/out_of_tree/build.py
@@ -9,27 +9,31 @@
 from pyodide_build.spec import _BuildSpecExports
 
 
-def prepare_build_dir(build_dir: Path) -> None:
+def _create_ignore_files(directory: Path) -> None:
+    directory.joinpath(".gitignore").write_text(
+        dedent("""\
+        # Created by pyodide-build
+        *
+    """),
+        encoding="utf-8",
+    )
+
+    directory.joinpath(".hgignore").write_text(
+        dedent("""\
+        # Created by pyodide-build
+        syntax: glob
+        **/*
+    """),
+        encoding="utf-8",
+    )
+
+
+def _prepare_build_dir(build_dir: Path) -> None:
     # create a persistent build dir in the source dir
-    # don't track the build dir in git (helps if building in a git/mercurial repo)
     build_dir.mkdir(exist_ok=True)
-    gitignore_path = build_dir / ".gitignore"
-    if not gitignore_path.exists():
-        with gitignore_path.open("w") as f:
-            f.write(
-                dedent("""\
-                    # Created by pyodide-build
-                    *""")
-            )
-    hgignore_path = build_dir / ".hgignore"
-    if not hgignore_path.exists():
-        with hgignore_path.open("w") as f:
-            f.write(
-                dedent("""\
-                    # Created by pyodide-build
-                    syntax: glob
-                    **/*""")
-            )
+    # don't track the build dir in version control,
+    # helps if building in a git/mercurial repo
+    _create_ignore_files(build_dir)
 
 
 def run(
@@ -55,7 +59,7 @@ def run(
     env.update(build_env.get_build_environment_vars(get_pyodide_root()))
 
     build_dir = srcdir / ".pyodide_build"
-    prepare_build_dir(build_dir)
+    _prepare_build_dir(build_dir)
 
     build_env_ctx = pypabuild.get_build_env(
         env=env,

From 920aec7a56a778df4bf25961ebff9056f1655803 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Apr 2025 16:20:03 +0530
Subject: [PATCH 30/32] `no_isolation` is no longer used

---
 pyodide_build/pypabuild.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pyodide_build/pypabuild.py b/pyodide_build/pypabuild.py
index 77eff0de..e3605ed6 100644
--- a/pyodide_build/pypabuild.py
+++ b/pyodide_build/pypabuild.py
@@ -286,7 +286,8 @@ def make_command_wrapper_symlinks(symlink_dir: Path) -> dict[str, str]:
 
 @contextmanager
 def _create_symlink_dir(
-    env: dict[str, str], build_dir: Path, no_isolation: bool = False
+    env: dict[str, str],
+    build_dir: Path,
 ):
     # Leave the symlinks in the build directory. This helps with reproducing.
     symlink_dir = build_dir / "pywasmcross_symlinks"
@@ -325,7 +326,7 @@ def get_build_env(
     args["exports"] = exports
     env = env.copy()
 
-    with _create_symlink_dir(env, build_dir, no_isolation) as symlink_dir:
+    with _create_symlink_dir(env, build_dir) as symlink_dir:
         env.update(make_command_wrapper_symlinks(symlink_dir))
         sysconfig_dir = Path(get_build_flag("TARGETINSTALLDIR")) / "sysconfigdata"
         args["PYTHONPATH"] = sys.path + [str(symlink_dir), str(sysconfig_dir)]

From ba3e8ba51f4df3fa83578c27e2135bbcac2eb74c Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Apr 2025 17:07:42 +0530
Subject: [PATCH 31/32] Add TODO for `_create_symlink_dir` context manager

---
 pyodide_build/pypabuild.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyodide_build/pypabuild.py b/pyodide_build/pypabuild.py
index e3605ed6..3a639722 100644
--- a/pyodide_build/pypabuild.py
+++ b/pyodide_build/pypabuild.py
@@ -284,6 +284,7 @@ def make_command_wrapper_symlinks(symlink_dir: Path) -> dict[str, str]:
     return env
 
 
+# TODO: a context manager is no longer needed here
 @contextmanager
 def _create_symlink_dir(
     env: dict[str, str],

From db53bdbe2c967edb64e1697366b859de76996839 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Apr 2025 17:25:00 +0530
Subject: [PATCH 32/32] Trigger [integration] tests