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fix: Handle extra white-space in `MatchSpec` (#3456) 

* test: Add non-regression test for #3453

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Minimal suboptimal fix

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Add edge cases to the env specification

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* test: Add `MatchSpec` parsing subcases

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* test: Complete `test_env_create_whitespace`

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Add kytea test case

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Merge replacement of binary operators

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Lint with pre-commit

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Adapt MatchSpec

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: Hind Montassif <hind.montassif@gmail.com>

* Remove redundant test

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: Hind Montassif <hind.montassif@gmail.com>

* Rename subcase

Co-authored-by: Hind-M <70631848+Hind-M@users.noreply.github.com>

* Adapt comparison on versions

Co-authored-by: Hind-M <70631848+Hind-M@users.noreply.github.com>

* Adapt test case

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

* Remove pytorch-cpu as it is not available on windows

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

---------

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
Co-authored-by: Hind Montassif <hind.montassif@gmail.com>
Co-authored-by: Hind-M <70631848+Hind-M@users.noreply.github.com>
This commit is contained in:
Julien Jerphanion 2024-09-19 16:54:58 +02:00 committed by GitHub
parent 6db44c8a64
commit 1c755675bf
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
4 changed files with 145 additions and 14 deletions
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54
libmamba/src/specs/match_spec.cpp
View File

@ -502,32 +502,58 @@ namespace mamba::specs
auto MatchSpec::parse(std::string_view str) -> expected_parse_t<MatchSpec>
{
auto parse_error = [&str](std::string_view err) -> tl::unexpected<ParseError>
std::string raw_match_spec_str = std::string(str);
raw_match_spec_str = util::strip(raw_match_spec_str);
// Remove any with space after binary operators, such as:
// - `openmpi-4.1.4-ha1ae619_102`'s improperly encoded `constrains`: "cudatoolkit >= 10.2"
// - `pytorch-1.13.0-cpu_py310h02c325b_0.conda`'s improperly encoded
// `constrains`: "pytorch-cpu = 1.13.0", "pytorch-gpu = 99999999"
// - `fipy-3.4.2.1-py310hff52083_3.tar.bz2`'s improperly encoded `constrains` or
// `dep`: ">=4.5.2"
// - `infokonoha-4.6.3-pyhd8ed1ab_0.tar.bz2`'s `kytea >=0.1.4, 0.2.0` -> `kytea
// >=0.1.4,0.2.0`
// TODO: this solution reallocates memory several times potentially, but the
// number of operators is small and the strings are short, so it must be fine.
// If needed it can be optimized so that the string is only copied once.
for (const std::string& op : { ">=", "<=", "==", ">", "<", "!=", "=", "==", "," })
{
return tl::make_unexpected(
ParseError(fmt::format(R"(Error parsing MatchSpec "{}": {}")", str, err))
);
const std::string& bad_op = op + " ";
while (raw_match_spec_str.find(bad_op) != std::string::npos)
{
raw_match_spec_str = raw_match_spec_str.substr(0, raw_match_spec_str.find(bad_op)) + op
+ raw_match_spec_str.substr(
raw_match_spec_str.find(bad_op) + bad_op.size()
);
}
}
auto parse_error = [&raw_match_spec_str](std::string_view err) -> tl::unexpected<ParseError>
{
return tl::make_unexpected(ParseError(
fmt::format(R"(Error parsing MatchSpec "{}": {}")", raw_match_spec_str, err)
));
};
static constexpr auto npos = std::string_view::npos;
str = util::strip(str);
if (str.empty())
raw_match_spec_str = util::strip(raw_match_spec_str);
if (raw_match_spec_str.empty())
{
return {};
}
// A plain URL like https://conda.anaconda.org/conda-forge/linux-64/pkg-6.4-bld.conda
if (has_archive_extension(str))
if (has_archive_extension(raw_match_spec_str))
{
return MatchSpec::parse_url(str);
return MatchSpec::parse_url(raw_match_spec_str);
}
// A URL with hash, generated by `mamba env export --explicit` like
// https://conda.anaconda.org/conda-forge/linux-64/pkg-6.4-bld.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
if (const auto idx = str.rfind(url_md5_sep); idx != npos)
if (const auto idx = raw_match_spec_str.rfind(url_md5_sep); idx != npos)
{
auto url = str.substr(0, idx);
auto hash = str.substr(idx + 1);
auto url = raw_match_spec_str.substr(0, idx);
auto hash = raw_match_spec_str.substr(idx + 1);
if (has_archive_extension(url))
{
return MatchSpec::parse_url(url).transform(
@ -552,7 +578,7 @@ namespace mamba::specs
// - ``namespace``
// - ``spec >=3 [attr="val", ...]``
{
auto maybe_chan_ns_spec = split_channel_namespace_spec(str);
auto maybe_chan_ns_spec = split_channel_namespace_spec(raw_match_spec_str);
if (!maybe_chan_ns_spec)
{
return parse_error(maybe_chan_ns_spec.error().what());
@ -572,7 +598,7 @@ namespace mamba::specs
out.m_channel = std::move(maybe_chan).value();
}
str = spec_str;
raw_match_spec_str = spec_str;
}
// Parse and apply bracket attributes ``attr="val"`` in ``pkg >=3 =mkl [attr="val", ...]``.
@ -581,7 +607,7 @@ namespace mamba::specs
auto ver_str = std::string_view();
auto bld_str = std::string_view();
{
auto maybe_pkg_ver_bld = rparse_and_set_matchspec_attributes(out, str);
auto maybe_pkg_ver_bld = rparse_and_set_matchspec_attributes(out, raw_match_spec_str);
if (!maybe_pkg_ver_bld)
{
return parse_error(maybe_pkg_ver_bld.error().what());

60
libmamba/tests/src/specs/test_match_spec.cpp
View File

@ -47,6 +47,66 @@ TEST_SUITE("specs::match_spec")
CHECK_EQ(ms.str(), "xtensor>=0.12.3");
}
SUBCASE("python > 3.11")
{
auto ms = MatchSpec::parse("python > 3.11").value();
CHECK_EQ(ms.name().str(), "python");
CHECK_EQ(ms.version().str(), ">3.11");
CHECK(ms.build_string().is_explicitly_free());
CHECK(ms.build_number().is_explicitly_free());
CHECK_EQ(ms.str(), "python>3.11");
}
SUBCASE("numpy < 2.0")
{
auto ms = MatchSpec::parse("numpy < 2.0").value();
CHECK_EQ(ms.name().str(), "numpy");
CHECK_EQ(ms.version().str(), "<2.0");
CHECK(ms.build_string().is_explicitly_free());
CHECK(ms.build_number().is_explicitly_free());
CHECK_EQ(ms.str(), "numpy<2.0");
}
SUBCASE("pytorch-cpu = 1.13.0")
{
auto ms = MatchSpec::parse("pytorch-cpu = 1.13.0").value();
CHECK_EQ(ms.name().str(), "pytorch-cpu");
CHECK_EQ(ms.version().str(), "=1.13.0");
CHECK(ms.build_string().is_explicitly_free());
CHECK(ms.build_number().is_explicitly_free());
CHECK_EQ(ms.str(), "pytorch-cpu=1.13.0");
}
SUBCASE("scipy >= 1.5.0, < 2.0.0")
{
auto ms = MatchSpec::parse("scipy >= 1.5.0, < 2.0.0").value();
CHECK_EQ(ms.name().str(), "scipy");
CHECK_EQ(ms.version().str(), ">=1.5.0,<2.0.0");
CHECK(ms.build_string().is_explicitly_free());
CHECK(ms.build_number().is_explicitly_free());
CHECK_EQ(ms.str(), "scipy[version=\">=1.5.0,<2.0.0\"]");
}
SUBCASE("scikit-learn >1.0.0")
{
auto ms = MatchSpec::parse("scikit-learn >1.0.0").value();
CHECK_EQ(ms.name().str(), "scikit-learn");
CHECK_EQ(ms.version().str(), ">1.0.0");
CHECK(ms.build_string().is_explicitly_free());
CHECK(ms.build_number().is_explicitly_free());
CHECK_EQ(ms.str(), "scikit-learn>1.0.0");
}
SUBCASE("kytea >=0.1.4, 0.2.0")
{
auto ms = MatchSpec::parse("kytea >=0.1.4, 0.2.0").value();
CHECK_EQ(ms.name().str(), "kytea");
CHECK_EQ(ms.version().str(), ">=0.1.4,==0.2.0");
CHECK(ms.build_string().is_explicitly_free());
CHECK(ms.build_number().is_explicitly_free());
CHECK_EQ(ms.str(), "kytea[version=\">=0.1.4,==0.2.0\"]");
}
SUBCASE("_libgcc_mutex 0.1 conda_forge")
{
auto ms = MatchSpec::parse("_libgcc_mutex 0.1 conda_forge").value();

7
micromamba/tests/env-extra-white-space.yaml Normal file
View File

@ -0,0 +1,7 @@
channels:
- conda-forge
dependencies:
- python > 3.11
- numpy < 2.0
- scipy >= 1.5.0, < 2.0.0
- scikit-learn >1.0.0

38
micromamba/tests/test_env.py
View File

@ -361,6 +361,7 @@ def test_env_update_pypi_with_conda_forge(tmp_home, tmp_root_prefix, tmp_path):
## See: https://github.com/mamba-org/mamba/issues/2059
pip_list_output = helpers.umamba_run("-p", env_prefix, "pip", "list", "--format=json")
pip_packages_list = yaml.safe_load(pip_list_output)
# When numpy 2.0.0 is installed using mamba,
# `numpy-2.0.0.dist-info/` is still created in `env_prefix/lib/pythonx.x/site-packages/` alongside `numpy-1.26.4.dist-info`
# therefore causing an unexpected result when listing the version.
@ -370,3 +371,40 @@ def test_env_update_pypi_with_conda_forge(tmp_home, tmp_root_prefix, tmp_path):
pkg["name"] == "numpy" and Version(pkg["version"]) >= Version("1.26.4")
for pkg in pip_packages_list
)
@pytest.mark.parametrize("shared_pkgs_dirs", [True], indirect=True)
def test_env_create_whitespace(tmp_home, tmp_root_prefix, tmp_path):
# Non-regression test for: https://github.com/mamba-org/mamba/issues/3453
env_prefix = tmp_path / "env-extra-white-space"
create_spec_file = tmp_path / "env-extra-white-space.yaml"
shutil.copyfile(__this_dir__ / "env-extra-white-space.yaml", create_spec_file)
res = helpers.run_env("create", "-p", env_prefix, "-f", create_spec_file, "-y", "--json")
assert res["success"]
# Check that the env was created
assert env_prefix.exists()
# Check that the env has the right packages
packages = helpers.umamba_list("-p", env_prefix, "--json")
assert any(
package["name"] == "python" and Version(package["version"]) > Version("3.11")
for package in packages
)
assert any(
package["name"] == "numpy" and Version(package["version"]) < Version("2.0")
for package in packages
)
assert any(
package["name"] == "scipy"
and Version("1.5.0") <= Version(package["version"]) < Version("2.0.0")
for package in packages
)
assert any(
package["name"] == "scikit-learn" and Version(package["version"]) > Version("1.0.0")
for package in packages
)