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fix: Clone pip packages with environment #4153

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fix: Clone pip packages with environment #4153

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108 changes: 82 additions & 26 deletions libmamba/src/api/create.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,11 @@
//
// The full license is in the file LICENSE, distributed with this software.

#include <fstream>
#include <iostream>

#include <yaml-cpp/yaml.h>

#include "mamba/api/configuration.hpp"
#include "mamba/api/create.hpp"
#include "mamba/api/install.hpp"
Expand Down Expand Up @@ -57,6 +60,7 @@ namespace mamba
void clone_environment(
Context& ctx,
ChannelContext& channel_context,
Configuration& config,
const fs::u8path& source_prefix,
bool create_env,
bool remove_prefix_on_failure
Expand All @@ -77,40 +81,85 @@ namespace mamba
}
const PrefixData& source_prefix_data = maybe_prefix_data.value();

std::vector<std::string> explicit_urls;
const auto records = source_prefix_data.sorted_records();
explicit_urls.reserve(records.size());

for (const auto& pkg : records)
// Export source environment to YAML format
TemporaryFile yaml_file("mamba_env_", ".yml");
{
if (pkg.package_url.empty())
YAML::Emitter out;
out << YAML::BeginMap;

// Add dependencies section
out << YAML::Key << "dependencies" << YAML::Value << YAML::BeginSeq;

// Add conda packages
const auto records = source_prefix_data.sorted_records();
for (const auto& pkg : records)
{
// Fallback to channel/platform/filename if possible.
if (pkg.channel.empty() || pkg.platform.empty() || pkg.filename.empty())
{
LOG_WARNING << "Skipping package without URL information while cloning: "
<< pkg.name;
continue;
}
const auto url = pkg.url_for_channel(pkg.channel);
explicit_urls.push_back(url);
out << fmt::format("{}={}={}", pkg.name, pkg.version, pkg.build_string);
}
else

// Add pip packages as a sub-map
const auto& pip_records = source_prefix_data.pip_records();
if (!pip_records.empty())
{
std::string url = pkg.package_url;
if (!pkg.sha256.empty())
out << YAML::BeginMap;
out << YAML::Key << "pip" << YAML::Value << YAML::BeginSeq;
for (const auto& [name, pkg] : pip_records)
{
url += "#sha256:" + pkg.sha256;
out << (pkg.name + "==" + pkg.version);
}
else if (!pkg.md5.empty())
{
url += "#" + pkg.md5;
}
explicit_urls.push_back(std::move(url));
out << YAML::EndSeq;
out << YAML::EndMap;
}

out << YAML::EndSeq;
out << YAML::EndMap;

// Write YAML to temporary file
std::ofstream yaml_out = open_ofstream(yaml_file.path());
yaml_out << out.c_str();
yaml_out.close();
}

install_explicit_specs(ctx, channel_context, explicit_urls, create_env, remove_prefix_on_failure);
// Read YAML file and populate config
const auto parse_result = detail::read_yaml_file(
ctx,
yaml_file.path().string(),
ctx.platform,
ctx.use_uv
);

// Populate config with parsed YAML contents
if (!parse_result.dependencies.empty())
{
auto& specs = config.at("specs").value<std::vector<std::string>>();
specs.insert(
specs.end(),
parse_result.dependencies.begin(),
parse_result.dependencies.end()
);
}

if (!parse_result.others_pkg_mgrs_specs.empty())
{
auto& others_pkg_mgrs_specs = config.at("others_pkg_mgrs_specs")
.value<std::vector<detail::other_pkg_mgr_spec>>();
others_pkg_mgrs_specs.insert(
others_pkg_mgrs_specs.end(),
parse_result.others_pkg_mgrs_specs.begin(),
parse_result.others_pkg_mgrs_specs.end()
);
}

// Install packages from config
const auto& install_specs_vec = config.at("specs").value<std::vector<std::string>>();
Comment on lines +153 to +154
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@jjerphan jjerphan Jan 29, 2026

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This is inspired from one of the install path, but we must not install those specifications modifying the configuration…

install_specs(
ctx,
channel_context,
config,
install_specs_vec,
create_env,
remove_prefix_on_failure
);
}
} // namespace

Expand Down Expand Up @@ -239,7 +288,14 @@ namespace mamba
{
const auto clone_value = clone_cfg.value<std::string>();
const auto source_prefix = compute_clone_source_prefix(ctx, clone_value);
clone_environment(ctx, channel_context, source_prefix, create_env, remove_prefix_on_failure);
clone_environment(
ctx,
channel_context,
config,
source_prefix,
create_env,
remove_prefix_on_failure
);
return;
}

Expand Down
18 changes: 13 additions & 5 deletions libmamba/src/api/utils.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -27,16 +27,16 @@ namespace mamba
{
tl::expected<command_args, std::runtime_error> get_pkg_mgr_install_command(
const std::string& name,
const std::string& target_prefix,
const fs::u8path& prefix,
const fs::u8path& spec_file,
pip::Update update
)
{
const auto get_python_path = [&]
{ return util::which_in("python", util::get_path_dirs(target_prefix)).string(); };
{ return util::which_in("python", util::get_path_dirs(prefix)).string(); };

const auto get_uv_path = [&]
{ return util::which_in("uv", util::get_path_dirs(target_prefix)).string(); };
{ return util::which_in("uv", util::get_path_dirs(prefix)).string(); };

command_args cmd = [&]
{
Expand Down Expand Up @@ -157,14 +157,21 @@ namespace mamba
{
specs_f << d.c_str() << '\n';
}
specs_f.flush();
specs_f.close();
}

// Use target_prefix to find pip/python executable
const fs::u8path& target_prefix = ctx.prefix_params.target_prefix;
// Ensure we use an absolute path for the requirements file
const fs::u8path specs_path = fs::absolute(specs.path());

command_args command = [&]
{
const auto maybe_command = get_pkg_mgr_install_command(
pkg_mgr,
ctx.prefix_params.target_prefix.string(),
specs.path(),
target_prefix,
specs_path,
update
);
if (maybe_command)
Expand Down Expand Up @@ -198,6 +205,7 @@ namespace mamba
fmt::print(LOG_INFO, "Calling: {}", fmt::join(command, " "));

auto [status, ec] = reproc::run(wrapped_command, options);

assert_reproc_success(options, status, ec);
if (status != 0)
{
Expand Down
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