make tarballs look more similar to conda-package-handling, add compression threads (#2177)

libmamba/include/mamba/core/mamba_fs.hpp

@@ -408,6 +408,11 @@ namespace fs
             return m_path.extension();
         }
 
+        u8path lexically_relative(const u8path& base) const
+        {
+            return m_path.lexically_relative(base);
+        }
+
         //---- Modifiers ----
 
         void clear() noexcept

libmamba/include/mamba/core/package_handling.hpp

@@ -25,9 +25,12 @@ namespace mamba
     void create_archive(const fs::u8path& directory,
                         const fs::u8path& destination,
                         compression_algorithm,
-                        int compression_level);
+                        int compression_level,
+                        int compression_threads,
+                        bool (*filter)(const fs::u8path&));
     void create_package(const fs::u8path& directory,
                         const fs::u8path& out_file,
+                        int compression_threads,
                         int compression_level);
 
     void extract_archive(const fs::u8path& file, const fs::u8path& destination);
@@ -37,7 +40,10 @@ namespace mamba
     void extract(const fs::u8path& file, const fs::u8path& destination);
     fs::u8path extract(const fs::u8path& file);
     void extract_subproc(const fs::u8path& file, const fs::u8path& dest);
-    bool transmute(const fs::u8path& pkg_file, const fs::u8path& target, int compression_level);
+    bool transmute(const fs::u8path& pkg_file,
+                   const fs::u8path& target,
+                   int compression_level,
+                   int compression_threads);
     bool validate(const fs::u8path& pkg_folder);
 }  // namespace mamba
 

libmamba/src/core/package_handling.cpp

@@ -84,12 +84,38 @@ namespace mamba
         return r;
     }
 
+    bool path_has_prefix(const fs::u8path& path, const fs::u8path& prefix)
+    {
+        auto pair = std::mismatch(path.std_path().begin(),
+                                  path.std_path().end(),
+                                  prefix.std_path().begin(),
+                                  prefix.std_path().end());
+        return pair.second == prefix.std_path().end();
+    }
+
+    int order(const fs::u8path& path)
+    {
+        int is_info = path_has_prefix(path, "info");
+        return !is_info;
+    }
+
+    int zip_order(const fs::u8path& path)
+    {
+        // sort info-...tar.zst file last in zip folder"
+        int init_order = starts_with(path.filename().string(), "info-");
+        // sort metadata.json first in zip folder
+        if (path.filename().string() == "metadata.json")
+            init_order = -1;
+        return init_order;
+    }
+
     // Bundle up all files in directory and create destination archive
     void create_archive(const fs::u8path& directory,
                         const fs::u8path& destination,
                         compression_algorithm ca,
                         int compression_level,
-                        bool (*filter)(const std::string&))
+                        int compression_threads,
+                        bool (*filter)(const fs::u8path&))
     {
         int r;
         struct archive* a;
@@ -127,10 +153,27 @@ namespace mamba
             archive_write_add_filter_zstd(a);
 
             if (compression_level < 1 || compression_level > 22)
-                throw std::runtime_error("zip compression level should be between 1 and 22");
+                throw std::runtime_error("zstd compression level should be between 1 and 22");
+
             std::string comp_level
                 = std::string("zstd:compression-level=") + std::to_string(compression_level);
-            archive_write_set_options(a, comp_level.c_str());
+
+            int res = archive_write_set_options(a, comp_level.c_str());
+            if (res != 0)
+            {
+                LOG_ERROR << "libarchive error (" << res << ") " << archive_error_string(a);
+            }
+
+            if (compression_threads > 2)
+            {
+                std::string comp_threads_level
+                    = std::string("zstd:threads=") + std::to_string(compression_threads);
+                res = archive_write_set_options(a, comp_threads_level.c_str());
+                if (res != 0)
+                {
+                    LOG_ERROR << "libarchive error (" << res << ") " << archive_error_string(a);
+                }
+            }
         }
 
         archive_write_open_filename(a, abs_out_path.string().c_str());
@@ -142,24 +185,42 @@ namespace mamba
         }
         fs::current_path(directory);
 
-        for (auto& dir_entry : fs::recursive_directory_iterator("."))
+        std::vector<std::pair<int, fs::u8path>> files;
+        if (ca != compression_algorithm::zip)
         {
-            // we only add empty directories to the archive
+            for (auto& dir_entry : fs::recursive_directory_iterator("."))
-            if (dir_entry.is_directory() && !fs::is_empty(dir_entry.path()))
             {
+                auto clean_path = dir_entry.path().lexically_relative("./");
+                files.push_back({ order(clean_path), clean_path });
+            }
+        }
+        else
+        {
+            // for zip files, sort `info` last
+            for (auto& dir_entry : fs::directory_iterator("."))
+            {
+                auto clean_path = dir_entry.path().lexically_relative("./");
+                files.push_back({ zip_order(clean_path), clean_path });
+            }
+        }
+
+        std::sort(files.begin(), files.end());
+
+        for (auto& order_pair : files)
+        {
+            const fs::u8path& path = order_pair.second;
+
+            // skip adding _empty_ directories (they are implicitly added by the files therein)
+            auto status = fs::symlink_status(path);
+            if (fs::is_directory(status) && !fs::is_empty(path) && !fs::is_symlink(status))
+            {
+                LOG_INFO << "Skipping " << path << " as it is a non-empty directory.";
                 continue;
             }
 
-            std::string p = dir_entry.path().string();
+            LOG_INFO << "Adding " << path << " to archive";
-            // do this in a better way?
+
-            if (p[0] == '.')
+            std::string p = path.string();
-            {
-                p = p.substr(1);
-            }
-            if (p[0] == '/')
-            {
-                p = p.substr(1);
-            }
             if (filter && filter(p))
             {
                 continue;
@@ -187,6 +248,11 @@ namespace mamba
             {
                 throw std::runtime_error(concat("libarchive error: ", archive_error_string(disk)));
             }
+
+            // clean out UID and GID
+            archive_entry_set_uid(entry, 0);
+            archive_entry_set_gid(entry, 0);
+
             if (archive_read_disk_descend(disk) < ARCHIVE_OK)
             {
                 throw std::runtime_error(concat("libarchive error: ", archive_error_string(disk)));
@@ -232,7 +298,8 @@ namespace mamba
     // note the info folder must have already been created!
     void create_package(const fs::u8path& directory,
                         const fs::u8path& out_file,
-                        int compression_level)
+                        int compression_level,
+                        int compression_threads)
     {
         fs::u8path out_file_abs = fs::absolute(out_file);
         if (ends_with(out_file.string(), ".tar.bz2"))
@@ -241,7 +308,8 @@ namespace mamba
                            out_file_abs,
                            bzip2,
                            compression_level,
-                           [](const std::string&) { return false; });
+                           compression_threads,
+                           [](const fs::u8path&) { return false; });
         }
         else if (ends_with(out_file.string(), ".conda"))
         {
@@ -250,12 +318,20 @@ namespace mamba
                            tdir.path() / concat("info-", out_file.stem().string(), ".tar.zst"),
                            zstd,
                            compression_level,
-                           [](const std::string& p) -> bool { return !starts_with(p, "info/"); });
+                           compression_threads,
+                           [](const fs::u8path& p) -> bool {
+                               return p.std_path().begin() != p.std_path().end()
+                                      && *p.std_path().begin() != "info";
+                           });
             create_archive(directory,
                            tdir.path() / concat("pkg-", out_file.stem().string(), ".tar.zst"),
                            zstd,
                            compression_level,
-                           [](const std::string& p) -> bool { return starts_with(p, "info/"); });
+                           compression_threads,
+                           [](const fs::u8path& p) -> bool {
+                               return p.std_path().begin() != p.std_path().end()
+                                      && *p.std_path().begin() == "info";
+                           });
 
             nlohmann::json pkg_metadata;
             pkg_metadata["conda_pkg_format_version"] = 2;
@@ -264,8 +340,12 @@ namespace mamba
             metadata_file << pkg_metadata;
             metadata_file.close();
 
-            create_archive(
+            create_archive(tdir.path(),
-                tdir.path(), out_file_abs, zip, 0, [](const std::string&) { return false; });
+                           out_file_abs,
+                           zip,
+                           0,
+                           compression_threads,
+                           [](const fs::u8path&) { return false; });
         }
     }
 
@@ -470,7 +550,10 @@ namespace mamba
         }
     }
 
-    bool transmute(const fs::u8path& pkg_file, const fs::u8path& target, int compression_level)
+    bool transmute(const fs::u8path& pkg_file,
+                   const fs::u8path& target,
+                   int compression_level,
+                   int compression_threads)
     {
         TemporaryDirectory extract_dir;
 
@@ -487,7 +570,7 @@ namespace mamba
             throw std::runtime_error("Unknown package format (" + pkg_file.string() + ")");
         }
 
-        create_package(extract_dir, target, compression_level);
+        create_package(extract_dir, target, compression_level, compression_threads);
         return true;
     }
 

libmambapy/libmambapy/__init__.pyi

@@ -1463,7 +1463,12 @@ def get_virtual_packages() -> typing.List[PackageInfo]:
 def sign(data: str, secret_key: str) -> str:
     pass
 
-def transmute(arg0: Path, arg1: Path, arg2: int) -> bool:
+def transmute(
+    source_package: Path,
+    destination_package: Path,
+    compression_level: int,
+    compression_threads: int = 1,
+) -> bool:
     pass
 
 MAMBA_CLEAN_ALL = 1

libmambapy/src/main.cpp

@@ -669,7 +669,19 @@ PYBIND11_MODULE(bindings, m)
 
     m.def("get_channels", &get_channels);
 
-    m.def("transmute", &transmute);
+    m.def("transmute",
+          &transmute,
+          py::arg("source_package"),
+          py::arg("destination_package"),
+          py::arg("compression_level"),
+          py::arg("compression_threads") = 1);
+
+    // fix extract from error_handling first
+    // auto package_handling_sm = m.def_submodule("package_handling");
+    // package_handling_sm.def("extract", &extract);
+    // package_handling_sm.def("create", &create_package, py::arg("directory"),
+    // py::arg("out_package"), py::arg("compression_level"), py::arg("compression_threads") = 1);
+
 
     m.def("get_virtual_packages", &get_virtual_packages);
 

mamba_package/src/package.cpp

@@ -16,6 +16,7 @@ set_package_command(CLI::App* com)
 {
     static std::string infile, dest;
     static int compression_level = -1;
+    static int compression_threads = 1;
 
     auto extract_subcom = com->add_subcommand("extract");
     extract_subcom->add_option("archive", infile, "Archive to extract");
@@ -35,6 +36,10 @@ set_package_command(CLI::App* com)
         "-c,--compression-level",
         compression_level,
         "Compression level from 0-9 (tar.bz2, default is 9), and 1-22 (conda, default is 15)");
+    compress_subcom->add_option(
+        "--compression-threads",
+        compression_threads,
+        "Compression threads (only relevant for .conda packages, default is 1)");
     compress_subcom->callback(
         [&]()
         {
@@ -45,7 +50,8 @@ set_package_command(CLI::App* com)
             if (ends_with(dest, ".conda") && compression_level == -1)
                 compression_level = 15;
 
-            create_package(fs::absolute(infile), fs::absolute(dest), compression_level);
+            create_package(
+                fs::absolute(infile), fs::absolute(dest), compression_level, compression_threads);
         });
 
     auto transmute_subcom = com->add_subcommand("transmute");
@@ -54,6 +60,10 @@ set_package_command(CLI::App* com)
         "-c,--compression-level",
         compression_level,
         "Compression level from 0-9 (tar.bz2, default is 9), and 1-22 (conda, default is 15)");
+    transmute_subcom->add_option(
+        "--compression-threads",
+        compression_threads,
+        "Compression threads (only relevant for .conda packages, default is 1)");
     transmute_subcom->callback(
         [&]()
         {
@@ -70,6 +80,7 @@ set_package_command(CLI::App* com)
                 dest = infile.substr(0, infile.size() - 8) + ".tar.bz2";
             }
             std::cout << "Transmuting " << fs::absolute(infile) << " to " << dest << std::endl;
-            transmute(fs::absolute(infile), fs::absolute(dest), compression_level);
+            transmute(
+                fs::absolute(infile), fs::absolute(dest), compression_level, compression_threads);
         });
 }

micromamba/environment-dev.yml

@@ -23,6 +23,7 @@ dependencies:
   - pytest-asyncio
   - pytest-lazy-fixture
   - pytest-xprocess
+  - conda-package-handling
   - pyyaml
   - spdlog
   - fmt

micromamba/src/package.cpp

@@ -7,6 +7,7 @@
 #include "common_options.hpp"
 
 #include "mamba/core/util.hpp"
+#include "mamba/api/configuration.hpp"
 #include "mamba/core/package_handling.hpp"
 
 using namespace mamba;  // NOLINT(build/namespaces)
@@ -16,47 +17,72 @@ set_package_command(CLI::App* subcom)
 {
     static std::string infile, dest;
     static int compression_level = -1;
+    static int compression_threads = 1;
+
+    init_general_options(subcom);
 
     auto extract_subcom = subcom->add_subcommand("extract");
+    init_general_options(extract_subcom);
     extract_subcom->add_option("archive", infile, "Archive to extract");
     extract_subcom->add_option("dest", dest, "Destination folder");
     extract_subcom->callback(
         [&]()
         {
-            std::cout << "Extracting " << fs::absolute(infile) << " to " << fs::absolute(dest)
+            // load verbose and other options to context
-                      << std::endl;
+            Configuration::instance().load();
+
+            Console::stream() << "Extracting " << fs::absolute(infile) << " to "
+                              << fs::absolute(dest) << std::endl;
             extract(fs::absolute(infile), fs::absolute(dest));
         });
 
     auto compress_subcom = subcom->add_subcommand("compress");
+    init_general_options(compress_subcom);
     compress_subcom->add_option("folder", infile, "Folder to compress");
     compress_subcom->add_option("dest", dest, "Destination (e.g. myfile-3.1-0.tar.bz2 or .conda)");
     compress_subcom->add_option(
         "-c,--compression-level",
         compression_level,
         "Compression level from 0-9 (tar.bz2, default is 9), and 1-22 (conda, default is 15)");
+    compress_subcom->add_option(
+        "--compression-threads",
+        compression_threads,
+        "Compression threads (only relevant for .conda packages, default is 1)");
     compress_subcom->callback(
         [&]()
         {
-            std::cout << "Compressing " << fs::absolute(infile) << " to " << dest << std::endl;
+            // load verbose and other options to context
+            Configuration::instance().load();
+
+            Console::stream() << "Compressing " << fs::absolute(infile) << " to " << dest
+                              << std::endl;
 
             if (ends_with(dest, ".tar.bz2") && compression_level == -1)
                 compression_level = 9;
             if (ends_with(dest, ".conda") && compression_level == -1)
                 compression_level = 15;
 
-            create_package(fs::absolute(infile), fs::absolute(dest), compression_level);
+            create_package(
+                fs::absolute(infile), fs::absolute(dest), compression_level, compression_threads);
         });
 
     auto transmute_subcom = subcom->add_subcommand("transmute");
+    init_general_options(transmute_subcom);
     transmute_subcom->add_option("infile", infile, "Folder to compress");
     transmute_subcom->add_option(
         "-c,--compression-level",
         compression_level,
         "Compression level from 0-9 (tar.bz2, default is 9), and 1-22 (conda, default is 15)");
+    transmute_subcom->add_option(
+        "--compression-threads",
+        compression_threads,
+        "Compression threads (only relevant for .conda packages, default is 1)");
     transmute_subcom->callback(
         [&]()
         {
+            // load verbose and other options to context
+            Configuration::instance().load();
+
             if (ends_with(infile, ".tar.bz2"))
             {
                 if (compression_level == -1)
@@ -69,7 +95,9 @@ set_package_command(CLI::App* subcom)
                     compression_level = 9;
                 dest = infile.substr(0, infile.size() - 8) + ".tar.bz2";
             }
-            std::cout << "Transmuting " << fs::absolute(infile) << " to " << dest << std::endl;
+            Console::stream() << "Transmuting " << fs::absolute(infile) << " to " << dest
-            transmute(fs::absolute(infile), fs::absolute(dest), compression_level);
+                              << std::endl;
+            transmute(
+                fs::absolute(infile), fs::absolute(dest), compression_level, compression_threads);
         });
 }

micromamba/tests/test_package.py

@@ -0,0 +1,209 @@
+import filecmp
+import platform
+import shutil
+import subprocess
+import tarfile
+import zipfile
+from pathlib import Path
+
+import pytest
+import zstandard
+from conda_package_handling import api as cph
+
+from .helpers import *
+
+
+@pytest.fixture
+def cph_test_file():
+    return Path(__file__).parent / "data" / "cph_test_data-0.0.1-0.tar.bz2"
+
+
+def print_diff_files(dcmp):
+    for name in dcmp.diff_files:
+        print(f"diff_file {name} found in {dcmp.left} and {dcmp.right}")
+    for name in dcmp.left_only:
+        print(f"file only found in LHS {dcmp.left} / {name}")
+    for name in dcmp.right_only:
+        print(f"file only found in RHS {dcmp.right} / {name}")
+
+    for sub_dcmp in dcmp.subdirs.values():
+        print_diff_files(sub_dcmp)
+
+
+def test_extract(cph_test_file: Path, tmp_path: Path):
+    (tmp_path / "cph").mkdir(parents=True)
+    (tmp_path / "mm").mkdir(parents=True)
+
+    shutil.copy(cph_test_file, tmp_path / "mm")
+    shutil.copy(cph_test_file, tmp_path / "cph")
+
+    mamba_exe = get_umamba()
+    subprocess.call(
+        [
+            mamba_exe,
+            "package",
+            "extract",
+            str(tmp_path / "mm" / cph_test_file.name),
+            str(tmp_path / "mm" / "cph_test_data-0.0.1-0"),
+        ]
+    )
+    cph.extract(
+        str(tmp_path / "cph" / cph_test_file.name),
+        dest_dir=str(tmp_path / "cph" / "cph_test_data-0.0.1-0"),
+    )
+
+    conda = set(
+        (p.relative_to(tmp_path / "cph") for p in (tmp_path / "cph").rglob("**/*"))
+    )
+    mamba = set(
+        (p.relative_to(tmp_path / "mm") for p in (tmp_path / "mm").rglob("**/*"))
+    )
+    assert conda == mamba
+
+    extracted = cph_test_file.name.removesuffix(".tar.bz2")
+    fcmp = filecmp.dircmp(tmp_path / "cph" / extracted, tmp_path / "mm" / extracted)
+    assert (
+        len(fcmp.left_only) == 0
+        and len(fcmp.right_only) == 0
+        and len(fcmp.diff_files) == 0
+    )
+    # fcmp.report_full_closure()
+
+
+def compare_two_tarfiles(tar1, tar2):
+    tar1_files = set(tar1.getnames())
+    tar2_files = set(tar2.getnames())
+    assert tar1_files == tar2_files
+
+    for f in tar1_files:
+        m1: tarfile.TarInfo = tar1.getmember(f)
+        m2 = tar2.getmember(f)
+        if platform.system() != "Windows":
+            if not m1.issym():
+                assert m1.mode == m2.mode
+            else:
+                if platform.system() == "Linux":
+                    assert m2.mode == 0o777
+                else:
+                    assert m1.mode == m2.mode
+            assert m1.mtime == m2.mtime
+
+        assert m2.uid == 0
+        assert m2.gid == 0
+        assert m1.size == m2.size
+
+        if m1.isfile():
+            assert tar1.extractfile(f).read() == tar2.extractfile(f).read()
+
+        if m1.islnk() or m1.issym():
+            assert m1.linkname == m2.linkname
+
+
+def assert_sorted(l):
+    assert l == sorted(l)
+
+
+def test_extract_compress(cph_test_file: Path, tmp_path: Path):
+    (tmp_path / "mm").mkdir(parents=True)
+
+    shutil.copy(cph_test_file, tmp_path / "mm")
+
+    mamba_exe = get_umamba()
+    out = tmp_path / "mm" / "out"
+    subprocess.call(
+        [
+            mamba_exe,
+            "package",
+            "extract",
+            str(tmp_path / "mm" / cph_test_file.name),
+            str(out),
+        ]
+    )
+    subprocess.call(
+        [
+            mamba_exe,
+            "package",
+            "compress",
+            str(out),
+            str(tmp_path / "mm" / "out.tar.bz2"),
+        ]
+    )
+
+    compare_two_tarfiles(
+        tarfile.open(cph_test_file), tarfile.open(tmp_path / "mm" / "out.tar.bz2")
+    )
+
+    fout = tarfile.open(tmp_path / "mm" / "out.tar.bz2")
+    names = fout.getnames()
+    assert "info/paths.json" in names
+
+    info_files = [f for f in names if f.startswith("info/")]
+    # check that info files are at the beginning
+    assert names[: len(info_files)] == info_files
+
+    # check that the rest is sorted
+    assert_sorted(names[len(info_files) :])
+    assert_sorted(names[: len(info_files)])
+
+
+def test_transmute(cph_test_file: Path, tmp_path: Path):
+    (tmp_path / "cph").mkdir(parents=True)
+    (tmp_path / "mm").mkdir(parents=True)
+
+    shutil.copy(cph_test_file, tmp_path)
+    shutil.copy(tmp_path / cph_test_file.name, tmp_path / "mm")
+
+    mamba_exe = get_umamba()
+    subprocess.call(
+        [mamba_exe, "package", "transmute", str(tmp_path / "mm" / cph_test_file.name)]
+    )
+    failed_files = cph.transmute(
+        str(tmp_path / cph_test_file.name), ".conda", out_folder=str(tmp_path / "cph")
+    )
+    assert len(failed_files) == 0
+
+    as_conda = cph_test_file.name.removesuffix(".tar.bz2") + ".conda"
+
+    cph.extract(str(tmp_path / "cph" / as_conda))
+    cph.extract(str(tmp_path / "mm" / as_conda))
+
+    conda = list((tmp_path / "cph").rglob("**/*"))
+    mamba = list((tmp_path / "mm").rglob("**/*"))
+
+    fcmp = filecmp.dircmp(
+        tmp_path / "cph" / "cph_test_data-0.0.1-0",
+        tmp_path / "mm" / "cph_test_data-0.0.1-0",
+    )
+    assert (
+        len(fcmp.left_only) == 0
+        and len(fcmp.right_only) == 0
+        and len(fcmp.diff_files) == 0
+    )
+    # fcmp.report_full_closure()
+
+    # extract zipfile
+    with zipfile.ZipFile(tmp_path / "mm" / as_conda, "r") as zip_ref:
+        l = zip_ref.namelist()
+
+        assert l[2].startswith("info-")
+        assert l[0] == "metadata.json"
+        assert l[1].startswith("pkg-")
+
+        zip_ref.extractall(tmp_path / "mm" / "zipcontents")
+
+    files = list((tmp_path / "mm" / "zipcontents").glob("**/*"))
+    for f in files:
+        if f.suffix == ".zst":
+            with open(f, mode="rb") as fi:
+                dcf = zstandard.ZstdDecompressor().stream_reader(fi)
+
+                with tarfile.open(fileobj=dcf, mode="r|") as z:
+                    assert_sorted(z.getnames())
+                    members = z.getmembers()
+                    for m in members:
+                        if f.name.startswith("info-"):
+                            assert m.name.startswith("info/")
+                        if not f.name.startswith("info-"):
+                            assert not m.name.startswith("info/")
+                        assert m.uid == 0
+                        assert m.gid == 0