zipfile repo: quick and dirty wip

.gitignore

@@ -7,6 +7,7 @@
 /var/spack/environments
 /var/spack/repos/*/index.yaml
 /var/spack/repos/*/lock
+/var/spack/repos/*/packages.zip
 /opt
 # Ignore everything in /etc/spack except /etc/spack/defaults
 /etc/spack/*

lib/spack/spack/cmd/repo.py

@@ -3,8 +3,13 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import filecmp
 import os
+import pathlib
 import sys
+import tempfile
+import zipfile
+from typing import List, Optional, Tuple
 
 import llnl.util.tty as tty
 
@@ -12,6 +17,7 @@
 import spack.repo
 import spack.util.path
 from spack.cmd.common import arguments
+from spack.util.archive import reproducible_zipfile_from_prefix
 
 description = "manage package source repositories"
 section = "config"
@@ -67,6 +73,12 @@ def setup_parser(subparser):
         help="configuration scope to modify",
     )
 
+    # Zip
+    zip_parser = sp.add_parser("zip", help=repo_zip.__doc__)
+    zip_parser.add_argument(
+        "namespace_or_path", help="namespace or path of a Spack package repository"
+    )
+
 
 def repo_create(args):
     """create a new package repository"""
@@ -109,31 +121,18 @@ def repo_add(args):
 def repo_remove(args):
     """remove a repository from Spack's configuration"""
     repos = spack.config.get("repos", scope=args.scope)
-    namespace_or_path = args.namespace_or_path
 
-    # If the argument is a path, remove that repository from config.
+    key, repo = _get_repo(repos, args.namespace_or_path)
-    canon_path = spack.util.path.canonicalize_path(namespace_or_path)
+
-    for repo_path in repos:
+    if not key:
-        repo_canon_path = spack.util.path.canonicalize_path(repo_path)
+        tty.die(f"No repository with path or namespace: {args.namespace_or_path}")
-        if canon_path == repo_canon_path:
+
-            repos.remove(repo_path)
+    repos.remove(key)
     spack.config.set("repos", repos, args.scope)
-            tty.msg("Removed repository %s" % repo_path)
+    if repo:
-            return
+        tty.msg(f"Removed repository {repo.root} with namespace '{repo.namespace}'")
-
+    else:
-    # If it is a namespace, remove corresponding repo
+        tty.msg(f"Removed repository {key}")
-    for path in repos:
-        try:
-            repo = spack.repo.from_path(path)
-            if repo.namespace == namespace_or_path:
-                repos.remove(path)
-                spack.config.set("repos", repos, args.scope)
-                tty.msg("Removed repository %s with namespace '%s'." % (repo.root, repo.namespace))
-                return
-        except spack.repo.RepoError:
-            continue
-
-    tty.die("No repository with path or namespace: %s" % namespace_or_path)
 
 
 def repo_list(args):
@@ -147,17 +146,77 @@ def repo_list(args):
             continue
 
     if sys.stdout.isatty():
-        msg = "%d package repositor" % len(repos)
+        tty.msg(f"{len(repos)} package repositor{'y.' if len(repos) == 1 else 'ies.'}")
-        msg += "y." if len(repos) == 1 else "ies."
-        tty.msg(msg)
 
     if not repos:
         return
 
     max_ns_len = max(len(r.namespace) for r in repos)
     for repo in repos:
-        fmt = "%%-%ds%%s" % (max_ns_len + 4)
+        print(f"{repo.namespace:<{max_ns_len}} {repo.root}")
-        print(fmt % (repo.namespace, repo.root))
+
+
+def repo_zip(args):
+    """zip a package repository to make it immutable and faster to load"""
+    key, _ = _get_repo(spack.config.get("repos"), args.namespace_or_path)
+
+    if not key:
+        tty.die(f"No repository with path or namespace: {args.namespace_or_path}")
+
+    try:
+        repo = spack.repo.from_path(key)
+    except spack.repo.RepoError:
+        tty.die(f"No repository at path: {key}")
+
+    def _zip_repo_skip(entry: os.DirEntry):
+        return entry.name == "__pycache__"
+
+    def _zip_repo_path_to_name(path: str) -> str:
+        # use spack/pkg/<repo>/* prefix and rename `package.py` as `__init__.py`
+        rel_path = pathlib.PurePath(path).relative_to(repo.packages_path)
+        if rel_path.name == "package.py":
+            rel_path = rel_path.with_name("__init__.py")
+        return str(rel_path)
+
+    # Create a zipfile in a temporary file
+    with tempfile.NamedTemporaryFile(delete=False, mode="wb", dir=repo.root) as f, zipfile.ZipFile(
+        f, "w", compression=zipfile.ZIP_DEFLATED
+    ) as zip:
+        reproducible_zipfile_from_prefix(
+            zip, repo.packages_path, skip=_zip_repo_skip, path_to_name=_zip_repo_path_to_name
+        )
+
+    packages_zip = os.path.join(repo.root, "packages.zip")
+    try:
+        # Inform the user whether or not the repo was modified since it was last zipped
+        if os.path.exists(packages_zip) and filecmp.cmp(f.name, packages_zip):
+            tty.msg(f"{repo.namespace}: {packages_zip} is up to date")
+            return
+        else:
+            os.rename(f.name, packages_zip)
+            tty.msg(f"{repo.namespace} was zipped: {packages_zip}")
+    finally:
+        try:
+            os.unlink(f.name)
+        except OSError:
+            pass
+
+
+def _get_repo(repos: List[str], path_or_name) -> Tuple[Optional[str], Optional[spack.repo.Repo]]:
+    """Find repo by path or namespace"""
+    canon_path = spack.util.path.canonicalize_path(path_or_name)
+    for path in repos:
+        if canon_path == spack.util.path.canonicalize_path(path):
+            return path, None
+
+    for path in repos:
+        try:
+            repo = spack.repo.from_path(path)
+        except spack.repo.RepoError:
+            continue
+        if repo.namespace == path_or_name:
+            return path, repo
+    return None, None
 
 
 def repo(parser, args):
@@ -167,5 +226,6 @@ def repo(parser, args):
         "add": repo_add,
         "remove": repo_remove,
         "rm": repo_remove,
+        "zip": repo_zip,
     }
     action[args.repo_command](args)

lib/spack/spack/patch.py

@@ -8,6 +8,7 @@
 import os.path
 import pathlib
 import sys
+import zipfile
 from typing import Any, Dict, Optional, Tuple, Type, Union
 
 import llnl.util.filesystem
@@ -20,7 +21,7 @@
 import spack.repo
 import spack.stage
 import spack.util.spack_json as sjson
-from spack.util.crypto import Checker, checksum
+from spack.util.crypto import Checker, checksum_stream
 from spack.util.executable import which, which_string
 
 
@@ -154,6 +155,9 @@ def __hash__(self) -> int:
         return hash(self.sha256)
 
 
+zipfilecache = {}
+
+
 class FilePatch(Patch):
     """Describes a patch that is retrieved from a file in the repository."""
 
@@ -193,9 +197,27 @@ def __init__(
             # Cannot use pkg.package_dir because it's a property and we have
             # classes, not instances.
             pkg_dir = os.path.abspath(os.path.dirname(cls.module.__file__))
-            path = os.path.join(pkg_dir, self.relative_path)
+            path = pathlib.Path(os.path.join(pkg_dir, self.relative_path))
-            if os.path.exists(path):
+
-                abs_path = path
+            if "packages.zip" in path.parts:
+                # check if it exists in the zip file.
+                idx = path.parts.index("packages.zip")
+                zip_path, entry_path = pathlib.PurePath(*path.parts[: idx + 1]), pathlib.PurePath(
+                    *path.parts[idx + 1 :]
+                )
+
+                lookup = zipfilecache.get(zip_path)
+                if lookup is None:
+                    zip = zipfile.ZipFile(zip_path, "r")
+                    namelist = set(zip.namelist())
+                    zipfilecache[zip_path] = (zip, namelist)
+                else:
+                    zip, namelist = lookup
+                if str(entry_path) in namelist:
+                    abs_path = str(path)
+                    break
+            elif path.exists():
+                abs_path = str(path)
                 break
 
         if abs_path is None:
@@ -215,7 +237,26 @@ def sha256(self) -> str:
             The sha256 of the patch file.
         """
         if self._sha256 is None and self.path is not None:
-            self._sha256 = checksum(hashlib.sha256, self.path)
+            path = pathlib.PurePath(self.path)
+            if "packages.zip" in path.parts:
+                # split in path to packages.zip and the path within the zip
+                idx = path.parts.index("packages.zip")
+                path_to_zip, path_in_zip = pathlib.PurePath(
+                    *path.parts[: idx + 1]
+                ), pathlib.PurePath(*path.parts[idx + 1 :])
+                lookup = zipfilecache.get(path_to_zip)
+                if lookup is None:
+                    zip = zipfile.ZipFile(path_to_zip, "r")
+                    namelist = set(zip.namelist())
+                    zipfilecache[path_to_zip] = (zip, namelist)
+                else:
+                    zip, namelist = lookup
+                f = zip.open(str(path_in_zip), "r")
+            else:
+                f = open(self.path, "rb")
+            self._sha256 = checksum_stream(hashlib.sha256, f)
+            f.close()
+
         assert isinstance(self._sha256, str)
         return self._sha256
 

lib/spack/spack/repo.py

@@ -26,6 +26,7 @@
 import types
 import uuid
 import warnings
+import zipimport
 from typing import Any, Dict, Generator, List, Optional, Set, Tuple, Type, Union
 
 import llnl.path
@@ -100,32 +101,6 @@ def get_data(self, path):
             return self.prepend.encode() + b"\n" + data
 
 
-class RepoLoader(_PrependFileLoader):
-    """Loads a Python module associated with a package in specific repository"""
-
-    #: Code in ``_package_prepend`` is prepended to imported packages.
-    #:
-    #: Spack packages are expected to call `from spack.package import *`
-    #: themselves, but we are allowing a deprecation period before breaking
-    #: external repos that don't do this yet.
-    _package_prepend = "from spack.package import *"
-
-    def __init__(self, fullname, repo, package_name):
-        self.repo = repo
-        self.package_name = package_name
-        self.package_py = repo.filename_for_package_name(package_name)
-        self.fullname = fullname
-        super().__init__(self.fullname, self.package_py, prepend=self._package_prepend)
-
-
-class SpackNamespaceLoader:
-    def create_module(self, spec):
-        return SpackNamespace(spec.name)
-
-    def exec_module(self, module):
-        module.__loader__ = self
-
-
 class ReposFinder:
     """MetaPathFinder class that loads a Python module corresponding to a Spack package.
 
@@ -165,10 +140,11 @@ def find_spec(self, fullname, python_path, target=None):
         if not fullname.startswith(ROOT_PYTHON_NAMESPACE):
             return None
 
-        loader = self.compute_loader(fullname)
+        result = self.compute_loader(fullname)
-        if loader is None:
+        if result is None:
             return None
-        return importlib.util.spec_from_loader(fullname, loader)
+        loader, actual_fullname = result
+        return importlib.util.spec_from_loader(actual_fullname, loader)
 
     def compute_loader(self, fullname):
         # namespaces are added to repo, and package modules are leaves.
@@ -187,16 +163,29 @@ def compute_loader(self, fullname):
                 # With 2 nested conditionals we can call "repo.real_name" only once
                 package_name = repo.real_name(module_name)
                 if package_name:
-                    return RepoLoader(fullname, repo, package_name)
+                    # annoyingly there is a many to one mapping for pkg module to file, have to
+                    # figure out how to deal with this properly.
+                    return (
+                        (repo.zipimporter, f"{namespace}.{package_name}")
+                        if repo.zipimporter
+                        else (
+                            _PrependFileLoader(
+                                fullname=fullname,
+                                path=repo.filename_for_package_name(package_name),
+                                prepend="from spack.package import *",
+                            ),
+                            fullname,
+                        )
+                    )
 
             # We are importing a full namespace like 'spack.pkg.builtin'
             if fullname == repo.full_namespace:
-                return SpackNamespaceLoader()
+                return SpackNamespaceLoader(), fullname
 
         # No repo provides the namespace, but it is a valid prefix of
         # something in the RepoPath.
         if is_repo_path and self.current_repository.by_namespace.is_prefix(fullname):
-            return SpackNamespaceLoader()
+            return SpackNamespaceLoader(), fullname
 
         return None
 
@@ -207,6 +196,7 @@ def compute_loader(self, fullname):
 repo_config_name = "repo.yaml"  # Top-level filename for repo config.
 repo_index_name = "index.yaml"  # Top-level filename for repository index.
 packages_dir_name = "packages"  # Top-level repo directory containing pkgs.
+packages_zip_name = "packages.zip"  # Top-level filename for zipped packages.
 package_file_name = "package.py"  # Filename for packages in a repository.
 
 #: Guaranteed unused default value for some functions.
@@ -216,9 +206,9 @@ def compute_loader(self, fullname):
 def packages_path():
     """Get the test repo if it is active, otherwise the builtin repo."""
     try:
-        return spack.repo.PATH.get_repo("builtin.mock").packages_path
+        return PATH.get_repo("builtin.mock").packages_path
-    except spack.repo.UnknownNamespaceError:
+    except UnknownNamespaceError:
-        return spack.repo.PATH.get_repo("builtin").packages_path
+        return PATH.get_repo("builtin").packages_path
 
 
 class GitExe:
@@ -1009,9 +999,14 @@ def check(condition, msg):
         self._names = self.full_namespace.split(".")
 
         packages_dir = config.get("subdirectory", packages_dir_name)
+        packages_zip = os.path.join(self.root, "packages.zip")
+        self.zipimporter = (
+            zipimport.zipimporter(packages_zip) if os.path.exists(packages_zip) else None
+        )
         self.packages_path = os.path.join(self.root, packages_dir)
         check(
-            os.path.isdir(self.packages_path), f"No directory '{packages_dir}' found in '{root}'"
+            self.zipimporter or os.path.isdir(self.packages_path),
+            f"No '{self.packages_path}' or '{packages_zip} found in '{root}'",
         )
 
         # Class attribute overrides by package name
@@ -1507,6 +1502,14 @@ def use_repositories(
         PATH = saved
 
 
+class SpackNamespaceLoader:
+    def create_module(self, spec):
+        return SpackNamespace(spec.name)
+
+    def exec_module(self, module):
+        module.__loader__ = self
+
+
 class MockRepositoryBuilder:
     """Build a mock repository in a directory"""
 

lib/spack/spack/stage.py

@@ -916,7 +916,7 @@ def interactive_version_filter(
     orig_url_dict = url_dict  # only copy when using editor to modify
     print_header = True
     VERSION_COLOR = spack.spec.VERSION_COLOR
-    while True:
+    while sys.stdin.isatty():
         if print_header:
             has_filter = version_filter != VersionList([":"])
             header = []
@@ -933,7 +933,9 @@ def interactive_version_filter(
                 num_new = sum(1 for v in sorted_and_filtered if v not in known_versions)
                 header.append(f"{llnl.string.plural(num_new, 'new version')}")
             if has_filter:
-                header.append(colorize(f"Filtered by {VERSION_COLOR}@@{version_filter}@."))
+                header.append(
+                    colorize(f"Filtered by {VERSION_COLOR}@@{version_filter}@. (clear with c)")
+                )
 
             version_with_url = [
                 colorize(

lib/spack/spack/util/archive.py

@@ -7,7 +7,9 @@
 import io
 import os
 import pathlib
+import shutil
 import tarfile
+import zipfile
 from contextlib import closing, contextmanager
 from gzip import GzipFile
 from typing import Callable, Dict, Tuple
@@ -228,3 +230,53 @@ def reproducible_tarfile_from_prefix(
                     tar.addfile(file_info, f)
 
         dir_stack.extend(reversed(new_dirs))  # we pop, so reverse to stay alphabetical
+
+
+def reproducible_zipfile_from_prefix(
+    zip: zipfile.ZipFile,
+    prefix: str,
+    *,
+    skip: Callable[[os.DirEntry], bool] = lambda entry: False,
+    path_to_name: Callable[[str], str] = default_path_to_name,
+) -> None:
+    """Similar to ``reproducible_tarfile_from_prefix`` but for zipfiles."""
+    dir_stack = [prefix]
+    while dir_stack:
+        dir = dir_stack.pop()
+
+        # Add the dir before its contents. zip.mkdir is Python 3.11.
+        dir_info = zipfile.ZipInfo(path_to_name(dir))
+        if not dir_info.filename.endswith("/"):
+            dir_info.filename += "/"
+        dir_info.external_attr = (0o40755 << 16) | 0x10
+        dir_info.file_size = 0
+        with zip.open(dir_info, "w") as dest:
+            dest.write(b"")
+
+        # Sort by name for reproducibility
+        with os.scandir(dir) as it:
+            entries = sorted(it, key=lambda entry: entry.name)
+
+        new_dirs = []
+        for entry in entries:
+            if skip(entry):
+                continue
+
+            if entry.is_dir(follow_symlinks=False):
+                new_dirs.append(entry.path)
+                continue
+
+            # symlink / hardlink support in ZIP is poor or non-existent: make copies.
+            elif entry.is_file(follow_symlinks=True):
+                file_info = zipfile.ZipInfo(path_to_name(entry.path))
+
+                # Normalize permissions like git
+                s = entry.stat(follow_symlinks=True)
+                file_info.external_attr = (0o755 if s.st_mode & 0o100 else 0o644) << 16
+                file_info.file_size = s.st_size
+                file_info.compress_type = zip.compression
+
+                with open(entry.path, "rb") as src, zip.open(file_info, "w") as dest:
+                    shutil.copyfileobj(src, dest)  # type: ignore[misc]
+
+        dir_stack.extend(reversed(new_dirs))  # we pop, so reverse to stay alphabetical

share/spack/spack-completion.bash

@@ -1748,7 +1748,7 @@ _spack_repo() {
     then
         SPACK_COMPREPLY="-h --help"
     else
-        SPACK_COMPREPLY="create list add remove rm"
+        SPACK_COMPREPLY="create list add remove rm zip"
     fi
 }
 
@@ -1792,6 +1792,15 @@ _spack_repo_rm() {
     fi
 }
 
+_spack_repo_zip() {
+    if $list_options
+    then
+        SPACK_COMPREPLY="-h --help"
+    else
+        _repos
+    fi
+}
+
 _spack_resource() {
     if $list_options
     then

share/spack/spack-completion.fish

@@ -2675,6 +2675,7 @@ complete -c spack -n '__fish_spack_using_command_pos 0 repo' -f -a list -d 'show
 complete -c spack -n '__fish_spack_using_command_pos 0 repo' -f -a add -d 'add a package source to Spack\'s configuration'
 complete -c spack -n '__fish_spack_using_command_pos 0 repo' -f -a remove -d 'remove a repository from Spack\'s configuration'
 complete -c spack -n '__fish_spack_using_command_pos 0 repo' -f -a rm -d 'remove a repository from Spack\'s configuration'
+complete -c spack -n '__fish_spack_using_command_pos 0 repo' -f -a zip -d 'zip a package repository to make it immutable and faster to load'
 complete -c spack -n '__fish_spack_using_command repo' -s h -l help -f -a help
 complete -c spack -n '__fish_spack_using_command repo' -s h -l help -d 'show this help message and exit'
 
@@ -2717,6 +2718,12 @@ complete -c spack -n '__fish_spack_using_command repo rm' -s h -l help -d 'show
 complete -c spack -n '__fish_spack_using_command repo rm' -l scope -r -f -a '_builtin defaults system site user command_line'
 complete -c spack -n '__fish_spack_using_command repo rm' -l scope -r -d 'configuration scope to modify'
 
+# spack repo zip
+set -g __fish_spack_optspecs_spack_repo_zip h/help
+complete -c spack -n '__fish_spack_using_command_pos 0 repo zip' $__fish_spack_force_files -a '(__fish_spack_repos)'
+complete -c spack -n '__fish_spack_using_command repo zip' -s h -l help -f -a help
+complete -c spack -n '__fish_spack_using_command repo zip' -s h -l help -d 'show this help message and exit'
+
 # spack resource
 set -g __fish_spack_optspecs_spack_resource h/help
 complete -c spack -n '__fish_spack_using_command_pos 0 resource' -f -a list -d 'list all resources known to spack (currently just patches)'

var/spack/repos/builtin/packages/chai/package.py

@@ -6,8 +6,7 @@
 import socket
 
 from spack.package import *
-
+from spack.pkg.builtin.blt import llnl_link_helpers
-from .blt import llnl_link_helpers
 
 
 class Chai(CachedCMakePackage, CudaPackage, ROCmPackage):

var/spack/repos/builtin/packages/raja/package.py

@@ -6,8 +6,7 @@
 import socket
 
 from spack.package import *
-
+from spack.pkg.builtin.blt import llnl_link_helpers
-from .blt import llnl_link_helpers
 
 
 # Starting with 2022.03.0, the only submodule we want to fetch is tpl/desul

var/spack/repos/builtin/packages/umpire/package.py

@@ -7,8 +7,7 @@
 import socket
 
 from spack.package import *
-
+from spack.pkg.builtin.blt import llnl_link_helpers
-from .blt import llnl_link_helpers
 
 
 class Umpire(CachedCMakePackage, CudaPackage, ROCmPackage):