From 865a5bfd442ff0e11366196b186ddf79c2f59268 Mon Sep 17 00:00:00 2001
From: Marius van Niekerk <marius.v.niekerk@gmail.com>
Date: Wed, 11 Oct 2023 17:45:30 -0400
Subject: [PATCH 1/4] Alphabetize the lockfile

---
 conda_lock/conda_lock.py               | 1 -
 conda_lock/lockfile/__init__.py        | 8 ++++++--
 conda_lock/lockfile/v2prelim/models.py | 3 +++
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/conda_lock/conda_lock.py b/conda_lock/conda_lock.py
index 239e909c7..45d701228 100644
--- a/conda_lock/conda_lock.py
+++ b/conda_lock/conda_lock.py
@@ -56,7 +56,6 @@
     is_micromamba,
 )
 from conda_lock.lockfile import (
-    UnknownLockfileVersion,
     parse_conda_lock_file,
     write_conda_lock_file,
 )
diff --git a/conda_lock/lockfile/__init__.py b/conda_lock/lockfile/__init__.py
index 65977d853..d1990ceb7 100644
--- a/conda_lock/lockfile/__init__.py
+++ b/conda_lock/lockfile/__init__.py
@@ -142,11 +142,15 @@ def parse_conda_lock_file(path: pathlib.Path) -> Lockfile:
         content = yaml.safe_load(f)
     version = content.pop("version", None)
     if version == 1:
-        return lockfile_v1_to_v2(LockfileV1.parse_obj(content))
+        lockfile = lockfile_v1_to_v2(LockfileV1.parse_obj(content))
+    elif version == 2:
+        lockfile = Lockfile.parse_obj(content)
     elif version is None:
         raise MissingLockfileVersion(f"{path} is missing a version")
     else:
         raise UnknownLockfileVersion(f"{path} has unknown version {version}")
+    lockfile.toposort_inplace()
+    return lockfile
 
 
 def write_conda_lock_file(
@@ -155,7 +159,7 @@ def write_conda_lock_file(
     metadata_choices: Optional[Collection[MetadataOption]],
     include_help_text: bool = True,
 ) -> None:
-    content.toposort_inplace()
+    content.alphasort_inplace()
     with path.open("w") as f:
         if include_help_text:
             categories = set(p.category for p in content.package)
diff --git a/conda_lock/lockfile/v2prelim/models.py b/conda_lock/lockfile/v2prelim/models.py
index 2cc35c26a..2b446f538 100644
--- a/conda_lock/lockfile/v2prelim/models.py
+++ b/conda_lock/lockfile/v2prelim/models.py
@@ -73,6 +73,9 @@ def __ror__(self, other: "Optional[Lockfile]") -> "Lockfile":
     def toposort_inplace(self) -> None:
         self.package = self._toposort(self.package)
 
+    def alphasort_inplace(self) -> None:
+        self.package.sort(key=lambda d: d.key())
+
     @staticmethod
     def _toposort(
         package: List[LockedDependency], update: bool = False

From d1a1c9c09fe18b6541c97db20ca26c49a4dc297e Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway1@tensorial.com>
Date: Mon, 20 Nov 2023 09:56:42 +0100
Subject: [PATCH 2/4] Add test that explicit lockfiles are toposorted

---
 tests/test_conda_lock.py | 57 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/tests/test_conda_lock.py b/tests/test_conda_lock.py
index 440da233b..402fa8b0e 100644
--- a/tests/test_conda_lock.py
+++ b/tests/test_conda_lock.py
@@ -42,6 +42,7 @@
     extract_input_hash,
     main,
     make_lock_spec,
+    render_lockfile_for_platform,
     run_lock,
 )
 from conda_lock.conda_solver import extract_json_object, fake_conda_environment
@@ -980,6 +981,62 @@ def test_parse_poetry_invalid_optionals(pyproject_optional_toml: Path):
     )
 
 
+def test_explicit_toposorted() -> None:
+    """Verify that explicit lockfiles are topologically sorted.
+
+    We write unified lockfiles in alphabetical order. This is okay because we store
+    the dependency information in the lockfile, so we have the necessary information
+    to perform topological sorting. However, explicit lockfiles do not store dependency
+    information, and thus need to be written in topological order.
+
+    Verifying topological ordering is very easy: we just need to make sure that each
+    package is written after all of its dependencies.
+    """
+    lockfile = parse_conda_lock_file(TEST_DIR / "test-toposort" / "conda-lock.yml")
+
+    # These are the individual lines as they appear in an explicit lockfile file
+    lines = render_lockfile_for_platform(
+        lockfile=lockfile,
+        kind="explicit",
+        platform="linux-64",
+        include_dev_dependencies=False,
+        extras=[],
+    )
+
+    # Packages are listed by URL, but we want to check by name.
+    url_to_name = {package.url: package.name for package in lockfile.package}
+    # For each package name we need the names of its dependencies
+    name_to_deps = {
+        package.name: set(package.dependencies.keys()) for package in lockfile.package
+    }
+
+    # We do a simulated installation run, and keep track of the packages
+    # that have been installed so far in installed_names
+    installed_names = set()
+
+    # Simulate installing each package in the order it appears in the lockfile.
+    # Verify that each package is installed after all of its dependencies.
+    for n, line in enumerate(lines):
+        if not line or line.startswith("#") or line.startswith("@EXPLICIT"):
+            continue
+        # Line should have the format url#hash
+        url = line.split("#")[0]
+        name = url_to_name[url]
+        deps = name_to_deps[name]
+
+        # Verify that all dependencies have been simulated-installed
+        for dep in deps:
+            if dep.startswith("__"):
+                # This is a virtual package, so we don't need to check it
+                continue
+            assert (
+                dep in installed_names
+            ), f"{n=}, {line=}, {name=}, {dep=}, {installed_names=}"
+
+        # Simulate installing the package
+        installed_names.add(name)
+
+
 def test_run_lock(
     monkeypatch: "pytest.MonkeyPatch", zlib_environment: Path, conda_exe: str
 ):

From 04cf04c0b00b67f62e32f20d0f4aeaedb4c20f75 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway1@tensorial.com>
Date: Mon, 20 Nov 2023 10:02:06 +0100
Subject: [PATCH 3/4] Fix mypy error

---
 tests/test_conda_lock.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_conda_lock.py b/tests/test_conda_lock.py
index 402fa8b0e..30aec861e 100644
--- a/tests/test_conda_lock.py
+++ b/tests/test_conda_lock.py
@@ -14,7 +14,7 @@
 
 from glob import glob
 from pathlib import Path
-from typing import Any, ContextManager, Dict, List, Tuple, Union
+from typing import Any, ContextManager, Dict, List, Set, Tuple, Union
 from unittest.mock import MagicMock
 from urllib.parse import urldefrag, urlsplit
 
@@ -1000,7 +1000,7 @@ def test_explicit_toposorted() -> None:
         kind="explicit",
         platform="linux-64",
         include_dev_dependencies=False,
-        extras=[],
+        extras=set(),
     )
 
     # Packages are listed by URL, but we want to check by name.
@@ -1012,7 +1012,7 @@ def test_explicit_toposorted() -> None:
 
     # We do a simulated installation run, and keep track of the packages
     # that have been installed so far in installed_names
-    installed_names = set()
+    installed_names: Set[str] = set()
 
     # Simulate installing each package in the order it appears in the lockfile.
     # Verify that each package is installed after all of its dependencies.

From bb6c7d15df08381215202d6b494630861a8fa93a Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway1@tensorial.com>
Date: Mon, 20 Nov 2023 12:07:49 +0100
Subject: [PATCH 4/4] Add missing lockfile

---
 tests/test-explicit-toposorted/conda-lock.yml | 1876 +++++++++++++++++
 .../test-explicit-toposorted/environment.yml  |   11 +
 tests/test_conda_lock.py                      |    4 +-
 3 files changed, 1890 insertions(+), 1 deletion(-)
 create mode 100644 tests/test-explicit-toposorted/conda-lock.yml
 create mode 100644 tests/test-explicit-toposorted/environment.yml

diff --git a/tests/test-explicit-toposorted/conda-lock.yml b/tests/test-explicit-toposorted/conda-lock.yml
new file mode 100644
index 000000000..ea244a5f8
--- /dev/null
+++ b/tests/test-explicit-toposorted/conda-lock.yml
@@ -0,0 +1,1876 @@
+# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT!
+#
+# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike
+# e.g. `conda env create`, the resulting environment will not change as new package versions become
+# available, unless you explicitly update the lock file.
+#
+# Install this environment as "YOURENV" with:
+#     conda-lock install -n YOURENV --file conda-lock.yml
+# To update a single package to the latest version compatible with the version constraints in the source:
+#     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
+# To re-solve the entire environment, e.g. after changing a version constraint in the source file:
+#     conda-lock -f environment.yml --lockfile conda-lock.yml
+version: 1
+metadata:
+  content_hash:
+    linux-64: cdf8d679a7bf335690de731d1e9ba558ca2144f51a11bfed31db5c6c991705de
+  channels:
+  - url: conda-forge
+    used_env_vars: []
+  platforms:
+  - linux-64
+  sources:
+  - environment.yml
+package:
+- name: __glibc
+  version: '2.17'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: file:///tmp/tmp1z4ph5xs/linux-64/__glibc-2.17-0.tar.bz2
+  hash:
+    md5: ''
+  category: main
+  optional: false
+- name: _libgcc_mutex
+  version: '0.1'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+  hash:
+    md5: d7c89558ba9fa0495403155b64376d81
+    sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
+  category: main
+  optional: false
+- name: _openmp_mutex
+  version: '4.5'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    _libgcc_mutex: '0.1'
+    libgomp: '>=7.5.0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+  hash:
+    md5: 73aaf86a425cc6e73fcf236a5a46396d
+    sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22
+  category: main
+  optional: false
+- name: blosc
+  version: 1.21.5
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libzlib: '>=1.2.13,<1.3.0a0'
+    lz4-c: '>=1.9.3,<1.10.0a0'
+    snappy: '>=1.1.10,<2.0a0'
+    zstd: '>=1.5.5,<1.6.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.5-h0f2a231_0.conda
+  hash:
+    md5: 009521b7ed97cca25f8f997f9e745976
+    sha256: e2b15b017775d1bda8edbb1bc48e545e45364edefa4d926732fc5488cc600731
+  category: main
+  optional: false
+- name: bzip2
+  version: 1.0.8
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda
+  hash:
+    md5: 69b8b6202a07720f448be700e300ccf4
+    sha256: 242c0c324507ee172c0e0dd2045814e746bb303d1eb78870d182ceb0abc726a8
+  category: main
+  optional: false
+- name: c-ares
+  version: 1.21.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.21.0-hd590300_0.conda
+  hash:
+    md5: c06fa0440048270817b9e3142cc661bf
+    sha256: dfe0e81d5462fced79fd0f99edeec94c9b27268cb04238638180981af2f889f1
+  category: main
+  optional: false
+- name: ca-certificates
+  version: 2023.11.17
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda
+  hash:
+    md5: 01ffc8d36f9eba0ce0b3c1955fa780ee
+    sha256: fb4b9f4b7d885002db0b93e22f44b5b03791ef3d4efdc9d0662185a0faafd6b6
+  category: main
+  optional: false
+- name: cairo
+  version: 1.18.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    fontconfig: '>=2.14.2,<3.0a0'
+    fonts-conda-ecosystem: ''
+    freetype: '>=2.12.1,<3.0a0'
+    icu: '>=73.2,<74.0a0'
+    libgcc-ng: '>=12'
+    libglib: '>=2.78.0,<3.0a0'
+    libpng: '>=1.6.39,<1.7.0a0'
+    libstdcxx-ng: '>=12'
+    libxcb: '>=1.15,<1.16.0a0'
+    libzlib: '>=1.2.13,<1.3.0a0'
+    pixman: '>=0.42.2,<1.0a0'
+    xorg-libice: '>=1.1.1,<2.0a0'
+    xorg-libsm: '>=1.2.4,<2.0a0'
+    xorg-libx11: '>=1.8.6,<2.0a0'
+    xorg-libxext: '>=1.3.4,<2.0a0'
+    xorg-libxrender: '>=0.9.11,<0.10.0a0'
+    zlib: ''
+  url: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda
+  hash:
+    md5: f907bb958910dc404647326ca80c263e
+    sha256: 142e2639a5bc0e99c44d76f4cc8dce9c6a2d87330c4beeabb128832cd871a86e
+  category: main
+  optional: false
+- name: cfitsio
+  version: 4.3.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    bzip2: '>=1.0.8,<2.0a0'
+    libcurl: '>=8.2.0,<9.0a0'
+    libgcc-ng: '>=12'
+    libgfortran-ng: ''
+    libgfortran5: '>=12.3.0'
+    libzlib: '>=1.2.13,<1.3.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/cfitsio-4.3.0-hbdc6101_0.conda
+  hash:
+    md5: 797554b8b7603011e8677884381fbcc5
+    sha256: c74938f1ade9b8f37b9fa8cc98a5b9262b325506f41d7492ad1d00146e0f1d08
+  category: main
+  optional: false
+- name: expat
+  version: 2.5.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libexpat: 2.5.0
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda
+  hash:
+    md5: 8b9b5aca60558d02ddaa09d599e55920
+    sha256: 36dfeb4375059b3bba75ce9b38c29c69fd257342a79e6cf20e9f25c1523f785f
+  category: main
+  optional: false
+- name: font-ttf-dejavu-sans-mono
+  version: '2.37'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+  hash:
+    md5: 0c96522c6bdaed4b1566d11387caaf45
+    sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b
+  category: main
+  optional: false
+- name: font-ttf-inconsolata
+  version: '3.000'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+  hash:
+    md5: 34893075a5c9e55cdafac56607368fc6
+    sha256: c52a29fdac682c20d252facc50f01e7c2e7ceac52aa9817aaf0bb83f7559ec5c
+  category: main
+  optional: false
+- name: font-ttf-source-code-pro
+  version: '2.038'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+  hash:
+    md5: 4d59c254e01d9cde7957100457e2d5fb
+    sha256: 00925c8c055a2275614b4d983e1df637245e19058d79fc7dd1a93b8d9fb4b139
+  category: main
+  optional: false
+- name: font-ttf-ubuntu
+  version: '0.83'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
+  hash:
+    md5: 19410c3df09dfb12d1206132a1d357c5
+    sha256: 470d5db54102bd51dbb0c5990324a2f4a0bc976faa493b22193338adb9882e2e
+  category: main
+  optional: false
+- name: fontconfig
+  version: 2.14.2
+  manager: conda
+  platform: linux-64
+  dependencies:
+    expat: '>=2.5.0,<3.0a0'
+    freetype: '>=2.12.1,<3.0a0'
+    libgcc-ng: '>=12'
+    libuuid: '>=2.32.1,<3.0a0'
+    libzlib: '>=1.2.13,<1.3.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda
+  hash:
+    md5: 0f69b688f52ff6da70bccb7ff7001d1d
+    sha256: 155d534c9037347ea7439a2c6da7c24ffec8e5dd278889b4c57274a1d91e0a83
+  category: main
+  optional: false
+- name: fonts-conda-ecosystem
+  version: '1'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    fonts-conda-forge: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+  hash:
+    md5: fee5683a3f04bd15cbd8318b096a27ab
+    sha256: a997f2f1921bb9c9d76e6fa2f6b408b7fa549edd349a77639c9fe7a23ea93e61
+  category: main
+  optional: false
+- name: fonts-conda-forge
+  version: '1'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    font-ttf-dejavu-sans-mono: ''
+    font-ttf-inconsolata: ''
+    font-ttf-source-code-pro: ''
+    font-ttf-ubuntu: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
+  hash:
+    md5: f766549260d6815b0c52253f1fb1bb29
+    sha256: 53f23a3319466053818540bcdf2091f253cbdbab1e0e9ae7b9e509dcaa2a5e38
+  category: main
+  optional: false
+- name: freetype
+  version: 2.12.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libpng: '>=1.6.39,<1.7.0a0'
+    libzlib: '>=1.2.13,<1.3.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda
+  hash:
+    md5: 9ae35c3d96db2c94ce0cef86efdfa2cb
+    sha256: b2e3c449ec9d907dd4656cb0dc93e140f447175b125a3824b31368b06c666bb6
+  category: main
+  optional: false
+- name: freexl
+  version: 2.0.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libexpat: '>=2.5.0,<3.0a0'
+    libgcc-ng: '>=12'
+    libiconv: '>=1.17,<2.0a0'
+    minizip: '>=4.0.1,<5.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/freexl-2.0.0-h743c826_0.conda
+  hash:
+    md5: 12e6988845706b2cfbc3bc35c9a61a95
+    sha256: 9213f60ba710ecfd3632ce47e036775c9f15ce80a6682ff63cbf12d9dddd5382
+  category: main
+  optional: false
+- name: gdal
+  version: 3.8.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    hdf5: '>=1.14.2,<1.14.3.0a0'
+    libgcc-ng: '>=12'
+    libgdal: 3.8.0
+    libstdcxx-ng: '>=12'
+    libxml2: '>=2.11.5,<2.12.0a0'
+    numpy: '>=1.26.0,<2.0a0'
+    openssl: '>=3.1.4,<4.0a0'
+    python: '>=3.12,<3.13.0a0'
+    python_abi: 3.12.*
+  url: https://conda.anaconda.org/conda-forge/linux-64/gdal-3.8.0-py312ha5e4baf_4.conda
+  hash:
+    md5: d6ae95a57c5030a804dab2849dda40e0
+    sha256: fbac0c4cf600d473ecce09443043e33aab64bdaaf12b27597031a87954364e14
+  category: main
+  optional: false
+- name: geos
+  version: 3.12.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/geos-3.12.0-h59595ed_0.conda
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diff --git a/tests/test-explicit-toposorted/environment.yml b/tests/test-explicit-toposorted/environment.yml
new file mode 100644
index 000000000..d714fa008
--- /dev/null
+++ b/tests/test-explicit-toposorted/environment.yml
@@ -0,0 +1,11 @@
+# Run conda-lock on this to pre-generate the alphabetized lockfile
+# on which we will test toposort. While we include a pip section here for
+# good measure, we won't actually test it since pip does its own toposort.
+channels:
+  - conda-forge
+platforms:
+  - linux-64
+dependencies:
+  - gdal
+  - pip:
+      - pydantic
diff --git a/tests/test_conda_lock.py b/tests/test_conda_lock.py
index 79e2200c4..482d645d3 100644
--- a/tests/test_conda_lock.py
+++ b/tests/test_conda_lock.py
@@ -1003,7 +1003,9 @@ def test_explicit_toposorted() -> None:
     Verifying topological ordering is very easy: we just need to make sure that each
     package is written after all of its dependencies.
     """
-    lockfile = parse_conda_lock_file(TEST_DIR / "test-toposort" / "conda-lock.yml")
+    lockfile = parse_conda_lock_file(
+        TEST_DIR / "test-explicit-toposorted" / "conda-lock.yml"
+    )
 
     # These are the individual lines as they appear in an explicit lockfile file
     lines = render_lockfile_for_platform(