Invalid/Temporary local packages unexpectedly appearing in conda-lock.yml

[zaneselvans]

Checklist

• [X] I added a descriptive title
• [X] I searched open reports and couldn't find a duplicate

What happened?

After updating to conda-lock v2.5.0 some odd new packages are showing up in our conda-lock.yml when it is regenerated via a GitHub action:

package:
  - name: __glibc
    version: "2.17"
    manager: conda
    platform: linux-64
    dependencies: {}
    url: file:///home/runner/work/_temp/tmp8q60deq6/linux-64/__glibc-2.17-0.tar.bz2
    hash:
      md5: ""
    category: main
    optional: false
  - name: __osx
    version: "11.0"
    manager: conda
    platform: osx-64
    dependencies: {}
    url: file:///home/runner/work/_temp/tmp8q60deq6/osx-64/__osx-11.0-0.tar.bz2
    hash:
      md5: ""
    category: main
    optional: false
  - name: __osx
    version: "11.0"
    manager: conda
    platform: osx-arm64
    dependencies: {}
    url: file:///home/runner/work/_temp/tmp8q60deq6/osx-arm64/__osx-11.0-0.tar.bz2
    hash:
      md5: ""
    category: main
    optional: false

I noticed that they exist because the lack of a hash value is causing the setup-micromamba GitHub action to fail with the following error:

  Empty environment created at prefix: /home/runner/micromamba/envs/pudl-dev
  critical libmamba either package 'package.info.hash.md5' or 'package.info.hash.sha256' must be specified, found none
  Error: The process '/home/runner/micromamba-bin/micromamba' failed with exit code 1

However, no packages named __osx or __glibc appear in the conda-lock.yml when I generate it locally using a similar command. The only obvious differences between the two environments are:

• The GitHub runners are running Linux, and my local environment is on an M1 Macbook Pro
• On the GitHub runner it is using conda-lock --micromamba while locally I'm using conda-lock --mamba. The command being used to generate the conda lockfiles / environment files:

conda-lock \
    --${mamba} \
    --file=pyproject.toml \
    --lockfile=environments/conda-lock.yml

However, running the above commands locally using --micromamba does not result in the __glibc or __osx packages appearing in conda-lock.yml

Conda Info

active environment : None
            shell level : 0
       user config file : /Users/zane/.condarc
 populated config files : /Users/zane/miniforge3/.condarc
                          /Users/zane/.condarc
          conda version : 23.9.0
    conda-build version : not installed
         python version : 3.10.12.final.0
       virtual packages : __archspec=1=arm64
                          __osx=14.1=0
                          __unix=0=0
       base environment : /Users/zane/miniforge3  (writable)
      conda av data dir : /Users/zane/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/zane/miniforge3/pkgs
                          /Users/zane/.conda/pkgs
       envs directories : /Users/zane/miniforge3/envs
                          /Users/zane/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.9.0 requests/2.31.0 CPython/3.10.12 Darwin/23.1.0 OSX/14.1
                UID:GID : 1000:20
             netrc file : None
           offline mode : False

Conda Config

==> /Users/zane/miniforge3/.condarc <==
channels:
  - conda-forge

==> /Users/zane/.condarc <==
auto_activate_base: False
default_python: 3.10
channel_priority: strict
channels:
  - conda-forge
  - defaults

Conda list

# packages in environment at /Users/zane/miniforge3:
#
# Name                    Version                   Build  Channel
annotated-types           0.6.0              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
boltons                   23.0.0             pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py310h1253130_0    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.19.1               hb547adb_0    conda-forge
ca-certificates           2023.11.17           hf0a4a13_0    conda-forge
cachecontrol              0.13.1             pyhd8ed1ab_0    conda-forge
cachecontrol-with-filecache 0.13.1             pyhd8ed1ab_0    conda-forge
cachy                     0.3.0              pyhd8ed1ab_1    conda-forge
certifi                   2023.11.17         pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h2399d43_3    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
click-default-group       1.2.4              pyhd8ed1ab_0    conda-forge
clikit                    0.6.2              pyhd8ed1ab_2    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     23.9.0          py310hbe9552e_0    conda-forge
conda-libmamba-solver     23.9.2             pyhd8ed1ab_0    conda-forge
conda-lock                2.5.0              pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
crashtest                 0.4.1              pyhd8ed1ab_0    conda-forge
cryptography              41.0.3          py310hdd3b5e7_0    conda-forge
distlib                   0.3.7              pyhd8ed1ab_0    conda-forge
ensureconda               1.4.3              pyhd8ed1ab_0    conda-forge
filelock                  3.13.1             pyhd8ed1ab_0    conda-forge
fmt                       10.1.1               h1995070_0    conda-forge
gitdb                     4.0.11             pyhd8ed1ab_0    conda-forge
gitpython                 3.1.40             pyhd8ed1ab_0    conda-forge
html5lib                  1.1                pyh9f0ad1d_0    conda-forge
icu                       73.2                 hc8870d7_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
jaraco.classes            3.3.0              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonpatch                 1.32               pyhd8ed1ab_0    conda-forge
jsonpointer               2.0                        py_0    conda-forge
keyring                   24.2.0          py310hbe9552e_1    conda-forge
krb5                      1.21.2               h92f50d5_0    conda-forge
libarchive                3.7.2                h82b9b87_0    conda-forge
libcurl                   8.4.0                h2d989ff_0    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
libmamba                  1.5.3                h0a6dc31_2    conda-forge
libmambapy                1.5.3           py310h3812fd7_2    conda-forge
libnghttp2                1.52.0               hae82a92_0    conda-forge
libsolv                   0.7.24               ha614eb4_3    conda-forge
libsqlite                 3.43.0               hb31c410_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libxml2                   2.11.5               h25269f3_1    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
lz4-c                     1.9.4                hb7217d7_0    conda-forge
lzo                       2.10              h642e427_1000    conda-forge
mamba                     1.5.3           py310ha5d4528_2    conda-forge
markupsafe                2.1.3           py310h2aa6e3c_1    conda-forge
more-itertools            10.1.0             pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.6           py310h38f39d4_0    conda-forge
ncurses                   6.4                  h7ea286d_0    conda-forge
openssl                   3.1.4                h0d3ecfb_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pastel                    0.2.1              pyhd8ed1ab_0    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pkginfo                   1.9.6              pyhd8ed1ab_0    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h8e9501a_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  2.4.2              pyhd8ed1ab_1    conda-forge
pydantic-core             2.10.1          py310had9acf8_0    conda-forge
pylev                     1.4.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.12         h01493a6_0_cpython    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pyyaml                    6.0.1           py310h2aa6e3c_1    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
reproc                    14.2.4               h1a8c8d9_0    conda-forge
reproc-cpp                14.2.4               hb7217d7_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.32         py310h2aa6e3c_0    conda-forge
ruamel.yaml.clib          0.2.7           py310h8e9501a_1    conda-forge
setuptools                68.1.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     5.0.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tomlkit                   0.12.2             pyha770c72_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   1.26.18            pyhd8ed1ab_0    conda-forge
virtualenv                20.24.6            pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
yaml-cpp                  0.8.0                h13dd4ca_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zstandard                 0.19.0          py310h8e9501a_0    conda-forge
zstd                      1.5.5                h4f39d0f_0    conda-forge

Additional Context

micromamba --config

channels:
  - conda-forge
  - defaults
channel_priority: strict
auto_activate_base: false

micromamba --version

1.5.3

[maresb]

Thanks for the report! Looks like we have a regression. :disappointed:

Please let me know if you figure out a reliable way to locally reproduce this.

For context, these are virtual packages.

[maresb]

Ah, I see the problem. Our toposort function was not just sorting, but also filtering out the virtual packages. I'll fix this...