conda-smithy
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conda-forge
Error with `register-ci` introduced in 3.38.0: `stderr: 'fatal: pathspec './disabled_appveyor.yml' did not match any files'`
Solution to issue cannot be found in the documentation.
- [X] I checked the documentation.
Issue
I often use register-ci locally to activate Azure builds for my feedstock forks. Today this surprisingly failed. I got the same error with both 3.39.1 and 3.38.0. Once I downgraded to 3.37.2, it worked as expected. Looking at the diff between 3.38.0 and 3.37.2, I don't see why the register-ci behavior should have changed.
Here is how I discovered the error:
git clone https://github.com/jdblischak/r-git2r-feedstock.git
cd r-git2r-feedstock/
export AZURE_ORG_OR_USER="jdblischak"
conda smithy register-ci --user "jdblischak" --feedstock_directory . --without-all --with-azure
## No circle token. Create a token at https://circleci.com/account/api and
## put it in ~/.conda-smithy/circle.token
## No appveyor token. Create a token at https://ci.appveyor.com/api-token and
## Put one in ~/.conda-smithy/appveyor.token
## No drone token. Create a token at https://cloud.drone.io/account and
## Put one in ~/.conda-smithy/drone.token
## No anaconda token. Create a token via
## anaconda auth --create --name conda-smithy --scopes "repos conda api"
## and put it in ~/.conda-smithy/anaconda.token
## Traceback (most recent call last):
## File "/home/wsl/mambaforge/bin/conda-smithy", line 10, in <module>
## sys.exit(main())
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/cli.py", line 758, in main
## args.subcommand_func(args)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/cli.py", line 334, in __call__
## forge_config = _load_forge_config(args.feedstock_directory, None)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/configure_feedstock.py", line 2400, in _load_forge_config
## config = _legacy_compatibility_checks(config, forge_dir)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/configure_feedstock.py", line 2290, in _legacy_compatibility_checks
## remove_file_or_dir(os.path.join(forge_dir, old_file))
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/feedstock_io.py", line 67, in remove_file_or_dir
## return remove_file(filename)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/feedstock_io.py", line 80, in remove_file
## repo.index.remove([filename])
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/git/index/util.py", line 73, in post_clear_cache_if_not_raised
## rval = func(self, *args, **kwargs)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/git/index/util.py", line 95, in check_default_index
## return func(self, *args, **kwargs)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/git/index/base.py", line 1029, in remove
## removed_paths = self.repo.git.rm(args, paths, **kwargs).splitlines()
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/git/cmd.py", line 986, in <lambda>
## return lambda *args, **kwargs: self._call_process(name, *args, **kwargs)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/git/cmd.py", line 1598, in _call_process
## return self.execute(call, **exec_kwargs)
## File "/home/wsl/mambaforge/lib/python3.10/site-packages/git/cmd.py", line 1388, in execute
## raise GitCommandError(redacted_command, status, stderr_value, stdout_value)
## git.exc.GitCommandError: Cmd('git') failed due to: exit code(128)
## cmdline: git rm --cached -- ./disabled_appveyor.yml
## stderr: 'fatal: pathspec './disabled_appveyor.yml' did not match any files'
git status
## On branch main
## Your branch is up to date with 'origin/main'.
##
## Changes to be committed:
## (use "git restore --staged <file>..." to unstage)
## new file: ./disabled_appveyor.yml
##
## Untracked files:
## (use "git add <file>..." to include in what will be committed)
## disabled_appveyor.yml
With conda-smithy 3.37.2, it worked as expected:
conda smithy register-ci --user "jdblischak" --feedstock_directory . --without-all --with-azure
## No circle token. Create a token at https://circleci.com/account/api and
## put it in ~/.conda-smithy/circle.token
## No appveyor token. Create a token at https://ci.appveyor.com/api-token and
## Put one in ~/.conda-smithy/appveyor.token
## No drone token. Create a token at https://cloud.drone.io/account and
## Put one in ~/.conda-smithy/drone.token
## No anaconda token. Create a token via
## anaconda auth --create --name conda-smithy --scopes "repos conda api"
## and put it in ~/.conda-smithy/anaconda.token
## WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22
## Adding in variants from internal_defaults
## CI Summary for jdblischak/r-git2r-feedstock (can take ~30s):
## Travis registration disabled.
## Circle registration disabled.
## * jdblischak/r-git2r-feedstock has been enabled on azure pipelines
## Appveyor registration disabled.
## Drone registration disabled.
## Cirun registration disabled.
## Heroku webservice registration disabled.
##
## CI services have been enabled. You may wish to regenerate the feedstock.
## Any changes will need commiting to the repo.
Installed packages
# The working config with conda-smithy 3.37.2.
# The only downgraded package was rattler-build-conda-compat from 1.2.1 to 0.2.5
# packages in environment at /home/wsl/mambaforge:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
anyio 4.4.0 pyhd8ed1ab_0 conda-forge
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
backports 1.0 pyhd8ed1ab_4 conda-forge
backports.strenum 1.3.1 pyhd8ed1ab_0 conda-forge
backports.tarfile 1.0.0 pyhd8ed1ab_1 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
black 24.8.0 py310hff52083_0 conda-forge
blinker 1.8.2 pyhd8ed1ab_0 conda-forge
boa 0.17.0 pyhd8ed1ab_3 conda-forge
boltons 24.0.0 pyhd8ed1ab_0 conda-forge
boolean.py 4.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py310hf71b8c6_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.33.1 heb4867d_0 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
chardet 5.2.0 py310hff52083_2 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cirun 0.30 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 24.7.1 py310hff52083_0 conda-forge
conda-build 24.5.1 py310hff52083_0 conda-forge
conda-forge-pinning 2024.09.09.07.32.13 hd8ed1ab_0 conda-forge
conda-index 0.5.0 pyhd8ed1ab_0 conda-forge
conda-libmamba-solver 24.7.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.3.0 pyh7900ff3_0 conda-forge
conda-package-streaming 0.10.0 pyhd8ed1ab_0 conda-forge
conda-smithy 3.37.2 unix_pyh707e725_1 conda-forge
conda-souschef 2.2.3 pyhd8ed1ab_0 conda-forge
cryptography 43.0.1 py310h6c63255_0 conda-forge
curl 8.9.1 h18eb788_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
deprecated 1.2.14 pyh1a96a4e_0 conda-forge
distlib 0.3.8 pyhd8ed1ab_0 conda-forge
distro 1.9.0 pyhd8ed1ab_0 conda-forge
editables 0.5 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
expat 2.6.3 h5888daf_0 conda-forge
filelock 3.16.0 pyhd8ed1ab_0 conda-forge
fmt 10.2.1 h00ab1b0_0 conda-forge
frozendict 2.4.4 py310hc51659f_0 conda-forge
gettext 0.22.5 he02047a_3 conda-forge
gettext-tools 0.22.5 he02047a_3 conda-forge
git 2.46.0 pl5321hb5640b7_0 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.43 pyhd8ed1ab_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
grayskull 2.6.0 pyhd8ed1ab_1 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hatch 1.12.0 pyhd8ed1ab_0 conda-forge
hatchling 1.25.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.5 pyhd8ed1ab_0 conda-forge
httpx 0.27.2 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
hyperlink 21.0.0 pyhd3deb0d_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.8 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.4.0 pyha770c72_0 conda-forge
importlib_metadata 8.4.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.4 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
isodate 0.6.1 pyhd8ed1ab_0 conda-forge
jaraco.classes 3.4.0 pyhd8ed1ab_1 conda-forge
jaraco.context 5.3.0 pyhd8ed1ab_1 conda-forge
jaraco.functools 4.0.0 pyhd8ed1ab_0 conda-forge
jeepney 0.8.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
json5 0.9.25 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py310hff52083_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
keyring 25.3.0 pyha804496_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
libarchive 3.7.4 hfca40fe_0 conda-forge
libasprintf 0.22.5 he8f35ee_3 conda-forge
libasprintf-devel 0.22.5 he8f35ee_3 conda-forge
libblas 3.9.0 23_linux64_openblas conda-forge
libcblas 3.9.0 23_linux64_openblas conda-forge
libcurl 8.9.1 hdb1bdb2_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.3 h5888daf_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.1.0 h77fa898_1 conda-forge
libgcc-ng 14.1.0 h69a702a_1 conda-forge
libgettextpo 0.22.5 he02047a_3 conda-forge
libgettextpo-devel 0.22.5 he02047a_3 conda-forge
libgfortran 14.1.0 h69a702a_1 conda-forge
libgfortran-ng 14.1.0 h69a702a_1 conda-forge
libgfortran5 14.1.0 hc5f4f2c_1 conda-forge
libglib 2.80.3 h315aac3_2 conda-forge
libgomp 14.1.0 h77fa898_1 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblapack 3.9.0 23_linux64_openblas conda-forge
liblief 0.14.1 hac33072_1 conda-forge
libmamba 1.5.9 h4cc3d14_0 conda-forge
libmambapy 1.5.9 py310h86cbe3b_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsolv 0.7.30 h3509ff9_0 conda-forge
libsqlite 3.46.1 hadc24fc_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.1.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.1.0 h4852527_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
license-expression 30.1.1 pyhd8ed1ab_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mamba 1.5.9 py310h51d5547_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py310ha75aee5_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
menuinst 2.1.2 py310hff52083_1 conda-forge
more-itertools 10.5.0 pyhd8ed1ab_0 conda-forge
msrest 0.6.21 pyh44b312d_0 conda-forge
mypy_extensions 1.0.0 pyha770c72_0 conda-forge
ncurses 6.5 he02047a_1 conda-forge
numpy 2.1.1 py310hd6e36ab_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
openssl 3.3.2 hb9d3cd8_0 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
patch 2.7.6 h7f98852_1002 conda-forge
patchelf 0.17.2 h58526e2_0 conda-forge
pathspec 0.12.1 pyhd8ed1ab_0 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pip 24.2 pyh8b19718_1 conda-forge
pkginfo 1.11.1 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.3.2 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
progressbar2 4.5.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.47 pyha770c72_0 conda-forge
prompt_toolkit 3.0.47 hd8ed1ab_0 conda-forge
psutil 6.0.0 py310ha75aee5_1 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
py-lief 0.14.1 py310h76e45a6_1 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py310h2372a71_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pycryptodome 3.20.0 py310hb0f0acc_0 conda-forge
pygithub 2.4.0 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pyjwt 2.9.0 pyhd8ed1ab_1 conda-forge
pynacl 1.5.0 py310ha75aee5_4 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytest 8.3.2 pyhd8ed1ab_0 conda-forge
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-libarchive-c 5.1 py310hff52083_1 conda-forge
python-utils 3.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 5_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py310ha75aee5_1 conda-forge
rapidfuzz 3.9.7 py310hf71b8c6_0 conda-forge
rattler-build 0.21.0 hbfb6850_0 conda-forge
rattler-build-conda-compat 0.2.5 pyhd8ed1ab_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
requests-oauthlib 2.0.0 pyhd8ed1ab_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
ripgrep 14.1.0 he8a937b_0 conda-forge
rpds-py 0.20.0 py310h505e2c1_1 conda-forge
ruamel.yaml 0.18.6 py310h2372a71_0 conda-forge
ruamel.yaml.clib 0.2.8 py310h2372a71_0 conda-forge
ruamel.yaml.jinja2 0.2.7 pyhd8ed1ab_0 conda-forge
scrypt 0.8.24 py310h6ec971a_1 conda-forge
secretstorage 3.3.3 py310hff52083_2 conda-forge
semver 3.0.2 pyhd8ed1ab_0 conda-forge
setuptools 73.0.1 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stdlib-list 0.10.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomli-w 1.0.0 pyhd8ed1ab_0 conda-forge
tomlkit 0.13.2 pyha770c72_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tqdm 4.66.5 pyhd8ed1ab_0 conda-forge
trove-classifiers 2024.7.2 pyhd8ed1ab_0 conda-forge
truststore 0.9.2 pyhd8ed1ab_0 conda-forge
typer 0.12.5 pyhd8ed1ab_0 conda-forge
typer-slim 0.12.5 pyhd8ed1ab_0 conda-forge
typer-slim-standard 0.12.5 hd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024a h8827d51_1 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
userpath 1.7.0 pyhd8ed1ab_0 conda-forge
uv 0.4.7 h0f3a69f_0 conda-forge
virtualenv 20.26.4 pyhd8ed1ab_0 conda-forge
vsts-python-api 0.1.25 pyhd8ed1ab_1 conda-forge
watchgod 0.7 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py310ha75aee5_1 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
zipp 3.20.1 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py310ha39cb0e_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Environment info
active environment : base
active env location : /home/wsl/mambaforge
shell level : 1
user config file : /home/wsl/.condarc
populated config files : /home/wsl/mambaforge/.condarc
conda version : 24.7.1
conda-build version : 24.5.1
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake
__conda=24.7.1=0
__glibc=2.35=0
__linux=5.15.153.1=0
__unix=0=0
base environment : /home/wsl/mambaforge (writable)
conda av data dir : /home/wsl/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/wsl/mambaforge/pkgs
/home/wsl/.conda/pkgs
envs directories : /home/wsl/mambaforge/envs
/home/wsl/.conda/envs
platform : linux-64
user-agent : conda/24.7.1 requests/2.32.3 CPython/3.10.14 Linux/5.15.153.1-microsoft-standard-WSL2 ubuntu/22.04.4 glibc/2.35 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.9
UID:GID : 1000:1000
netrc file : None
offline mode : False
I ran into this same error again today with conda-smithy 3.43.0 when trying to locally run register-ci on the feedstock jdblischak/cellxgene-census-feedstock. Again I worked around it by downgrading to conda-smithy 3.37.2.
I'm still confused why this error started between 3.37.2 and 3.38.0. The functions _legacy_compatibility_checks, remove_file_or_dir, and remove_file haven't been touched in over a year. See below for links to git blame
https://github.com/conda-forge/conda-smithy/blame/52af540b1e3d9781893498ec5ce90f58c4c0d8e6/conda_smithy/configure_feedstock.py#L2275 https://github.com/conda-forge/conda-smithy/blame/52af540b1e3d9781893498ec5ce90f58c4c0d8e6/conda_smithy/feedstock_io.py#L65 https://github.com/conda-forge/conda-smithy/blame/52af540b1e3d9781893498ec5ce90f58c4c0d8e6/conda_smithy/feedstock_io.py#L75
Same issue here with latest version. I would be interested in a fix.
Thank you for reporting that.
Interesting development. I was once again able to run conda smithy register-ci with version 3.46.1 🎉
conda smithy --version
## 3.46.1
export AZURE_ORG_OR_USER="jdblischak"
conda smithy register-ci --user "jdblischak" --feedstock_directory . --without-all --with-azure
## * jdblischak/r-seurat-feedstock has been enabled on azure pipelines
I wanted to know which version fixed the problem. The last I had tried was 4.43.0, which was still failing. However, I wasn't able to easily determine this. That's because unlike the functional conda-smithy 3.37.0, which can be re-run over and over again in the same feedstock, 3.46.1 cannot be re-run after the initial activation.
conda smithy --version
## 3.46.1
# Re-running in a feedstock that has already enabled azure pipelines
export AZURE_ORG_OR_USER="jdblischak"
conda smithy register-ci --user "jdblischak" --feedstock_directory . --without-all --with-azure
## _pygit2.GitError: invalid data in index - invalid entry
Here's the full traceback:
Traceback (most recent call last):
File "/home/wsl/mambaforge/bin/conda-smithy", line 10, in <module>
sys.exit(main())
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/cli.py", line 767, in main
args.subcommand_func(args)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/cli.py", line 337, in __call__
forge_config = _load_forge_config(args.feedstock_directory, None)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/configure_feedstock.py", line 2516, in _load_forge_config
config = _legacy_compatibility_checks(config, forge_dir)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/configure_feedstock.py", line 2391, in _legacy_compatibility_checks
remove_file_or_dir(os.path.join(forge_dir, old_file))
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/feedstock_io.py", line 86, in remove_file_or_dir
return remove_file(filename)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/feedstock_io.py", line 99, in remove_file
touch_file(filename)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/feedstock_io.py", line 80, in touch_file
with write_file(filename) as fh:
File "/home/wsl/mambaforge/lib/python3.10/contextlib.py", line 142, in __exit__
next(self.gen)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/conda_smithy/feedstock_io.py", line 75, in write_file
repo.index.add(index_path)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/pygit2/repository.py", line 647, in index
check_error(err, io=True)
File "/home/wsl/mambaforge/lib/python3.10/site-packages/pygit2/errors.py", line 66, in check_error
raise GitError(message)
_pygit2.GitError: invalid data in index - invalid entry
And here is a demonstration that conda-smithy 3.37 has no trouble re-running in an already enabled feedstock:
mamba create --yes -n bisect-smithy conda-smithy=3.37
# Have to use conda-smithy when running outside the base env
conda smithy --version
## 3.46.1
conda-smithy --version
## 3.37.2
export AZURE_ORG_OR_USER="jdblischak"
conda-smithy register-ci --user "jdblischak" --feedstock_directory . --without-all --with-azure
## * jdblischak/r-seurat-feedstock already enabled on azure pipelines
So today I ran register-ci with conda-smithy 3.47.0. It was able to create the new pipeline in Azure pipelines. Furthermore, I was able to run it repeatedly without error in the same feedstock after the initial setup (unlike last time with 3.46.1; see above). However, I don't see any changes between 3.46.1 and 3.47.0 that would have affected the behavior of register-ci. And indeed, when I downgraded to conda-smithy 3.46.1, I was able to run register-ci in the already-registered feedstock without error.
So the good news is that this issue appears to have been resolved. And the bad news is that all of these errors are likely due to changes in dependencies, making it difficult to ensure it will continue to work in the future.