Initial runfile changes cwd to lowercase version which fails all code needing case sensitive paths

[DeltaMod]

I am using the latest version of Spyder through Anaconda, but this problem started with the first version of spyder 6+.
On launch, my path is correctly reflected in the working directory field
if I import os in the console, and use os.getcwd() it outputs a correctly formatted uppercase cwd (C://Users/Myname).
If I then run an empty script, I see the following command in the console

%runfile 'C:/Users/MyName/PathToPlace/EmptyScript.py' --wdir

My console working directory has now been swapped to:

'c:\\users\\myname\\pathtoplace"

which means that any commands that need winbows style path formatting fails. Is there a secret option I missed that stops this from happening? Right now, all of my code that uses os.listdir() and os.getcwd() to get filelists for plotting data can't be used because cwd is reflected incorrectly.
I thought it might be a package problem, but like I said, if I run a script that contains literally nothing, it changes my cwd.

Temporary solution currently is:
If you try to right click your tab and choose "set console working directory" it swaps to the uppercase path, then immediately back to a lowercase one... unless you swap to another file tab, choose "set console working directory", then swap back to your target file and do the same thing.
Now it works, but why?

Permanent solution currently is:
Downgrade to 5.5.1, which works flawlessly in comparison.

output of pip list in case it's relevant

Package Version ------------------------------- ------------------- aext-assistant 4.1.0 aext-assistant-server 4.1.0 aext-core 4.1.0 aext-core-server 4.1.0 aext-panels 4.1.0 aext-panels-server 4.1.0 aext-project-filebrowser-server 4.1.0 aext-share-notebook 4.1.0 aext-share-notebook-server 4.1.0 aext-shared 4.1.0 aext-toolbox 4.1.0 aiofiles 22.1.0 aiohappyeyeballs 2.4.4 aiohttp 3.11.10 aiosignal 1.2.0 aiosqlite 0.18.0 alabaster 0.7.16 alembic 1.13.3 anaconda-anon-usage 0.5.0 anaconda-cli-base 0.4.2 anaconda-client 1.13.0 anaconda-cloud-auth 0.7.2 anaconda-navigator 2.6.4 anaconda-project 0.11.1 annotated-types 0.6.0 anyio 4.6.2 archspec 0.2.3 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 arrow 1.3.0 astroid 3.3.8 astropy 6.0.0 astropy-iers-data 0.2024.3.11.18.33.3 asttokens 2.0.5 async-lru 2.0.4 async-timeout 5.0.1 asyncssh 2.17.0 atomicwrites 1.4.0 attrs 24.3.0 autopep8 2.0.4 babel 2.16.0 backports.functools-lru-cache 1.6.4 backports.tempfile 1.0 backports.weakref 1.0.post1 beautifulsoup4 4.12.3 binaryornot 0.4.4 black 24.10.0 bleach 6.2.0 bokeh 3.6.2 boltons 24.1.0 Bottleneck 1.4.2 Brotli 1.0.9 cairocffi 1.7.1 certifi 2025.1.31 cffi 1.17.1 chardet 4.0.0 charset-normalizer 3.3.2 click 8.1.7 cloudpickle 3.0.0 colorama 0.4.6 comm 0.2.1 conda 25.1.1 conda-build 25.1.2 conda-content-trust 0.2.0 conda_index 0.5.0 conda-libmamba-solver 25.1.1 conda-pack 0.7.1 conda-package-handling 2.4.0 conda_package_streaming 0.11.0 conda-repo-cli 1.0.137 conda-token 0.5.0+1.g2209e04 conda-verify 3.4.2 configparser 7.0.0 contourpy 1.2.0 cookiecutter 2.6.0 cryptography 44.0.1 cssselect2 0.7.0 cycler 0.12.1 datefinder 0.7.3 dateparser 1.2.0 debugpy 1.8.11 decorator 5.1.1 defusedxml 0.7.1 Deprecated 1.2.13 diff-match-patch 20200713 dill 0.3.8 distro 1.9.0 DMU 0.3.8 docstring-to-markdown 0.11 docutils 0.18.1 entrypoints 0.4 et-xmlfile 1.1.0 exceptiongroup 1.2.0 executing 0.8.3 fastjsonschema 2.20.0 filelock 3.13.1 flake8 7.1.1 fonttools 4.49.0 frozendict 2.4.2 frozenlist 1.5.0 future 1.0.0 greenlet 3.1.1 h11 0.14.0 h5py 3.10.0 hdf5storage 0.1.19 httpcore 1.0.2 httpx 0.27.0 idna 3.7 imagej 0.3.2 imagesize 1.4.1 imglyb 2.1.0 importlib_metadata 8.5.0 inflection 0.5.1 intervaltree 3.1.0 ipykernel 6.29.5 ipython 8.30.0 ipython-genutils 0.2.0 isort 5.13.2 jaraco.classes 3.2.1 jedi 0.19.2 jellyfish 1.1.3 jgo 1.0.6 Jinja2 3.1.5 JPype1 1.5.0 json5 0.9.25 jsonpatch 1.33 jsonpointer 2.1 jsonschema 4.23.0 jsonschema-specifications 2023.7.1 jupyter_client 8.6.3 jupyter_core 5.7.2 jupyter-events 0.10.0 jupyter-lsp 2.2.0 jupyter_server 2.14.1 jupyter_server_fileid 0.9.0 jupyter_server_terminals 0.4.4 jupyter_server_ydoc 0.8.0 jupyter-ydoc 0.2.5 jupyterlab 4.3.4 jupyterlab-pygments 0.1.2 jupyterlab_server 2.27.3 keyring 24.3.1 kiwisolver 1.4.5 labeling 0.1.14 latex2excel 0.1.dev0 latexcodec 2.0.1 libarchive-c 5.1 libmambapy 2.0.5 linkify-it-py 2.0.0 lxml 5.3.0 Mako 1.2.3 Markdown 3.4.1 markdown-it-py 2.2.0 MarkupSafe 3.0.2 mat73 0.63 matplotlib 3.8.3 matplotlib-inline 0.1.6 mccabe 0.7.0 mdit-py-plugins 0.3.0 mdurl 0.1.0 menuinst 2.2.0 mistune 2.0.4 mkl_fft 1.3.11 mkl_random 1.2.8 mkl-service 2.4.0 more-itertools 10.3.0 mpl-axes-aligner 1.3 multidict 6.1.0 mypy-extensions 1.0.0 natsort 8.3.1 navigator-updater 0.5.1 nb_conda_kernels 2.5.2 nbclassic 1.1.0 nbclient 0.8.0 nbconvert 7.16.4 nbformat 5.10.4 nest-asyncio 1.6.0 notebook 7.3.2 notebook_shim 0.2.3 numexpr 2.10.1 numpy 1.26.4 numpydoc 1.7.0 opencv-python 4.9.0.80 openpyxl 3.1.2 overrides 7.4.0 packaging 24.2 pandas 2.2.2 pandocfilters 1.5.0 panel 1.6.0 param 2.2.0 parso 0.8.4 pathspec 0.10.3 pexpect 4.8.0 pickleshare 0.7.5 pillow 11.1.0 pip 25.0.1 pkce 1.0.3 pkginfo 1.11.2 plasTeX 3.0 platformdirs 3.10.0 pluggy 1.5.0 ply 3.11 prometheus_client 0.21.0 prompt-toolkit 3.0.43 propcache 0.2.0 psutil 5.9.0 ptyprocess 0.7.0 pure-eval 0.2.2 py-slvs 1.0.6 pycodestyle 2.12.1 pycosat 0.6.6 pycparser 2.21 pydantic 2.10.3 pydantic_core 2.27.1 pydantic-settings 2.6.1 pydocstyle 6.3.0 pyerfa 2.0.1.1 pyflakes 3.2.0 PyGithub 2.4.0 Pygments 2.15.1 pyimagej 1.5.0 PyJWT 2.10.1 pylatexenc 2.10 pylint 3.3.3 pylint-venv 3.0.3 pyls-spyder 0.4.0 PyMySQL 1.1.1 PyNaCl 1.5.0 pyparsing 3.1.2 PyQt5 5.15.10 PyQt5_sip 12.13.0 PyQtWebEngine 5.15.6 PySocks 1.7.1 python-dateutil 2.9.0.post0 python-dotenv 0.21.0 python-json-logger 3.2.1 python-lsp-black 2.0.0 python-lsp-jsonrpc 1.1.2 python-lsp-server 1.12.0 python-slugify 5.0.2 pytoolconfig 1.2.6 pytz 2024.1 pyuca 1.2 pyvips 2.2.3 pyviz_comms 3.0.2 pywin32 308 pywin32-ctypes 0.2.2 pywinpty 2.0.14 PyYAML 6.0.2 pyzmq 26.2.0 QDarkStyle 3.2.3 qstylizer 0.2.2 QtAwesome 1.3.1 qtconsole 5.6.1 QtPy 2.4.1 readchar 4.0.5 referencing 0.30.2 regex 2024.5.15 reportlab 4.2.2 requests 2.32.3 requests-toolbelt 1.0.0 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rich 13.9.4 rope 1.12.0 rpds-py 0.22.3 Rtree 1.0.1 ruamel.yaml 0.18.6 ruamel.yaml.clib 0.2.8 ruamel-yaml-conda 0.17.21 scipy 1.12.0 scyjava 1.10.0 semver 3.0.2 Send2Trash 1.8.2 sentry-sdk 2.18.0 setuptools 69.0.3 shellingham 1.5.0 sip 6.7.12 six 1.16.0 sniffio 1.3.0 snowballstemmer 2.2.0 sortedcontainers 2.4.0 soupsieve 2.5 Sphinx 7.3.7 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.10 spyder 6.0.3 spyder-kernels 3.0.2 SQLAlchemy 2.0.37 stack-data 0.2.0 superqt 0.6.7 svglib 1.5.1 svgutils 0.3.4 svgwrite 1.4.3 tabulate 0.9.0 terminado 0.17.1 text-unidecode 1.3 textdistance 4.6.3 three-merge 0.1.1 tifffile 2024.2.12 tinycss2 1.4.0 toml 0.10.2 tomli 2.0.1 tomlkit 0.13.2 tornado 6.4.2 tqdm 4.67.1 traitlets 5.14.3 truststore 0.10.0 typer 0.9.0 typing_extensions 4.12.2 tzdata 2023.3 tzlocal 5.2 uc-micro-py 1.0.1 ujson 5.10.0 Unidecode 1.3.8 urllib3 2.3.0 watchdog 4.0.2 wcwidth 0.2.5 webencodings 0.5.1 websocket-client 1.8.0 whatthepatch 1.0.2 wheel 0.45.1 win-inet-pton 1.1.0 wrapt 1.17.0 xarray 2024.9.0 xlrd 2.0.1 xyzservices 2022.9.0 y-py 0.6.2 yapf 0.40.2 yarl 1.18.0 ypy-websocket 0.8.4 zipp 3.21.0 zstandard 0.23.0

[ccordoba12]

Hey @DeltaMod, thanks for reporting. We were not aware of this problem, so thanks for bringing it up to our attention.

We'll try to fix it in 6.0.6, to be released in a couple of months.

[ccordoba12]

@dalthviz, are you able to reproduce this one?

[dalthviz]

I think I was able to reproduce this:

I guess is caused due to the path after running a file being set as the working directory with a normalized version of the path (maybe at some point os.path.normcase is being used 🤔)