Closed Eddymorphling closed 11 months ago
adamltyson
commented
11 months ago Hi @Eddymorphling. @willGraham01 may be able to correct me, but I think brainglobe-workflows isn't on PyPI. You should be able to install it with:
pip install git+https://github.com/brainglobe/brainglobe-workflowsOr if you want to edit your installation:
git clone https://github.com/brainglobe/brainglobe-workflows
cd brainglobe-workflows
pip install -e .
Eddymorphling
commented
11 months ago pip install git+https://github.com/brainglobe/brainglobe-workflows
Ah didn't know. Installing via gitseems to work! Thanks!
adamltyson
commented
11 months ago We should document this better though. This package is still early in development though, so expect a few bumps along the road. Feel free to join our developer chat if you have any issues as an early adopter of V2.
Eddymorphling
commented
11 months ago Sorry @adamltyson. Going back to this again here. Has the cellfinder CLI changed? When I try to run the CLI I get an error
'cellfinder' is not recognized as an internal or external command,
operable program or batch file.
I also noticed that brainglobe-workflows only installed the cellfinder-core package but the cellfinder package is missing
adamltyson
commented
11 months ago My apologies. I think our blog post is slightly premature. The cellfinder CLI hasn't migrated to this package yet. You're safe to use the "original" cellfinder CLI for the time being. @willGraham01 knows more, but I think this package should be updated soon.
Eddymorphling
commented
11 months ago Ah ok. No worries. Thanks for letting me know :) I will keep an eye out on the for any new updates and will use the old one for now.
willGraham01
commented
11 months ago Sorry for the confusion Eddymorphling!
I think our blog post is slightly premature. The cellfinder CLI hasn't migrated to this package yet.
Yeah as @adamltyson said, we've not quite migrated cellfinder into this package yet, but will do so once this PR is approved.
brainglobe-workflows isn't on PyPI
Yep it's not yet made it to PyPI. It will become installable via pip install brainglobe-workflows once the update above goes in.
Eddymorphling
commented
10 months ago Hi @adamltyson and @willGraham01 .
A happy new year! Sorry to bug you with this again. I am trying to setup a new conda env with the new releases of Brainglobe, cellfinder and Brainglobe-workflows. I thought of setting up everything from scratch on a new conda env rather than tweaking my old one. I am trying to set this up on a virtual Linux machine that runs on my HPC to use GPU resources when running cellfinder.
I followed the instructions that I found over here . Here are the steps in brief to setup a new env.
conda create --name brainglobe python=3.10 followed byconda activate brainglobepython -m pip install brainreg[napari]pip install brainglobe-workflowsAfter following the above steps,I ran Brainreg napari plugin but end up with the following error
RuntimeError: Failed to import command at 'brainreg.napari.register:brainreg_register': No module named 'brainglobe_napari_io.cellfinder.reader_dir'
Strangely, I do not see the cellfinder plugin in napari or in my pip list. Am I doing something wrong or did I miss installing any other packages? Below is my pip list just in case. Thank you once again.
Package Version
----------------------------- ------------
absl-py 2.0.0
alabaster 0.7.13
app-model 0.2.4
appdirs 1.4.4
asttokens 2.4.1
astunparse 1.6.3
attrs 23.2.0
Babel 2.14.0
bg-atlasapi 1.0.2
bg_space 0.6.0
blosc2 2.4.0
brainglobe-napari-io 0.3.1
brainglobe-segmentation 1.1.0
brainglobe-utils 0.3.2
brainglobe-workflows 1.0.0
brainreg 1.0.1
build 1.0.3
cachetools 5.3.2
cachey 0.2.1
cellfinder-core 0.5.1
certifi 2023.11.17
charset-normalizer 3.3.2
click 8.1.7
cloudpickle 3.0.0
comm 0.2.1
configobj 5.0.8
dask 2023.12.1
debugpy 1.8.0
decorator 5.1.1
docstring-parser 0.15
docutils 0.17.1
exceptiongroup 1.2.0
executing 2.0.1
fancylog 0.3.0
flatbuffers 23.5.26
freetype-py 2.4.0
fsspec 2023.12.2
gast 0.4.0
google-auth 2.26.0
google-auth-oauthlib 0.4.6
google-pasta 0.2.0
grpcio 1.60.0
h5py 3.10.0
HeapDict 1.0.1
hsluv 5.0.4
idna 3.6
imageio 2.33.1
imagesize 1.4.1
imio 0.3.0
importlib-metadata 7.0.1
in-n-out 0.1.9
ipykernel 6.28.0
ipython 8.19.0
jedi 0.19.1
Jinja2 3.1.2
joblib 1.3.2
jsonschema 4.20.0
jsonschema-specifications 2023.12.1
jupyter_client 8.6.0
jupyter_core 5.7.0
keras 2.11.0
kiwisolver 1.4.5
lazy_loader 0.3
libclang 16.0.6
llvmlite 0.41.1
locket 1.0.0
magicgui 0.8.1
Markdown 3.5.1
markdown-it-py 3.0.0
MarkupSafe 2.1.3
matplotlib-inline 0.1.6
mdurl 0.1.2
meshio 5.3.4
msgpack 1.0.7
multiprocessing-logging 0.3.4
mypy-extensions 1.0.0
napari 0.4.18
napari-console 0.0.9
napari-plugin-engine 0.2.0
napari-svg 0.1.10
natsort 8.4.0
ndindex 1.7
nest-asyncio 1.5.8
networkx 3.2.1
nibabel 5.2.0
npe2 0.7.3
nptyping 2.5.0
numba 0.58.1
numexpr 2.8.8
numpy 1.26.3
numpydoc 1.5.0
oauthlib 3.2.2
opt-einsum 3.3.0
packaging 23.2
pandas 2.1.4
parso 0.8.3
partd 1.4.1
pexpect 4.9.0
pillow 10.2.0
Pint 0.23
pip 23.3.1
platformdirs 4.1.0
pooch 1.8.0
prompt-toolkit 3.0.43
protobuf 3.19.6
psutil 5.9.7
psygnal 0.9.5
ptyprocess 0.7.0
pure-eval 0.2.2
py-cpuinfo 9.0.0
pyasn1 0.5.1
pyasn1-modules 0.3.0
pyconify 0.1.6
pydantic 1.10.13
pydantic-compat 0.1.2
Pygments 2.17.2
pynrrd 1.0.0
PyOpenGL 3.1.7
pyproject_hooks 1.0.0
PyQt5 5.15.10
PyQt5-Qt5 5.15.2
PyQt5-sip 12.13.0
python-dateutil 2.8.2
pytz 2023.3.post1
PyYAML 6.0.1
pyzmq 25.1.2
qtconsole 5.5.1
QtPy 2.4.1
referencing 0.32.0
requests 2.31.0
requests-oauthlib 1.3.1
rich 13.7.0
rpds-py 0.16.2
rsa 4.9
scikit-image 0.22.0
scikit-learn 1.3.2
scipy 1.11.4
setuptools 68.2.2
six 1.16.0
slurmio 0.1.1
snowballstemmer 2.2.0
Sphinx 4.5.0
sphinxcontrib-applehelp 1.0.4
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
stack-data 0.6.3
superqt 0.6.1
tables 3.9.2
tensorboard 2.11.2
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorflow 2.11.1
tensorflow-estimator 2.11.0
tensorflow-io-gcs-filesystem 0.35.0
termcolor 2.4.0
threadpoolctl 3.2.0
tifffile 2023.12.9
tomli 2.0.1
tomli_w 1.0.0
toolz 0.12.0
tornado 6.4
tqdm 4.66.1
traitlets 5.14.1
treelib 1.7.0
typer 0.9.0
typing_extensions 4.9.0
tzdata 2023.4
urllib3 2.1.0
vispy 0.12.2
wcwidth 0.2.12
Werkzeug 3.0.1
wheel 0.41.2
wrapt 1.16.0
zipp 3.17.0
Hi @Eddymorphling, sorry about this! An update to brainreg is on it's way. Should be sorted by tommorow and I'll update you.
Eddymorphling
commented
10 months ago Thank you for the quick feedback @adamltyson. You guys are the best!
adamltyson
commented
10 months ago @Eddymorphling could you try pip install brainreg -U. I think this should be fixed now.
adamltyson
commented
10 months ago Also, a warning that we're in the middle of restructuring everything, so I'm afraid there may be lots of issues like this for the next few weeks.
Eddymorphling
commented
10 months ago @Eddymorphling could you try
pip install brainreg -U. I think this should be fixed now.
Yes, this fixed it. Thank you.
Can I still use the cellfinder CLI with my current setup? Or should I replace use brainmapper instead in the CLI..
adamltyson
commented
10 months ago From now on, please use brainmapper. It's exactly the same though, just a change of name.
Eddymorphling
commented
10 months ago Got it. Will do so. I will also keep an eye for any updates.
Eddymorphling
commented
10 months ago Hi @adamltyson Is there a way to run Cellfinder training via CLI? If yes, could you please share the documentation for this? Thank you.
Eddymorphling
commented
10 months ago Nevermind found it here
Hi folks,
Thank you for the work done so far on Brainglobe v1.
I have been using the previous versions of brainreg/cellfinder using CLIs and now am trying to setup
Brainglobe-workflows. I was able to setup the newbrainregwithout any issues in a new conda env. But when I try to installBrainglobe-worksflowsin the same env usingpipit throws an error (below). Seems like its not able to find the package? Any suggestions?Thanks!