[BUG] Brainglobe-workflows not found?

[Eddymorphling]

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 new brainreg without any issues in a new conda env. But when I try to install Brainglobe-worksflows in the same env using pip it throws an error (below). Seems like its not able to find the package? Any suggestions?

ERROR: Could not find a version that satisfies the requirement brainglobe-workflows (from versions: none)
ERROR: No matching distribution found for brainglobe-workflows

Thanks!

[adamltyson]

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-workflows

Or if you want to edit your installation:

git clone https://github.com/brainglobe/brainglobe-workflows
cd brainglobe-workflows
pip install -e .

[Eddymorphling]

pip install git+https://github.com/brainglobe/brainglobe-workflows

Ah didn't know. Installing via git seems to work! Thanks!

[adamltyson]

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]

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]

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]

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]

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]

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.

1. Setting up a new env - conda create --name brainglobe python=3.10 followed by conda activate brainglobe
2. Installing "new" brainreg - python -m pip install brainreg[napari]
3. Installing brainglobe-workflows - pip install brainglobe-workflows
4. Start napari.

After 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

[adamltyson]

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]

Thank you for the quick feedback @adamltyson. You guys are the best!

[adamltyson]

@Eddymorphling could you try pip install brainreg -U. I think this should be fixed now.

[adamltyson]

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]

@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]

From now on, please use brainmapper. It's exactly the same though, just a change of name.

[Eddymorphling]

Got it. Will do so. I will also keep an eye for any updates.

[Eddymorphling]

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]

Nevermind found it here