The python2.7 was so older that i can not install the module that your workflow need

[honghh2018]

Hi, developer
I want to return the spring_dev, but i get the module miss error, like below:

this module can not be install by pip.i already had solve the the preprocessing_python and the helper_functions module.
but the tables can not be solved by myself. it was complicated than i though.
Hope you help to fix this issue.
Best
Hanhuihong

[honghh2018]

Hi @calebweinreb @AllonMKlein everybody,
Had anyone hear this?

Best
Hanhuihong

[honghh2018]

Hi @AllonMKlein,
how can i do for this issue?

[calebweinreb]

There are no immediate plans for an upgrade to python3. Can you try installing the tables module via conda? ```conda install pytables```. This worked for me using python 2.7

…

On Thu, Jan 6, 2022 at 6:45 AM Alec hong ***@***.***> wrote: Hi @AllonMKlein <https://github.com/AllonMKlein>, how can i do for this issue? — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MUHLH5EZLLHXSGU6CDUUV6EVANCNFSM5LHDSTAQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[honghh2018]

Hi @calebweinreb ,
Excellent, it work on my virtual environmnt. you are bloody genius, and tremendously give me a mega help for this urgent project.
Thanks, God bless you
Best

[honghh2018]

Hi @calebweinreb ,
There is another issue showing up.
the code lying below:

#Save merged samples
merge_setup = {'/Dataset_v1':sample_list}
for s, smerge in merge_setup.items():
print smerge
t0 = time.time()
print t0
print '________________', s

cell_ix = np.in1d(samp_id_flat, smerge)

run_all_spring_1_6(E[cell_ix,:],
                 list(merged_list), s, main_spring_dir, normalize=False, tot_counts_final = total_counts[cell_ix],
                 min_counts = 3, min_cells = 3, min_vscore_pctl = 90, 
                 show_vscore_plot = True, num_pc = 50, pca_method = '', k_neigh=4, use_approxnn = False,
                 output_spring = True, num_force_iter = 2000,
                 cell_groupings = {'Sample': list(samp_id_flat[cell_ix])})

print time.time() - t0

np.save(main_spring_dir + s + '/cell_filter.npy', np.nonzero(cell_ix)[0])
np.savetxt(main_spring_dir + s + '/cell_filter.txt', np.nonzero(cell_ix)[0], fmt='%i')

print time.time() - t0

the error showing below:

['CTRL2', 'FI_3M', 'SRR8872326', 'SRR8872330', 'WT5M1', 'WT6W', 'F20_3M', 'PRT17', 'SRR8872327', 'SRR8872331', 'WT15M', 'WT5M2', 'WT9M']
1643102870.03
________________ /Dataset_v1
Filtering genes
Using 1835 genes
Running PCA
Building kNN graph
kNN built in 192.32610 sec
Saving SPRING files to /share/nas1/Data/Users/honghh/temp/spring-dev/test_data/Dataset_v1
{'Total Counts': array([1149, 2069, 2547, ..., 1361, 1552, 727])}

TypeError Traceback (most recent call last)
in ()
14 show_vscore_plot = True, num_pc = 50, pca_method = '', k_neigh=4, use_approxnn = False,
15 output_spring = True, num_force_iter = 2000,
---> 16 cell_groupings = {'Sample': list(samp_id_flat[cell_ix])})
17
18 print time.time() - t0

in run_all_spring_1_6(E, gene_list, sample_name, save_dir, base_ix, normalize, exclude_dominant_frac, min_counts, min_cells, min_vscore_pctl, show_vscore_plot, exclude_gene_names, num_pc, pca_method, pca_norm, k_neigh, cell_groupings, num_force_iter, output_spring, precomputed_pca, gene_filter, custom_colors, exclude_corr_genes_list, exclude_corr_genes_minCorr, dist_metric, use_approxnn, run_doub_detector, dd_k, dd_frac, dd_approx, tot_counts_final)
113 save_spring_dir_sparse_hdf5(E, [], 0, gene_list, save_path,
114 custom_colors = custom_colors, edges=list(links),
--> 115 cell_groupings = cell_groupings)
116 else:
117 save_spring_dir_sparse_hdf5(E, [], 0, gene_list, save_path,

TypeError: save_spring_dir_sparse_hdf5() got multiple values for keyword argument 'custom_colors'

how can i fix this issue?
Any advices would be appreciated.
Best,
Hanhuihong

[calebweinreb]

Can you send the data and notebook that led to the error? (calebsw@gmail.com)

[honghh2018]

Hi @calebweinreb ,
The ipynb file and the data had been sent to you from the 939869915@qq.com email.
Hope the reply.
Best
Hanhuihong

[honghh2018]

Hi @calebweinreb ,
Had any advices for this circumstance?

Best,
Hanhuihong

[honghh2018]

Hi @calebweinreb
Is data had received ?
Had anyone feedback this issue? if having any question please let me know. I am be glad to help.

[honghh2018]

Had anyone hear this circumstance？

[calebweinreb]

Hi, I'm very sorry for the late reply. In regard to the specific error, it seems to arise because save_spring_dir_sparse_hdf5 is defined as taking 4 position arguments and 2 keyword arguments, whereas in run_all_spring_1_6 it is being called with 5 positional arguments. Zooming out, it seems like this notebook is using functions that were copied from within cgi_bin? The code in cgi_bin is only intended for our web backend. To generate SPRING plots locally using a notebook, we recommend one of the recipes in the data_prep directory (e.g. https://github.com/AllonKleinLab/SPRING_dev/blob/master/data_prep/spring_example_pbmc4k.ipynb). All the helper functions for these notebooks should be imported from spring_helper.py

…

On Mon, Feb 7, 2022 at 3:46 AM Alec hong ***@***.***> wrote: Had anyone hear this circumstance？ — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MVBVUKMSVJODAKTVCLUZ6BERANCNFSM5LHDSTAQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[honghh2018]

Very grateful for the reply.
I have carefully checked the spring_example_pbmc4k.ipynb but found the weird question,
It can not found the spring_helper directory when Running the header of the notebook with from spring_helper import * .
It is strange that download the spring_dev software, because of the module of spring_helper can not be imported properly with conda environment.

%pylab inline
File "", line 1
%pylab inline
^
SyntaxError: invalid syntax
from spring_helper import *
Traceback (most recent call last):
File "", line 1, in
ImportError: No module named spring_helper
from doublet_detector import *
Traceback (most recent call last):
File "", line 1, in
ImportError: No module named doublet_detector
from collections import defaultdict

the spring setup following you github project workflow

Best,
Hanhuihong

[calebweinreb]

Since SPRING is not 'installed' in the environment, all the imports have to be from files that are in the current directory (or at least you need to add the path to them using sys.path.append). Is the spring_helpers.py file in the same directory that you are running the notebook from?

…

On Mon, Feb 7, 2022 at 9:43 PM Alec hong ***@***.***> wrote: Very grateful for the reply. I have carefully checked the spring_example_pbmc4k.ipynb but found the weird question, It can not found the spring_helper directory when Running the header of the notebook with from spring_helper import * . It is stranger that download the spring_dev software, because of the module of spring_helper can not be imported properly with conda environment. %pylab inline File "", line 1 %pylab inline ^ SyntaxError: invalid syntax from spring_helper import * Traceback (most recent call last): File "", line 1, in ImportError: No module named spring_helper from doublet_detector import * Traceback (most recent call last): File "", line 1, in ImportError: No module named doublet_detector from collections import defaultdict the spring setup following you github project workflow Best, Hanhuihong — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MU5ACWCOONF66SKNJLU2B7N5ANCNFSM5LHDSTAQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[honghh2018]

Hi @calebweinreb ,
Thanks the advices, The issue have be solved by your alert. I manually create a prep_data dir and bring the helper_funciton.py into it and then import it.
This way can work well.
Hope the Best for you
My friends