TypeError: __init__() got an unexpected keyword argument 'dist_std_local'

[HuangDDU]

A good job! The result and plot is interseting! When I run the tutorial(https://pyvia.readthedocs.io/en/latest/ViaJupyter_Toy_Multifurcating.html) with Jupyter Notebook, I meet some troubles.

#define parameters
ncomps, knn, random_seed, dataset, root_user  =30,20, 42,'toy', ['M1']
[](url)
v0 = VIA(adata_counts.obsm['X_pca'][:, 0:ncomps], true_label, jac_std_global=0.15, dist_std_local=1,
             knn=knn, cluster_graph_pruning_std=1, too_big_factor=0.3, root_user=root_user, preserve_disconnected=True, dataset='group',
             random_seed=random_seed)#, piegraph_arrow_head_width=0.2,             piegraph_edgeweight_scalingfactor=1.0)  
v0.run_VIA()

I got the following error

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks/Basic tutorial.ipynb 单元格 11 line 4
      [1](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20tutorial.ipynb#X10sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0) #define parameters
      [2](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20tutorial.ipynb#X10sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1) ncomps, knn, random_seed, dataset, root_user  =30,20, 42,'toy', ['M1']
----> [4](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20tutorial.ipynb#X10sdnNjb2RlLXJlbW90ZQ%3D%3D?line=3) v0 = VIA(adata_counts.obsm['X_pca'][:, 0:ncomps], true_label, dist_std_local=1,
      [5](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20tutorial.ipynb#X10sdnNjb2RlLXJlbW90ZQ%3D%3D?line=4)              knn=knn, cluster_graph_pruning_std=1, too_big_factor=0.3, root_user=root_user, preserve_disconnected=True, dataset='group',
      [6](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20tutorial.ipynb#X10sdnNjb2RlLXJlbW90ZQ%3D%3D?line=5)              random_seed=random_seed)#, piegraph_arrow_head_width=0.2,             piegraph_edgeweight_scalingfactor=1.0)  
      [7](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20tutorial.ipynb#X10sdnNjb2RlLXJlbW90ZQ%3D%3D?line=6) v0.run_VIA()

TypeError: __init__() got an unexpected keyword argument 'dist_std_local'

My python is 3.8.18 and pyVIA version is 0.1.94. The pyVIA version is the latest version following by pypi(https://pypi.org/project/pyVIA/) and github repository setup.py. May be version 2 is not upload?

(via) huang@yu:~/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks$ pip list | grep pyVIA
pyVIA                     0.1.94
(via) huang@yu:~/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks$ python
Python 3.8.18 | packaged by conda-forge | (default, Oct 10 2023, 15:44:36)

I enter into the core.py VIA.init(...) where no parameter jac_std_global and cluster_graph_pruning_std appear.May be wrong source code version is uploaded? I will be pleasure to get your response.

[ShobiStassen]

Hi there,

I have changed some the of parameter names to be more intuitive (and updating the documents too). Have you followed the syntax in: https://pyvia.readthedocs.io/en/latest/ViaJupyter_Toy_Multifurcating.html

And

https://pyvia.readthedocs.io/en/latest/mESC_timeseries.html

This has different parameter names than those you wrote in your message. 0.1.94 pyvia is a soft launch of Via2.0 so you will be able to plot all the Atlas views and pathways (syntax examples and usage also in the Cartography tutorials)

Let me know how you get on Shobi

On Tue, 24 Oct 2023, 10:57 HuangDDU, @.***> wrote:

A good @job https://github.com/job! The result and plot is interseting! When I run the tutorial( https://pyvia.readthedocs.io/en/latest/ViaJupyter_Toy_Multifurcating.html) with Jupyter Notebook, I meet some troubles.

define parameters

ncomps, knn, random_seed, dataset, root_user =30,20, 42,'toy', ['M1'] v0 = VIA(adata_counts.obsm['X_pca'][:, 0:ncomps], true_label, jac_std_global=0.15, dist_std_local=1, knn=knn, cluster_graph_pruning_std=1, too_big_factor=0.3, root_user=root_user, preserve_disconnected=True, dataset='group', random_seed=random_seed)#, piegraph_arrow_head_width=0.2, piegraph_edgeweight_scalingfactor=1.0) v0.run_VIA()

I got the following error

---

TypeError Traceback (most recent call last) /home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks/Basic tutorial.ipynb 单元格 11 line 4 1 #define parameters 2 ncomps, knn, random_seed, dataset, root_user =30,20, 42,'toy', ['M1'] ----> 4 v0 = VIA(adata_counts.obsm['X_pca'][:, 0:ncomps], true_label, dist_std_local=1, 5 knn=knn, cluster_graph_pruning_std=1, too_big_factor=0.3, root_user=root_user, preserve_disconnected=True, dataset='group', 6 random_seed=random_seed)#, piegraph_arrow_head_width=0.2, piegraph_edgeweight_scalingfactor=1.0) 7 v0.run_VIA()

TypeError: init() got an unexpected keyword argument 'dist_std_local'

My python is 3.8.18 and pyVIA version is 0.1.94. The pyVIA version is the latest version following by pypi(https://pypi.org/project/pyVIA/) and github repository setup.py. May be version 2 is not upload?

(via) @.:~/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks$ pip list | grep pyVIA pyVIA 0.1.94 (via) @.:~/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks$ python Python 3.8.18 | packaged by conda-forge | (default, Oct 10 2023, 15:44:36)

I enter into the core.py VIA.init(...) where no parameter jac_std_global and cluster_graph_pruning_std appear.May be wrong source code version is uploaded? I will be pleasure to get your response.

— Reply to this email directly, view it on GitHub https://github.com/ShobiStassen/VIA/issues/47, or unsubscribe https://github.com/notifications/unsubscribe-auth/AISI4SBDOHLQLTMUHHC7MBDYA4OB5AVCNFSM6AAAAAA6M6Q4A2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2TQMZSGYZTKMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[HuangDDU]

Thanks for your reply, I stil have some problems flowed by your instruction https://pyvia.readthedocs.io/en/latest/ViaJupyter_Toy_Multifurcating.html.

1. The first cell of the turtoral aim to import package, where core_via2 package is not available while the old pyVIA.core is useful

   # from core_via2 import * #to be released soon # unuseful
   from pyVIA.core import *

   The the most plots can be reproducted. However, few plots function is error. Such as the Overall trajectory section

   # draw overall pseudotime and main trajectories
   plot_trajectory_curves(via_object=v0)# or set  embedding=embedding_of_your_choice
   plt.show()

   
   ---------------------------------------------------------------------------
   AttributeError                            Traceback (most recent call last)
   /home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter Notebooks/Basic workflow.ipynb 单元格 23 line 2
     [1](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20workflow.ipynb#Y122sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0) # draw overall pseudotime and main trajectories
   ----> [2](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20workflow.ipynb#Y122sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1) plot_trajectory_curves(via_object=v0)# or set  embedding=embedding_of_your_choice
     [3](vscode-notebook-cell://ssh-remote%2B192.168.1.2/home/huang/PyCode/scRNA/VIA/VIA-master/Jupyter%20Notebooks/Basic%20workflow.ipynb#Y122sdnNjb2RlLXJlbW90ZQ%3D%3D?line=2) plt.show()

File ~/.conda/envs/via/lib/python3.8/site-packages/pyVIA/plotting_via.py:2743, in plot_trajectory_curves(via_object, embedding, idx, title_str, draw_all_curves, arrow_width_scale_factor, scatter_size, scatter_alpha, linewidth, marker_edgewidth, cmap_pseudotime, dpi, highlight_terminal_states, use_maxout_edgelist) 2740 y_val = y_val.reshape((len(y_val), -1)) 2741 xp = np.linspace(minx, maxx, 500) -> 2743 gam50 = pg.LinearGAM(n_splines=4, spline_order=3, lam=10).gridsearch(x_val, y_val) 2744 XX = gam50.generate_X_grid(term=0, n=500) 2745 preds = gam50.predict(XX)

File ~/.local/lib/python3.8/site-packages/pygam/pygam.py:1894, in GAM.gridsearch(self, X, y, weights, return_scores, keep_best, objective, progress, **paramgrids) 1892 coef = models[-1].coef 1893 gam.setparams(coef=coef, force=True, verbose=False) -> 1894 gam.fit(X, y, weights) 1896 except ValueError as error: 1897 msg = str(error) + '\non model with params:\n' + str(param_grid)

File ~/.local/lib/python3.8/site-packages/pygam/pygam.py:920, in GAM.fit(self, X, y, weights) 917 self.statistics_['m_features'] = X.shape[1] 919 # optimize --> 920 self._pirls(X, y, weights) 921 # if self._opt == 0: 922 # self._pirls(X, y, weights) 923 # if self._opt == 1: 924 # self._pirls_naive(X, y) 925 return self

File ~/.local/lib/python3.8/site-packages/pygam/pygam.py:686, in GAM._pirls(self, X, Y, weights) 669 def _pirls(self, X, Y, weights): 670 """ 671 Performs stable PIRLS iterations to estimate GAM coefficients 672 (...) 684 None 685 """ --> 686 modelmat = self._modelmat(X) # build a basis matrix for the GLM 687 n, m = modelmat.shape 689 # initialize GLM coefficients if model is not yet fitted

File ~/.local/lib/python3.8/site-packages/pygam/pygam.py:459, in GAM._modelmat(self, X, term) 437 """ 438 Builds a model matrix, B, out of the spline basis for each feature 439 (...) 453 containing model matrix of the spline basis for selected features 454 """ 455 X = check_X(X, nfeats=self.statistics['m_features'], 456 edge_knots=self.edgeknots, dtypes=self.dtype, 457 features=self.feature, verbose=self.verbose) --> 459 return self.terms.build_columns(X, term=term)

File ~/.local/lib/python3.8/site-packages/pygam/terms.py:1719, in TermList.build_columns(self, X, term, verbose) 1717 columns = [] 1718 for term_id in term: -> 1719 columns.append(self._terms[term_id].build_columns(X, verbose=verbose)) 1720 return sp.sparse.hstack(columns, format='csc')

File ~/.local/lib/python3.8/site-packages/pygam/terms.py:784, in SplineTerm.build_columns(self, X, verbose) 768 """construct the model matrix columns for the term 769 770 Parameters (...) 780 scipy sparse array with n rows 781 """ 782 X[:, self.feature][:, np.newaxis] --> 784 splines = b_spline_basis(X[:, self.feature], 785 edge_knots=self.edgeknots, 786 spline_order=self.spline_order, 787 n_splines=self.n_splines, 788 sparse=True, 789 periodic=self.basis in ['cp'], 790 verbose=verbose) 792 if self.by is not None: 793 splines = splines.multiply(X[:, self.by][:, np.newaxis])

File ~/.local/lib/python3.8/site-packages/pygam/utils.py:649, in b_spline_basis(x, edge_knots, n_splines, spline_order, sparse, periodic, verbose) 646 aug_knots[-1] += 1e-9 # want last knot inclusive 648 # prepare Haar Basis --> 649 bases = (x >= aug_knots[:-1]).astype(np.int) * \ 650 (x < aug_knots[1:]).astype(np.int) 651 bases[-1] = bases[-2][::-1] # force symmetric bases at 0 and 1 653 # do recursion from Hastie et al. vectorized

File ~/.conda/envs/via/lib/python3.8/site-packages/numpy/init.py:305, in getattr(attr) 300 warnings.warn( 301 f"In the future np.{attr} will be defined as the " 302 "corresponding NumPy scalar.", FutureWarning, stacklevel=2) 304 if attr in former_attrs: --> 305 raise AttributeError(former_attrs[attr]) 307 # Importing Tester requires importing all of UnitTest which is not a 308 # cheap import Since it is mainly used in test suits, we lazy import it 309 # here to save on the order of 10 ms of import time for most users 310 # 311 # The previous way Tester was imported also had a side effect of adding 312 # the full numpy.testing namespace 313 if attr == 'testing':

AttributeError: module 'numpy' has no attribute 'int'. np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

The above problem may be from wrong package of numpy version or the import action in first cell.

2. Can you please synchronize the readthdoc and GitHub repository notebooks so I can run the tutorial code more easily?

3. What's more, other notebook updates is keenly awaited.

Looking forward for your reply!

[HuangDDU]

Can you solve these problems

[ShobiStassen]

Hi @HuangDDU ,

1. the latest version 0.1.94 onwards of Via will have the functionality of Via 2.0, it's just a soft launch at the moment. So you can go ahead and use import pyVIA.core and you will get Via 2.0
2. I am not getting your error message when I run plot_trajectory_curves(). This is the numpy and pygam version i have: numpy == 1.24.3 and pygam 0.9.0. I just tried when i updated this tutorial let me know if you still have issues
3. generally the RTD pages will be up to date and i'll remove some of the notebooks from github to avoid confusion