[ANN] Spyder 4.0 fifth public beta release

[Carlos Córdoba]

Hi all,

On the behalf of the Spyder Project Contributors, I’m pleased to announce the fifth beta of our next major version: Spyder 4.0.

We’ve been working on this version for almost three years now and as far as we know it’s working very well. There are still several bugs to squash but we encourage all people who like the bleeding edge to give it a try. This beta version is released 6 weeks after Spyder 4.0 beta4 and it includes more than 540 commits.

Spyder 4.0 comes with several interesting and exciting new features. The most important ones are:

• Main Window

  • Dark theme for the entire application.
  • A new Plots pane to browse all inline figures generated by the IPython console.
  • Rename the following panes:
    • Static code analysis to Code Analysis
    • File explorer to Files
    • Find in files to Find
    • History log to History
    • Project explorer to Project
  • Create a separate window when undocking all panes.
  • Show current conda environment (if any) in the status bar.

• Editor

  • Code folding.
  • Indentation guides.
  • A class/method/function lookup panel. This can be shown in the menu Source > Show selector for classes and functions.
  • Autosave functionality to recover unsaved files after a crash.
  • Code completion and linting are provided by the Python Language Server.

• IPython Console

  • Run files in an empty namespace.
  • Create dedicated consoles for Pylab, Sympy and Cython.
  • Run cells through a new function called runcell.
  • Run cells by name.

• Debugger

  • runfile and runcell can be called when the debugger is active.
  • Debug cells by pressing Alt+Shift+Return.
  • Permanent history.
  • Syntax highlighting.

• Variable Explorer

  • New viewer to inspect any Python object in a tree-like view.
  • Filter variables by name or type.
  • MultiIndex support in the Dataframe viewer.
  • Support for all Pandas indexes.
  • Support for sets.
  • Support for Numpy object arrays.

• Files

  • Associate external applications to open specific file extensions.
  • Context menu action to open files externally.
  • Multi-select functionality with Ctrl/Shift + mouse click.
  • Copy/paste files and their absolute or relative paths.
  • Use special icons for different file types.

• Outline

  • Show cells grouped in sections.
  • Add default name to all cells.

For a more complete list of changes, please see our changelog

You can easily install this beta if you use Anaconda by running:

conda update qt pyqt
conda install -c spyder-ide spyder=4.0.0b5

Or you can use pip with this command:

pip install --pre -U spyder

Enjoy!
Carlos

​

[Stephen P. Molnar]

I am using the Spyder4.0.0b5 IDE with Python 3.7.3 and have encountered, what to me at least, is a rather strange problem.

The code, at this point is:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Apr  8 15:17:07 2017

@author: comp

"""
#import numpy as np
#import matplotlib.pyplot as plt
import pandas as pd

name = input("Enter Molecule ID: ")

print(name)

ligand_file = name+'_apo-1acl.RMSD'

print('Ligand file = ',ligand_file)

data = pd.read_table('ligand_file',skiprows = 7)

print(data)

The input file, in this example, 17-3_apo-1acl.RMSD is:

    RMSD TABLE
    __________

_____________________________________________________________________
     |      |      |           |         |                 |
Rank | Sub- | Run  | Binding   | Cluster | Reference       | Grep
     | Rank |      | Energy    | RMSD    | RMSD            | Pattern
_____|______|______|___________|_________|_________________|___________
   1      1      8       -7.23      0.00     93.07           RANKING
   1      2      9       -6.79      1.39     92.64           RANKING
   2      1     16       -7.18      0.00     93.19           RANKING
   3      1      2       -6.93      0.00     93.38           RANKING
   3      2     17       -6.84      0.23     93.45           RANKING
   4      1     15       -6.55      0.00     91.83           RANKING
   4      2      7       -6.34      0.33     91.77           RANKING
   5      1      5       -6.41      0.00     93.05           RANKING
   6      1      3       -6.36      0.00     92.84           RANKING
   6      2     10       -6.28      0.47     92.92           RANKING
   6      3      6       -6.27      0.43     92.82           RANKING
   6      4     18       -6.25      0.32     92.88           RANKING
   6      5     13       -6.24      0.96     92.75           RANKING
   6      6      1       -6.24      0.87     92.60           RANKING
   6      7     14       -6.21      0.51     92.90           RANKING
   6      8     11       -6.14      0.98     92.78           RANKING
   6      9     20       -6.11      0.71     92.67           RANKING
   6     10     19       -6.01      1.36     93.00           RANKING
   7      1     12       -6.30      0.00     93.28           RANKING
   8      1      4       -5.85      0.00     92.97           RANKING
_______________________________________________________________________

The output at this point is:

Enter Molecule ID: 17-3
17-3
Ligand file =  17-3_apo-1acl.RMSD
Traceback (most recent call last):

  File "<ipython-input-3-48de0a8fd907>", line 1, in <module>
runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.', wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable')

  File "/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py", line 827, in runfile
    execfile(filename, namespace)

  File "/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py", line 110, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.", line 23, in <module>
    data = pd.read_table('ligand_file',skiprows = 7)

  File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 685, in parser_f
    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 457, in _read
    parser = TextFileReader(fp_or_buf, **kwds)

  File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 895, in __init__
    self._make_engine(self.engine)

  File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 1135, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)

  File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 1917, in __init__
    self._reader = parsers.TextReader(src, **kwds)

  File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.__cinit__

  File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source

FileNotFoundError: [Errno 2] File b'ligand_file' does not exist: b'ligand_file'


However, if I change the data = line to:

data = pd.read_table('13-7_apo-1acl.RMSD',skiprows = 7)

The output is:

runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.', wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable')

Enter Molecule ID: 13-7
13-7
Ligand file =  13-7_apo-1acl.RMSD
_____|______|______|___________|_________|_________________|___________
0      1      1      8       -7.23      0.00 9...
1      1      2      9       -6.79      1.39 9...
2      2      1     16       -7.18      0.00 9...
3      3      1      2       -6.93      0.00 9...
4      3      2     17       -6.84      0.23 9...
5      4      1     15       -6.55      0.00 9...
6      4      2      7       -6.34      0.33 9...
7      5      1      5       -6.41      0.00 9...
8      6      1      3       -6.36      0.00 9...
9      6      2     10       -6.28      0.47 9...
10     6      3      6       -6.27      0.43 9...
11     6      4     18       -6.25      0.32 9...
12     6      5     13       -6.24      0.96 9...
13     6      6      1       -6.24      0.87 9...
14     6      7     14       -6.21      0.51 9...
15     6      8     11       -6.14      0.98 9...
16     6      9     20       -6.11      0.71 9...
17     6     10     19       -6.01      1.36 9...
18     7      1     12       -6.30      0.00 9...
19     8      1      4       -5.85      0.00 9...
20 ______________________________________________...

I have used the ligand_file = line in other Python script that has worked without any errors.

Google has not been a solution in his case.  Pointers towards wolutions to this problem will be much appreciated.

Thanks in advance.

--
Stephen P. Molnar, Ph.D.            Life is a fuzzy set
http://www.Molecular-Modeling.net   Multivariate and stochastic
614.312.7528 (c)
Skype:  smolnar1

[Björn Johansson]

Seems file name is:

17-3_apo-1acl.RMSD in the first case and

13-7_apo-1acl.RMSD in the second ?

[Michiel Karrenbelt]

look like you are passing a string instead of a variable

data = pd.read_table('ligand_file', skiprows=7)

should be

data = pd.read_table(ligand_file, skiprows=7)

[bcolsen]

In your read table line you have quotes around your variable name so pandas is looking for a file named 'ligand_file' instead of the string the the variable is pointing to. Just remove the quotes and you'll be good to go.

[Stephen P. Molnar]

Thanks for the reply.

The first file was a mistake.

The problem was due to quotes around the file name. The problem has been solved.

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--

Stephen P. Molnar, Ph.D.            Life is a fuzzy set

Foundation for Chemistry            Multivariate and stochastic
http://www.Molecular-Modeling.net
614.312.7528 (c)
Skype:  smolnar1