Bug#1085363: bioxtasraw: Python SyntaxWarning

Graham Inggs ginggs at debian.org
Fri Oct 18 17:29:13 BST 2024 

Source: bioxtasraw
Version: 2.2.2-2
User: debian-python at lists.debian.org
Usertags: syntaxwarning

Hi Maintainer

The SyntaxWarning below were emitted when this package was tested with
pipuarts[1].

Regards
Graham


[1] https://piuparts.debian.org/sid/source/b/bioxtasraw.html


  Setting up python3-bioxtasraw (2.2.2-2) ...
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:467:
SyntaxWarning: invalid escape sequence '\s'
    five_col_fit =
re.compile('\s*\d*[.]\d*[+eE-]*\d+\s+-?\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:468:
SyntaxWarning: invalid escape sequence '\s'
    three_col_fit =
re.compile('\s*\d*[.]\d*[+eE-]*\d+\s+-?\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:469:
SyntaxWarning: invalid escape sequence '\s'
    two_col_fit =
re.compile('\s*\d*[.]\d*[+eE-]*\d+\s+-?\d*[.]\d*[+eE-]*\d+\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:471:
SyntaxWarning: invalid escape sequence '\s'
    results_fit =
re.compile('\s*Current\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s*\d*[.]?\d*[+eE-]*\d*\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:473:
SyntaxWarning: invalid escape sequence '\s'
    te_fit = re.compile('\s*Total\s+[Ee]stimate\s*:\s+\d*[.]\d+\s*\(?[A-Za-z\s]+\)?\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:474:
SyntaxWarning: invalid escape sequence '\d'
    te_num_fit = re.compile('\d*[.]\d+')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:475:
SyntaxWarning: invalid escape sequence '\s'
    te_quality_fit = re.compile('[Aa][A-Za-z\s]+\)?\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:477:
SyntaxWarning: invalid escape sequence '\s'
    p_rg_fit = re.compile('\s*Real\s+space\s*\:?\s*Rg\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*\+-\s*\d*[.]\d+[+eE-]*\d*')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:478:
SyntaxWarning: invalid escape sequence '\s'
    q_rg_fit = re.compile('\s*Reciprocal\s+space\s*\:?\s*Rg\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:480:
SyntaxWarning: invalid escape sequence '\s'
    p_i0_fit = re.compile('\s*Real\s+space\s*\:?[A-Za-z0-9\s\.,+-=]*\(0\)\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*\+-\s*\d*[.]\d+[+eE-]*\d*')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:481:
SyntaxWarning: invalid escape sequence '\s'
    q_i0_fit = re.compile('\s*Reciprocal\s+space\s*\:?[A-Za-z0-9\s\.,+-=]*\(0\)\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:629:
SyntaxWarning: invalid escape sequence '\s'
    iq_pattern =
re.compile('\s*\d*[.]\d*[+eE-]*\d+\s+-?\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:713:
SyntaxWarning: invalid escape sequence '\s'
    iq_pattern =
re.compile('\s*\d*[.]\d*[+eE-]*\d+\s+-?\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/DENSS.py:788:
SyntaxWarning: invalid escape sequence '\s'
    iq_pattern =
re.compile('\s*\d*[.]\d*[+eE-]*\d+\s+-?\d*[.]\d*[+eE-]*\d+\s+\d*[.]\d*[+eE-]*\d+\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:395:
SyntaxWarning: invalid escape sequence '\l'
    self.subplotLabels = [('Guinier', '$q^2$', '$\ln(I(q))$', .1),
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:396:
SyntaxWarning: invalid escape sequence '\D'
    ('Normalized Residual', '$q^2$', '$\Delta \ln (I(q))/\sigma (q)$', 0.1)]
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:398:
SyntaxWarning: invalid escape sequence '\l'
    self.subplotLabels = [('Guinier', '$q^2$', '$\ln(I(q))$', .1),
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:399:
SyntaxWarning: invalid escape sequence '\D'
    ('Residual', '$q^2$', '$\Delta \ln (I(q))$', 0.1)]
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:3780:
SyntaxWarning: invalid escape sequence '\i'
    subplotLabels = [('Integrated Area of q*I(q)', 'q', '$\int q \cdot
I(q) dq$', 'VC')]
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:4095:
SyntaxWarning: invalid escape sequence '\D'
    '$\Delta I(q)/\sigma (q)$', 0.1))
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:4097:
SyntaxWarning: invalid escape sequence '\D'
    subplotLabels.append(('Residual', '$q$', '$\Delta I(q)$', 0.1))
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:7839:
SyntaxWarning: invalid escape sequence '\D'
    ax1.set_ylabel('$\Delta I(q)/\sigma (q)$')
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:7841:
SyntaxWarning: invalid escape sequence '\D'
    ax1.set_ylabel('$\Delta I(q)$')
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:10339:
SyntaxWarning: invalid escape sequence '\c'
    ax0.set_ylabel('$\chi^2$', fontsize='small')
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:10351:
SyntaxWarning: invalid escape sequence '\m'
    ax2.set_ylabel('Support Volume ($\mathrm{\AA^{3}}$)', fontsize='small')
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:10461:
SyntaxWarning: invalid escape sequence '\m'
    ax0.plot([resx],[0.5],'ro', label='Resolution = %.2f $\mathrm{\AA}$'%resn)
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17041:
SyntaxWarning: invalid escape sequence '\c'
    ('Mean Error Weighted $\chi^2$', 'Index', '$\chi^2$', 0.1),
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17041:
SyntaxWarning: invalid escape sequence '\c'
    ('Mean Error Weighted $\chi^2$', 'Index', '$\chi^2$', 0.1),
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17087:
SyntaxWarning: invalid escape sequence '\c'
    b = self.subplots['Mean Error Weighted $\chi^2$']
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17103:
SyntaxWarning: invalid escape sequence '\c'
    b = self.subplots['Mean Error Weighted $\chi^2$']
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17168:
SyntaxWarning: invalid escape sequence '\c'
    b = self.subplots['Mean Error Weighted $\chi^2$']
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17253:
SyntaxWarning: invalid escape sequence '\c'
    b = self.subplots['Mean Error Weighted $\chi^2$']
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17344:
SyntaxWarning: invalid escape sequence '\c'
    b = self.subplots['Mean Error Weighted $\chi^2$']
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:17383:
SyntaxWarning: invalid escape sequence '\c'
    self.subplots['Mean Error Weighted $\chi^2$'],
  /usr/lib/python3/dist-packages/bioxtasraw/RAWAnalysis.py:21329:
SyntaxWarning: invalid escape sequence '\s'
    self.bottom_plot.set_ylabel('I/$\sigma$')
  /usr/lib/python3/dist-packages/bioxtasraw/RAWPlot.py:1424:
SyntaxWarning: invalid escape sequence '\l'
    'guinier'     : ('Guinier', '$q^2$ [1/A^2]', '$\ln(I(q)$'),
  /usr/lib/python3/dist-packages/bioxtasraw/SASCalc.py:373:
SyntaxWarning: invalid escape sequence '\i'
    """Calculates the volume of correlation as the ratio of i0 to $\int q*I dq$
  /usr/lib/python3/dist-packages/bioxtasraw/SASCalc.py:1065:
SyntaxWarning: invalid escape sequence '\s'
    dammif_re = 'ATSAS\s*\d+[.]\d+[.]\d*'
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:392:
SyntaxWarning: invalid escape sequence '\d'
    timeMonitorPattern = re.compile('\d*-second\s[a-z]*\s[()A-Z,]*\s\d*\s\d*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:393:
SyntaxWarning: invalid escape sequence '\s'
    closedShutterCountPattern = re.compile('closed\s\d*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:394:
SyntaxWarning: invalid escape sequence '\s'
    datePattern = re.compile('#D\s.*\n')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1223:
SyntaxWarning: invalid escape sequence '\s'
    start_match = '\s*'
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1224:
SyntaxWarning: invalid escape sequence '\s'
    end_match = '\s*$'
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1225:
SyntaxWarning: invalid escape sequence '\+'
    num_match = '[\+-]?\d+\.?\d*[+eE-]*\d*'
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1226:
SyntaxWarning: invalid escape sequence '\s'
    sep_match = '\s*[\s,]\s*'
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1227:
SyntaxWarning: invalid escape sequence '\s'
    alt_sep_match = '\s*[\s,]?\s*'
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1760:
SyntaxWarning: invalid escape sequence '\s'
    results_fit =
re.compile('\s*Current\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s+\d*[.]\d*[+eE-]*\d*\s*\d*[.]?\d*[+eE-]*\d*\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1762:
SyntaxWarning: invalid escape sequence '\s'
    te_fit = re.compile('\s*Total\s+[Ee]stimate\s*:\s+\d*[.]\d+\s*\(?[A-Za-z\s]+\)?\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1763:
SyntaxWarning: invalid escape sequence '\d'
    te_num_fit = re.compile('\d*[.]\d+')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1764:
SyntaxWarning: invalid escape sequence '\s'
    te_quality_fit = re.compile('[Aa][A-Za-z\s]+\)?\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1766:
SyntaxWarning: invalid escape sequence '\s'
    p_rg_fit = re.compile('\s*Real\s+space\s*\:?\s*Rg\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*\+-\s*\d*[.]\d+[+eE-]*\d*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1767:
SyntaxWarning: invalid escape sequence '\s'
    q_rg_fit = re.compile('\s*Reciprocal\s+space\s*\:?\s*Rg\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1769:
SyntaxWarning: invalid escape sequence '\s'
    p_i0_fit = re.compile('\s*Real\s+space\s*\:?[A-Za-z0-9\s\.,+-=]*\(0\)\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*\+-\s*\d*[.]\d+[+eE-]*\d*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1770:
SyntaxWarning: invalid escape sequence '\s'
    q_i0_fit = re.compile('\s*Reciprocal\s+space\s*\:?[A-Za-z0-9\s\.,+-=]*\(0\)\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:1772:
SyntaxWarning: invalid escape sequence '\s'
    alpha_fit =
re.compile('\s*Current\s+ALPHA\s*\:?\s*\=?\s*\d*[.]\d+[+eE-]*\d*\s*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:2659:
SyntaxWarning: invalid escape sequence '\s'
    res_pattern =
re.compile('\s*Ensemble\s*Resolution\s*=?\s*\d+\.?\d*\s*\+?-?\s*\d+\s*[a-zA-Z]*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:2730:
SyntaxWarning: invalid escape sequence '\s'
    cluster_pattern = re.compile('\s*Cluster\s*\d')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:2731:
SyntaxWarning: invalid escape sequence '\s'
    distance_pattern = re.compile('\s*\d\s*\d\s*\d+[.]\d+\s*$')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:3185:
SyntaxWarning: invalid escape sequence '\s'
    param_pattern = re.compile('[a-zA-Z0-9_]*\s*[:]\s+.*')
  /usr/lib/python3/dist-packages/bioxtasraw/SASFileIO.py:3250:
SyntaxWarning: invalid escape sequence '\s'
    param_pattern = re.compile('[a-zA-Z0-9_]*\s*[:]\s+.*')

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