Closed picca closed 5 months ago
Hello, when byte-compiling the cctbx python modules, I got a few warnings
Chjeers
Fred
Paramétrage de python3-cctbx (2023.12+ds2+~3.17.0+ds1-1) ... /usr/lib/python3/dist-packages/cctbx/command_line/find_reticular_twin_laws.py:37: SyntaxWarning: invalid escape sequence '\%' print(""" /usr/lib/python3/dist-packages/gltbx/util.py:61: SyntaxWarning: invalid escape sequence '\d' vers_pat = re.compile("^((\d+)\.(\d+))(?:\.(\d+))?(?: (.*))?$") /usr/lib/python3/dist-packages/iotbx/command_line/explore_metric_symmetry.py:339: SyntaxWarning: invalid escape sequence '\ ' print(" /%4i %4i %4i \ "%(mat[0][0],mat[0][1],mat[0][2]), file=log) /usr/lib/python3/dist-packages/iotbx/command_line/explore_metric_symmetry.py:341: SyntaxWarning: invalid escape sequence '\%' print(" \%4i %4i %4i / "%(mat[2][0],mat[2][1],mat[2][2]), file=log) /usr/lib/python3/dist-packages/iotbx/logfiles.py:19: SyntaxWarning: invalid escape sequence '\%' return float(re.sub("\%$", "", value)) /usr/lib/python3/dist-packages/iotbx/logfiles.py:474: SyntaxWarning: invalid escape sequence '\d' elif re.match("^\d", line): /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:7: SyntaxWarning: invalid escape sequence '\{' """ Iterator to generate strings of length n_chars, using upper-case, /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:45: SyntaxWarning: invalid escape sequence '\/' special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" /usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py:409: SyntaxWarning: invalid escape sequence '\P' test_ncs_spec = '''\ /usr/lib/python3/dist-packages/libtbx/auto_build/bootstrap.py:455: SyntaxWarning: invalid escape sequence '\s' if re.match('remote\s*=', line.strip()): /usr/lib/python3/dist-packages/libtbx/auto_build/bootstrap.py:457: SyntaxWarning: invalid escape sequence '\s' if re.match('rebase\s*=', line.strip()): /usr/lib/python3/dist-packages/libtbx/auto_build/install_base_packages.py:840: SyntaxWarning: invalid escape sequence '\$' configure_args.append("LDFLAGS=-Wl,-rpath=\$$ORIGIN/../lib") /usr/lib/python3/dist-packages/libtbx/fastentrypoints.py:43: SyntaxWarning: invalid escape sequence '\.' TEMPLATE = '''\ /usr/lib/python3/dist-packages/libtbx/fastentrypoints.py:92: SyntaxWarning: invalid escape sequence '\.' filename = re.sub('\.pyc$', '.py', __file__) /usr/lib/python3/dist-packages/libtbx/file_clutter.py:12: SyntaxWarning: invalid escape sequence '\w' '^ from [ ]+ __future__ [ ]+ import [ \w,]+ division', re.VERBOSE) /usr/lib/python3/dist-packages/libtbx/file_clutter.py:14: SyntaxWarning: invalid escape sequence '\w' '^ from [ ]+ __future__ [ ]+ import [ \w,]+ absolute_import', re.VERBOSE) /usr/lib/python3/dist-packages/libtbx/file_clutter.py:16: SyntaxWarning: invalid escape sequence '\w' '^ from [ ]+ __future__ [ ]+ import [ \w,]+ print_function', re.VERBOSE) /usr/lib/python3/dist-packages/libtbx/queuing_system_utils/processing/polling.py:282: SyntaxWarning: invalid escape sequence '\?' pattern = "^.*?(?=<\?xml)", /usr/lib/python3/dist-packages/mmtbx/command_line/show_r_factors_by_shell.py:106: SyntaxWarning: invalid escape sequence '\(' first_label_non_anom = re.sub("\(.*", "", labels[0]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:777: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', list[resid_count]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:779: SyntaxWarning: invalid escape sequence '\w' n=re.search('\w', list[resid_count + 1]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:816: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', list[2 * a]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:823: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', list[2 * a]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1191: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1194: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][4]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1499: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs[i][j][0]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1501: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs[i][j][3]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1503: SyntaxWarning: invalid escape sequence '\S' m=re.search('\S+', MASTER_Basepairs[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1505: SyntaxWarning: invalid escape sequence '\S' m=re.search('\S+', MASTER_Basepairs[i][j][5]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1823: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', LIST[r][s][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1825: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', LIST[r][s][4]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1879: SyntaxWarning: invalid escape sequence '\/' ma=re.compile('\/+') /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1988: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary_line[2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1991: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary_line[4]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2318: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2324: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2892: SyntaxWarning: invalid escape sequence '\S' m=re.search('\S+', new_list_end[b][0]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2979: SyntaxWarning: invalid escape sequence '\d' search = '\d+' /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2981: SyntaxWarning: invalid escape sequence '\w' search = '\w+' /usr/lib/python3/dist-packages/prime/postrefine/mod_gui_frames.py:750: SyntaxWarning: invalid escape sequence '\A' self.bmult_axes.set_xlabel("Resolution ($\AA$)") /usr/lib/python3/dist-packages/scitbx/math/fliege_mayer_900_ylm.py:1: SyntaxWarning: invalid escape sequence '\i' """ /usr/lib/python3/dist-packages/wxtbx/info_panels.py:208: SyntaxWarning: invalid escape sequence '\s' str_value = re.sub("\s*\*\*\*", "", str_value) /usr/lib/python3/dist-packages/wxtbx/info_panels.py:418: SyntaxWarning: invalid escape sequence '\s' str_value = re.sub("\s*\*\*\*", "", str_value) /usr/lib/python3/dist-packages/wxtbx/phil_controls/choice.py:18: SyntaxWarning: invalid escape sequence '\*' choices = [ re.sub("\*", "", choice) for choice in choices ] /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:23: SyntaxWarning: invalid escape sequence '\s' re_energy = re.compile("photon_energy_eV\s=\s([0-9]+\.[0-9]+)") /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:24: SyntaxWarning: invalid escape sequence '\s' re_uc = re.compile("""Cell\sparameters\s /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:33: SyntaxWarning: invalid escape sequence '\s' re_miller = re.compile("""\s*(-?[0-9]{1,3}) /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:41: SyntaxWarning: invalid escape sequence '\s' re_lattice_type = re.compile("lattice_type\s=\s([a-zA-Z]+)") /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:42: SyntaxWarning: invalid escape sequence '\s' re_centering = re.compile("centering\s=\s([A-Z])") /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:45: SyntaxWarning: invalid escape sequence '\s' re_Astar = re.compile("""astar\s=\s*(-?\+?[0-9]+\.[0-9]+) /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:48: SyntaxWarning: invalid escape sequence '\s' re_Bstar = re.compile("""bstar\s=\s*(-?\+?[0-9]+\.[0-9]+) /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:51: SyntaxWarning: invalid escape sequence '\s' re_Cstar = re.compile("""cstar\s=\s*(-?\+?[0-9]+\.[0-9]+) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1124: SyntaxWarning: invalid escape sequence '\D' plt.title("2d histogram of $\Delta$ %s vs azimuthal angle"%caption) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1126: SyntaxWarning: invalid escape sequence '\D' plt.ylabel("$\Delta$ %s ($\mu$m)"%caption) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1266: SyntaxWarning: invalid escape sequence '\A' plt.title(u"%d: Ewald offset ($\AA^{-1}$) vs $2\\theta$ on %d spots"%(expt_id, len(two_thetas))) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1267: SyntaxWarning: invalid escape sequence '\c' plt.xlabel(u"$2\\theta (\circ)$") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1268: SyntaxWarning: invalid escape sequence '\A' plt.ylabel(u"Ewald offset ($\AA^{-1}$)") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1294: SyntaxWarning: invalid escape sequence '\s' plt.title(u"Binned $I/\sigma_I$ vs. Ewald offset") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1295: SyntaxWarning: invalid escape sequence '\A' plt.xlabel(u"Ewald offset ($\AA^{-1}$)") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1296: SyntaxWarning: invalid escape sequence '\s' plt.ylabel(u"Median $I/\sigma_I$") /usr/lib/python3/dist-packages/xfel/command_line/experiment_residuals.py:203: SyntaxWarning: invalid escape sequence '\D' cbar.ax.set_title("$\Delta \psi$") /usr/lib/python3/dist-packages/xfel/cxi/cspad_ana/mod_filter.py:52: SyntaxWarning: invalid escape sequence '\d' p_old = re.compile("\d{4}-\d{2}-\d{2}T\d{2}:\d{2}Z\d{2}\.\d{3}") /usr/lib/python3/dist-packages/xfel/cxi/cspad_ana/mod_filter.py:53: SyntaxWarning: invalid escape sequence '\d' p_new = re.compile("\d{17}") /usr/lib/python3/dist-packages/xfel/cxi/cxi_cc.py:132: SyntaxWarning: invalid escape sequence '\d' """Get the R1 factor according to this formula /usr/lib/python3/dist-packages/xfel/merging/application/statistics/intensity_resolution_statistics_cxi.py:350: SyntaxWarning: invalid escape sequence '\d' """Get the R1 factor according to this formula /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1022: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1024: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*[Qq][Uu][Aa][Dd]\s+\d+\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1026: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*[Ss][Ee][Nn][Ss][Oo][Rr]\s+[Xx]\s+[Yy]\s+[Zz]\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1028: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*\d+\s+[+-]?\d+\s+[+-]?\d+\s+[+-]?\d+\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/ui/components/xfel_gui_plotter.py:393: SyntaxWarning: invalid escape sequence '\A' AA = "a-edge (%.2f +/- %.2f $\AA$)" % (flex.mean(a), /usr/lib/python3/dist-packages/xfel/ui/components/xfel_gui_plotter.py:395: SyntaxWarning: invalid escape sequence '\A' BB = "b-edge (%.2f +/- %.2f $\AA$)" % (flex.mean(b), /usr/lib/python3/dist-packages/xfel/ui/components/xfel_gui_plotter.py:397: SyntaxWarning: invalid escape sequence '\A' CC = "c-edge (%.2f +/- %.2f $\AA$)" % (flex.mean(c), /usr/lib/python3/dist-packages/xfel/ui/db/merging_log_scraper.py:106: SyntaxWarning: invalid escape sequence '\A' ax1.set_xlabel(u'Resolution ${\AA}$') /usr/lib/python3/dist-packages/xfel/ui/db/merging_log_scraper.py:189: SyntaxWarning: invalid escape sequence '\A' ax2.set_ylabel(u"Resolution ($\AA$")
Hello, when byte-compiling the cctbx python modules, I got a few warnings
Chjeers
Fred