--- Dependency check [begin] --- --- Dependency check [end] --- --- Distribution check [begin] --- Version 1.2.1 - 2024-10-18 (AI) Information: this ChangeLog entry matches the version number: Version 1.2.1 - 2024-10-18 (AI) Information: ./config/pyrgsspecplot.par is an XML parameter file, I cannot yet validate it. Skipped. Warning: pyrgsspecplot - missing lyt files. Now checking git repository... --- Distribution check [end] --- sed -e "s/DOC/pyrgsspecplot/" -e "s/TYPE/devel/" < \ /workspaces/xmm_sas/packages/sas/doc/lib/package.tex | /workspaces/xmm_sas/packages/sas/bin/texcombine | \ /workspaces/xmm_sas/packages/sas/bin/fixdoc -type=devel pyrgsspecplot 1.2.1 pyrgsspecplot 22.0.0-6da3b52c5-20241025 > pyrgsspecplot.tex including sasdevel... including sasglobal... including pyrgsspecplot_description... latex pyrgsspecplot < /dev/null > makedoc.log || ( cat makedoc.log ; exit 1 ) bibtex pyrgsspecplot < /dev/null > makedoc.log make[5]: [/workspaces/xmm_sas/Make.include:1062: pyrgsspecplot.ps.gz] Error 2 (ignored) latex pyrgsspecplot < /dev/null > makedoc.log || ( cat makedoc.log ; exit 1 ) latex pyrgsspecplot < /dev/null > makedoc.log || ( cat makedoc.log ; exit 1 ) dvips -o pyrgsspecplot.ps pyrgsspecplot > makedoc.log 2>&1 || ( cat makedoc.log ; exit 1 ) dvipdf pyrgsspecplot > makedoc.log 2>&1 || ( cat makedoc.log ; continue ) gzip -f pyrgsspecplot.ps SASRELDIR=../../.. ;\ export SASRELDIR ;\ latex2html -nouse_pdftex -init_file /workspaces/xmm_sas/packages/sas/doc/lib/latex2html.init pyrgsspecplot > /dev/null texexpand V2020 (Released January 1, 2020) Warning: No implementation found for option: `version' for `sasdoc' package Warning: No implementation found for option: `version' for `sasdoc' package This is dvips(k) 2021.1 (TeX Live 2022/dev) Copyright 2021 Radical Eye Software (www.radicaleye.com) ' TeX output 2024.10.25:1609' -> images.ps . [1] /usr/bin/echo "" mkpkgidx -t . > /dev/null || (rm -f pyrgsspecplot/index.pl ; exit 1) pointer=pyrgsspecplot/ChangeLog ; \ target=../../../packages/pyrgsspecplot/ChangeLog ; \ if [ -f $target -a \( ! -h $pointer \) ] ; then \ ln -s ../$target $pointer ; \ fi rm pyrgsspecplot.tex Testing testpyrgsspecplot ... FAILED Message: will run ./testpyrgsspecplot for no longer than 600 seconds. ============================= test session starts ============================== platform linux -- Python 3.12.4, pytest-8.3.3, pluggy-1.5.0 -- /sasbuild/tools/python-3.12.4/bin/python3 cachedir: .pytest_cache rootdir: /workspaces/xmm_sas/packages/pyrgsspecplot plugins: anyio-4.6.2.post1 collecting ... collected 8 items test_pyrgsspecplot.py::test_collect_fits_info PASSED [ 12%] test_pyrgsspecplot.py::test_get_src_label_and_offaxes PASSED [ 25%] test_pyrgsspecplot.py::test_lambda2beta PASSED [ 37%] test_pyrgsspecplot.py::test_general FAILED [ 50%] test_pyrgsspecplot.py::test_general_grouping PASSED [ 62%] test_pyrgsspecplot.py::test_general_PDF FAILED [ 75%] test_pyrgsspecplot.py::test_general_lambda PASSED [ 87%] test_pyrgsspecplot.py::test_general_lambda_rebin PASSED [100%] =================================== FAILURES =================================== _________________________________ test_general _________________________________ def test_general(): parsed = dict() parsed.update({'mincounts' : '2'}) parsed.update({'group' : 'no'}) parsed.update({'rebin' : 'no'}) parsed.update({'sourceid' : '1'}) parsed.update({'device' : '/pdf'}) parsed.update({'plotfile' : './out/spec_py.pdf'}) parsed.update({'dark_mode' : 'yes'}) parsed.update({'spectrumsets' : 'SPECTRUM0101.FIT SPECTRUM0102.FIT'}) parsed.update({'sourcelistset' : 'rgssources.ds'}) > rgsspecplot.run(parsed) test_pyrgsspecplot.py:52: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:811: in run status = sasplt.merge_pdf(pdf_files, plotfile + '.{}'.format(out_format)) ../../../lib/python/pysas/pysasplot_utils/pysasplot_utils.py:678: in merge_pdf merger = PdfMerger() /sasbuild/tools/python-3.12.4/lib/python3.12/site-packages/pypdf/_merger.py:42: in __init__ deprecation_with_replacement("PdfMerger", "PdfWriter", "5.0.0") /sasbuild/tools/python-3.12.4/lib/python3.12/site-packages/pypdf/_utils.py:384: in deprecation_with_replacement deprecation( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ msg = 'PdfMerger is deprecated and was removed in pypdf 5.0.0. Use PdfWriter instead.' def deprecation(msg: str) -> None: > raise DeprecationError(msg) E pypdf.errors.DeprecationError: PdfMerger is deprecated and was removed in pypdf 5.0.0. Use PdfWriter instead. /sasbuild/tools/python-3.12.4/lib/python3.12/site-packages/pypdf/_utils.py:371: DeprecationError ----------------------------- Captured stdout call ----------------------------- Executing /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py {'mincounts': '2', 'group': 'no', 'rebin': 'no', 'sourceid': '1', 'device': '/pdf', 'plotfile': './out/spec_py.pdf', 'dark_mode': 'yes', 'spectrumsets': 'SPECTRUM0101.FIT SPECTRUM0102.FIT', 'sourcelistset': 'rgssources.ds'} FRACEXP is missing. fracexp = 1 No re-binning needed for this Light Curve. Input / Output time bins ratio : 1 lambda_val [ 7114.6475792 29173.9794912 6772.69043547 17191.61785237 21175.38405337 3714.35891191 30596.4214802 ] cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39] 15489.455078125 cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 5 10 15 20 25 30 35 40] 15489.455078125 lambda_major: [0.03737833 0.04519873 0.05185345 0.0577469 0.06309278 0.06802031 0.07261471 0.07693568] betamin 0.0300083328038454 betarange 0.05000000055588331 amjorpos [0.14739988 0.30380788 0.4369023 0.55477139 0.66168895 0.76023957 0.85212755 0.93854698] energy major pos: [ 48.9938328 70.24840399 98.58783225 123.38483197 164.71316485 247.36983059 495.33982784] FRACEXP is missing. fracexp = 1 No re-binning needed for this Light Curve. Input / Output time bins ratio : 1 lambda_val [ 7114.6475792 29173.9794912 6772.69043547 17191.61785237 21175.38405337 3714.35891191 30596.4214802 ] cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39] 15489.455078125 cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 5 10 15 20 25 30 35 40] 15489.455078125 lambda_major: [0.03737833 0.04519873 0.05185345 0.0577469 0.06309278 0.06802031 0.07261471 0.07693568] betamin 0.0300083328038454 betarange 0.05000000055588331 amjorpos [0.14739988 0.30380788 0.4369023 0.55477139 0.66168895 0.76023957 0.85212755 0.93854698] energy major pos: [ 48.9938328 70.24840399 98.58783225 123.38483197 164.71316485 247.36983059 495.33982784] ----------------------------- Captured stderr call ----------------------------- pyrgsspecplot - WARNING - Mismatch between device parameter and the extension given in the plotfile parameter. pdf will be used. pyrgsspecplot - WARNING - SPECDELT not found pyrgsspecplot - WARNING - SPECPIX not found pyrgsspecplot - WARNING - SPECVAL not found QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-sasbuild' pyrgsspecplot - WARNING - SPECDELT not found pyrgsspecplot - WARNING - SPECPIX not found pyrgsspecplot - WARNING - SPECVAL not found ------------------------------ Captured log call ------------------------------- WARNING pyrgsspecplot:logger.py:158 Mismatch between device parameter and the extension given in the plotfile parameter. pdf will be used. INFO pyrgsspecplot:logger.py:158 Evaluating file SPECTRUM0101.FIT. DEBUG pyrgsspecplot:logger.py:158 Filtering data using pyutils... DEBUG pyrgsspecplot:logger.py:158 Getting source label and offaxis values from rgssources.ds with id 1. WARNING pyrgsspecplot:logger.py:158 SPECDELT not found WARNING pyrgsspecplot:logger.py:158 SPECPIX not found WARNING pyrgsspecplot:logger.py:158 SPECVAL not found DEBUG pyrgsspecplot:logger.py:158 RATE-like spectrum... DEBUG pyrgsspecplot:logger.py:158 Looking for XMM misc data... DEBUG pyrgsspecplot:logger.py:158 Starting graph processing... DEBUG pyrgsspecplot:logger.py:158 Getting passed data. DEBUG pyrgsspecplot:logger.py:158 Only one table for error and data. DEBUG pyrgsspecplot:logger.py:158 1 3000 DEBUG pyrgsspecplot:logger.py:158 Saving /workspaces/xmm_sas/packages/pyrgsspecplot/test/out/spec_py_1_TEMP_SPECPLOT.pdf. INFO pyrgsspecplot:logger.py:158 Evaluating file SPECTRUM0102.FIT. DEBUG pyrgsspecplot:logger.py:158 Filtering data using pyutils... DEBUG pyrgsspecplot:logger.py:158 Getting source label and offaxis values from rgssources.ds with id 1. WARNING pyrgsspecplot:logger.py:158 SPECDELT not found WARNING pyrgsspecplot:logger.py:158 SPECPIX not found WARNING pyrgsspecplot:logger.py:158 SPECVAL not found DEBUG pyrgsspecplot:logger.py:158 RATE-like spectrum... DEBUG pyrgsspecplot:logger.py:158 Looking for XMM misc data... DEBUG pyrgsspecplot:logger.py:158 Starting graph processing... DEBUG pyrgsspecplot:logger.py:158 Getting passed data. DEBUG pyrgsspecplot:logger.py:158 Only one table for error and data. DEBUG pyrgsspecplot:logger.py:158 1 3000 DEBUG pyrgsspecplot:logger.py:158 Saving /workspaces/xmm_sas/packages/pyrgsspecplot/test/out/spec_py_2_TEMP_SPECPLOT.pdf. INFO pyrgsspecplot:logger.py:158 Merging existing PDFs... _______________________________ test_general_PDF _______________________________ def test_general_PDF(): parsed = dict() parsed.update({'mincounts' : '5'}) parsed.update({'group' : 'no'}) parsed.update({'rebin' : 'yes'}) parsed.update({'sourceid' : '1'}) parsed.update({'device' : 'pdf'}) parsed.update({'plotfile' : './out/spec_pyrebin5.pdf'}) parsed.update({'dark_mode' : 'yes'}) parsed.update({'spectrumsets' : 'SPECTRUM0101.FIT, SPECTRUM0102.FIT'}) parsed.update({'sourcelistset' : 'rgssources.ds'}) > rgsspecplot.run(parsed) test_pyrgsspecplot.py:82: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:811: in run status = sasplt.merge_pdf(pdf_files, plotfile + '.{}'.format(out_format)) ../../../lib/python/pysas/pysasplot_utils/pysasplot_utils.py:678: in merge_pdf merger = PdfMerger() /sasbuild/tools/python-3.12.4/lib/python3.12/site-packages/pypdf/_merger.py:42: in __init__ deprecation_with_replacement("PdfMerger", "PdfWriter", "5.0.0") /sasbuild/tools/python-3.12.4/lib/python3.12/site-packages/pypdf/_utils.py:384: in deprecation_with_replacement deprecation( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ msg = 'PdfMerger is deprecated and was removed in pypdf 5.0.0. Use PdfWriter instead.' def deprecation(msg: str) -> None: > raise DeprecationError(msg) E pypdf.errors.DeprecationError: PdfMerger is deprecated and was removed in pypdf 5.0.0. Use PdfWriter instead. /sasbuild/tools/python-3.12.4/lib/python3.12/site-packages/pypdf/_utils.py:371: DeprecationError ----------------------------- Captured stdout call ----------------------------- Executing /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py {'mincounts': '5', 'group': 'no', 'rebin': 'yes', 'sourceid': '1', 'device': 'pdf', 'plotfile': './out/spec_pyrebin5.pdf', 'dark_mode': 'yes', 'spectrumsets': 'SPECTRUM0101.FIT, SPECTRUM0102.FIT', 'sourcelistset': 'rgssources.ds'} lambda_val [ 7114.6475792 29173.9794912 6772.69043547 17191.61785237 21175.38405337 3714.35891191 30596.4214802 ] cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39] 15489.455078125 cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 5 10 15 20 25 30 35 40] 15489.455078125 lambda_major: [0.03737833 0.04519873 0.05185345 0.0577469 0.06309278 0.06802031 0.07261471 0.07693568] betamin 0.03002499947069736 betarange 0.05000833388930929 amjorpos [0.14704204 0.30342398 0.43649622 0.55434566 0.66124541 0.75977961 0.85165227 0.93805731] energy major pos: [ 48.98533524 70.2363646 98.5710704 123.36393798 164.68538395 247.32827588 495.25695168] lambda_val [ 7114.6475792 29173.9794912 6772.69043547 17191.61785237 21175.38405337 3714.35891191 30596.4214802 ] cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39] 15489.455078125 cosbeta = np.cos(alpha0 + offaxis) + order * lambda_values / d 0.0274606216698885 -4.9101003e-05 -1 [ 5 10 15 20 25 30 35 40] 15489.455078125 lambda_major: [0.03737833 0.04519873 0.05185345 0.0577469 0.06309278 0.06802031 0.07261471 0.07693568] betamin 0.03002499947069736 betarange 0.05000833388930929 amjorpos [0.14704204 0.30342398 0.43649622 0.55434566 0.66124541 0.75977961 0.85165227 0.93805731] energy major pos: [ 48.98533524 70.2363646 98.5710704 123.36393798 164.68538395 247.32827588 495.25695168] ----------------------------- Captured stderr call ----------------------------- pyrgsspecplot - WARNING - Mismatch between device parameter and the extension given in the plotfile parameter. pdf will be used. pyrgsspecplot - WARNING - SPECDELT not found pyrgsspecplot - WARNING - SPECPIX not found pyrgsspecplot - WARNING - SPECVAL not found pyrgsspecplot - WARNING - SPECDELT not found pyrgsspecplot - WARNING - SPECPIX not found pyrgsspecplot - WARNING - SPECVAL not found ------------------------------ Captured log call ------------------------------- WARNING pyrgsspecplot:logger.py:158 Mismatch between device parameter and the extension given in the plotfile parameter. pdf will be used. INFO pyrgsspecplot:logger.py:158 Evaluating file SPECTRUM0101.FIT. DEBUG pyrgsspecplot:logger.py:158 Filtering data using pyutils... DEBUG pyrgsspecplot:logger.py:158 Getting source label and offaxis values from rgssources.ds with id 1. WARNING pyrgsspecplot:logger.py:158 SPECDELT not found WARNING pyrgsspecplot:logger.py:158 SPECPIX not found WARNING pyrgsspecplot:logger.py:158 SPECVAL not found DEBUG pyrgsspecplot:logger.py:158 RATE-like spectrum... INFO pyrgsspecplot:logger.py:158 Rebinning for file SPECTRUM0101.FIT. DEBUG pyrgsspecplot:logger.py:158 Running rebbin_min_counts. DEBUG pyrgsspecplot:logger.py:158 Looking for XMM misc data... DEBUG pyrgsspecplot:logger.py:158 Starting graph processing... DEBUG pyrgsspecplot:logger.py:158 Getting passed data. DEBUG pyrgsspecplot:logger.py:158 Rebinned - separated tables for error and data. DEBUG pyrgsspecplot:logger.py:158 1 2694 DEBUG pyrgsspecplot:logger.py:158 Saving /workspaces/xmm_sas/packages/pyrgsspecplot/test/out/spec_pyrebin5_1_TEMP_SPECPLOT.pdf. INFO pyrgsspecplot:logger.py:158 Evaluating file SPECTRUM0102.FIT. DEBUG pyrgsspecplot:logger.py:158 Filtering data using pyutils... DEBUG pyrgsspecplot:logger.py:158 Getting source label and offaxis values from rgssources.ds with id 1. WARNING pyrgsspecplot:logger.py:158 SPECDELT not found WARNING pyrgsspecplot:logger.py:158 SPECPIX not found WARNING pyrgsspecplot:logger.py:158 SPECVAL not found DEBUG pyrgsspecplot:logger.py:158 RATE-like spectrum... INFO pyrgsspecplot:logger.py:158 Rebinning for file SPECTRUM0102.FIT. DEBUG pyrgsspecplot:logger.py:158 Running rebbin_min_counts. DEBUG pyrgsspecplot:logger.py:158 Looking for XMM misc data... DEBUG pyrgsspecplot:logger.py:158 Starting graph processing... DEBUG pyrgsspecplot:logger.py:158 Getting passed data. DEBUG pyrgsspecplot:logger.py:158 Rebinned - separated tables for error and data. DEBUG pyrgsspecplot:logger.py:158 1 2705 DEBUG pyrgsspecplot:logger.py:158 Saving /workspaces/xmm_sas/packages/pyrgsspecplot/test/out/spec_pyrebin5_2_TEMP_SPECPLOT.pdf. INFO pyrgsspecplot:logger.py:158 Merging existing PDFs... =============================== warnings summary =============================== test/test_pyrgsspecplot.py::test_general test/test_pyrgsspecplot.py::test_general test/test_pyrgsspecplot.py::test_general_PDF test/test_pyrgsspecplot.py::test_general_PDF /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:705: RuntimeWarning: invalid value encountered in multiply counts_p = exposuret * rate_p test/test_pyrgsspecplot.py::test_general_grouping /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:750: RuntimeWarning: overflow encountered in scalar add summed_channels[bin_c] = summed_channels[bin_c] + channel_p[i - 1] test/test_pyrgsspecplot.py::test_general_grouping /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:762: RuntimeWarning: invalid value encountered in divide channel = np.divide(summed_channels, n_channels) test/test_pyrgsspecplot.py::test_general_grouping test/test_pyrgsspecplot.py::test_general_lambda test/test_pyrgsspecplot.py::test_general_lambda_rebin /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:180: UserWarning: set_ticklabels() should only be used with a fixed number of ticks, i.e. after set_ticks() or using a FixedLocator. ax1.xaxis.set_ticklabels(np.around(lamb_values, 2)) test/test_pyrgsspecplot.py::test_general_PDF test/test_pyrgsspecplot.py::test_general_PDF test/test_pyrgsspecplot.py::test_general_lambda_rebin /workspaces/xmm_sas/lib/python/pysas/pyrgsspecplot/pyrgsspecplot.py:284: RuntimeWarning: overflow encountered in scalar add newchannel[k] = newchannel[k] + t[i][xcol] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED test_pyrgsspecplot.py::test_general - pypdf.errors.DeprecationError: P... FAILED test_pyrgsspecplot.py::test_general_PDF - pypdf.errors.DeprecationErro... ================== 2 failed, 6 passed, 12 warnings in 12.57s =================== Error while running ./testpyrgsspecplot ERROR: one of the tests failed