orbeckst
commented
4 years ago I can't reproduce the failure in the following environment
- MDA 1.0.0
- conda with Python 3.8.5
- macOS 10.12
- duecredit 0.8.0 (fresh
pip install duecredit)
I'll check other configurations.
However, can you try updating duecredit as the first obvious difference (even though I doubt that this is the problem, that's one cause to check).
Output
pytest --disable-pytest-warnings --pyargs MDAnalysisTests -k test_data
========================================================= test session starts ==========================================================
platform darwin -- Python 3.8.5, pytest-6.0.2, py-1.9.0, pluggy-0.13.1
rootdir: ~/tmp/mda
plugins: hypothesis-5.28.0
collected 16326 items / 16308 deselected / 2 skipped / 16 selected
analysis/test_data.py . [ 5%]
auxiliary/test_xvg.py .... [ 27%]
coordinates/test_dlpoly.py . [ 33%]
coordinates/test_dms.py . [ 38%]
coordinates/test_gro.py . [ 44%]
coordinates/test_lammps.py .. [ 55%]
coordinates/test_timestep_api.py . [ 61%]
coordinates/test_trj.py . [ 66%]
coordinates/test_trz.py . [ 72%]
utils/test_datafiles.py ... [ 88%]
utils/test_imports.py .. [100%]
====================================== 18 passed, 2 skipped, 16308 deselected, 1 warning in 8.74s ======================================
DueCredit Report:
- Molecular simulation analysis library / MDAnalysis (v 1.0) [1, 2]
- ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 1.0) [3]
- Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hbonds.hbond_autocorrel (v 1.0) [4]
- HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole (v 1.0) [5, 6, 7]
- Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 1.0) [8]
- LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 1.0) [2]
- Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 1.0) [9]
- QCProt implementation / MDAnalysis.lib.qcprot (v 1.0) [10, 11]
- Description of recent updates and new functionality in MDAnalysis since release 0.7.2 (March 2011) up to release 0.16.0 (April 2017). Please cite together with Michaud-Agrawal et al 2011. , Description of MDAnalysis up to release 0.7.2 (March 2011), including the basic philosophy of the library and the LeafletFinder algorithm. Please cite together with Gowers et al 2016. / MDAnalysis/ (v None) [12, 2]
- Scientific tools library / numpy (v 1.14.2) [13]
3 packages cited
7 modules cited
0 functions cited
References
----------
[1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy.
[2] Michaud-Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327.
[3] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415.
[4] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22), p.224907.
[5] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460.
[6] Smart, O.S. et al., 1996. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics, 14(6), pp.354–360.
[7] Stelzl, L.S. et al., 2014. Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY. Journal of Molecular Biology, 426(3), pp.735–751.
[8] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857.
[9] Seyler, S.L. et al., 2015. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways E. Tajkhorshid, ed.. PLOS Computational Biology, 11(10), p.1004568.
[10] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480.
[11] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563.
[12] Gowers, R.J. et al., 2016. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall & S. Rostrup, eds. Proceedings of the 15th Python in Science Conference. pp. 102–109.
[13] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
drew-parsons
yarikoptic
Expected behavior
MDAnalysis has been configured so that when pytest is run, it runs duecredit after completion. The references reported by duecredit should be cited cleanly without triggering a reporting error.
Actual behavior
When pytest is launched, all tests successfully run (or skip/xfail as needed), no fails. After completing tests, MDAnalysis launches a duecredit report. This fails, apparently due to misconfigured reference entries.
The pytest run itself returns error code 0, so the problem is not registering as an "error" as such, as far as pytest goes. But the report of
ERRORED: not enough values to unpackis disconcerting and the Logging error does go to stderr so could be interpreted by some systems as a test fail.Any variation of pytest (including
pytest --collect-only) triggers the duecredit report with the same broken citations. Test output on test_data.py only (selected since it has only 1 test) is:It might be easier to see which citations are causing the problem by hiding stderr:
Code to reproduce the behavior
(on Debian, that's
pytest-3 -k test_data.py)or any other variation of
pytest.Current version of MDAnalysis
python -V)? Python 3.8.6rc1