The journey...

28 Aug 2017

With the end of GSoC coding period only a couple of days away, lets have a look at what I’ve been able to accomplish so far. My project, as I initially told, was divided into three main parts.

Removing nose as a dependency
- nose is no longer required for the TravisCI build to pass. We have completely shifted to pytest.
Improving performance and bringing down the execution time taken by the TravisCI build.
- Have brought down the execution time significantly. The TravisCI build that used to take ~45-50 mins(and sometimes timeout due to the 50min time limit) now completes in ~20 minutes! We no longer have to restart builds and hope they complete.
- Have completely ported 7 out of 8 modules in MDAnalysisTests to follow the pytest style. The coordinates module is still work-in-progress and needs some more refining. I am working on it as of now and hope to complete it in a week.
Refactoring format specific reader/writer classes to make them follow the same base API (Optional).
- Unfortunately, I couldn’t make time to take this on. Thanks to the community for pointing out, during the application phase, that I might not be able to get here!

Let’s have a look at some numbers. I’ve opened a total of 112 PRs and have got 128 commits merged as of today. Lines of code is an interesting story - I’ve managed to delete more lines than I’ve added! Less code == Less maintenance effort.

In the end, GSoC has been a great experience. I’ve picked up a couple of things about programming and testing while working with the community and this has certainly helped me grow as a developer. My project wouldn’t have been possible without all the valuable help I got along the way. A huge, huge thanks to my mentors and the whole community for all the help, ideas and discussions along the way.

So what’s next? First of all, I’ll complete my work on the coordinates module. Once that’s done, I plan to take on Part 3 of my proposal - Refactoring format specific reader/writer classes to make them follow the same base API. Though I won’t be able to dedicate as much time as I’ve been doing during the GSoC coding period, I’ll try to keep working on this regularly.

Finally here’s a list of all the PRs that I worked on during the summer -

#1370 Break build packagewise
#1413 Port lib/test_util.py to pytest
#1414 Port coordinates module
#1417 Port formats module to pytest
#1418 Run the pytest testsuite in parallel
#1420 Port topology module
#1434 Port utils module to pytest
#1439 Port auxiliary module to pytest
#1441 Fix coverage drop in coordinates module
#1443 Port core module to pytest
#1450 Port analysis module to pytes
#1464 Pytest Style: test_altloc.py
#1465 Pytest style: test_datafiles.py
#1466 Pytest Style: test_deprecated.py
#1467 Pytest Style: test_log.py
#1468 Pytest Style: test_modelling.py
#1469 Pytest Style: test_nuclinfo.py
#1470 Pytest Style: test_persistence.py
#1471 Pytest Style: test_selections.py
#1472 Pytest Style: test_streamio.py
#1473 Pytest Style: test_imports.py
#1480 Dropping nose as a dependency
#1492 Pytest Style: auxiliary/base.py
#1493 Pytest Style: test_xvg.py
#1494 Pytest Style: test_util.py
#1526 Pytest Style: topology/base.py
#1527 Pytest Style: topology/test_crd.py
#1535 Pytest Style: core/test_atom.py
#1539 Pytest Style analysis/test_hole.py
#1540 Pytest Style analysis/test_diffusionmap.py
#1541 Pytest style analysis/test_distances.py
#1542 Pytest Style analysis/test_gnm.py
#1543 Pytest Style analysis/test_density.py
#1544 Pytest Style analysis/test_hbonds.py
#1545 Pytest Style analysis/test_contacts.py
#1546 Pytest Style analysis/test_align.py
#1547 Pytest Style analysis/test_base.py
#1548 Pytest Style analysis/test_lineardensity.py
#1549 Pytest Style analysis/test_nuclinfo.py
#1550 Pytest Style analysis/test_helanal.py
#1551 Pytest Style analysis/test_leaflet.py
#1568 Pytest style analysis/test_persistencelength.py
#1569 Pytest Style analysis/test_psa.py
#1570 Pytest Style analysis/test_rdf.py
#1571 Pytest Style analysis/test_waterdynamics.py
#1574 Remove dependency from nose
#1586 Pytest Style topology/test_dlpoly.py
#1587 Pytest Style topology/test_dms.py
#1588 Pytest Style topology/test_gms.py
#1590 Pytest Style topology/test_gro.py
#1592 Pytest Style topology/test_guessers.py
#1593 Pytest Style topology/test_hoomdxml.py
#1595 Pytest Style topology/test_mmtf.py
#1596 Pytest Style topology/test_lammpsdata.py
#1597 Pytest Style topology/test_mol2.py
#1598 Pytest Style topology/test_pdb.py
#1599 Pytest Style topology/test_pdbqt.py
#1600 Pytest Style topology/test_pqr.py
#1601 Pytest Style topology/test_psf.py
#1602 Pytest Style topology/test_top.py
#1604 Pytest Style topology/test_topology_base.py
#1605 PEP8 fixes topology/test_topology_str_types.py
#1607 Pytest Style topology/test_xpdb.py
#1608 Pytest Style topology/test_xyz.py
#1610 Pytest Style analysis/test_rms.py
#1611 Pytest Style analysis/test_hydrogenbondautocorrel.py
#1620 Pytest Style core/test_topologyattrs.py
#1621 Pytest Stylecore/test_topology.py
#1622 Pytest Style core/test_segmentgroup.py
#1623 Pytest Style core/test_segment.py
#1624 Pytest Style core/test_residuegroup.py
#1625 Pytest Style core/test_residue.py
#1626 Pytest Style core/test_requires.py
#1627 Pytest Style core/test_index_dtype.py
#1628 Pytest Style core/test_groups.py
#1629 Pytest Style core/test_group_traj_access.py
#1633 Pytest Style core/test_fragments.py
#1634 Pytest Style core/test_atomselections.py
#1637 Pytest Style coordinates/test_dlpoly.py
#1638 Pytest Style coordinates/test_dms.py
#1639 Pytest Style coordinates/test_gms.py
#1640 Pytest Style coordinates/test_chainreader.py
#1641 Pytest Style coordinates/test_crd.py
#1644 Pytest Style coordinates/test_lammps.py
#1645 Pytest Style coordinates/test_memory.py
#1646 Pytest Style coordinates/test_mmtf.py
#1647 Pytest Style coordinates/test_netcdf.py & coordinates/test_trj.py
#1648 Pytest Style coordinates/test_null.py
#1649 Pytest Style coordinates/test_pdbqt.py
#1650 Pytest Style coordinates/test_timestep_api.py
#1652 Pytest Style coordinates/test_trz.py
#1653 PEP8 fixes for coordinates/test_txyz.py
#1654 Pytest Style coordinates/test_writer_registration.py
#1656 Pytest Style coordinates/test_xyz.py
#1606 Pytest Style topology/test_tprparser.py (WIP)
#1609 Pytest Style TestEncore (WIP)
#1619 Pytest Style core/test_updating_atomgroup.py (WIP)
#1635 Pytest Style core/test_atomgroup.py (WIP)
#1642 Remove yield based tests (WIP)
#1651 Pytest Style coordinates/test_trj.py (WIP)
#1655 Pytest Style coordinates/test_xdr.py (WIP)

That’s it for now, see ya later!

Utkarsh Bansal

The journey...