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Add support for reading Desmond DTR (Anton) trajectories #796

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merged 37 commits into from
Feb 7, 2020

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drroe
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@drroe drroe commented Feb 7, 2020

Makes use of the DTR plugin from VMD (used with permission) under the hood. Supports only reads at present, but does work in parallel. There is no test yet since the smallest DTR trajectory I have is ~4 GB - will have to add a test in the future.

…omple properly without too much modification
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lgtm-com bot commented Feb 7, 2020

This pull request introduces 1 alert when merging 9fc1266 into 40b4820 - view on LGTM.com

new alerts:

  • 1 for FIXME comment

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hainm commented Feb 7, 2020

image

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lgtm-com bot commented Feb 7, 2020

This pull request introduces 1 alert when merging 2243603 into 40b4820 - view on LGTM.com

new alerts:

  • 1 for FIXME comment

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lgtm-com bot commented Feb 7, 2020

This pull request introduces 2 alerts when merging 7db4d5f into 40b4820 - view on LGTM.com

new alerts:

  • 1 for Missing header guard
  • 1 for FIXME comment

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drroe commented Feb 7, 2020

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hainm commented Feb 7, 2020

uhm, not sure. I already exclude the parallel tests
pytest -vs --ignore=test_parallel_pmap --ignore=test_run_mpi.py --ignore=test_energy/test_pmap_sander.py --ignore=test_parallel_mpi --ignore=test_actionlist.py
let's try to finish this (switch to py3): #790

PS: I have never had this issue with pytraj on linux (either from travis or from my docker image).

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hainm commented Feb 7, 2020

uhm, It's not a python version issue either.

This PR run with python 3.

platform linux -- Python 3.7.4, pytest-5.3.5, py-1.8.1, pluggy-0.13.1 -- /opt/conda/bin/python

cachedir: .pytest_cache

rootdir: /iscratch/jenkins-cpu/workspace/amber-github/pytraj

collecting ... cpptraj_test_dir /cpptraj/test

test_vs_cpptraj

test_frame_indices

test_simplified_codes

test_dssp_allatoms

/iscratch/jenkins-cpu/workspace/amber-github/pytraj/tests/test_energy

amberhome 

collected 420 items



run_simple_test.py::TestRunnable::test_Dataset try to make all dataset stuff

PASSED

run_simple_test.py::TestRunnable::test_create_ try to make all analysis objects

PASSED

run_simple_test.py::TestRunnable::test_create_actions try to make all action objects

PASSED

run_simple_test.py::TestRunnable::test_geometry try to make structure-related objects

PASSED

run_simple_test.py::TestRunnable::test_import try to load sample data

try to make all action objects

try to make all analysis objects

try to make all dataset stuff

try to make structure-related objects

try to create Trajectory-like objects

other stuff. throw all tests don't belong anywhere else here

OK

PASSED

run_simple_test.py::TestRunnable::test_loading PASSED

run_simple_test.py::TestRunnable::test_other other stuff. throw all tests don't belong anywhere else here

PASSED

test_crdframes.py::TestCrdFrames::test_crdframes PASSED

test_createcrd.py::TestCreateCRD::test_autoimage_rms_strip Sending interrupt signal to process

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drroe commented Feb 7, 2020

Jenkins fail is a pytraj hang - merging.

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2 participants