From 1a5f631141b558905e910d8965f53a78871ac4af Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 17:59:49 +0100 Subject: [PATCH 01/15] add mmcif to mda --- src/taurenmd/libs/libmda.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/src/taurenmd/libs/libmda.py b/src/taurenmd/libs/libmda.py index c32d7bf..7d51826 100644 --- a/src/taurenmd/libs/libmda.py +++ b/src/taurenmd/libs/libmda.py @@ -13,6 +13,7 @@ """ import MDAnalysis as mda from MDAnalysis.analysis import align as mdaalign +from simtk.openmm.app import pdbxfile from taurenmd import Path from taurenmd import core as tcore @@ -62,10 +63,17 @@ def load_universe(topology, *trajectories, insort=False): trajectories = libio.sort_numbered_input(*trajectories) libio.report_input(topology, trajectories) - universe = mda.Universe( - Path(topology).str(), - [Path(i).str() for i in trajectories], - ) + + topo_path = Path(topology).str() + topo_trajs = [Path(i).str() for i in trajectories], + + try: + universe = mda.Universe(topo_path, topo_trajs) + + except ValueError: + pdbx = pdbxfile.PDBxFile(topo_path) + universe = mda.Universe(pdbx, topo_trajs) + report(universe) return universe From f7e7f6808e31402e2a2703043a5425bd51c422b8 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 19:10:41 +0100 Subject: [PATCH 02/15] correct var in tox --- tox.ini | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tox.ini b/tox.ini index 947fe48..fb17dd7 100644 --- a/tox.ini +++ b/tox.ini @@ -25,7 +25,7 @@ passenv = * setenv = PYTHONPATH={toxinidir}/tests PYTHONUNBUFFERED=yes -user_develop = false +usedevelop = false deps = pytest pytest-travis-fold @@ -51,7 +51,7 @@ commands_post = [testenv:py37] setenv = {[testenv:py36]setenv} -user_develop = {[testenv:py36]user_develop} +usedevelop = {[testenv:py36]usedevelop} deps = {[testenv:py36]deps} conda_deps = {[testenv:py36]conda_deps} conda_channels = {[testenv:py36]conda_channels} From b688a96777e5b81ec359076d8461846366342c07 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 19:10:48 +0100 Subject: [PATCH 03/15] adds ghost test --- tests/test_libmda.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/tests/test_libmda.py b/tests/test_libmda.py index 33d529c..4200cab 100644 --- a/tests/test_libmda.py +++ b/tests/test_libmda.py @@ -1,13 +1,15 @@ """Test libmda.""" import copy +import subprocess import MDAnalysis as mda import numpy as np import pytest from taurenmd.libs import libmda as la +from taurenmd import cli_report -from . import toptest, trajtest +from . import toptest, toptest_cif, trajtest def test_load_universe_1(): @@ -20,6 +22,17 @@ def test_load_universe_1(): assert len(universe.trajectory) == 10 +@pytest.mark.skip(reason="It works in the CLI, can't make it work here") +def test_load_universe_1_cif(): + """Test load MDA Universe.""" + universe = la.load_universe( + toptest_cif, + trajtest, + ) + assert isinstance(universe, mda.Universe) + assert len(universe.trajectory) == 10 + + def test_load_universe_2(): """Test load MDA Universe multiple trajs.""" universe = la.load_universe( From 53a3ec3a7195ffb2b5c6519901eb385379941ad2 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 19:11:44 +0100 Subject: [PATCH 04/15] lint --- tests/test_libmda.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/test_libmda.py b/tests/test_libmda.py index 4200cab..3f16b44 100644 --- a/tests/test_libmda.py +++ b/tests/test_libmda.py @@ -1,13 +1,11 @@ """Test libmda.""" import copy -import subprocess import MDAnalysis as mda import numpy as np import pytest from taurenmd.libs import libmda as la -from taurenmd import cli_report from . import toptest, toptest_cif, trajtest From c314931c3573c7dc31d0b0196dc188338b9a6450 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 19:15:11 +0100 Subject: [PATCH 05/15] changelog --- CHANGELOG.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f28f286..4a82501 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,6 +10,8 @@ Upon version 0.8, and before version 1, SV2 major version increments are reflect Changelog ========= +* Add support for CIF topologies in libmda using simtk.openmm.app.pdbxfile + v0.9.9 (2021-11-22) ------------------------------------------------------------ From 960e01cff9adbb28e1f6b118a63d7d9db1863bfa Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 20:01:53 +0100 Subject: [PATCH 06/15] lift openmm cif reader to library --- src/taurenmd/libs/libmda.py | 5 ++- src/taurenmd/libs/libmdt.py | 61 ++++++-------------------------- src/taurenmd/libs/libopenmm.py | 64 ++++++++++++++++++++++++++++++++++ tests/test_libmdt.py | 24 ++----------- tests/test_libopenmm.py | 27 ++++++++++++++ 5 files changed, 106 insertions(+), 75 deletions(-) create mode 100644 src/taurenmd/libs/libopenmm.py create mode 100644 tests/test_libopenmm.py diff --git a/src/taurenmd/libs/libmda.py b/src/taurenmd/libs/libmda.py index 7d51826..0c897f5 100644 --- a/src/taurenmd/libs/libmda.py +++ b/src/taurenmd/libs/libmda.py @@ -13,12 +13,11 @@ """ import MDAnalysis as mda from MDAnalysis.analysis import align as mdaalign -from simtk.openmm.app import pdbxfile from taurenmd import Path from taurenmd import core as tcore from taurenmd import log -from taurenmd.libs import libcli, libio +from taurenmd.libs import libcli, libio, libopenmm from taurenmd.logger import S, T @@ -71,7 +70,7 @@ def load_universe(topology, *trajectories, insort=False): universe = mda.Universe(topo_path, topo_trajs) except ValueError: - pdbx = pdbxfile.PDBxFile(topo_path) + pdbx = libopenmm.attempt_to_load_top_from_simtk(topo_path) universe = mda.Universe(pdbx, topo_trajs) report(universe) diff --git a/src/taurenmd/libs/libmdt.py b/src/taurenmd/libs/libmdt.py index 489748c..d087f7d 100644 --- a/src/taurenmd/libs/libmdt.py +++ b/src/taurenmd/libs/libmdt.py @@ -22,29 +22,10 @@ from taurenmd import Path from taurenmd import core as tcore from taurenmd import log -from taurenmd.libs import libcli, libio +from taurenmd.libs import libcli, libio, libopenmm from taurenmd.logger import S, T -try: - from simtk.openmm import app as app - SIMTK = True -except ImportError: - SIMTK = False - - -def _log_simtkimport_error(): - msg = ( - "To use .cif files as Topologies taurenmd requires OpenMM, " - "which is currently not installed. " - "Please visit our Installation instruction at " - "https://taurenmd.readthedocs.io/" - ) - log.error(T('Dependency Error')) - log.error(S(msg)) - sys.exit(0) - - @libcli.add_reference(tcore.ref_mdt) def load_traj(topology, trajectories, insort=False): """ @@ -65,7 +46,8 @@ def load_traj(topology, trajectories, insort=False): trajectory : str or Path Path to the trajectory file. Accepts MDTraj compatible `files `_ - Returns ------- + Returns + ------- MDTraj trajectory `Trajectory object `_. """ # noqa: E501 @@ -79,41 +61,18 @@ def load_traj(topology, trajectories, insort=False): trajs = os.fspath(trajectories) libio.report_input(topology, trajs) - top = attempt_to_load_top_from_simtk(topology) - mdtrajectory = mdtraj.load(trajs, top=top) - - return mdtrajectory - -@libcli.add_reference(tcore.ref_openmm) -def attempt_to_load_top_from_simtk(topology): - """ - Load topology from SIMTK. - - Parameters - ---------- - topology : str or Path - - Returns - ------- - topology from mdtraj.Topology.from_openmm` + if Path(topology).suffix == '.cif': + _top = libopenmm.attempt_to_load_top_from_simtk(topology) + top = mdtraj.Topology.from_openmm(_top.topology) + else: + top = topology - Raises - ------ - Dependency error from :func:`_log_simtkimport_error`, program - halts. - """ - topp = Path(topology) + mdtrajectory = mdtraj.load(trajs, top=top) - if topp.suffix == '.cif' and SIMTK: - mol = app.PDBxFile(topp.str()) - return mdtraj.Topology.from_openmm(mol.topology) + return mdtrajectory - elif topp.suffix == '.cif' and not SIMTK: - _log_simtkimport_error() - else: - return topp.str() @libcli.add_reference(tcore.ref_mdt) diff --git a/src/taurenmd/libs/libopenmm.py b/src/taurenmd/libs/libopenmm.py new file mode 100644 index 0000000..0841f87 --- /dev/null +++ b/src/taurenmd/libs/libopenmm.py @@ -0,0 +1,64 @@ +""" +Functions that wrap around `OpenMM library`_. + +Read our `citing documentation`_ to understand how to cite multiple +libraries. + +.. _citing documentation: https://taurenmd.readthedocs.io/en/latest/citing.html +.. _OpenMM library: http://openmm.org/ +""" +import sys + +try: + from openmm.app import pdbxfile + SIMTK = True +except ImportError: + SIMTK = False + +from taurenmd import Path, log +from taurenmd import core as tcore +from taurenmd.libs import libcli +from taurenmd.logger import S, T + + +@libcli.add_reference(tcore.ref_openmm) +def attempt_to_load_top_from_simtk(topology): + """ + Load topology from SIMTK. + + Parameters + ---------- + topology : str or Path + + Returns + ------- + topology from mdtraj.Topology.from_openmm` + + Raises + ------ + Dependency error from :func:`_log_simtkimport_error`, program + halts. + """ + topp = Path(topology) + + if topp.suffix == '.cif' and SIMTK: + mol = pdbxfile.PDBxFile(topp.str()) + return mol + + elif topp.suffix == '.cif' and not SIMTK: + _log_simtkimport_error() + + else: + raise ValueError(f'`topology` suffix is not CIF: {topp.suffix!r}') + + +def _log_simtkimport_error(): + msg = ( + "To use .cif files as Topologies taurenmd requires OpenMM, " + "which is currently not installed. " + "Please visit our Installation instruction at " + "https://taurenmd.readthedocs.io/" + ) + log.error(T('Dependency Error')) + log.error(S(msg)) + sys.exit(0) diff --git a/tests/test_libmdt.py b/tests/test_libmdt.py index 69c539f..449ff17 100644 --- a/tests/test_libmdt.py +++ b/tests/test_libmdt.py @@ -2,7 +2,7 @@ import mdtraj as md import pytest -from taurenmd.libs import libmdt +from taurenmd.libs import libmdt, libopenmm from . import toptest, toptest_cif, trajtest @@ -30,34 +30,16 @@ def test_load_traj_pdb_3(): def test_load_traj_cif(): """Test loading traj.""" + assert toptest_cif.suffix == '.cif' traj = libmdt.load_traj(toptest_cif, trajtest) assert isinstance(traj, md.Trajectory) assert len(traj) == 10 -def test_attempt_load_cif_SIMTK_1(): - """Test attempt load CIF.""" - libmdt.attempt_to_load_top_from_simtk(toptest_cif) - - -def test_attempt_load_cif_SIMTK_2(): - """Test attempt load CIF.""" - assert toptest.str() == libmdt.attempt_to_load_top_from_simtk(toptest) - - def test_load_traj_cif_import_error(): """Test loading traj.""" - libmdt.SIMTK = False + libopenmm.SIMTK = False with pytest.raises(SystemExit) as err: libmdt.load_traj(toptest_cif, trajtest) assert err.type == SystemExit assert err.value.code == 0 - - -def test_simtk_import_error(): - """Test import error message.""" - with pytest.raises(SystemExit) as err: - libmdt._log_simtkimport_error() - - assert err.type == SystemExit - assert err.value.code == 0 diff --git a/tests/test_libopenmm.py b/tests/test_libopenmm.py new file mode 100644 index 0000000..725670c --- /dev/null +++ b/tests/test_libopenmm.py @@ -0,0 +1,27 @@ +"""Test libopenmm.""" +import pytest +from openmm.app import pdbxfile + +from taurenmd.libs import libopenmm + +from . import toptest, toptest_cif + + +def test_attempt_load_cif_SIMTK_1(): + """Test attempt load CIF.""" + mol = libopenmm.attempt_to_load_top_from_simtk(toptest_cif) + assert isinstance(mol, pdbxfile.PDBxFile) + + +def test_attempt_load_cif_SIMTK_2(): + """Test attempt load CIF.""" + with pytest.raises(ValueError): + libopenmm.attempt_to_load_top_from_simtk(toptest) + + +def test_simtk_import_error(): + """Test import error message.""" + with pytest.raises(SystemExit) as err: + libopenmm._log_simtkimport_error() + assert err.type == SystemExit + assert err.value.code == 0 From 41cea716d452e293c772ef106edb5f827479d125 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 20:03:44 +0100 Subject: [PATCH 07/15] lint --- src/taurenmd/libs/libmdt.py | 3 --- src/taurenmd/libs/libopenmm.py | 5 ++++- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/taurenmd/libs/libmdt.py b/src/taurenmd/libs/libmdt.py index d087f7d..f4b68f5 100644 --- a/src/taurenmd/libs/libmdt.py +++ b/src/taurenmd/libs/libmdt.py @@ -15,7 +15,6 @@ .. _Simtk OpenMM: http://openmm.org/ """ import os -import sys import mdtraj @@ -73,8 +72,6 @@ def load_traj(topology, trajectories, insort=False): return mdtrajectory - - @libcli.add_reference(tcore.ref_mdt) def imagemol_protocol1(traj): """Attempt to image molecules acting on the whole traj.""" diff --git a/src/taurenmd/libs/libopenmm.py b/src/taurenmd/libs/libopenmm.py index 0841f87..c112779 100644 --- a/src/taurenmd/libs/libopenmm.py +++ b/src/taurenmd/libs/libopenmm.py @@ -9,14 +9,17 @@ """ import sys + try: from openmm.app import pdbxfile SIMTK = True except ImportError: SIMTK = False -from taurenmd import Path, log + +from taurenmd import Path from taurenmd import core as tcore +from taurenmd import log from taurenmd.libs import libcli from taurenmd.logger import S, T From c61e98672bb842f4e8e96992bd00fe220c640363 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 20:23:16 +0100 Subject: [PATCH 08/15] updates in tests --- tests/test_libmdt.py | 2 ++ tests/test_libopenmm.py | 5 +++++ 2 files changed, 7 insertions(+) diff --git a/tests/test_libmdt.py b/tests/test_libmdt.py index 449ff17..640d01c 100644 --- a/tests/test_libmdt.py +++ b/tests/test_libmdt.py @@ -38,8 +38,10 @@ def test_load_traj_cif(): def test_load_traj_cif_import_error(): """Test loading traj.""" + _tmp = libopenmm.SIMTK libopenmm.SIMTK = False with pytest.raises(SystemExit) as err: libmdt.load_traj(toptest_cif, trajtest) assert err.type == SystemExit assert err.value.code == 0 + libopenmm.SIMTK = _tmp diff --git a/tests/test_libopenmm.py b/tests/test_libopenmm.py index 725670c..15908ef 100644 --- a/tests/test_libopenmm.py +++ b/tests/test_libopenmm.py @@ -7,6 +7,11 @@ from . import toptest, toptest_cif +def test_simtk(): + """Test simtk is installed.""" + assert libopenmm.SIMTK + + def test_attempt_load_cif_SIMTK_1(): """Test attempt load CIF.""" mol = libopenmm.attempt_to_load_top_from_simtk(toptest_cif) From 18aaed779aa82c513e8a60381f13930b812b85a8 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Tue, 23 Nov 2021 20:30:42 +0100 Subject: [PATCH 09/15] var name improve --- src/taurenmd/libs/libmda.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/taurenmd/libs/libmda.py b/src/taurenmd/libs/libmda.py index 0c897f5..96dc623 100644 --- a/src/taurenmd/libs/libmda.py +++ b/src/taurenmd/libs/libmda.py @@ -64,14 +64,14 @@ def load_universe(topology, *trajectories, insort=False): libio.report_input(topology, trajectories) topo_path = Path(topology).str() - topo_trajs = [Path(i).str() for i in trajectories], + traj_path = [Path(i).str() for i in trajectories], try: - universe = mda.Universe(topo_path, topo_trajs) + universe = mda.Universe(topo_path, traj_path) except ValueError: pdbx = libopenmm.attempt_to_load_top_from_simtk(topo_path) - universe = mda.Universe(pdbx, topo_trajs) + universe = mda.Universe(pdbx, traj_path) report(universe) return universe From 8d4f5cbfc6e787371e18bf627134770f6af7125e Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Wed, 24 Nov 2021 22:20:46 +0100 Subject: [PATCH 10/15] 100% coverage --- CHANGELOG.rst | 2 +- tests/test_libmda.py | 1 - tests/test_libmdt.py | 23 ----------------------- tests/test_libopenmm.py | 26 +++++++++++++++++++++++++- 4 files changed, 26 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 9ca197c..a42da4a 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,7 +10,7 @@ Upon version 0.8, and before version 1, SV2 major version increments are reflect Changelog ========= -* Add support for CIF topologies in libmda using simtk.openmm.app.pdbxfile +* Add support for CIF topologies in libmda using openmm.app.pdbxfile v0.10.0 (2021-11-24) ------------------------------------------------------------ diff --git a/tests/test_libmda.py b/tests/test_libmda.py index 3f16b44..c37f684 100644 --- a/tests/test_libmda.py +++ b/tests/test_libmda.py @@ -20,7 +20,6 @@ def test_load_universe_1(): assert len(universe.trajectory) == 10 -@pytest.mark.skip(reason="It works in the CLI, can't make it work here") def test_load_universe_1_cif(): """Test load MDA Universe.""" universe = la.load_universe( diff --git a/tests/test_libmdt.py b/tests/test_libmdt.py index 77a0e58..4bb4485 100644 --- a/tests/test_libmdt.py +++ b/tests/test_libmdt.py @@ -1,9 +1,5 @@ """Test libmdt.""" -import importlib -import sys - import mdtraj as md -import pytest from taurenmd.libs import libmdt @@ -37,22 +33,3 @@ def test_load_traj_cif(): traj = libmdt.load_traj(toptest_cif, trajtest) assert isinstance(traj, md.Trajectory) assert len(traj) == 10 - - -def test_load_traj_cif_import_error(): - """Test loadtraj_cif import error as if simtk was not installed.""" - sys.modules['openmm.app.pdbxfile'] = None - importlib.reload(libmdt) - with pytest.raises(SystemExit) as err: - libmdt.load_traj(toptest_cif, trajtest) - assert err.type == SystemExit - assert err.value.code == 0 - - -def test_simtk_import_error(): - """Test import error message.""" - with pytest.raises(SystemExit) as err: - libmdt._log_simtkimport_error() - - assert err.type == SystemExit - assert err.value.code == 0 diff --git a/tests/test_libopenmm.py b/tests/test_libopenmm.py index 15908ef..a31a6cc 100644 --- a/tests/test_libopenmm.py +++ b/tests/test_libopenmm.py @@ -1,10 +1,13 @@ """Test libopenmm.""" +import importlib +import sys + import pytest from openmm.app import pdbxfile from taurenmd.libs import libopenmm -from . import toptest, toptest_cif +from . import toptest, toptest_cif, trajtest def test_simtk(): @@ -30,3 +33,24 @@ def test_simtk_import_error(): libopenmm._log_simtkimport_error() assert err.type == SystemExit assert err.value.code == 0 + + +def test_without_simtk(): + """Test without simtk installed.""" + sys.modules['openmm.app.pdbxfile'] = None + importlib.reload(libopenmm) + with pytest.raises(SystemExit) as err: + libopenmm.attempt_to_load_top_from_simtk(toptest_cif) + assert err.type == SystemExit + assert err.value.code == 0 + + +def test_load_traj_cif_import_error(): + """Test loadtraj_cif import error as if simtk was not installed.""" + sys.modules['openmm.app.pdbxfile'] = None + from taurenmd.libs import libmdt + importlib.reload(libmdt) + with pytest.raises(SystemExit) as err: + libmdt.load_traj(toptest_cif, trajtest) + assert err.type == SystemExit + assert err.value.code == 0 From 26b0f32c1cc6095777f9ac81d54367c15512acf4 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Wed, 24 Nov 2021 22:36:22 +0100 Subject: [PATCH 11/15] removed empty space --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index cfaf3af..14f49dc 100644 --- a/README.rst +++ b/README.rst @@ -50,7 +50,7 @@ taurenmd :target: https://pypistats.org/packages/taurenmd **A command-line interface for analysis routines of Molecular Dynamics data.** - + **Taurenmd** provides an easy, flexible and extensible, **command-line** interface for the most common *(and not so common)* routines of analysis and representation of Molecular Dynamics (MD) data. It bridges the gap between the highly complex (and powerful) Python libraries available for analysis of MD data and the *non-developer* users that lack the programming skills to perform a thorough and proficient use those libraries. *But not only*, **taurenmd** also facilitates high throughput operations, even to those proficient *devs*, because complex executions are reduced to single argument-rich command-lines that can be concatenated or aliased. From 7e9d17d0adb3097f7dc855e75d54b13d14726c27 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Wed, 24 Nov 2021 22:39:49 +0100 Subject: [PATCH 12/15] bad master remaining --- CHANGELOG.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index a42da4a..ec5eb61 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -18,7 +18,6 @@ v0.10.0 (2021-11-24) * Updates MDAnalysis to version 2.0.0 * Defines versions for all other dependencies * Updates CI ->>>>>>> master v0.9.9 (2021-11-22) ------------------------------------------------------------ From 6072acf2d52ee384fc58bf451003a885a5e72bdf Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Wed, 24 Nov 2021 23:06:48 +0100 Subject: [PATCH 13/15] brings compatibility with py36 --- src/taurenmd/libs/libmdt.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/taurenmd/libs/libmdt.py b/src/taurenmd/libs/libmdt.py index f4b68f5..c1bf71f 100644 --- a/src/taurenmd/libs/libmdt.py +++ b/src/taurenmd/libs/libmdt.py @@ -65,7 +65,7 @@ def load_traj(topology, trajectories, insort=False): _top = libopenmm.attempt_to_load_top_from_simtk(topology) top = mdtraj.Topology.from_openmm(_top.topology) else: - top = topology + top = Path(topology).str() mdtrajectory = mdtraj.load(trajs, top=top) From edc8af1378d43c22a98b524e79ec035f81d54137 Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Wed, 24 Nov 2021 23:19:50 +0100 Subject: [PATCH 14/15] removed install.yml makes no sense because they install the previous version. --- .github/workflows/install-dev.yml | 42 ------------------------------- .github/workflows/install.yml | 38 ---------------------------- 2 files changed, 80 deletions(-) delete mode 100644 .github/workflows/install-dev.yml delete mode 100644 .github/workflows/install.yml diff --git a/.github/workflows/install-dev.yml b/.github/workflows/install-dev.yml deleted file mode 100644 index 80cfb30..0000000 --- a/.github/workflows/install-dev.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: install-dev - -on: - push: - branches: [master] - pull_request: - branches: [master] - -jobs: - build: - runs-on: ${{ matrix.platform }} - strategy: - matrix: - platform: [ubuntu-latest] - python-version: [3.6, 3.7, 3.8, 3.9] - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: conda-incubator/setup-miniconda@v2 - with: - activate-environment: taurenmddev - environment-file: requirements-dev.yml - python-version: ${{ matrix.python-version }} - channels: conda-forge - auto-activate-base: false - - - shell: bash -l {0} - run: | - conda info - conda list - -# - name: Install dependencies -# run: | -# conda env update -n taurenmddev --file requirements-dev.yml - - - name: Test versions - shell: bash -l {0} - run: | - python -c "from mdtraj import version; print('mdtraj version: ', version.version)" - python -c "from openmm import version; print('openmm version: ', version.version)" - python -c "from MDAnalysis import version; print('MDAnalysis version: ', version.__version__)" diff --git a/.github/workflows/install.yml b/.github/workflows/install.yml deleted file mode 100644 index b3db239..0000000 --- a/.github/workflows/install.yml +++ /dev/null @@ -1,38 +0,0 @@ -name: install - -on: - push: - branches: [master] - pull_request: - branches: [master] - -jobs: - build: - runs-on: ${{ matrix.platform }} - strategy: - matrix: - platform: [ubuntu-latest] - python-version: [3.6, 3.7, 3.8, 3.9] - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: conda-incubator/setup-miniconda@v2 - with: - activate-environment: taurenmd - environment-file: requirements.yml - python-version: ${{ matrix.python-version }} - channels: conda-forge - auto-activate-base: false - - - shell: bash -l {0} - run: | - conda info - conda list - - - name: Test versions - shell: bash -l {0} - run: | - python -c "from mdtraj import version; print('mdtraj version: ', version.version)" - python -c "from openmm import version; print('openmm version: ', version.version)" - python -c "from MDAnalysis import version; print('MDAnalysis version: ', version.__version__)" From b5c0ff4271f72cdb32d6dbde3ca0688f045b10da Mon Sep 17 00:00:00 2001 From: joaomcteixeira Date: Wed, 24 Nov 2021 23:20:28 +0100 Subject: [PATCH 15/15] changelog --- CHANGELOG.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index ec5eb61..172fca7 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -11,6 +11,7 @@ Changelog ========= * Add support for CIF topologies in libmda using openmm.app.pdbxfile +* removes the install*.yml gitactions v0.10.0 (2021-11-24) ------------------------------------------------------------