From 4fc067095a4b0aff945bcb429e6dbb0431106466 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 31 Jan 2020 11:37:09 +0000 Subject: [PATCH 1/6] Update align.py --- package/MDAnalysis/analysis/align.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index 405b39a1b8f..fc74cbf73c9 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -536,6 +536,10 @@ class AlignTraj(AnalysisBase): `filename`. One can also use the same universe if one wants to fit to the current frame. + .. versionchanged:: 1.0.0 + `save()` has now been removed, as an alternative use `np.savetxt()` on + :class:AlignTraj.rmsd. + """ def __init__(self, mobile, reference, select='all', filename=None, From 4cb191be110a86c9c6807ef5c5813e929aa678e6 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 31 Jan 2020 12:10:13 +0000 Subject: [PATCH 2/6] fixes save and filename --- package/MDAnalysis/analysis/align.py | 24 ++++++------------- .../MDAnalysisTests/analysis/test_align.py | 11 --------- 2 files changed, 7 insertions(+), 28 deletions(-) diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index fc74cbf73c9..d8d9610e1be 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -537,8 +537,8 @@ class AlignTraj(AnalysisBase): current frame. .. versionchanged:: 1.0.0 - `save()` has now been removed, as an alternative use `np.savetxt()` on - :class:AlignTraj.rmsd. + ``save()`` has now been removed, as an alternative use ``np.savetxt()`` + on ``:class:AlignTraj.rmsd``. """ @@ -617,6 +617,9 @@ def __init__(self, mobile, reference, select='all', filename=None, already a :class:`MemoryReader` then it is *always* treated as if ``in_memory`` had been set to ``True``. + .. versionchanged:: 1.0.0 + Default ``filename`` has now been changed to the current directory. + .. deprecated:: 0.19.1 Default ``filename`` directory will change in 1.0 to the current directory. @@ -639,13 +642,8 @@ def __init__(self, mobile, reference, select='all', filename=None, logger.info("Moved mobile trajectory to in-memory representation") else: if filename is None: - # DEPRECATED in 0.19.1 - # Change in 1.0 - # - # fn = os.path.split(mobile.trajectory.filename)[1] - # filename = prefix + fn - path, fn = os.path.split(mobile.trajectory.filename) - filename = os.path.join(path, prefix + fn) + fn = os.path.split(mobile.trajectory.filename)[1] + filename = prefix + fn logger.info('filename of rms_align with no filename given' ': {0}'.format(filename)) @@ -703,14 +701,6 @@ def _conclude(self): if not self._verbose: logging.disable(logging.NOTSET) - @deprecate(release="0.19.0", remove="1.0") - def save(self, rmsdfile): - """save rmsd as a numpy array - """ - # these are the values of the new rmsd between the aligned trajectory - # and reference structure - np.savetxt(rmsdfile, self.rmsd) - logger.info("Wrote RMSD timeseries to file %r", rmsdfile) class AverageStructure(AnalysisBase): """RMS-align trajectory to a reference structure using a selection, diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py index 56f34f183e7..c8fd4bbf6af 100644 --- a/testsuite/MDAnalysisTests/analysis/test_align.py +++ b/testsuite/MDAnalysisTests/analysis/test_align.py @@ -211,8 +211,6 @@ def test_rmsd_custom_weights(self, universe, reference): assert_almost_equal(rmsd[1], rmsd_weights[1], 6) def test_AlignTraj_outfile_default(self, universe, reference): - # NOTE: Remove the line os.remove() with release 1.0, - # when the default behavior of AlignTraj changes. with tempdir.in_tempdir(): reference.trajectory[-1] x = align.AlignTraj(universe, reference) @@ -220,7 +218,6 @@ def test_AlignTraj_outfile_default(self, universe, reference): assert os.path.basename(x.filename) == 'rmsfit_adk_dims.dcd' finally: x._writer.close() - os.remove(x.filename) def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir): reference.trajectory[-1] @@ -250,9 +247,6 @@ def test_AlignTraj(self, universe, reference, tmpdir): x = align.AlignTraj(universe, reference, filename=outfile).run() fitted = mda.Universe(PSF, outfile) - rmsd_outfile = str(tmpdir.join('rmsd')) - x.save(rmsd_outfile) - assert_almost_equal(x.rmsd[0], 6.9290, decimal=3) assert_almost_equal(x.rmsd[-1], 5.2797e-07, decimal=3) @@ -262,11 +256,6 @@ def test_AlignTraj(self, universe, reference, tmpdir): self._assert_rmsd(reference, fitted, 0, 6.929083044751061) self._assert_rmsd(reference, fitted, -1, 0.0) - # superficially check saved file rmsd_outfile - rmsd = np.loadtxt(rmsd_outfile) - assert_array_almost_equal(rmsd, x.rmsd, - err_msg="saved RMSD not correct") - def test_AlignTraj_weighted(self, universe, reference, tmpdir): outfile = str(tmpdir.join('align_test.dcd')) x = align.AlignTraj(universe, reference, From 7e4983ac3167d9b41c6a7ff7067f32f086fcd97d Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 31 Jan 2020 12:18:34 +0000 Subject: [PATCH 3/6] changelog --- package/CHANGELOG | 2 ++ 1 file changed, 2 insertions(+) diff --git a/package/CHANGELOG b/package/CHANGELOG index b9c624a4dad..acb792bfc96 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -19,6 +19,8 @@ mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira * 0.21.0 Fixes + * AlignTraj `save()` method has been removed and the `filename` variable now + defaults to the current working directory. * PDBWriter now uses first character of segid as ChainID (Issue #2224) * Adds a more detailed warning when attempting to read chamber-style parm7 files (Issue #2475) From 311e89b3c684883b35eb242b7f65a2b8c55217bf Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 31 Jan 2020 13:58:28 +0000 Subject: [PATCH 4/6] remove deprecate import --- package/MDAnalysis/analysis/align.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index d8d9610e1be..7c39806333c 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -204,7 +204,7 @@ from MDAnalysis.exceptions import SelectionError, SelectionWarning import MDAnalysis.analysis.rms as rms from MDAnalysis.coordinates.memory import MemoryReader -from MDAnalysis.lib.util import get_weights, deprecate +from MDAnalysis.lib.util import get_weights from .base import AnalysisBase From c1b39e16ad1ca242c25c8a0c2745543449733bf3 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 31 Jan 2020 14:38:48 +0000 Subject: [PATCH 5/6] docstring change --- package/MDAnalysis/analysis/align.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index 7c39806333c..ad0a8f6e35d 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -538,7 +538,7 @@ class AlignTraj(AnalysisBase): .. versionchanged:: 1.0.0 ``save()`` has now been removed, as an alternative use ``np.savetxt()`` - on ``:class:AlignTraj.rmsd``. + on :attr:`rmsd`. """ From 7126ab6a76b91c9d488633b21acc2685a3bdc49c Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 31 Jan 2020 15:09:00 +0000 Subject: [PATCH 6/6] A change not a fix --- package/CHANGELOG | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index acb792bfc96..eefec05b213 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -19,8 +19,6 @@ mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira * 0.21.0 Fixes - * AlignTraj `save()` method has been removed and the `filename` variable now - defaults to the current working directory. * PDBWriter now uses first character of segid as ChainID (Issue #2224) * Adds a more detailed warning when attempting to read chamber-style parm7 files (Issue #2475) @@ -78,6 +76,8 @@ Enhancements convert between a parmed.Structure and MDAnalysis Universe (PR #2404) Changes + * AlignTraj `save()` method has been removed and the `filename` variable now + defaults to the current working directory (Issues #2099, #1745, #2443) * The fasta2select now always assumes that the gap character in a sequence is "-" (Issue #2448, PR #2457)