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yuxuanzhuang committed Jun 8, 2020
2 parents e9121df + 3f7f5d3 commit 91b28f4
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -39,6 +39,9 @@ authors.py
# ignore files from tests
.hypothesis/

# duecredit
.duecredit.p

# editors and IDEs
*.sw[a-z]
*~
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57 changes: 57 additions & 0 deletions azure-pipelines.yml
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@@ -0,0 +1,57 @@
trigger:
# start a new build for every push
batch: False
branches:
include:
- develop
paths:
include:
- '*'

pr:
branches:
include:
- '*' # must quote since "*" is a YAML reserved character; we want a string


jobs:
- job: Windows
condition: and(succeeded(), ne(variables['Build.SourceBranch'], 'refs/heads/master')) # skip for PR merges
pool:
vmImage: 'VS2017-Win2016'
strategy:
maxParallel: 4
matrix:
Python37-32bit-full:
PYTHON_VERSION: '3.7'
PYTHON_ARCH: 'x86'
BITS: 32
steps:
- task: UsePythonVersion@0
inputs:
versionSpec: $(PYTHON_VERSION)
addToPath: true
architecture: $(PYTHON_ARCH)
- script: python -m pip install --upgrade pip setuptools wheel
displayName: 'Install tools'
- script: >-
python -m pip install
cython
matplotlib
numpy
pytest
pytest-xdist
scikit-learn
scipy
displayName: 'Install dependencies'
- powershell: |
cd package
python setup.py install
cd ..\testsuite
python setup.py install
cd ..
displayName: 'Build MDAnalysis'
- powershell: |
cd testsuite
pytest .\MDAnalysisTests --disable-pytest-warnings -n 2 -rsx
displayName: 'Run MDAnalysis Test Suite'
2 changes: 2 additions & 0 deletions package/AUTHORS
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Expand Up @@ -145,6 +145,8 @@ Chronological list of authors
- Ameya Harmalkar
- Shakul Pathak
- Andrea Rizzi
- William Glass
- Marcello Sega

External code
-------------
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31 changes: 29 additions & 2 deletions package/CHANGELOG
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Expand Up @@ -17,11 +17,23 @@ mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira
PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,
Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria,
ss62171, Luthaf, yuxuanzhuang, abhishandy, mlnance, shfrz, orbeckst,
wvandertoorn, cbouy, AmeyaHarmalkar, Oscuro-Phoenix, andrrizzi
wvandertoorn, cbouy, AmeyaHarmalkar, Oscuro-Phoenix, andrrizzi, WG150,
tylerjereddy, Marcello-Sega

* 0.21.0

Fixes
* MOL2Writer now accepts both Universes and AtomgGroups (Issue #2717)
* Use user-provided `remark` in `XYZWriter` (Issue #2692)
* Added more informative error messages about topology attributes
(Issue #2565)
* Made NoDataError a subclass of ValueError *and* AttributeError
(Issue #2635)
* Fixed select_atoms("around 0.0 ...") selections and capped_distance
causing a segfault (Issue #2656 PR #2665)
* `PDBWriter` writes unitary `CRYST1` record (cubic box with sides of 1 Å)
when `u.dimensions` is `None` or `np.zeros(6)` (Issue #2679, PR #2685)
* Ensures principal_axes() returns axes with the right hand convention (Issue #2637)
* Fixed retrieval of auxiliary information after getting the last timestep
of the trajectory (Issue #2674, PR #2683).
* n_components correctly selects PCA components (Issue #2623)
Expand Down Expand Up @@ -86,6 +98,8 @@ Fixes
* Contact Analysis class respects PBC (Issue #2368)

Enhancements
* Added support for FHI-AIMS input files (PR #2705)
* vastly improved support for 32-bit Windows (PR #2696)
* Added methods to compute the root-mean-square-inner-product of subspaces
and the cumulative overlap of a vector in a subspace for PCA (PR #2613)
* Added .frames and .times arrays to AnalysisBase (Issue #2661)
Expand Down Expand Up @@ -132,6 +146,18 @@ Enhancements
the capability to allow intermittent behaviour (PR #2256)

Changes
* Unused `MDAnalysis.lib.mdamath._angle` has been removed (Issue #2650)
* Refactored dihedral selections and Ramachandran.__init__ to speed up
dihedral selections for faster tests (Issue #2671, PR #2706)
* Removes the deprecated `t0`, `tf`, and `dtmax` from
:class:Waterdynamics.SurvivalProbability. Instead the `start`, `stop` and
`tau_max` keywords should be passed to
:meth:`Waterdynamics.SurvivalProbability.run`. Furthermore, the `stop`
keyword is now exclusive instead of inclusive (Issue #2524).
* :meth:`align.fasta2select` now writes `alnfilename` and `treefilename` to
the current working directory (Issue #2701)
* Removes duplicate `NUMBER_TO_ELEMENTS` table from topology._elements,
`Z2SYMB` from topology.tables should now be used instead (Issue #2699)
* Deprecated :class:`ProgressMeter` and replaced it with :class:`ProgressBar` using
the tqdm package (Issue #928, PR #2617). Also fixes issue #2504.
* Removed `details` from `ClusteringMethod`s (Issue #2575, PR #2620)
Expand Down Expand Up @@ -189,7 +215,8 @@ Deprecations
* analysis.density.density_from_Universe() (remove in 2.0)
* analysis.density.notwithin_coordinates_factory() (remove in 2.0)
* analysis.density.density_from_PDB and BfactorDensityCreator (remove in 2.0)

* Writer.write_next_timestep is deprecated, use write() instead (remove in 2.0)
* Writer.write(Timestep) is deprecated, use either a Universe or AtomGroup

09/05/19 IAlibay, richardjgowers

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5 changes: 4 additions & 1 deletion package/MDAnalysis/__init__.py
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Expand Up @@ -177,7 +177,10 @@
_SELECTION_WRITERS = {}
_CONVERTERS = {}
# Registry of TopologyAttributes
_TOPOLOGY_ATTRS = {}
_TOPOLOGY_ATTRS = {} # {attrname: cls}
_TOPOLOGY_TRANSPLANTS = {} # {name: [attrname, method, transplant class]}
_TOPOLOGY_ATTRNAMES = {} # {lower case name w/o _ : name}


# Storing anchor universes for unpickling groups
import weakref
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8 changes: 6 additions & 2 deletions package/MDAnalysis/analysis/align.py
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Expand Up @@ -1033,6 +1033,10 @@ def fasta2select(fastafilename, is_aligned=False,
.. _ClustalW: http://www.clustal.org/
.. _STAMP: http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
.. versionchanged:: 1.0.0
Passing `alnfilename` or `treefilename` as `None` will create a file in
the current working directory.
"""
if is_aligned:
logger.info("Using provided alignment {}".format(fastafilename))
Expand All @@ -1042,10 +1046,10 @@ def fasta2select(fastafilename, is_aligned=False,
else:
if alnfilename is None:
filepath, ext = os.path.splitext(fastafilename)
alnfilename = filepath + '.aln'
alnfilename = os.path.basename(filepath) + '.aln'
if treefilename is None:
filepath, ext = os.path.splitext(alnfilename)
treefilename = filepath + '.dnd'
treefilename = os.path.basename(filepath) + '.dnd'
run_clustalw = Bio.Align.Applications.ClustalwCommandline(
clustalw,
infile=fastafilename,
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