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Merged
richardjgowers merged 21 commits into from
Mar 10, 2020
Merged

Add Chemfiles as a coordinate reader/writer #1862

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240c3d3
Add a dot between filename and extension
Apr 10, 2018
1862eff
Implement CHEMFILES reader and writer
Apr 10, 2018
65c5c86
Add chemfiles to conda dependencies on CI
Mar 28, 2019
ad5d199
Allow passing the format name to chemfiles
Luthaf May 8, 2019
b450ee3
Add documentation to the code
Luthaf May 15, 2019
634e326
Convert MDAnalysis topology to chemfiles when writing
Luthaf May 15, 2019
ca33ab2
added standard XYZ tests via Chemfiles
richardjgowers Jul 8, 2019
5eadec7
minor tweaks to get tests passing
richardjgowers Jul 8, 2019
b4410db
Also translate segindex attribute to property
Luthaf Feb 10, 2020
93ddfd7
Move version checking inside a function
Luthaf Feb 11, 2020
6f195ae
Documentation improvements
Luthaf Feb 11, 2020
c3d5321
Add a test when opening a file without extension
Luthaf Feb 11, 2020
eaf172c
Add a comment about unit conversion
Luthaf Feb 11, 2020
359ea4e
Add a test checking that velocities and unit cell are written
Luthaf Feb 12, 2020
b1aa7d2
made chemfiles optional dependency using FORMAT_HINT
richardjgowers Feb 18, 2020
55e97e7
properly skip chemfiles tests if bad version too
richardjgowers Feb 18, 2020
8fcdc23
changelog and authors
richardjgowers Feb 18, 2020
0338863
fixed logic in chemfiles skipping
richardjgowers Feb 21, 2020
85b7ac1
Merge branch 'develop' into chemfiles
richardjgowers Feb 26, 2020
570e191
TST: skip test if wrong chemfiles version is installed.
kain88-de Mar 10, 2020
7f6395f
Merge branch 'develop' into chemfiles
richardjgowers Mar 10, 2020
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2 changes: 1 addition & 1 deletion .appveyor.yml
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Expand Up @@ -10,7 +10,7 @@ cache:
environment:
global:
CONDA_CHANNELS: conda-forge
CONDA_DEPENDENCIES: pip setuptools wheel cython mock six biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov
CONDA_DEPENDENCIES: pip setuptools wheel cython mock six biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov chemfiles
PIP_DEPENDENCIES: gsd==1.9.3 duecredit parmed
DEBUG: "False"
MINGW_64: C:\mingw-w64\x86_64-6.3.0-posix-seh-rt_v5-rev1\mingw64\bin
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4 changes: 2 additions & 2 deletions .travis.yml
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Expand Up @@ -28,7 +28,7 @@ env:
- SETUP_CMD="${PYTEST_FLAGS}"
- BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
- CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
- CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12"
- CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles"
- CONDA_CHANNELS='biobuilds conda-forge'
- CONDA_CHANNEL_PRIORITY=True
- PIP_DEPENDENCIES="duecredit parmed"
Expand Down Expand Up @@ -66,7 +66,7 @@ matrix:
INSTALL_HOLE="false"

- env: NAME="python 2.7"
PYTHON_VERSION=2.7
PYTHON_VERSION=2.7
CODECOV="true"
NUMPY_VERSION=1.16
SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
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2 changes: 1 addition & 1 deletion package/AUTHORS
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Expand Up @@ -128,6 +128,7 @@ Chronological list of authors
2020
- Charlie Cook
- Yuanyu Chang
- Guillaume Fraux
- Ivan Hristov
- Michael Quevillon
- Hao Tian
Expand All @@ -136,7 +137,6 @@ Chronological list of authors
- Shubham Sharma



External code
-------------

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3 changes: 2 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -16,7 +16,7 @@ The rules for this file:
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
ss62171, Luthaf

* 0.21.0

Expand Down Expand Up @@ -66,6 +66,7 @@ Fixes
* Fixed example docs for polymer persistence length (#2582)

Enhancements
* Added ability to use Chemfiles as a trajectory reader backend (PR #1862)
* New analysis.hole2 module for HOLE interfacing. Contains a function (hole)
for running HOLE on singular PDB files and class (HoleAnalysis) for
trajectories (PR #2523)
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1 change: 1 addition & 0 deletions package/MDAnalysis/coordinates/__init__.py
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Expand Up @@ -716,6 +716,7 @@ class can choose an appropriate reader automatically.
from . import base
from .core import reader, writer
from . import chain
from . import chemfiles
from . import CRD
from . import DCD
from . import DLPoly
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