Add Chemfiles as a coordinate reader/writer (#1862)

* Implement CHEMFILES reader and writer Co-authored-by: richardjgowers <[email protected]> Co-authored-by: Max Linke <[email protected]>
MDAnalysis · Mar 10, 2020 · e416aa7 · e416aa7
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commit e416aa7
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Showing 11 changed files with 661 additions and 8 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -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

diff --git a/.travis.yml b/.travis.yml
@@ -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"
@@ -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"

diff --git a/package/AUTHORS b/package/AUTHORS
@@ -128,6 +128,7 @@ Chronological list of authors
 2020
   - Charlie Cook
   - Yuanyu Chang
+  - Guillaume Fraux
   - Ivan Hristov
   - Michael Quevillon
   - Hao Tian
@@ -136,7 +137,6 @@ Chronological list of authors
   - Shubham Sharma
 
 
-
 External code
 -------------
 

diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -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
 
@@ -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)

diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py
@@ -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