add h5md format (#2787)

* Fixes #762
* add H5MD coordinate reader (supports parallel MPI in principle but is not well tested at the moment, see #2865)
* added test h5md datafiles:  real example (derived from cobrotoxin.trr) and synthetic example for MultiframeReaderTest reader tests
* add tests (MultiframeReaderTest and custom)
* add documentation (example and parallel MPI)
* added h5py into conda dependencies and pyh5md into pip dependencies
* update CHANGELOG
* update AUTHORS

.appveyor.yml

@@ -10,7 +10,7 @@ cache:
 environment:
     global:
         CONDA_CHANNELS: conda-forge
-        CONDA_DEPENDENCIES: pip setuptools wheel cython biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov chemfiles tqdm tidynamics>=1.0.0 rdkit>=2020.03.1
+        CONDA_DEPENDENCIES: pip setuptools wheel cython biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov chemfiles tqdm tidynamics>=1.0.0 rdkit>=2020.03.1 h5py
         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
@@ -22,7 +22,7 @@ environment:
         # is fixed in ci-helpers https://github.com/astropy/ci-helpers/issues/406
         # MINICONDA_VERSION: "latest"
         MPLBACKEND: "agg"
-        
+
     matrix:
         - PYTHON_VERSION: 3.6
           PYTHON_ARCH: 64

.travis.yml

@@ -30,7 +30,7 @@ env:
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
     - CONDA_MIN_DEPENDENCIES="mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"
@@ -151,7 +151,7 @@ after_success:
     fi
 
   # can't use test here since this leads to travis fails even though the build passes
-  # turn off blocking as it causes large writes to stdout to fail 
+  # turn off blocking as it causes large writes to stdout to fail
   # (see https://github.com/travis-ci/travis-ci/issues/4704)
   - |
     if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] ; then
@@ -162,4 +162,3 @@ after_success:
       cd -
       bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs_via_travis.sh;
     fi
-

azure-pipelines.yml

@@ -20,7 +20,7 @@ jobs:
   pool:
     vmImage: 'VS2017-Win2016'
   variables:
-    MPLBACKEND: agg    
+    MPLBACKEND: agg
   strategy:
     matrix:
         Python37-32bit-full:
@@ -54,6 +54,7 @@ jobs:
       pytest-xdist
       scikit-learn
       scipy
+      h5py
       tqdm
     displayName: 'Install dependencies'
   # TODO: recent rdkit is not on PyPI
@@ -64,7 +65,7 @@ jobs:
       duecredit
       gsd==1.9.3
       joblib
-      GridDataFormats 
+      GridDataFormats
       mmtf-python
       networkx
       parmed

package/AUTHORS

@@ -147,6 +147,7 @@ Chronological list of authors
   - Andrea Rizzi
   - William Glass
   - Marcello Sega
+  - Edis Jakupovic
 
 External code
 -------------

package/CHANGELOG

@@ -21,7 +21,7 @@ The rules for this file:
 Fixes
   * Bond attribute is no longer set if PDB file contains no CONECT records
     (Issue #2832)
-  * ResidueAttrs now have Atom as a target class by default; ICodes and 
+  * ResidueAttrs now have Atom as a target class by default; ICodes and
     Molnums now have default target_classes (#2803, PR #2805)
   * Selections on emtpy AtomGroups now return an empty AtomGroup instead of an
     error (Issue #2765)
@@ -36,8 +36,8 @@ Fixes
     density=True; the keyword was available since 0.19.0 but with incorrect
     semantics and not documented and did not produce correct results (Issue
     #2811, PR #2812)
-  * In hydrogenbonds.hbond_analysis.HydrogenbondAnalysis an AttributeError 
-    was thrown when finding D-H pairs via the topology if `hydrogens` was an 
+  * In hydrogenbonds.hbond_analysis.HydrogenbondAnalysis an AttributeError
+    was thrown when finding D-H pairs via the topology if `hydrogens` was an
     empty AtomGroup (Issue #2848)
   * Fixed the DMSParser, allowing the creation of multiple segids sharing
     residues with identical resids (Issue #1387, PR #2872)    
@@ -60,6 +60,7 @@ Enhancements
   * Added Hydrogen Bond Lifetime keyword "between" (PR #2791)
   * Dead code removed from the TPR parser and increased test coverage (PR #2840)
   * TPR parser exposes the elements topology attribute (PR #2858, see Issue #2553)
+  * Added `H5MDReader` to coordinate readers (Issue #762, PR #2787)
 
 Changes
   * deprecated NumPy type aliases have been replaced with their actual types