AuxReader for EDR Files

.github/actions/setup-deps/action.yaml

@@ -76,6 +76,8 @@ inputs:
     default: 'pytest-cov<=2.10.1'
   pytest-xdist:
     default: 'pytest-xdist'
+  pyedr:
+    default: 'pyedr'
   # pip-install optional dependencies
   duecredit:
     default: 'duecredit'
@@ -132,14 +134,15 @@ runs:
         else
           conda install ${CONDA_DEPS}
         fi
-          
+
     - name: pip_install
       shell: bash -l {0}
       env:
         PIP_MIN_DEPS: |
           ${{ inputs.coverage }}
           ${{ inputs.pytest-cov }}
           ${{ inputs.pytest-xdist }}
+          ${{ inputs.pyedr }}
         PIP_OPT_DEPS: |
           ${{ inputs.duecredit }}
           ${{ inputs.parmed }}
@@ -150,7 +153,6 @@ runs:
         else
           PIP_DEPS="${PIP_MIN_DEPS} ${{ inputs.extra-pip-deps }}"
         fi
-        
+
         # do the install
         pip install ${PIP_DEPS}
-

azure-pipelines.yml

@@ -96,6 +96,7 @@ jobs:
       tqdm
       threadpoolctl
       fasteners
+      pyedr
     displayName: 'Install dependencies'
   # for wheel install testing, we pin to an
   # older NumPy, the oldest version we support and that

maintainer/conda/environment.yml

@@ -33,3 +33,4 @@ dependencies:
       - msmb_theme==1.2.0
       - sphinx-sitemap==1.0.2
       - packaging
+      - pyedr

package/CHANGELOG

@@ -14,7 +14,7 @@ The rules for this file:
 
 ------------------------------------------------------------------------------
 ??/??/?? IAlibay, PicoCentauri, orbeckst, hmacdope, rmeli, miss77jun, rzhao271,
-         yuxuanzhuang, hsadia538
+         yuxuanzhuang, hsadia538, BFedder
 
  * 2.3.0
 
@@ -36,6 +36,8 @@ Enhancements
     (CZI Performance track, PR #3683)
   * Refactor make_downshift_arrays with vector operation in numpy(PR #3724)
   * Optimize topology serialization/construction by lazy-building _RA and _SR.
+  * A new AuxReader for the GROMACS EDR file format was implemented.
+    (Issue # 3629, PR # 3749)
 
 Changes
   * To add additional optional packages for different file formats when
@@ -45,6 +47,10 @@ Changes
     as per NEP29 (PR #3737)
   * Narrowed variable scope to reduce use of OpenMP `private` clause (PR #3706, PR
     #3728)
+  * `MDAnalysis.coordinates.base.add_auxiliary()` now supports adding of
+    multiple auxiliary data points at the same time. To this end, an additional
+    `auxterm` argument is now available. Adding all data found in the auxiliary
+    data source is possible by passing `auxname="*"`. (PR #3749)
 
 Deprecations
   * The extras_requires target "AMBER" for `pip install ./package[AMBER]`
@@ -109,7 +115,7 @@ Enhancements
   * Added equations for `center_of_mass` and `center_of_geometry`to
     documentation (PR #3671)
   * Added `center_of_charge` attribute (PR #3671)
-  * Added `frames` argument to AnalysisBase.run to allow analysis to run on 
+  * Added `frames` argument to AnalysisBase.run to allow analysis to run on
     arbitrary list of frames (Issue #1985)
   * LinearDensity now works with updating AtomGroups (Issue #2508, PR #3617)
   * Link PMDA in documentation (PR #3652)