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

@@ -13,7 +13,8 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, Luthaf, hmacdope, rafaelpap, jbarnoud
+
+??/??/?? IAlibay, Luthaf, hmacdope, rafaelpap, jbarnoud, BFedder
 
  * 2.4.0
 
@@ -22,10 +23,21 @@ Fixes
   * Upgrade to chemfiles 0.10.3 (Issue #3798)
 
 Enhancements
+  * MDAnalysis.units now has a lookup dictionary called MDANALYSIS_BASE_UNITS
+    where unit types like length or speed are mapped to their base units in
+    MDAnalysis (i.e. "A" or "A/ps")
+  * A new AuxReader for the GROMACS EDR file format was implemented.
+    (Issue # 3629, PR # 3749)
   * Added benchmarks for bonds topology attribute (Issue #3785, PR #3806)
 
 
 Changes
+ * `MDAnalysis.coordinates.base.add_auxiliary()` now supports adding of
+    multiple auxiliary data points at the same time. To this end, the API was
+    rewritten and now expects dictionaries of `desired attribute name`:
+    `name in auxiliary data file` as input. Adding all data found in the
+    auxiliary data source is possible by omitting the dictionary and explicitly
+    passing the AuxReader instance as `auxdata`. (PR #3749)
   * The "AMBER" entry in setup.py's extra_requires has now been removed. Please
     use `pip install ./package[extra_formats]` instead (PR #3810)
   * `Universe.empty` emmits less warnings (PR #3814)
@@ -35,7 +47,6 @@ Deprecations
 
 08/29/22 IAlibay, PicoCentauri, orbeckst, hmacdope, rmeli, miss77jun, rzhao271,
          yuxuanzhuang, hsadia538, lilyminium
-
  * 2.3.0
 
 Fixes