Merge remote-tracking branch 'upstream/develop' into memory-reader-repr

Author: ljwoods2

.github/actions/build-src/action.yaml

@@ -63,8 +63,8 @@ runs:
         which python
         which pip
         pip list
-        conda info
-        conda list
+        micromamba info
+        micromamba list
 
     - name: build_mda_main
       shell: bash -l {0}

.github/workflows/deploy.yaml

@@ -40,6 +40,7 @@ jobs:
           - [ubuntu-22.04, manylinux_x86_64, x86_64]
           - [macos-11, macosx_*, x86_64]
           - [windows-2019, win_amd64, AMD64]
+          - [macos-14, macosx_*, arm64]
         python: ["cp39", "cp310", "cp311", "cp312"]
     defaults:
       run:
@@ -50,7 +51,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.2
+        uses: pypa/cibuildwheel@v2.16.5
         with:
           package-dir: package
         env:

.github/workflows/gh-ci-cron.yaml

@@ -224,7 +224,7 @@ jobs:
         fail-fast: false
         matrix:
           os: [ubuntu, macos]
-          python-version: ["3.9", "3.10", "3.11"]
+          python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v4
 
@@ -264,14 +264,17 @@ jobs:
   pypi-latest-release:
     # A set of runner to check that the latest conda release works as expected
     if: "github.repository == 'MDAnalysis/mdanalysis'"
-    runs-on: ${{ matrix.os }}-latest
+    runs-on: ${{ matrix.os }}
     timeout-minutes: 60
     strategy:
         fail-fast: false
         matrix:
-          os: [ubuntu, macos, windows]
-          python-version: ["3.9", "3.10", "3.11"]
+          os: [ubuntu-latest, macos-latest, macos-14, windows-latest]
+          python-version: ["3.9", "3.10", "3.11", "3.12"]
           wheels: ['true', 'false']
+          exclude:
+          - os: "macos-14"
+            python-version: "3.9"
     steps:
       # Checkout to have access to local actions (i.e. setup-os)
     - uses: actions/checkout@v4

.github/workflows/gh-ci.yaml

@@ -34,9 +34,14 @@ jobs:
           include:
             - name: macOS_monterey_py311
               os: macOS-12
-              python-version: "3.11"
+              python-version: "3.12"
               full-deps: true
               codecov: true
+            - name: macOS_14_arm64_py312
+              os: macOS-14
+              python-version: "3.12"
+              full-deps: false
+              codecov: true
             - name: numpy_min
               os: ubuntu-latest
               python-version: 3.9

package/CHANGELOG

@@ -14,21 +14,24 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, ljwoods2
+??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
+         ljwoods2
 
  * 2.8.0
 
 Fixes
+ * Fix ChainReader `__repr__()` method when sub-reader is MemoryReader 
+   (Issue #3349, PR #4407)
  * Fix bug in PCA preventing use of `frames=...` syntax (PR #4423)
  * Fix `analysis/diffusionmap.py` iteration through trajectory to iteration
    over `self._sliced_trajectory`, hence supporting
    `DistanceMatrix.run(frames=...)` (PR #4433)
  * Fix doctest errors of lib/picklable_file_io.py (Issue #3925, PR #4371)
  * Fix deploy action to use the correct version of the pypi upload action.
- * Fix ChainReader `__repr__()` method when sub-reader is MemoryReader 
-   (Issue #3349, PR #4407)
 
 Enhancements
+ * Documented the r0 attribute in the `Contacts` class and added the 
+   `n_initial_contacts` attribute, with documentation. (Issue #2604, PR #4415)
 
 Changes
  * As per NEP29, the minimum version of numpy has been raised to 1.23.

package/MDAnalysis/analysis/contacts.py

@@ -405,6 +405,13 @@ def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
              Show detailed progress of the calculation if set to ``True``; the
              default is ``False``.
 
+        Attributes
+        ----------
+        n_initial_contacts : int
+             Total number of initial contacts.
+        r0 : list[numpy.ndarray]
+             List of distance arrays between reference groups.
+
         Notes
         -----
 
@@ -455,6 +462,9 @@ def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
                                                 box=self._get_box(refA.universe)))
                 self.initial_contacts.append(contact_matrix(self.r0[-1], radius))
 
+        self.n_initial_contacts = self.initial_contacts[0].sum()
+
+
     @staticmethod
     def _get_atomgroup(u, sel):
         select_error_message = ("selection must be either string or a "

testsuite/MDAnalysisTests/analysis/test_contacts.py

@@ -375,6 +375,16 @@ def test_warn_deprecated_attr(self, universe):
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert_equal(CA1.timeseries, CA1.results.timeseries)
 
+    @pytest.mark.parametrize("datafiles, expected", [((PSF, DCD), 0),
+                                                     ([TPR, XTC], 41814)])
+    def test_n_initial_contacts(self, datafiles, expected):
+        """Test for n_initial_contacts attribute"""
+        u = mda.Universe(*datafiles)
+        select = ('protein', 'not protein')
+        refgroup = (u.select_atoms('protein'), u.select_atoms('not protein'))
+
+        r = contacts.Contacts(u, select=select, refgroup=refgroup)
+        assert_equal(r.n_initial_contacts, expected)
 
 def test_q1q2():
     u = mda.Universe(PSF, DCD)