Merge branch 'develop' into fix-ci-deps

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

@@ -56,6 +56,8 @@ inputs:
     default: 'chemfiles-python>=0.9'
   clustalw:
     default: 'clustalw=2.1'
+  dask:
+    default: 'dask'
   distopia:
     default: 'distopia>=0.2.0'
   h5py:
@@ -125,6 +127,7 @@ runs:
           ${{ inputs.biopython }}
           ${{ inputs.chemfiles-python }}
           ${{ inputs.clustalw }}
+          ${{ inputs.dask }}
           ${{ inputs.distopia }}
           ${{ inputs.gsd }}
           ${{ inputs.h5py }}

.github/dependabot.yaml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

.github/workflows/darkerbot.yaml

@@ -23,7 +23,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
@@ -32,7 +32,7 @@ jobs:
           pip install PyGithub
 
       - name: 'Download artifact'
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({

.github/workflows/deploy.yaml

@@ -201,7 +201,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.8.10
+        uses: pypa/gh-action-pypi-publish@v1.10.0
 
   upload_pypi_mdanalysistests:
     if: |
@@ -227,7 +227,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/gh-action-pypi-publish@v1.8.10
+        uses: pypa/gh-action-pypi-publish@v1.10.0
         with:
           packages_dir: testsuite/dist
 

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

@@ -206,7 +206,7 @@ jobs:
       with:
         os-type: "ubuntu"
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -302,7 +302,7 @@ jobs:
       with:
         os-type: ${{ matrix.os }}
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/gh-ci.yaml

@@ -123,7 +123,7 @@ jobs:
 
     - name: codecov
       if: matrix.codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
@@ -240,7 +240,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: 3.11
 

.github/workflows/labels.yaml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-    - uses: actions/labeler@v3
+    - uses: actions/labeler@v5
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"
         configuration-path: ".github/pr_path_labeler.yml"

.github/workflows/linters.yaml

@@ -31,13 +31,13 @@ jobs:
       with:
         fetch-depth: 0
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: "3.10"
 
     - name: darker-main-code
       id: darker-main-code
-      uses: akaihola/darker@1.6.1
+      uses: akaihola/darker@v2.1.1
       continue-on-error: true
       with:
         version: "~=1.6.1"
@@ -48,7 +48,7 @@ jobs:
 
     - name: darker-test-code
       id: darker-test-code
-      uses: akaihola/darker@1.6.1
+      uses: akaihola/darker@v2.1.1
       continue-on-error: true
       with:
         version: "~=1.6.1"
@@ -58,7 +58,7 @@ jobs:
         lint: "flake8"
 
     - name: get-pr-info
-      uses: actions/github-script@v6
+      uses: actions/github-script@v7
       with:
         script:
             const prNumber = context.payload.number;
@@ -90,7 +90,7 @@ jobs:
       run: cat darker_results/status.json
 
     - name: upload-status
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: darkerlint
         path: darker_results/
@@ -104,7 +104,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: "3.10"
 

LICENSE

@@ -1765,6 +1765,33 @@ PyQCPROT
     OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
+==========================================================================
+
+DSSP module code for protein secondary structure assignment
+ - analysis/dssp/pydssp_numpy.py
+
+MIT License
+
+Copyright (c) 2022 Shintaro Minami
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
 ==========================================================================
 
 MDAnalysis logo (see doc/sphinx/source/logos)

azure-pipelines.yml

@@ -101,7 +101,7 @@ jobs:
     displayName: 'pin to older NumPy (wheel test)'
     condition: and(succeeded(), ne(variables['NUMPY_MIN'], ''))
   - script: >-
-      python -m pip install
+      python -m pip install -vvv
       biopython
       "chemfiles>=0.10,<0.10.4"
       duecredit
@@ -112,8 +112,8 @@ jobs:
       networkx
       parmed
       pytng>=0.2.3
-      tidynamics>=1.0.0
       rdkit>=2020.03.1
+      tidynamics>=1.0.0
     displayName: 'Install additional dependencies for 64-bit tests'
     condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
   - script: >-

package/AUTHORS

@@ -240,7 +240,10 @@ Chronological list of authors
   - Sampurna Mukherjee
   - Leon Wehrhan
   - Valerij Talagayev
-
+  - Kurt McKee
+  - Fabian Zills
+  - Laksh Krishna Sharma
+  - Matthew Davies
 
 
 External code

package/CHANGELOG

@@ -16,11 +16,25 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
-         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher
+         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
+         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies
 
  * 2.8.0
 
 Fixes
+ * Catch higher dimensional indexing in GroupBase & ComponentBase (Issue #4647)
+ * Do not raise an Error reading H5MD files with datasets like
+   `observables/<particle>/<property>` (part of Issue #4598, PR #4615)
+ * Fix failure in double-serialization of TextIOPicklable file reader.
+   (Issue #3723, PR #3722)
+ * Fix failure to preserve modification of coordinates after serialization,
+   e.g. with transformations
+   (Issue #4633, PR #3722)
+ * Fix PSFParser error when encoutering string-like resids
+ * (Issue #2053, Issue #4189 PR #4582)
+ * Fix `MDAnalysis.analysis.align.AlignTraj` not accepting writer kwargs
+   (Issue #4564, PR #4565)
+ * Fix #4259 via removing argument `parallelizable` of `NoJump` transformation.
  * Fix doctest errors of analysis/pca.py related to rounding issues 
    (Issue #3925, PR #4377)
  * Convert openmm Quantity to raw value for KE and PE in OpenMMSimulationReader.
@@ -39,6 +53,11 @@ Fixes
  * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
 
 Enhancements
+ * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
+   (Issue #4158, PR #4304)
+ * explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
+ * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
+ * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`
    (PR #4531)
  * Improved performance of PDBWriter (Issue #2785, PR #4472)
@@ -49,6 +68,10 @@ Enhancements
    DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
 
 Changes
+ * The `fetch_mmtf` method has been removed as the REST API service
+   for MMTF files has ceased to exist (Issue #4634)
+ * MDAnalysis now builds against numpy 2.0 rather than the
+   minimum supported numpy version (PR #4620)
  * As per SPEC0 the minimum supported Python version has been raised
    to 3.10 (PR #4502)
  * MDAnalysis.analysis.hole2 is now directly imported from the mdakit
@@ -66,6 +89,8 @@ Changes
    numpy.testing.assert_allclose #4438)
 
 Deprecations
+ * The MMTF Reader is deprecated and will be removed in version 3.0
+   as the MMTF format is no longer supported (Issue #4634)
  * The MDAnalysis.analysis.waterdynamics module has been deprecated in favour
    of the waterdynamics MDAKit and will be removed in version 3.0.0 (PR #4404)
  * The MDAnalysis.analysis.psa module has been deprecated in favour of

package/MDAnalysis/__init__.py

@@ -150,7 +150,7 @@
 
 """
 
-__all__ = ['Universe', 'Writer', 'fetch_mmtf',
+__all__ = ['Universe', 'Writer',
            'AtomGroup', 'ResidueGroup', 'SegmentGroup']
 
 import logging
@@ -209,7 +209,6 @@
 from .coordinates.core import writer as Writer
 
 # After Universe import
-from .coordinates.MMTF import fetch_mmtf
 from . import converters
 
 from .due import due, Doi, BibTeX

package/MDAnalysis/analysis/__init__.py

@@ -23,6 +23,7 @@
 
 __all__ = [
     'align',
+    'backends',
     'base',
     'contacts',
     'density',
@@ -45,6 +46,7 @@
     'pca',
     'psa',
     'rdf',
+    'results',
     'rms',
     'waterdynamics',
 ]

package/MDAnalysis/analysis/align.py

@@ -681,6 +681,7 @@ class AlignTraj(AnalysisBase):
     def __init__(self, mobile, reference, select='all', filename=None,
                  prefix='rmsfit_', weights=None,
                  tol_mass=0.1, match_atoms=True, strict=False, force=True, in_memory=False,
+                 writer_kwargs=None,
                  **kwargs):
         """Parameters
         ----------
@@ -720,6 +721,8 @@ def __init__(self, mobile, reference, select='all', filename=None,
         verbose : bool (optional)
              Set logger to show more information and show detailed progress of
              the calculation if set to ``True``; the default is ``False``.
+        writer_kwargs : dict (optional)
+            kwarg dict to be passed to the constructed writer
 
 
         Attributes
@@ -780,6 +783,9 @@ def __init__(self, mobile, reference, select='all', filename=None,
            :attr:`rmsd` results are now stored in a
            :class:`MDAnalysis.analysis.base.Results` instance.
 
+        .. versionchanged:: 2.8.0
+           Added ``writer_kwargs`` kwarg dict to pass to the writer
+
         """
         select = rms.process_selection(select)
         self.ref_atoms = reference.select_atoms(*select['reference'])
@@ -816,10 +822,12 @@ def __init__(self, mobile, reference, select='all', filename=None,
             self.ref_atoms, self.mobile_atoms, tol_mass=tol_mass,
             strict=strict, match_atoms=match_atoms)
 
+        if writer_kwargs is None:
+            writer_kwargs = {}
         # with self.filename == None (in_memory), the NullWriter is chosen
         # (which just ignores input) and so only the in_memory trajectory is
         # retained
-        self._writer = mda.Writer(self.filename, natoms)
+        self._writer = mda.Writer(self.filename, natoms, **writer_kwargs)
 
         self._weights = get_weights(self.ref_atoms, weights)
 
@@ -1661,4 +1669,4 @@ def get_atoms_byres(g, match_mask=np.logical_not(mismatch_mask)):
                 logger.error(errmsg)
                 raise SelectionError(errmsg)
 
-    return ag1, ag2
+    return ag1, ag2