mdakits are now optional deps

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

@@ -66,15 +66,6 @@ runs:
         micromamba info
         micromamba list
 
-    - name: mda_deps
-      shell: bash -l {0}
-      run: |
-        # Install mdakit deps that depend on MDA
-        python -m pip install --no-deps \
-            waterdynamics   \
-            pathsimanalysis \
-            mdahole2
-
     - name: build_mda_main
       shell: bash -l {0}
       run: |

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

@@ -96,10 +96,16 @@ inputs:
   # pip-install optional dependencies
   duecredit:
     default: 'duecredit'
+  mdahole2:
+    default: 'mdahole2'
   parmed:
     default: 'parmed'
+  pathsimanalysis:
+    default: 'pathsimanalysis'
   pyedr:
     default: 'pyedr>=0.7.0'
+  waterdynamics:
+    default: 'waterdynamics'
 
 runs:
   using: "composite"

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

@@ -67,11 +67,6 @@ jobs:
             pytest                   \
             pytest-xdist             \
             pytest-timeout
-        # deps that depend on MDA
-        python -m pip install --no-deps \
-            waterdynamics   \
-            pathsimanalysis \
-            mdahole2
 
     - name: pre_install_list_deps
       run: python -m pip list

package/CHANGELOG

@@ -38,6 +38,11 @@ Enhancements
 
 
 Changes
+ * MDANalysis.analysis.psa, MDAnalysis.analysis.waterdynamics and
+   MDAnalysis.analysis.hole2 are now no longer available by default in
+   MDAnalysis. You will need to install their respective MDAKits to
+   keep using them. Please note that they will be fully removed in
+   MDAnalysis v3.0 (Issue #4899, PR #4953).
  * Changed `fasteners` dependency to  `filelock` (Issue #4797, PR #4800)
  * Codebase is now formatted with black (version `24`) (PR #4886)
 

package/MDAnalysis/analysis/hole2/__init__.py

@@ -36,14 +36,23 @@
 
 """
 import warnings
-from mdahole2.analysis.hole import hole, HoleAnalysis
-from mdahole2.analysis import utils, templates
-from mdahole2.analysis.utils import create_vmd_surface
 
-wmsg = (
-    "Deprecated in version 2.8.0\n"
-    "MDAnalysis.analysis.hole2 is deprecated in favour of the "
-    "MDAKit madahole2 (https://www.mdanalysis.org/mdahole2/) "
-    "and will be removed in MDAnalysis version 3.0.0"
-)
-warnings.warn(wmsg, category=DeprecationWarning)
+try:
+    from mdahole2.analysis.hole import hole, HoleAnalysis
+    from mdahole2.analysis import utils, templates
+    from mdahole2.analysis.utils import create_vmd_surface
+except ImportError:
+    wmsg = (
+        "Please install the mdahole2 mdakit to use it in MDAnalysis.\n"
+        "More details can be found here: "
+        "https://www.mdanalysis.org/mdahole2/getting_started.html"
+    )
+    warnings.warn(wmsg, category=UserWarning)
+else:
+    wmsg = (
+        "Deprecated in version 2.8.0\n"
+        "MDAnalysis.analysis.hole2 is deprecated in favour of the "
+        "MDAKit madahole2 (https://www.mdanalysis.org/mdahole2/) "
+        "and will be removed in MDAnalysis version 3.0.0"
+    )
+    warnings.warn(wmsg, category=DeprecationWarning)

package/MDAnalysis/analysis/psa.py

@@ -46,28 +46,35 @@
 
 import warnings
 
-from pathsimanalysis import (
-    get_path_metric_func,
-    sqnorm,
-    get_msd_matrix,
-    reshaper,
-    get_coord_axes,
-    hausdorff,
-    hausdorff_wavg,
-    hausdorff_avg,
-    hausdorff_neighbors,
-    discrete_frechet,
-    dist_mat_to_vec,
-    Path,
-    PSAPair,
-    PSAnalysis,
-)
-
-
-wmsg = (
-    "Deprecation in version 2.8.0:\n"
-    "MDAnalysis.analysis.psa is deprecated in favour of the MDAKit "
-    "PathSimAnalysis (https://github.com/MDAnalysis/PathSimAnalysis) "
-    "and will be removed in MDAnalysis version 3.0.0"
-)
-warnings.warn(wmsg, category=DeprecationWarning)
+try:
+    from pathsimanalysis import (
+        get_path_metric_func,
+        sqnorm,
+        get_msd_matrix,
+        reshaper,
+        get_coord_axes,
+        hausdorff,
+        hausdorff_wavg,
+        hausdorff_avg,
+        hausdorff_neighbors,
+        discrete_frechet,
+        dist_mat_to_vec,
+        Path,
+        PSAPair,
+        PSAnalysis,
+    )
+except ImportError:
+    wmsg = (
+        "Please install the PathSimAnalysis mdakit to use it in MDAnalysis.\n"
+        "More details can be found here: "
+        "https://www.mdanalysis.org/PathSimAnalysis/getting_started.html"
+    )
+    warnings.warn(wmsg, category=UserWarning)
+else:
+    wmsg = (
+        "Deprecation in version 2.8.0:\n"
+        "MDAnalysis.analysis.psa is deprecated in favour of the MDAKit "
+        "PathSimAnalysis (https://github.com/MDAnalysis/PathSimAnalysis) "
+        "and will be removed in MDAnalysis version 3.0.0"
+    )
+    warnings.warn(wmsg, category=DeprecationWarning)

package/MDAnalysis/analysis/waterdynamics.py

@@ -41,18 +41,25 @@
 """
 import warnings
 
-from waterdynamics.waterdynamics import (
-    WaterOrientationalRelaxation,
-    AngularDistribution,
-    MeanSquareDisplacement,
-    SurvivalProbability,
-)
-
-
-wmsg = (
-    "Deprecation in version 2.8.0\n"
-    "MDAnalysis.analysis.waterdynamics is deprecated in favour of the "
-    "MDAKit waterdynamics (https://www.mdanalysis.org/waterdynamics/) "
-    "and will be removed in MDAnalysis version 3.0.0"
-)
-warnings.warn(wmsg, category=DeprecationWarning)
+try:
+    from waterdynamics.waterdynamics import (
+        WaterOrientationalRelaxation,
+        AngularDistribution,
+        MeanSquareDisplacement,
+        SurvivalProbability,
+    )
+except ImportError:
+    wmsg = (
+        "Please install the waterdynamics mdakit to use it in MDAnalysis.\n"
+        "More details can be found here: "
+        "https://www.mdanalysis.org/waterdynamics/getting_started.html"
+    )
+    warnings.warn(wmsg, category=UserWarning)
+else:
+    wmsg = (
+        "Deprecation in version 2.8.0\n"
+        "MDAnalysis.analysis.waterdynamics is deprecated in favour of the "
+        "MDAKit waterdynamics (https://www.mdanalysis.org/waterdynamics/) "
+        "and will be removed in MDAnalysis version 3.0.0"
+    )
+    warnings.warn(wmsg, category=DeprecationWarning)

package/pyproject.toml

@@ -40,9 +40,6 @@ dependencies = [
     'packaging',
     'filelock',
     'mda-xdrlib',
-    'waterdynamics',
-    'pathsimanalysis',
-    'mdahole2',
 ]
 keywords = [
     "python", "science", "chemistry", "biophysics", "molecular-dynamics",
@@ -86,6 +83,9 @@ analysis = [
     "scikit-learn",
     "tidynamics>=1.0.0",
     'networkx>=2.0',
+    'waterdynamics',
+    'pathsimanalysis',
+    'mdahole2',
 ]
 doc = [
     "sphinx",

testsuite/MDAnalysisTests/analysis/test_hole2.py

@@ -26,9 +26,24 @@
 import pytest
 
 from MDAnalysis.analysis import hole2
+from MDAnalysisTests.util import import_not_available
 
 
+@pytest.mark.skipif(
+    import_not_available("mdahole2"),
+    reason="Test skipped because mdahole2 is not found",
+)
 def test_moved_to_mdakit_warning():
     wmsg = "MDAnalysis.analysis.hole2 is deprecated"
     with pytest.warns(DeprecationWarning, match=wmsg):
         reload(hole2)
+
+
+@pytest.mark.skipif(
+    not import_not_available("mdahole2"),
+    reason="Test skipped because mdahole2 is found",
+)
+def test_install_mdakit_warning():
+    wmsg = "Please install"
+    with pytest.warns(UserWarning, match=wmsg):
+        reload(hole2)

testsuite/MDAnalysisTests/analysis/test_psa.py

@@ -25,9 +25,24 @@
 import pytest
 
 from MDAnalysis.analysis import psa
+from MDAnalysisTests.util import import_not_available
 
 
+@pytest.mark.skipif(
+    import_not_available("pathsimanalysis"),
+    reason="Test skipped because PathSimAnalysis is not found",
+)
 def test_moved_to_mdakit_warning():
     wmsg = "MDAnalysis.analysis.psa is deprecated in favour of the MDAKit"
     with pytest.warns(DeprecationWarning, match=wmsg):
         reload(psa)
+
+
+@pytest.mark.skipif(
+    not import_not_available("pathsimanalysis"),
+    reason="Test skipped because PathSimAnalysis is found",
+)
+def test_install_mdakit_warning():
+    wmsg = "Please install"
+    with pytest.warns(UserWarning, match=wmsg):
+        reload(psa)

testsuite/MDAnalysisTests/analysis/test_waterdynamics.py

@@ -24,9 +24,24 @@
 import pytest
 
 from MDAnalysis.analysis import waterdynamics
+from MDAnalysisTests.util import import_not_available
 
 
+@pytest.mark.skipif(
+    import_not_available("waterdynamics"),
+    reason="Test skipped because waterdynamics is not found",
+)
 def test_moved_to_mdakit_warning():
     wmsg = "MDAnalysis.analysis.waterdynamics is deprecated"
     with pytest.warns(DeprecationWarning, match=wmsg):
         reload(waterdynamics)
+
+
+@pytest.mark.skipif(
+    not import_not_available("waterdynamics"),
+    reason="Test skipped because waterdynamics is found",
+)
+def test_install_mdakit_warning():
+    wmsg = "Please install"
+    with pytest.warns(UserWarning, match=wmsg):
+        reload(waterdynamics)

testsuite/MDAnalysisTests/utils/test_duecredit.py

@@ -31,6 +31,7 @@
 import MDAnalysis as mda
 from MDAnalysis.coordinates.H5MD import HAS_H5PY
 from MDAnalysisTests.datafiles import MMTF, TPR_xvf, H5MD_xvf
+from MDAnalysisTests.util import import_not_available
 
 # duecredit itself is not needed in the name space but this is a
 # convenient way to skip all tests if duecredit is not installed
@@ -64,11 +65,6 @@ def test_duecredit_collector_primary(self, module, path, citekey):
     @pytest.mark.parametrize(
         "module,path,citekey",
         [
-            (
-                "MDAnalysis.analysis.psa",
-                "pathsimanalysis.psa",
-                "10.1371/journal.pcbi.1004568",
-            ),
             (
                 "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
                 "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
@@ -101,6 +97,16 @@ def test_duecredit_collector_analysis_modules(self, module, path, citekey):
         importlib.import_module(module)
         assert mda.due.citations[(path, citekey)].cites_module == True
 
+    @pytest.mark.skipif(
+        import_not_available("pathsimanalysis"),
+        reason="Test skipped because PathSimAnalysis is not found",
+    )
+    def test_duecredit_psa(self):
+        importlib.import_module("MDAnalysis.analysis.psa")
+        path = "pathsimanalysis.psa"
+        citekey = "10.1371/journal.pcbi.1004568"
+        assert mda.due.citations[(path, citekey)].cites_module == True
+
     def test_duecredit_mmtf(self):
         # doesn't trigger on import but on use of either parser or reader
         u = mda.Universe(MMTF)