Deprecate PSA and replace with PathSimAnalysis mdakit (#4403)

* PSA is now deprecated and for now has been replaced with an import to the MDAKit PathSimAnalysis

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

@@ -39,6 +39,8 @@ inputs:
     default: 'numpy'
   packaging:
     default: 'packaging'
+  pathsimanalysis:
+    default: 'pathsimanalysis'
   pip:
     default: 'pip'
   pytest:
@@ -116,6 +118,7 @@ runs:
           ${{ inputs.mmtf-python }}
           ${{ inputs.numpy }}
           ${{ inputs.packaging }}
+          ${{ inputs.pathsimanalysis }}
           ${{ inputs.pip }}
           ${{ inputs.pytest }}
           ${{ inputs.scipy }}

package/CHANGELOG

@@ -29,6 +29,9 @@ Changes
    is used from python 3.9 to 3.11 (Issue #4401, PR #4402)
 
 Deprecations
+ * The MDAnalysis.analysis.psa module has been deprecated in favour of
+   the PathSimAnalysis MDAKit and will be removed in version 3.0.0
+   (PR #4403)
 
 
 12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith,