Merge branch 'MDAnalysis:main' into main

.gitignore

@@ -132,3 +132,5 @@ dmypy.json
 
 # workflow storage
 json-statuses/
+
+.DS_Store

docs/source/conf.py

@@ -119,7 +119,8 @@
     'main.js',
 ]
 
-html_logo = "_static/logos/mdanalysis-logo-200x150.png"
+html_logo = "_static/logos/mdakits-logo-1563x1563.png"
+html_favicon = "_static/logos/mdakits-logo.ico"
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

mdakits/lipyds/status.yaml

@@ -7,11 +7,11 @@ badges:
   transformation: false
   writer: false
 develop:
-  install_mdakit: true
+  install_mdakit: false
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 33
+  numfails: 40
   run_tests: false
 latest:
   install_mdakit: true

mdakits/prolif/status.yaml

@@ -11,8 +11,8 @@ develop:
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 0
-  run_tests: true
+  numfails: 6
+  run_tests: false
 latest:
   install_mdakit: true
   install_mdanalysis: true

mdakits/propkatraj/status.yaml

@@ -11,12 +11,12 @@ develop:
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 0
-  run_tests: true
+  numfails: 2
+  run_tests: false
 latest:
   install_mdakit: true
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 0
-  run_tests: true
+  numfails: 2
+  run_tests: false

mdakits/spyrmsdkit/metadata.yaml

@@ -0,0 +1,52 @@
+project_name: spyrmsdkit
+
+authors:
+  - https://github.com/RMeli/spyrmsdkit/blob/main/AUTHORS.md
+
+maintainers:
+  - RMeli
+
+## str: a free form description of the mdakit
+description:
+    spyrmsdkit allows to compute symmetry-corrected RMSDs with spyrmsd on MD trajectories
+
+## List(str): a list of keywords which describe the mdakit
+keywords:
+  - spyrmsd
+  - RMSD
+  - symmetry-corrected RMSD
+  - drug discovery
+
+license: GPL-2.0-or-later
+
+project_home: https://github.com/RMeli/spyrmsdkit/
+
+documentation_home: https://spyrmsd.readthedocs.io
+
+documentation_type: API
+
+#install:
+#  - pip install spyrmsdkit
+
+src_install:
+  - pip install git+https://github.com/RMeli/spyrmsdkit@main
+
+import_name: spyrmsdkit
+
+python_requires: ">=3.10"
+
+## str: a specification for the range of MDAnalysis versions supported by this MDAKit
+mdanalysis_requires: ">=2.0.0"
+
+run_tests:
+  - pytest --pyargs spyrmsdkit
+
+test_dependencies:
+  - mamba install pytest MDAnalysisTests
+
+development_status: Production
+
+publications:
+  - https://doi.org/10.1186/s13321-020-00455-2
+
+changelog: https://github.com/RMeli/spyrmsdkit/blob/main/CHANGELOG.md

mdakits/spyrmsdkit/status.yaml

@@ -0,0 +1,22 @@
+badges:
+  analysis: false
+  converter: false
+  coverage: false
+  reader: false
+  topology: false
+  transformation: false
+  writer: false
+develop:
+  install_mdakit: true
+  install_mdanalysis: true
+  install_python: true
+  install_test_deps: true
+  numfails: 0
+  run_tests: true
+latest:
+  install_mdakit: true
+  install_mdanalysis: true
+  install_python: true
+  install_test_deps: true
+  numfails: 0
+  run_tests: true

mdakits/template/metadata.yaml

@@ -19,7 +19,7 @@ project_name: MYPROJECT
 
 ## List(str): a link to the authors file (preferred) or a list of authors 
 authors:
-  - https://github.com/GH_HOST_ACCOUNT/MYPROJECT/blob/main/AUTHORS
+  - https://github.com/GH_HOST_ACCOUNT/MYPROJECT/blob/main/AUTHORS.md
 
 ## List(str): a list of maintainers
 ## Please note these _must_ be GitHub handles
@@ -73,7 +73,7 @@ src_install:
 import_name: MYPACKAGE
 
 ## str: a specification for the range of Python versions supported by this MDAKit
-python_requires: ">=3.9"
+python_requires: ">=3.10"
 
 ## str: a specification for the range of MDAnalysis versions supported by this MDAKit
 mdanalysis_requires: ">=2.0.0"

mdakits/transport-analysis/status.yaml

@@ -11,12 +11,12 @@ develop:
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 0
-  run_tests: true
+  numfails: 3
+  run_tests: false
 latest:
   install_mdakit: true
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 0
-  run_tests: true
+  numfails: 3
+  run_tests: false