Bring over use_cpctools patch.

.github/workflows/publish_release.yaml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: python -m build

.github/workflows/tests.yaml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: ruff .
@@ -22,7 +22,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: mypy .
@@ -32,7 +32,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: ruff format --check .
@@ -42,7 +42,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: pytest --cov=src --cov-report term-missing
@@ -52,7 +52,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: make -C docs doctest

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
     os: ubuntu-22.04
     tools:
-      python: "3.11"
+      python: "3.10"
 
 sphinx:
     configuration: docs/source/conf.py

README.rst

@@ -9,6 +9,15 @@ To get ``dynsight``, you can install it with pip::
 
     $ pip install dynsight
 
+
+Examples
+========
+
+There are examples available in the ``examples/`` directory of this repository.
+
+There are also examples available in the ``cpctools`` repository
+`here <https://github.com/GMPavanLab/cpctools/tree/main/Examples>`
+
 How To Cite
 ===========
 
@@ -27,7 +36,14 @@ Publications
 Acknowledgements
 ================
 
-Developed in GMP
-ERC
-NextGenEU
-Daniele Rapetti
+We developed this code when working in the Pavan group,
+https://www.gmpavanlab.com/, whose members often provide very valuable
+feedback, which we gratefully acknowledge.
+
+Much of the original code in ``cpctools`` was written by Daniele Rapetti (Iximiel).
+
+The work was funded by the European Union and ERC under projects DYNAPOL and the
+NextGenerationEU project, CAGEX.
+
+.. figure:: docs/source/_static/EU_image.png
+

docs/source/data_processing.rst

@@ -0,0 +1,31 @@
+Data processing
+===============
+
+
+SOAP distances
+--------------
+
+.. toctree::
+  :maxdepth: 1
+
+
+  kernelsoap <_autosummary/dynsight.data_processing.kernelsoap>
+  simplekernelsoap <_autosummary/dynsight.data_processing.simplekernelsoap>
+  soapdistance <_autosummary/dynsight.data_processing.soapdistance>
+  soapdistancenormalized <_autosummary/dynsight.data_processing.soapdistancenormalized>
+  simplesoapdistance <_autosummary/dynsight.data_processing.simplesoapdistance>
+
+Classification
+--------------
+
+.. toctree::
+  :maxdepth: 1
+
+  createreferencesfromtrajectory <_autosummary/dynsight.data_processing.createreferencesfromtrajectory>
+  getdistancebetween <_autosummary/dynsight.data_processing.getdistancebetween>
+  getdistancesfromref <_autosummary/dynsight.data_processing.getdistancesfromref>
+  getdistancesfromrefnormalized <_autosummary/dynsight.data_processing.getdistancesfromrefnormalized>
+  mergereferences <_autosummary/dynsight.data_processing.mergereferences>
+  savereferences <_autosummary/dynsight.data_processing.savereferences>
+  getreferencesfromdataset <_autosummary/dynsight.data_processing.getreferencesfromdataset>
+  applyclassification <_autosummary/dynsight.data_processing.applyclassification>

docs/source/hdf5er.rst

@@ -0,0 +1,10 @@
+HDF5er
+======
+
+
+.. toctree::
+  :maxdepth: 1
+
+  mda_to_hdf5 <_autosummary/dynsight.hdf5er.mda_to_hdf5>
+  universe_to_hdf5 <_autosummary/dynsight.hdf5er.universe_to_hdf5>
+  create_universe_from_slice <_autosummary/dynsight.hdf5er.create_universe_from_slice>

docs/source/index.rst

@@ -3,6 +3,16 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+.. toctree::
+   :hidden:
+   :caption: dynsight
+   :maxdepth: 2
+
+   SOAPify <soapify>
+   timeSOAP <time_soap>
+   LENS <lens>
+   data processing <data_processing>
+   HDF5er <hdf5er>
 
 .. toctree::
   :hidden:
@@ -35,6 +45,14 @@ To get :mod:`.dynsight`, you can install it with pip::
 
   $ pip install dynsight
 
+Dependencies
+............
+
+The main dependancies are for SOAP analysis:
+
+* `cpctools <https://github.com/GMPavanLab/cpctools>`_
+* `dscribe (1.2.0 - 1.2.2) <https://singroup.github.io/dscribe/latest/>`_
+
 Developer Setup
 ...............
 
@@ -57,6 +75,30 @@ Overview
 
 To be written.
 
+Examples
+--------
+
+There are simplified examples available in the
+`examples <https://github.com/GMPavanLab/dynsight/tree/main/examples>`_
+directory of this repository.
+
+There are also examples available in the ``cpctools`` repository
+`here <https://github.com/GMPavanLab/cpctools/tree/main/Examples>`_.
+
+
+
+Acknowledgements
+----------------
+
+We developed this code when working in the Pavan group,
+https://www.gmpavanlab.com/, whose members often provide very valuable
+feedback, which we gratefully acknowledge.
+
+Much of the original code in ``cpctools`` was written by Daniele Rapetti (Iximiel).
+
+The work was funded by the European Union and ERC under projects DYNAPOL and the
+NextGenerationEU project, CAGEX.
+
 Indices and tables
 ------------------
 

docs/source/lens.rst

@@ -0,0 +1,9 @@
+LENS
+====
+
+
+.. toctree::
+  :maxdepth: 1
+
+  list_neighbours_along_trajectory <_autosummary/dynsight.lens.list_neighbours_along_trajectory>
+  neighbour_change_in_time <_autosummary/dynsight.lens.neighbour_change_in_time>

docs/source/soapify.rst

@@ -0,0 +1,24 @@
+SOAPify
+=======
+
+This package uses `cpctools` to run SOAP (add citation) analysis on molecular
+systems.
+
+Saponify
+--------
+
+.. toctree::
+  :maxdepth: 1
+
+  saponify_trajectory <_autosummary/dynsight.soapify.saponify_trajectory>
+  saponify_multiple_trajectories <_autosummary/dynsight.soapify.saponify_multiple_trajectories>
+
+
+Utilities
+---------
+
+.. toctree::
+  :maxdepth: 1
+
+  get_soap_settings <_autosummary/dynsight.soapify.get_soap_settings>
+  fill_soap_vector_from_dscribe <_autosummary/dynsight.soapify.fill_soap_vector_from_dscribe>

docs/source/time_soap.rst

@@ -0,0 +1,9 @@
+timeSOAP
+========
+
+.. toctree::
+  :maxdepth: 1
+
+  timesoap <_autosummary/dynsight.time_soap.timesoap>
+  timesoapsimple <_autosummary/dynsight.time_soap.timesoapsimple>
+  gettimesoapsimple <_autosummary/dynsight.time_soap.gettimesoapsimple>