Release 0.1.0

CITATION.cff

@@ -0,0 +1,31 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: FEflow
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Iván
+    family-names: Pulido Sánchez
+    orcid: 'https://orcid.org/0000-0002-7178-8136'
+  - given-names: Irfan
+    family-names: Alibay
+    orcid: 'https://orcid.org/0000-0001-5787-9130'
+  - given-names: David
+    family-names: Dotson
+    orcid: 'https://orcid.org/0000-0001-5879-2942'
+  - given-names: Richard
+    family-names: Gowers
+    orcid: 'https://orcid.org/0000-0002-3241-1846'
+  - given-names: Hannah
+    family-names: Baumann
+    orcid: 'https://orcid.org/0000-0002-1736-7744'
+  - given-names: Michael M.
+    family-names: Henry
+    orcid: 'https://orcid.org/0000-0002-3870-9993'
+repository-code: 'https://github.com/choderalab/feflow'
+version: '0.1'
+date-released: '2024-07-29'

README.md

@@ -12,8 +12,23 @@ Recipes, utilities, and protocols for molecular free energy calculations using t
 Copyright (c) 2023, ChoderaLab
 
 
-#### Acknowledgements
+### Acknowledgements
 [Choderalab -- Perses](https://github.com/choderalab/perses)
+
 [Open Free energy Consortium](https://openfree.energy/)
+
 Project based on the
 [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.
+
+### References
+[1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
+
+[2] Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex
+Ivy Zhang, Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser, Sukrit Singh, and John D. Chodera
+Journal of Chemical Theory and Computation 2023 19 (15), 4863-4882
+DOI: 10.1021/acs.jctc.3c00333
+
+[3] Chodera, J. et al., 2023. choderalab/openmmtools: 0.23.1.
+
+[4] Eastman, P. et al., 2017. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics R. Gentleman, ed.. PLOS Computational Biology, 13(7), p.1005659.
+

docs/CHANGELOG.rst

@@ -0,0 +1,11 @@
+=================
+feflow Change Log
+=================
+
+.. current developments
+
+v0.1
+====================
+
+First release. Base implementation of Nonequilibrium cycling protocol.
+

docs/api.rst

@@ -1,7 +1,13 @@
 API Documentation
 =================
 
+.. module:: feflow
+    :no-index:
+
 .. autosummary::
-   :toctree: autosummary
+    :toctree: autosummary
+    :recursive:
 
-   feflow.canvas
+    feflow.protocols
+    feflow.settings
+    feflow.utils

docs/conf.py

@@ -24,10 +24,10 @@
 
 project = "feflow"
 copyright = (
-    "2023, Iván Pulido. Project structure based on the "
+    "2023, ChoderaLab. Project structure based on the "
     "Computational Molecular Science Python Cookiecutter version 1.1"
 )
-author = "Iván Pulido"
+author = "ChoderaLab"
 
 # The short X.Y version
 version = ""

feflow/__init__.py

@@ -3,4 +3,4 @@
 
 from importlib.metadata import version
 
-__version__ = version("openfe")
+__version__ = version("feflow")

feflow/protocols/nonequilibrium_cycling.py

@@ -33,10 +33,15 @@
 from ..utils.data import serialize, deserialize
 
 # Specific instance of logger for this module
-# logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__)
 
 
 class SetupUnit(ProtocolUnit):
+    """
+    Initial unit of the protocol. Sets up a Nonequilibrium cycling simulation given the chemical
+    systems, mapping and settings.
+    """
+
     @staticmethod
     def _check_states_compatibility(state_a, state_b):
         """
@@ -431,8 +436,9 @@ def _execute(self, ctx, *, protocol, state_a, state_b, mapping, **inputs):
 
 class CycleUnit(ProtocolUnit):
     """
-    Monolithic unit for simulation. It runs a single NEQ cycle simulation from chemical systems
-    and stores the work computed in numpy-formatted files, to be analyzed by a result unit.
+    Monolithic unit for the cycle part of the simulation.
+    It runs a number of NEq cycles from the outputs of a setup unit and stores the work computed in
+    numpy-formatted files, to be analyzed by a result unit.
     """
 
     @staticmethod

feflow/settings/nonequilibrium_cycling.py

@@ -1,8 +1,5 @@
 """
 Settings objects for the different protocols using gufe objects.
-
-This module implements the objects that will be needed to run relative binding free
-energy calculations using perses.
 """
 
 from typing import Optional

news/TEMPLATE.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

rever.xsh

@@ -0,0 +1,7 @@
+$PROJECT = $GITHUB_REPO = 'feflow'
+$GITHUB_ORG = 'choderalab'
+
+$ACTIVITIES = ['changelog']
+
+$CHANGELOG_FILENAME = 'docs/CHANGELOG.rst'
+$CHANGELOG_TEMPLATE = 'TEMPLATE.rst'