wepy2: Refactor and test suite

.dvc/.gitignore

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvc/config

@@ -0,0 +1,4 @@
+[core]
+    remote = idp-dvc-gs
+['remote "idp-dvc-gs"']
+    url = gs://examol-idp-prod-dvc/dvcstore-wepy2

.dvcignore

@@ -0,0 +1,3 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.envrc

@@ -0,0 +1,3 @@
+source_env_if_exists .envrc.local
+. ./.venv/bin/activate
+

.gitignore

@@ -287,5 +287,6 @@ tags
 .vim
 
 # End of https://www.gitignore.io/api/vim
-uv.lock
 _output
+.envrc.local
+_tmp

AUTHORS.org → AUTHORS.md

@@ -1,10 +1,10 @@
-* Credits
+# Credits
 
-** Development Lead
+## Development Lead
 
 Samuel D. Lotz <samuel.lotz@salotz.info>
 
-** Contributors
+## Contributors
 
 Alex Dickson
 Nazanin Donyapour

CONTRIBUTING.md

@@ -1,4 +1,40 @@
-# Contributing 
+# CONTRIBUTING
+
+```
+uv sync --all-extras
+```
+
+To test against other python versions run this first for each version
+you are interested in:
+
+```
+uv sync --python 3.11 --all-extras
+```
+
+
+## Tests
+
+The standard test run like:
+
+```
+uv run --all-extras pytest tests/unit
+```
+
+The flake finder flag will enable running certain tests multiple
+times. Typically for parallel routines which intermittently fail.
+
+You can test on other python versions like:
+
+```
+uv run --python 3.11 --all-extras pytest --flake-finder tests/unit
+```
+
+The `--flake-finder` flag will run things multiple times to see if
+they are flaky.
+
+
+
+# Contributing (OLD)
 
 Developing on wepy
 

README.md

@@ -0,0 +1,62 @@
+<a href="https://doi.org/10.5281/zenodo.3973431"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3973431.svg" alt="DOI"></a>
+
+# Weighted Ensemble Python: wepy
+
+![Wepy Logo](./info/logo/wepy.svg)
+
+
+[Documentation](https://adicksonlab.github.io/wepy/index.html)
+
+Modular implementation and framework for running weighted ensemble (WE)
+simulations in pure python, where the aim is to have simple things
+simple and complicated things possible. The latter being the priority.
+
+The goal of the architecture is that it should be highly modular to
+allow extension, but provide a "killer app" for most uses that just
+works, no questions asked.
+
+Comes equipped with support for
+[OpenMM](https://github.com/pandegroup/openmm) molecular dynamics,
+parallelization using multiprocessing, the
+[WExplore](http://pubs.acs.org/doi/abs/10.1021/jp411479c) and
+[REVO](https://pubmed.ncbi.nlm.nih.gov/31255090/) (Resampling
+Ensembles by Variance Optimization) resampling algorithms, and an HDF5
+file format and library for storing and querying your WE datasets that
+can be used from the command line.
+
+The deeper architecture of `wepy` is intended to be loosely coupled,
+so that unforeseen use cases can be accomodated, but tightly
+integrated for the most common of use cases, i.e. molecular dynamics.
+
+This allows freedom for fast development of new methods.
+
+## Installation
+
+Also see: [Installation Instructions](info/installation.org)
+
+```shell
+pip install wepy
+
+# for openmm and MD related packages
+pip install 'wepy[md]'
+```
+
+## Citations
+
+Current [Zenodo DOI](https://zenodo.org/badge/latestdoi/101077926).
+
+Cite software as:
+
+```
+Samuel D. Lotz, Nazanin Donyapour, Alex Dickson, Tom Dixon, Nicole Roussey, & Rob Hall. (2020, August 4). ADicksonLab/wepy: 1.0.0 Major version release (Version v1.0.0). Zenodo. http://doi.org/10.5281/zenodo.3973431
+```
+
+Accompanying journal article:
+
+- [ACS Omega](https://pubs.acs.org/doi/abs/10.1021/acsomega.0c03892) article
+
+
+
+
+
+

info/users_guide.org

@@ -583,7 +583,7 @@ We see that ReceptorDistance is inheriting from the ~Distance~ class,
 which is defined as such:
 
 #+BEGIN_SRC python
-  class Distance(object):
+  class Distance:
       """Abstract Base class for Distance classes."""
 
       def __init__(self):
@@ -615,7 +615,7 @@ as being equivalent to:
 We notice that the ~Distance~ class defines this method ~distance~:
 
 #+BEGIN_SRC python
-  class Distance(object):
+  class Distance:
       ...
 
       def distance(self, state_a, state_b):
@@ -634,7 +634,7 @@ it still has access to it.
 We notice that ~Distance~ also defines the method ~image_distance~:
 
 #+BEGIN_SRC python
-  class Distance(object):
+  class Distance:
 
       ...
 
@@ -1040,7 +1040,7 @@ weights of walkers in an ensemble (a simple list container).
 The implementation is very simple:
 
 #+begin_src python
-class Walker(object):
+class Walker:
 
     def __init__(self, state, weight):
 
@@ -1077,7 +1077,7 @@ it doesn't directly inherit from the actual ~WalkerState~ class.
 The implementation is very simple:
 
 #+begin_src python
-  class WalkerState(object):
+  class WalkerState:
 
       def __init__(self, **kwargs):
           self._data = kwargs
@@ -1478,8 +1478,8 @@ handle new ones, e.g.:
 
 #+end_src
 
-In addition to the ABC ~Reporter~ class the ~FileReporter~ and
-~ProgressiveFileReporter~ are very useful to inherit from as they
+In addition to the ABC ~Reporter~ class the ~FileReporterABC~ and
+~ProgressiveFileReporterABC~ are very useful to inherit from as they
 handle some file path and file mode logic, the latter updates modes to
 allow for repeated writes to the same file for each cycle of a
 simulation.
@@ -1489,9 +1489,9 @@ specific to its own function and all the handling of filenames is done
 by a call to the superclass constructor:
 
 #+begin_src python
-  from wepy.reporter.reporter import ProgressiveFileReporter
+  from wepy.reporter.reporter import ProgressiveFileReporterABC
 
-  class DashboardReporter(ProgressiveFileReporter):
+  class DashboardReporter(ProgressiveFileReporterABC):
 
       def __init__(self,
                    step_time=None,
@@ -1524,7 +1524,7 @@ then using a simple for-loop to sequentially compute the segments:
 
 #+begin_src python
 
-  class Mapper(object):
+  class Mapper:
 
       def init(self, segment_func):