Rename EnsEquil to a3fe

.gitattributes

@@ -1 +1 @@
-EnsEquil/_version.py export-subst
+a3fe/_version.py export-subst

.github/CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into this EnsEquil. 
+describes how to merge code changes into this a3fe. 
 
 ## Getting Started
 
@@ -19,7 +19,7 @@ describes how to merge code changes into this EnsEquil.
   [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
   with the branch name relating to the feature you are going to add.
 * When you are ready for others to examine and comment on your new feature,
-  navigate to your fork of EnsEquil on GitHub and open a [pull
+  navigate to your fork of a3fe on GitHub and open a [pull
   request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
   after you launch a PR from one of your fork's branches, all
   subsequent commits to that branch will be added to the open pull request
@@ -29,7 +29,7 @@ describes how to merge code changes into this EnsEquil.
 * If you're providing a new feature, you must add test cases and documentation.
 * When the code is ready to go, make sure you run the test suite using pytest.
 * When you're ready to be considered for merging, check the "Ready to go"
-  box on the PR page to let the EnsEquil devs know that the changes are complete.
+  box on the PR page to let the a3fe devs know that the changes are complete.
   The code will not be merged until this box is checked, the continuous
   integration returns checkmarks,
   and multiple core developers give "Approved" reviews.

.github/workflows/CI.yaml

@@ -52,7 +52,7 @@ jobs:
         # conda setup requires this special shell
         shell: bash -l {0}
         run: |
-          pytest -v --cov=EnsEquil --cov-report=xml --color=yes EnsEquil/tests/
+          pytest -v --cov=a3fe --cov-report=xml --color=yes a3fe/tests/
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3

.lgtm.yml

@@ -9,4 +9,4 @@ path_classifiers:
     - versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
     - devtools/*
   generated:
-    - EnsEquil/_version.py
+    - a3fe/_version.py

README.md

@@ -1,40 +1,40 @@
-EnsEquil
+a3fe
 ==============================
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/fjclark/EnsEquil/workflows/CI/badge.svg)](https://github.com/fjclark/EnsEquil/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/fjclark/EnsEquil/branch/main/graph/badge.svg?token=UMH0OUSUJY)](https://codecov.io/gh/fjclark/EnsEquil)
+[![GitHub Actions Build Status](https://github.com/fjclark/a3fe/workflows/CI/badge.svg)](https://github.com/fjclark/a3fe/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/fjclark/a3fe/branch/main/graph/badge.svg?token=UMH0OUSUJY)](https://codecov.io/gh/fjclark/a3fe)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Documentation Status](https://readthedocs.org/projects/ensequil/badge/?version=latest)](https://ensequil.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/a3fe/badge/?version=latest)](https://a3fe.readthedocs.io/en/latest/?badge=latest)
 
 A package for running adaptive alchemical absolute binding free energy calculations with SOMD based on an ensemble of simulations. This requires the SLURM scheduling system.
 
 ### Installation
 
-EnsEquil depends on SLURM for scheduling jobs, and on GROMACS for running initial equilibration simulations. Please ensure that your have sourced your GMXRC or loaded your GROMACS module before proceeding with the installation.
+a3fe depends on SLURM for scheduling jobs, and on GROMACS for running initial equilibration simulations. Please ensure that your have sourced your GMXRC or loaded your GROMACS module before proceeding with the installation.
 
 We first need to install the [BioSimSpace](https://biosimspace.openbiosim.org/) dependencies using mamba (or conda). SOMD, which is used to run the simulations, is contained within Sire, which will be installed as a dependency of BioSimSpace.
 ```bash
-mamba create -n ensequil -c conda-forge -c openbiosim/label/dev biosimspace
-mamba activate ensequil
+mamba create -n a3fe -c conda-forge -c openbiosim/label/dev biosimspace
+mamba activate a3fe
 ```
-Now download EnsEquil, install, and test:
+Now download a3fe, install, and test:
  ```bash
- git clone https://github.com/fjclark/EnsEquil.git
- cd EnsEquil
+ git clone https://github.com/fjclark/a3fe.git
+ cd a3fe
  pip install .
- pytest EnsEquil
+ pytest a3fe
  ```
 
 ### Quick Start
 
-- Activate your EnsEquil conda environment 
+- Activate your a3fe conda environment 
 - Create a base directory for the calculation and create an directory called `input` within this
 - Move your input files into the the input directory. For example, if you have parameterised AMBER-format input files, name these bound_param.rst7, bound_param.prm7, free_param.rst7, and free_param.prm7. For more details see the documentation.
-- Copy run somd.sh and template_config.sh from EnsEquil/EnsEquil/data/example_run_dir to your `input` directory, making sure to the SLURM options in run_somd.sh so that the jobs will run on your cluster
+- Copy run somd.sh and template_config.sh from a3fe/a3fe/data/example_run_dir to your `input` directory, making sure to the SLURM options in run_somd.sh so that the jobs will run on your cluster
 - In the calculation base directory, run the following python code, either through ipython or as a python script (you will likely want to run the script with `nohup`or use ipython through tmux to ensure that the calculation is not killed when you lose connection)
 
 ```python
-import EnsEquil as ee 
+import a3fe as ee 
 calc = ee.Calculation()
 calc.setup()
 calc.get_optimal_lam_vals()

EnsEquil/__init__.py → a3fe/__init__.py

@@ -1,7 +1,15 @@
 """A package for running free energy calculations with SOMD with automated equilibration detection based on an ensemble of simulations."""
 
+# This package was previously named "EnsEquil". To allow objects pickled with the
+# old name to be unpickled with the new name, we set EnsEquil to point to a3fe.
+import sys as _sys
+
+_sys.modules["EnsEquil"] = _sys.modules["a3fe"]
+
+
 # Run imports
 from ._version import __version__
+
 # Pdb helper import
 from .read import *
 from .run import *

a3fe/_version.py

@@ -0,0 +1 @@
+__version__ = "1.0.0+414.g1520022.dirty"

EnsEquil/analyse/detect_equil.py → a3fe/analyse/detect_equil.py

@@ -950,7 +950,7 @@ def dummy_check_equil_multiwindow(
 ) -> _Tuple[bool, _Optional[float]]:  # type: ignore
     """
     Becuse "check_equil_multiwindow" checks multiple windows at once and sets the _equilibrated
-    and _equil_time attributes of the lambda windows, but EnsEquil was written based on per-window
+    and _equil_time attributes of the lambda windows, but a3fe was written based on per-window
     checks, we need a dummy function which just reads the attributes of the lambda window and
     assumes that they have already been set by "check_equil_multiwindow".