Rename 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

@@ -1,41 +1,43 @@
-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)
 
+<img src="./a3fe_logo.png" alt="Alt text" style="width: 50%; height: 50%;">
+
 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 
-calc = ee.Calculation()
+import a3fe as a3 
+calc = a3.Calculation()
 calc.setup()
 calc.get_optimal_lam_vals()
 calc.run()

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/compare.py → a3fe/analyse/compare.py

@@ -1,12 +1,14 @@
 """Functionality for comparing two or more simulation runners."""
 
 
-import numpy as _np
-from ..run._utils import SimulationRunnerIterator as _SimulationRunnerIterator
+from typing import List as _List
+from typing import Tuple as _Tuple
+from typing import Union as _Union
 
+import numpy as _np
 from scipy.stats import levene as _levene
 
-from typing import List as _List, Tuple as _Tuple, Union as _Union
+from ..run._utils import SimulationRunnerIterator as _SimulationRunnerIterator
 
 __all__ = [
     "get_comparitive_convergence_data",

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".
 

EnsEquil/analyse/mbar.py → a3fe/analyse/mbar.py

@@ -16,11 +16,11 @@
 
 import numpy as _np
 
+from ..read._process_somd_files import \
+    read_mbar_gradients as _read_mbar_gradients
 from ..read._process_somd_files import read_mbar_result as _read_mbar_result
-from ..read._process_somd_files import (
-    write_truncated_sim_datafile as _write_truncated_sim_datafile,
-    read_mbar_gradients as _read_mbar_gradients,
-)
+from ..read._process_somd_files import \
+    write_truncated_sim_datafile as _write_truncated_sim_datafile
 
 
 def run_mbar(

EnsEquil/analyse/plot.py → a3fe/analyse/plot.py

@@ -29,24 +29,23 @@
 from typing import Optional as _Optional
 from typing import Tuple as _Tuple
 
-import matplotlib.pyplot as _plt
-import matplotlib.colors as _colors
 import matplotlib.cm as _cm
+import matplotlib.colors as _colors
+import matplotlib.pyplot as _plt
 import numpy as _np
 import pandas as _pd
 import scipy.stats as _stats
-from scipy.stats import kruskal as _kruskal
 import seaborn as _sns
+from scipy.stats import kruskal as _kruskal
 
 from ..read._process_somd_files import read_mbar_pmf as _read_mbar_pmf
 from ..read._process_somd_files import read_overlap_mat as _read_overlap_mat
+from ..run._utils import SimulationRunnerIterator as _SimulationRunnerIterator
+from .compare import \
+    get_comparitive_convergence_data as _get_comparitive_convergence_data
 from .process_grads import GradientData
 from .rmsd import get_rmsd as _get_rmsd
-from .compare import (
-    get_comparitive_convergence_data as _get_comparitive_convergence_data,
-)
 from .waters import get_av_waters_stage as _get_av_waters_stage
-from ..run._utils import SimulationRunnerIterator as _SimulationRunnerIterator
 
 
 def general_plot(

EnsEquil/analyse/process_grads.py → a3fe/analyse/process_grads.py

@@ -12,9 +12,8 @@
 import numpy as _np
 from scipy.constants import gas_constant as _R
 
-from .autocorrelation import (
-    get_statistical_inefficiency as _get_statistical_inefficiency,
-)
+from .autocorrelation import \
+    get_statistical_inefficiency as _get_statistical_inefficiency
 from .mbar import run_mbar as _run_mbar
 
 

EnsEquil/analyse/rmsd.py → a3fe/analyse/rmsd.py

@@ -7,13 +7,13 @@
 import subprocess as _subprocess
 from tempfile import TemporaryDirectory as _TemporaryDirectory
 from typing import List as _List
-from typing import Tuple as _Tuple
 from typing import Optional as _Optional
+from typing import Tuple as _Tuple
 
 import BioSimSpace as _BSS
+import MDAnalysis.transformations as _trans
 import numpy as _np
 from MDAnalysis import Universe as _Universe
-import MDAnalysis.transformations as _trans
 from MDAnalysis.analysis.rms import RMSD as _RMSD
 
 

EnsEquil/analyse/waters.py → a3fe/analyse/waters.py

@@ -1,18 +1,15 @@
 """Functions to analyse binding site waters."""
 
-from typing import (
-    List as _List,
-    Tuple as _Tuple,
-    Optional as _Optional,
-    Callable as _Callable,
-)
-
 import glob as _glob
-import MDAnalysis as _mda
-import numpy as _np
 import os as _os
-
 from multiprocessing import Pool as _Pool
+from typing import Callable as _Callable
+from typing import List as _List
+from typing import Optional as _Optional
+from typing import Tuple as _Tuple
+
+import MDAnalysis as _mda
+import numpy as _np
 
 
 def get_av_waters_simulation(