Sphinx & Plotting Documentation

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,36 @@
+import sys
+import os
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'safep'
+copyright = '2024, Brannigan Lab'
+author = 'Brannigan Lab'
+release = '0.1.3'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+      'sphinx.ext.autodoc', 
+      'sphinx.ext.napoleon', 
+      'autodocsumm', 
+      'sphinx.ext.coverage'
+]
+auto_doc_default_options = {'autosummary': True}
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+sys.path.insert(0,  os.path.abspath('../safep'))
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme' # read the docs theme. This variable is 'default' by default.
+
+html_static_path = ['_static']

docs/getting-started.rst

@@ -0,0 +1,37 @@
+getting-started
+===============
+
+.. toctree::
+   :maxdepth: 4
+
+Introduction
+------------
+SAFEP-related scripts and tools
+
+These scripts and notebooks are broadly applicable to FEP analysis.
+
+A complete tutorial is available at:
+`SAFEP Tutorial <https://doi.org/10.33011/livecoms.5.1.2067>`_.
+
+Installation
+------------
+
+.. Installation:
+0. Clone this repository
+1. Enter the repository directory
+2. Run ``pip install .``
+
+OR
+
+0. Run ``pip install git+https://github.com/BranniganLab/safep.git``
+
+Notebooks
+----------
+- BAR_Estimator_Basic: General use FEP analysis. Includes cumulative dG estimates, error estimates, and measures of convergence.
+- BAR_Estimator_Expanded: Extended functionality including bootstrapped error estimates, kernel estimation of dL distributions, and more.
+
+
+Examples
+----------
+Sample data is available in Sample_Notebooks/Sample_Data or from the alchemtest package.
+

docs/index.rst

@@ -0,0 +1,23 @@
+.. safep documentation master file, created by
+   sphinx-quickstart on Wed Mar 27 13:57:58 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to safep's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   getting-started
+   modules
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/modules.rst

@@ -0,0 +1,7 @@
+safep
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   safep

docs/requirements.txt

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+autodocsumm
+sphinx_rtd_theme
+safep
+numpy
+pandas
+matplotlib
+scipy
+alchemlyb
+pymbar
+natsort
+tqdm

docs/safep.rst

@@ -0,0 +1,69 @@
+safep package
+=============
+
+Submodules
+----------
+
+safep.AFEP\_parse module
+------------------------
+
+.. automodule:: safep.AFEP_parse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+safep.TI module
+---------------
+
+.. automodule:: safep.TI
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+safep.estimators module
+-----------------------
+
+.. automodule:: safep.estimators
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+safep.fileIO module
+-------------------
+
+.. automodule:: safep.fileIO
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+safep.helpers module
+--------------------
+
+.. automodule:: safep.helpers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+safep.plotting module
+---------------------
+
+.. automodule:: safep.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+safep.processing module
+-----------------------
+
+.. automodule:: safep.processing
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: safep
+   :members:
+   :undoc-members:
+   :show-inheritance:

pyproject.toml

@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+dependencies = [
+    'numpy>=1.22.0',
+    'pandas>=1.4.0', 
+    'alchemlyb==2.0.0', 
+    'matplotlib>=3.5.0', 
+    'natsort>=7.1.0', 
+    'tqdm',
+    ]
+
+name = 'safep'
+version = "0.1.4"
+
+authors = [{name='Brannigan Lab', email='[email protected]'}]
+
+description = 'Tools for Analyzing and Debugging (SA)FEP calculations'
+readme = "README.md"
+
+requires-python = ">=3.10"
+
+classifiers = [
+    'Development Status :: 4 - Beta',
+	'Intended Audience :: Science/Research',
+	'Operating System :: POSIX :: Linux',        
+	'Programming Language :: Python :: 3.12',
+	"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+	"Operating System :: OS Independent",
+]
+
+[project.urls]
+Homepage = "https://github.com/BranniganLab/safep"
+Issues = "https://github.com/BranniganLab/safep/issues"

safep/fileIO.py

@@ -65,9 +65,9 @@ def read_FEPOUT(fileName, step=1):
             if line[0] == '#':
                 frame = 0
                 #print(line)
-                Lambda = re.search('LAMBDA SET TO (\d+(\.\d+)*)', line)
-                Lambda2 = re.search('LAMBDA2 (\d+(\.\d+)*)', line)
-                LambdaIDWS = re.search('LAMBDA_IDWS (\d+(\.\d+)*)', line)
+                Lambda = re.search(r'LAMBDA SET TO (\d+(\.\d+)*)', line)
+                Lambda2 = re.search(r'LAMBDA2 (\d+(\.\d+)*)', line)
+                LambdaIDWS = re.search(r'LAMBDA_IDWS (\d+(\.\d+)*)', line)
                 if Lambda:
                     L = Lambda.group(1)
                     #print(f'L={L}')