Merge branch 'develop' into HydrogenBondAnalysis

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Autoformat all files using `black`
+8f061e7da99eb78353e9392d6929673da5b352a3

.github/workflows/black.yaml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.github/workflows/ci.yaml

@@ -32,20 +32,17 @@ jobs:
 
         os: [ubuntu-latest]
         python-version: ["3.10"]
-        gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1"]
+        gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1"]
         include:
-          - os: ubuntu-latest
-            python-version:  "3.7"
-            gromacs-version: "2021.1"
           - os: ubuntu-latest
             python-version: "3.8"
-            gromacs-version: "2021.1"
+            gromacs-version: "2023.1"
           - os: ubuntu-latest
             python-version: "3.9"
-            gromacs-version: "2021.1"
+            gromacs-version: "2023.1"
           - os: macos-latest
             python-version: "3.10"
-            gromacs-version: "2021.1"
+            gromacs-version: "2023.1"
 
     env:
       MPLBACKEND: agg
@@ -55,13 +52,17 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: mamba environment and package installation
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: devtools/conda-envs/test_env.yaml
-        channel-priority: "flexible"
+        condarc: |
+           channels:
+              - conda-forge
+              - bioconda
+           channel_priority: flexible
         cache-downloads: true
-        cache-env: true
-        extra-specs: |
+        cache-environment: true
+        create-args: >-
            python=${{ matrix.python-version }}
           
     - name: Python version information
@@ -78,8 +79,10 @@ jobs:
          python -m pip install pybol
 
     - name: Install GROMACS (${{ matrix.gromacs-version }})
+      # include mdanalysis here AGAIN to work around micromamba removing mdanalysis 
+      # while downgrading libxml2 (see issue #252)
       run: |
-         micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl
+         micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl mdanalysis
 
     - name: Install package (with no dependencies)
       run: |

.gitignore

@@ -12,3 +12,6 @@ dist
 doc/examples/benzene/Equilibrium/
 .coverage
 coverage.xml
+*.lock
+*.npz
+dir.csv

.vscode/extensions.json

@@ -0,0 +1,6 @@
+{
+    "recommendations": [
+        "ms-python.black-formatter",
+        "ms-python.python"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "[python]": {
+        "editor.formatOnSave": true
+    }
+}

AUTHORS

@@ -39,3 +39,7 @@ their first commit. GitHub handle is optional.
 
 - Cade Duckworth (cadeduckworth)
 
+2023
+----
+
+- Alexander Moriarty (@a-ws-m)

CHANGES

@@ -5,11 +5,16 @@ CHANGES for MDPOW
 Add summary of changes for each release. Use ISO 8061 dates. Reference
 GitHub issues numbers and PR numbers.
 
-2022-??-??    0.9.0
-cadeduckworth, orbeckst, VOD555
+2023-??-??    0.9.0
+cadeduckworth, orbeckst, VOD555, a-ws-m
 
 Changes
 
+* added support for Python 3.10 (#202)
+* dropped testing on Python 3.6 (PR #220, #202)
+* dropped testing on Python 3.7 (minimally supported Python >= 3.8, #248)
+* support Gromacs 2022.4 and 2023.1 (#256)
+* use pymbar >= 4 and alchemlyb >= 2 (#246)
 * for ensemble.EnsembleAnalysis._single_frame() 
   changed 'pass' to 'raise NotImplementedError' (#216)
 * for ensemble.EnsembleAnalysis._single_universe() 
@@ -18,16 +23,38 @@ Changes
   and use _single_frame OR _single_universe (#216)
 * _prepare_universe and _conclude_universe removed from 
   EnsembleAnalysis.run() method, no longer needed (per comments, #199)
-* added support for Python 3.10
-* dropped testing on Python 3.6 
+* internal log_banner() now uses logger as argument (PR #247)
+* use `black` formatter for codebase (#271)
+
+Enhancements
+
+* convert figure components to SVG, save as individual PDFs,
+  and generate PDF of all figures combined in one file,
+  for workflows dihedrals module (#243)
+* add RDKit mol object to dihedrals plot with dihedral atom
+  indices labeled and dihedral atom group bonds highlighted
+  for workflows dihedrals module (#243)
+* new workflows registry that contains each EnsembleAnalysis for which
+  a workflows module exists, for use with workflows base module (#229)
+* new workflows base module that provides iterative workflow use for
+  directories that contain multiple projects (#229)
+* new workflows module (#217)
+* new automated dihedral analysis workflow (detect dihedrals with SMARTS,
+  analyze with EnsembleAnalysis, and generate seaborn violinplots) (#217)
+* new workflows.base.guess_elements() function to guess elements
+  from masses (PR #264)  
+* add new exit_on_error=False|True argument to run.runMD_or_exit() so
+  that failures just raise exceptions and not call sys.exit() (PR #249)
 
 Fixes
 
+* for mdpow.workflows.dihedrals.periodic_angle() implement .copy(deep=True)
+  to explicitly make a copy DataFrame of the data for angle padding (#242)
 * fix rcoulomb in CHARMM energy minimization MDP template file (PR #210)
 * fix ensemble.EnsembleAnalysis.check_groups_from_common_ensemble (#212)
 
 
-2021-01-03    0.8.0
+2022-01-03    0.8.0
 ALescoulie, orbeckst
 
 Changes

INSTALL.rst

@@ -2,7 +2,7 @@
  Quick installation instructions for *MDPOW*
 =============================================
 
-MDPOW is compatible with Python 3.7+ and tested
+MDPOW is compatible with Python >=3.8 and tested
 on Ubuntu and Mac OS.
 
 We recommend that you install MDPOW in a virtual environment.
@@ -28,11 +28,11 @@ GROMACS_.
 Conda environment with pre-requisites
 -------------------------------------
 
-Make a conda environment with the latest packages for Python 3.7 and
+Make a conda environment with the latest packages for Python 3.8 or
 higher with the name *mdpow*; this installs the larger dependencies that are
 pre-requisites for MDPOW::
 
-  conda create -c conda-forge -n mdpow  numpy scipy matplotlib mdanalysis pyyaml alchemlyb pandas gromacswrapper
+  conda create -c conda-forge -n mdpow  numpy scipy matplotlib seaborn mdanalysis pyyaml alchemlyb pandas gromacswrapper rdkit
   conda activate mdpow
 
 Install MDPOW with ``pip``::

README.rst

@@ -2,10 +2,11 @@
  README for MDPOW
 ===================
 
-|build| |cov| |docs|
+|build| |cov| |docs| |black| |zenodo|
 
 .. |P_ow| replace:: *P*\ :sub:`OW`
 .. |P_cw| replace:: *P*\ :sub:`CW`
+.. |P_tw| replace:: *P*\ :sub:`TW`  
 
 *MDPOW* is a python package that automates the calculation of
 solvation free energies via molecular dynamics (MD) simulations. In
@@ -14,7 +15,8 @@ coefficients. Currently implemented:
 
 - *water-octanol* partition coefficient (|P_ow|)
 - *water-cyclohexane* partition coefficient (|P_cw|)
-
+- *water-toluene* partition coefficient (|P_tw|)
+
 Calculations are performed with the Gromacs_ MD software package
 [#GromacsWrapperNote]_. Currently, *OPLS-AA*, *CHARMM/CGENFF*, and
 *AMBER/GAFF* parameters are supported.
@@ -44,10 +46,10 @@ Installation
 ------------
 
 See `INSTALL`_ for detailed instructions. MDPOW currently supports and
-is tested with Python 3.7 to 3.9.
+is tested with Python 3.8 to 3.10.
 
 You will also need `Gromacs`_ (currently tested with versions 4.6.5,
-2018, 2020, 2021 but 2016 and 2019 should also work).
+2018, 2020, 2021, 2022, 2023 but 2016 and 2019 should also work).
 
 
 Development version
@@ -72,9 +74,14 @@ Source code
 *MDPOW* is open source and published under the `GNU General Public License
 v3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .
 
+We use `black`_ for uniform code formatting.
+
 .. _`GNU General Public License v3`:
    http://www.gnu.org/licenses/gpl-3.0.html
 
+.. _`black`: https://github.com/psf/black
+
+
 Footnotes
 ---------
 
@@ -92,5 +99,13 @@ Footnotes
 .. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest
    :target: http://mdpow.readthedocs.org/en/latest/?badge=latest
    :alt: Documentation
+
+.. |zenodo| image:: https://zenodo.org/badge/44999898.svg
+   :target: https://zenodo.org/badge/latestdoi/44999898
+   :alt: Zenodo
+
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :target: https://github.com/psf/black	 
+   :alt: black   
 
 .. _INSTALL: INSTALL.rst

devtools/conda-envs/test_env.yaml

@@ -14,10 +14,16 @@ dependencies:
 - mdanalysis >=2
 - numkit
 - gromacswrapper
-- alchemlyb <2
+- alchemlyb >=2
+- pymbar >=4
+- rdkit
+- seaborn
+- svgutils
+- cairosvg
+- pypdf
 
   # Testing
 - pytest
 - pytest-pep8
 - pytest-cov
-- codecov  
+- codecov

doc/examples/benzene/session.py

@@ -1,31 +1,39 @@
 import mdpow.equil
+
 S = mdpow.equil.WaterSimulation(molecule="BNZ")
 S.topology("benzene.itp")
 S.solvate(struct="benzene.pdb")
 S.energy_minimize()
-S.MD_relaxed(runtime=5)   # should be at least 1e3 ps for production not just 5 ps
+S.MD_relaxed(runtime=5)  # should be at least 1e3 ps for production not just 5 ps
 
 # run simulation externally or use MDrunner
 # (see docs for using mpi etc)
 import gromacs
-r = gromacs.run.MDrunner(dirname=S.dirs['MD_relaxed'], deffnm="md", c="md.pdb", cpi=True, append=True, v=True)
-r.run()   # runs mdrun in the python shell
+
+r = gromacs.run.MDrunner(
+    dirname=S.dirs["MD_relaxed"], deffnm="md", c="md.pdb", cpi=True, append=True, v=True
+)
+r.run()  # runs mdrun in the python shell
 
 
-S.MD(runtime=10, qscript=['local.sh'])  # should be at least 10e3 ps for production, not just 10 ps
+S.MD(
+    runtime=10, qscript=["local.sh"]
+)  # should be at least 10e3 ps for production, not just 10 ps
 # run simulation
-r = gromacs.run.MDrunner(dirname=S.dirs['MD_NPT'], deffnm="md", c="md.pdb", cpi=True, append=True, v=True)
-r.run()   # runs mdrun in the python shell
+r = gromacs.run.MDrunner(
+    dirname=S.dirs["MD_NPT"], deffnm="md", c="md.pdb", cpi=True, append=True, v=True
+)
+r.run()  # runs mdrun in the python shell
 
 
 import mdpow.fep
+
 gwat = mdpow.fep.Ghyd(simulation=S, runtime=10)
 gwat.setup()
 
 # run multiple simulations on cluster
 
 
-
 O = mdpow.equil.OctanolSimulation(molecule="BNZ")
 O.topology("benzene.itp")
 O.solvate(struct="benzene.pdb")

doc/requirements.txt

@@ -4,5 +4,12 @@ scipy
 pandas
 pyyaml
 GromacsWrapper>=0.5.1
-alchemlyb
+alchemlyb>=2
+pymbar>=4
 mdanalysis
+rdkit
+seaborn
+matplotlib
+svgutils
+cairosvg
+pypdf

doc/sphinx/source/analysis.txt

@@ -20,12 +20,11 @@ all FEP simulations. They then make data available (typically, as a
 :class:`pandas.DataFrame`).
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
 
    analysis/solvation
    analysis/dihedral
 
-
 .. _framework:   
 
 Ensemble Analysis Framework
@@ -45,10 +44,9 @@ in more detail in [Lescoulie2021]_.
 .. toctree::
    :maxdepth: 1
 
-   analysis/ensemble_analysis	      
+   analysis/ensemble_analysis
    analysis/ensemble
 
-
 References
 ----------
 .. [Lescoulie2021] A. Lescoulie, "SPIDAL Summer REU 2021: Upgrading MDPOW and