Merge branch 'develop' into HydrogenBondAnalysis

.git-blame-ignore-revs

@@ -1,2 +1,3 @@
 # Autoformat all files using `black`
 8f061e7da99eb78353e9392d6929673da5b352a3
+91078a63c64ec9a1c2de7f72a835813b888d1c73

.github/workflows/ci.yaml

@@ -26,33 +26,33 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # only test all GROMACS version on the oldest and latest
-        # Python to keep the testing matrix manageable and only use 2
-        # macos runners (latest GROMACS, oldest and latest Python)
+        # only test all GROMACS version on the latest
+        # Python to keep the testing matrix manageable and only use 1
+        # macos runners (latest GROMACS, latest Python)
 
         os: [ubuntu-latest]
-        python-version: ["3.10"]
-        gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1"]
+        python-version: ["3.12"]
+        gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1", "2024.3"]
         include:
           - os: ubuntu-latest
-            python-version: "3.8"
-            gromacs-version: "2023.1"
+            python-version: "3.10"
+            gromacs-version: "2024.3"
           - os: ubuntu-latest
-            python-version: "3.9"
-            gromacs-version: "2023.1"
+            python-version: "3.11"
+            gromacs-version: "2024.3"	    
           - os: macos-latest
-            python-version: "3.10"
-            gromacs-version: "2023.1"
+            python-version: "3.12"
+            gromacs-version: "2024.3"
 
     env:
       MPLBACKEND: agg
 
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: mamba environment and package installation
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: devtools/conda-envs/test_env.yaml
         condarc: |
@@ -93,7 +93,7 @@ jobs:
         pytest -v --durations=20 --cov=mdpow --cov-report=xml --color=yes ./mdpow/tests
 
     - name: Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

.github/workflows/deploy.yaml

@@ -0,0 +1,57 @@
+name: Build and upload to PyPi
+
+on:
+  push:
+    tags:
+      - "*"
+  release:
+    types:
+      - published
+
+jobs:
+  test_pypi_push:
+    environment:
+      name: TestPyPi
+      url: https://test.pypi.org/p/MDPOW
+    permissions:
+      id-token: write
+    if: |
+      github.repository == 'Becksteinlab/MDPOW' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
+    name: "TestPyPi: Build and upload pure Python wheels"
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: testpypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        with:
+          test_submission: true
+          package_name: 'MDPOW'
+          module_name: 'mdpow'
+          tests: false
+
+  pypi_push:
+    environment:
+      name: PyPi
+      url: https://pypi.org/p/MDPOW
+    permissions:
+      id-token: write
+    if: |
+      github.repository == 'Becksteinlab/MDPOW' &&
+      (github.event_name == 'release' && github.event.action == 'published')
+    name: "PyPi: Build and upload pure Python wheels"
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: pypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'release' && github.event.action == 'published'
+        with:        
+          package_name: 'MDPOW'
+          module_name: 'mdpow'
+          tests: false

.gitignore

@@ -15,3 +15,11 @@ coverage.xml
 *.lock
 *.npz
 dir.csv
+
+# Files for the Martini example that can be downloaded at runtime
+doc/examples/martini/*
+!doc/examples/martini/*.mdp
+!doc/examples/martini/*.ipynb
+!doc/examples/martini/water.gro
+!doc/examples/martini/octanol.gro
+!doc/examples/martini/benzene.pdb

.readthedocs.yaml

@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: doc/sphinx/source/conf.py
@@ -13,9 +18,12 @@ sphinx:
 formats:
    - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
+# install package
 python:
-   version: 3.8
    install:
-   - requirements: doc/requirements.txt
-   system_packages: true
+      - method: pip
+        path: .
+
+conda:
+    environment: devtools/conda-envs/readthedocs.yaml
+

.vscode/settings.json

@@ -1,5 +1,10 @@
 {
     "[python]": {
         "editor.formatOnSave": true
-    }
+    },
+    "python.testing.pytestArgs": [
+        "mdpow"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
 }

AUTHORS

@@ -42,4 +42,4 @@ their first commit. GitHub handle is optional.
 2023
 ----
 
-- Alexander Moriarty (@a-ws-m)
+- Alexander Moriarty (a-ws-m)

CHANGES

@@ -5,15 +5,19 @@ CHANGES for MDPOW
 Add summary of changes for each release. Use ISO 8061 dates. Reference
 GitHub issues numbers and PR numbers.
 
-2023-??-??    0.9.0
+2024-10-11    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)
+* change in TI implementation in fep.Gsolv.analysis(): scipy.integrate.simpson()
+  now always uses Cartwright's approach to compute the last interval instead of
+  the old `even="last"` behavior. This change **may lead to small numerical 
+  differences in output** (#281)
+* added testing/support for Python 3.10 (#202) to 3.12 (#283)
+* dropped testing/support for Python 3.9 (#286), 3.8 (#281), 3.7 (#248),
+  3.6 (PR #220, #202)
+* support Gromacs 2022.4 and 2023.1 (#256) and 2024.3 (PR #290)
 * use pymbar >= 4 and alchemlyb >= 2 (#246)
 * for ensemble.EnsembleAnalysis._single_frame() 
   changed 'pass' to 'raise NotImplementedError' (#216)
@@ -25,6 +29,22 @@ Changes
   EnsembleAnalysis.run() method, no longer needed (per comments, #199)
 * internal log_banner() now uses logger as argument (PR #247)
 * use `black` formatter for codebase (#271)
+* implemented `forcefields.Forcefield` class (#267)
+  - facilitates users using non-default forcefields without changing package
+    code  
+  - `equil.Simulation` has new `ff_class` argument
+  - each `Forcefield` has unique `default_water_model`, replacing global
+    `DEFAULT_WATER_MODEL`
+  - `get_solvent_model()` and `get_solvent_identifier()` take either `str` or
+    `Forcefield` type for the `forcefield` argument    
+  - both functions also use the `Forcefield`-specific `default_water_model`
+    (fixes #112)  
+* `forcefields.DEFAULT_WATER_MODEL` removed (#267)
+* changed `system.top` and `system_octwet.top` to act as templates and added
+  `.template` suffix (#267)  
+* removed `forcefields.get_ff_paths()` (#267)
+* changed `forcefields.get_solvent_identifier()`: will raise `ValueError`
+  instead of returning `None` (#267)
 
 Enhancements
 
@@ -52,6 +72,11 @@ Fixes
   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)
+* updated versioneer (#285)
+* fix that simulation stages cannot be restarted after error (#272)
+* fix that testing resource data files were not packaged at all; they are now
+  included with the sdist (tar.gz) (23 MiB) but excluded from the wheel (whl)
+  (2.3 MiB) (#293)
 
 
 2022-01-03    0.8.0

INSTALL.rst

@@ -28,7 +28,7 @@ GROMACS_.
 Conda environment with pre-requisites
 -------------------------------------
 
-Make a conda environment with the latest packages for Python 3.8 or
+Make a conda environment with the latest packages for Python 3.10 or
 higher with the name *mdpow*; this installs the larger dependencies that are
 pre-requisites for MDPOW::
 

MANIFEST.in

@@ -1,7 +1,7 @@
-include   setup.py setup.cfg COPYING INSTALL README.rst AUTHORS CHANGES
-recursive-include   doc *.html *.css *.js *.txt *.inv *.png
+include   setup.py setup.cfg COPYING INSTALL.rst README.rst AUTHORS CHANGES
+include   versioneer.py
+include   mdpow/_version.py
 graft     mdpow/templates/
 graft     mdpow/top/
-graft     mdpow/top/oplsaa.ff/
-include versioneer.py
-include mdpow/_version.py
+graft     mdpow/tests/testing_resources/
+global-exclude *.py[cod]

README.rst

@@ -46,10 +46,10 @@ Installation
 ------------
 
 See `INSTALL`_ for detailed instructions. MDPOW currently supports and
-is tested with Python 3.8 to 3.10.
+is tested with Python 3.10 to 3.12.
 
 You will also need `Gromacs`_ (currently tested with versions 4.6.5,
-2018, 2020, 2021, 2022, 2023 but 2016 and 2019 should also work).
+2018, 2020, 2021, 2022, 2023, 2024 but 2016 and 2019 should also work).
 
 
 Development version

devtools/conda-envs/readthedocs.yaml

@@ -0,0 +1,26 @@
+name: readthedocs
+channels:
+- conda-forge
+dependencies:
+- python >=3.10
+- six
+- numpy
+- scipy >=1.11.0
+- matplotlib-base
+- pandas
+- scikit-learn
+- pyyaml
+- mdanalysis >=2
+- numkit
+- gromacswrapper
+- alchemlyb >=2
+- pymbar >=4
+- rdkit
+- seaborn
+- svgutils
+- cairosvg
+- pypdf
+
+# sphinx and RTD
+- sphinx
+- sphinx_rtd_theme

devtools/conda-envs/test_env.yaml

@@ -6,7 +6,7 @@ dependencies:
 - python
 - six
 - numpy
-- scipy
+- scipy >=1.11.0
 - matplotlib-base
 - pandas
 - scikit-learn
@@ -22,7 +22,7 @@ dependencies:
 - cairosvg
 - pypdf
 
-  # Testing
+# Testing
 - pytest
 - pytest-pep8
 - pytest-cov

doc/examples/martini/benzene.pdb

@@ -0,0 +1,13 @@
+REMARK    GENERATED BY TRJCONV
+TITLE     This is an auto generated system
+REMARK    THIS IS A SIMULATION BOX
+CRYST1  150.000  150.000  180.000  90.00  90.00  90.00 P 1           1
+MODEL        1
+ATOM      1  R1  BENZ    1      30.920   6.600  24.160  1.00  0.00            
+ATOM      2  R2  BENZ    1      28.820   5.000  23.610  1.00  0.00            
+ATOM      3  R3  BENZ    1      29.860   6.580  21.680  1.00  0.00            
+TER
+ENDMDL
+CONECT    1    2
+CONECT    2    3
+CONECT    1    3

doc/examples/martini/em.mdp

@@ -0,0 +1,17 @@
+include          =  
+integrator       =  steep
+dt               =  0.02
+nsteps           =  1000
+nstxout          =  0
+nstvout          =  0
+nstlog           =  100 
+nstxtcout        =  100
+xtc-precision    =  1000
+rlist            =  1.0
+coulombtype      =  Reaction-Field
+rcoulomb         =  1.0
+epsilon_r        =  15
+vdw-type         =  cutoff
+vdw-modifier     =  Potential-shift-verlet
+rvdw             =  1.0
+constraints = none

doc/examples/martini/eq.mdp

@@ -0,0 +1,24 @@
+include          =  
+dt               =  0.005 
+nsteps           =  25000
+nstxout          =  0 
+nstvout          =  0
+nstlog           =  1000
+nstxout-compressed  = 1000
+cutoff-scheme    =  Verlet
+coulombtype      =  Reaction-Field
+rcoulomb         =  1.1
+epsilon_r        =  15 
+vdw-type         =  cutoff
+vdw-modifier     =  Potential-shift-verlet 
+rvdw             =  1.1 
+tcoupl           =  v-rescale 
+tc-grps          =  System
+tau-t            =  1.0
+ref-t            =  300
+Pcoupl           =  c-rescale
+Pcoupltype       =  isotropic
+tau-p            =  3.0
+compressibility  =  3e-4
+ref-p            =  1.0
+refcoord_scaling =  all