Merge branch 'master' into auto_mod_mapping

.github/workflows/deploy.yml

@@ -14,26 +14,25 @@ env:
 
 jobs:
   build:
-
     runs-on: ubuntu-20.04
 
     strategy:
       matrix:
-       py_version: ["3.8", "3.9", "3.10", "3.11"]
+       py_version: ["3.9", "3.10", "3.11", "3.12"]
        include:
-         - py_version: "3.8"
-           WITH_CODECOV: true
          - py_version: "3.9"
            WITH_CODECOV: true
          - py_version: "3.10"
            WITH_CODECOV: true
          - py_version: "3.11"
            WITH_CODECOV: true
+         - py_version: "3.12"
+           WITH_CODECOV: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.py_version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.py_version }}
         cache: pip
@@ -54,6 +53,7 @@ jobs:
       run: |
         coverage run $(which pytest) -vv --hypothesis-show-statistics
         coverage report --omit='*/bin/pytest'
+        coverage xml
         
     - if: ${{ matrix.WITH_CODECOV }}
       name: Upload coverage codecov   
@@ -68,11 +68,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
         cache: pip
         cache-dependency-path: |
           **/setup.cfg
@@ -93,11 +93,11 @@ jobs:
       runs-on: ubuntu-latest
 
       steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-           python-version: '3.11'
+           python-version: '3.x'
            cache: pip
            cache-dependency-path: |
              **/setup.cfg
@@ -118,37 +118,33 @@ jobs:
   deploy:
     needs: [build, lint, docs]
     runs-on: ubuntu-latest
-
+    environment:
+      name: pypi
+      url: https://pypi.org/p/vermouth
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+      with:
+        fetch-tags: true
+        fetch-depth: 0
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
         cache: pip
         cache-dependency-path: |
           **/setup.cfg
           **/requirements-*.txt
           **/pyproject.toml
-        
+    - name: Install dependencies
+      run: |
+        pip install --upgrade setuptools pip
+        pip install --upgrade .
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
-        pip install pbr
-         
+      run: |
+        python3 -m pip install build pbr --user
     - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        
-    - name: Publish package to PyPI
+      run: python3 -m build --sdist --wheel --outdir dist/
+    - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -16,26 +16,25 @@ env:
 
 jobs:
   build:
-
     runs-on: ubuntu-20.04
 
     strategy:
       matrix:
-       py_version: ["3.8", "3.9", "3.10", "3.11"]
+       py_version: ["3.9", "3.10", "3.11", "3.12"]
        include:
-         - py_version: "3.8"
-           WITH_CODECOV: true
          - py_version: "3.9"
            WITH_CODECOV: true
          - py_version: "3.10"
            WITH_CODECOV: true
          - py_version: "3.11"
            WITH_CODECOV: true
+         - py_version: "3.12"
+           WITH_CODECOV: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.py_version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.py_version }}
         cache: pip
@@ -71,11 +70,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
         cache: pip
         cache-dependency-path: |
           **/setup.cfg
@@ -96,11 +95,11 @@ jobs:
       runs-on: ubuntu-latest
 
       steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-           python-version: '3.11'
+           python-version: '3.x'
            cache: pip
            cache-dependency-path: |
              **/setup.cfg
@@ -116,3 +115,39 @@ jobs:
         run: | 
           mkdir -p doc/source/_static
           sphinx-build -EnW -b html doc/source/ doc/build/html
+
+  deploy:
+    needs: [build, lint, docs]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/vermouth
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-tags: true
+        fetch-depth: 0
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: pip
+        cache-dependency-path: |
+          **/setup.cfg
+          **/requirements-*.txt
+          **/pyproject.toml
+    - name: Install dependencies
+      run: |
+        pip install --upgrade setuptools pip
+        pip install --upgrade .
+    - name: Install pypa/build
+      run: |
+        python3 -m pip install build pbr --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build --sdist --wheel --outdir dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

pyproject.toml

@@ -4,6 +4,7 @@ requires = [
         "setuptools >= 30.3.0",
         "pbr",
     ]
+build-backend = "pbr.build"
 
 [tool.pytest.ini_options]
 addopts = "--import-mode=importlib"

setup.cfg

@@ -17,10 +17,10 @@ classifier =
     License :: OSI Approved :: Apache Software License
     Operating System :: OS Independent
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Topic :: Scientific/Engineering :: Bio-Informatics
     Topic :: Scientific/Engineering :: Chemistry
 keywords = martini MD martinize

vermouth/data/mappings/his.charmm.mapping

@@ -0,0 +1,30 @@
+[ block ]
+[ from ]
+charmm
+[ to ]
+martini22
+
+[ from blocks ]
+HIS
+
+[ to blocks ]
+HSE
+
+[ mapping ]
+  N    BB
+ HN    BB
+ CA    BB
+ HA    BB
+ CB   SC1
+HB1   SC1
+HB2   SC1
+CD2   SC2
+HD2   SC2
+ CG   SC1
+NE2   SC2
+HE2   SC2
+ND1   SC3
+CE1   SC3
+HE1   SC3
+  C    BB
+  O    BB

vermouth/data/mappings/his.gromos.mapping

@@ -0,0 +1,27 @@
+[ block ]
+[ from ]
+gromos
+[ to ]
+martini22
+
+[ from blocks ]
+HIS
+
+[ to blocks ]
+HSE
+
+[ mapping ]
+  N    BB
+  H    BB
+ CA    BB
+ CB   SC1
+ CG   SC1
+ND1   SC3
+HD1   SC3
+CD2   SC2
+HD2   SC2
+CE1   SC3
+HE1   SC3
+NE2   SC2
+  C    BB
+  O    BB