Migrate openforcefield to openff.toolkit (#803).

.gitattributes

@@ -1 +1 @@
-openforcefield/_version.py export-subst
+openff/toolkit/_version.py export-subst

.github/pull_request_template.md

@@ -1,5 +1,5 @@
 - [ ] Tag issue being addressed
-- [ ] Add [tests](https://github.com/openforcefield/openforcefield/tree/master/openforcefield/tests)
-- [ ] Update docstrings/[documentation](https://github.com/openforcefield/openforcefield/tree/master/docs), if applicable
+- [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/master/openff/toolkit/tests)
+- [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/master/docs), if applicable
 - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase
-- [ ] Update [changelog](https://github.com/openforcefield/openforcefield/blob/master/docs/releasehistory.rst)
+- [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/master/docs/releasehistory.rst)

.github/workflows/CI.yml

@@ -17,7 +17,7 @@ on:
 
 jobs:
   test:
-    if: (github.event_name == 'schedule' && github.repository == 'openforcefield/openforcefield') || (github.event_name != 'schedule')
+    if: (github.event_name == 'schedule' && github.repository == 'openforcefield/openff-toolkit') || (github.event_name != 'schedule')
     name: Test on ${{ matrix.cfg.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.cfg.rdkit }}, OpenEye=${{ matrix.cfg.openeye }}
     runs-on: ${{ matrix.cfg.os }}
     strategy:
@@ -51,8 +51,8 @@ jobs:
       OPENEYE: ${{ matrix.cfg.openeye }}
       PYVER: ${{ matrix.python-version }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openforcefield
-      PYTEST_ARGS: -r fE --tb=short --cov=openforcefield --cov-config=setup.cfg --cov-append --cov-report=xml
+      PACKAGE: openff
+      PYTEST_ARGS: -r fE --tb=short --cov=openff --cov-config=setup.cfg --cov-append --cov-report=xml
       NB_ARGS: -v --nbval-lax --ignore=examples/deprecated
 
     steps:
@@ -106,41 +106,41 @@ jobs:
       - name: Install package
         shell: bash -l {0}
         run: |
-          python -m pip install --no-deps -v .
+          python setup.py develop --no-deps
 
       - name: Check installed toolkits
         shell: bash -l {0}
         run: |
           if [[ "$OPENEYE" == true ]]; then
-            python -c "from openforcefield.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
+            python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
           fi
           if [[ "$OPENEYE" == false ]]; then
             if [[ $(conda list | grep openeye-toolkits) ]]; then
               conda remove --force openeye-toolkits --yes
             fi
-            python -c "from openforcefield.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye unexpectedly found'"
+            python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye unexpectedly found'"
           fi
           if [[ "$RDKIT" == true ]]; then
-            python -c "from openforcefield.utils.toolkits import RDKIT_AVAILABLE; assert RDKIT_AVAILABLE, 'RDKit unavailable'"
+            python -c "from openff.toolkit.utils.toolkits import RDKIT_AVAILABLE; assert RDKIT_AVAILABLE, 'RDKit unavailable'"
           fi
           if [[ "$RDKIT" == false ]]; then
             if [[ $(conda list | grep rdkit) ]]; then
               conda remove --force rdkit --yes
             fi
-            python -c "from openforcefield.utils.toolkits import RDKIT_AVAILABLE; assert not RDKIT_AVAILABLE, 'RDKit unexpectedly found'"
+            python -c "from openff.toolkit.utils.toolkits import RDKIT_AVAILABLE; assert not RDKIT_AVAILABLE, 'RDKit unexpectedly found'"
           fi
 
       - name: Check links
         shell: bash -l {0}
         if: ${{ matrix.cfg.rdkit == 'true' && matrix.cfg.openeye == 'TRUE' }}
         run: |
-          pytest -r fE --tb=short openforcefield/tests/test_links.py
+          pytest -r fE --tb=short openff/toolkit/tests/test_links.py
 
       - name: Run unit tests
         shell: bash -l {0}
         run: |
-          PYTEST_ARGS+=" --ignore=openforcefield/tests/test_examples.py"
-          PYTEST_ARGS+=" --ignore=openforcefield/tests/test_links.py"
+          PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_examples.py"
+          PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_links.py"
           if [[ "$RDKIT" == true && "$OPENEYE" == true ]]; then
             PYTEST_ARGS+="--doctest-modules"
           fi
@@ -153,12 +153,14 @@ jobs:
             PYTEST_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
             PYTEST_ARGS+=" --ignore=examples/QCArchive_interface"
           fi
-          pytest $PYTEST_ARGS openforcefield/tests/test_examples.py
+          pytest $PYTEST_ARGS openff/toolkit/tests/test_examples.py
 
       - name: Run example notebooks
         shell: bash -l {0}
         run: |
           NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs"
+          # XFail until a new `openmmforcefields` build is made which depends on `openff-toolkit`.
+          NB_ARGS+=" --ignore=examples/swap_amber_parameters"
           if [[ "$RDKIT" == false ]]; then
             NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
             NB_ARGS+=" --ignore=examples/conformer_energies"

.github/workflows/conda.yml

@@ -31,7 +31,7 @@ jobs:
       OPENEYE: ${{ matrix.openeye }}
       PYVER: ${{ matrix.python-version }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openforcefield
+      PACKAGE: openff-toolkit
 
     steps:
       - uses: actions/checkout@v2
@@ -82,13 +82,13 @@ jobs:
         shell: bash -l {0}
         run: |
           if [[ "$OPENEYE" == true ]]; then
-            python -c "from openforcefield.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
+            python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
           fi
           if [[ "$OPENEYE" == false ]]; then
             if [[ $(conda list | grep openeye-toolkits) ]]; then
               conda remove --force openeye-toolkits --yes
             fi
-            python -c "from openforcefield.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye unexpectedly found'"
+            python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye unexpectedly found'"
           fi
 
       - name: Check that correct OFFTK version was installed
@@ -97,8 +97,8 @@ jobs:
           # Go up one directory to ensure that we don't just load the OFFTK from the checked-out repo
           cd ../
 
-          export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openforcefield.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
-          export FOUND_VER=$(python -c "import openforcefield; print(openforcefield.__version__)")
+          export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
+          export FOUND_VER=$(python -c "import openff.toolkit; print(openff.toolkit.__version__)")
 
           echo "Latest tag is"
           echo $LATEST_TAG
@@ -110,12 +110,12 @@ jobs:
             exit 1
           fi
 
-          cd openforcefield
+          cd openff/toolkit
 
       - name: Test the package
         shell: bash -l {0}
         run: |
-          export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openforcefield.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
+          export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
           # Checkout the state of the repo as of the last release
           git fetch --tags
           git checkout tags/$LATEST_TAG
@@ -125,10 +125,10 @@ jobs:
           ls
 
           if [[ "$OPENEYE" == true ]]; then
-            python -c "import openforcefield; print(openforcefield.__file__)"
+            python -c "import openff.toolkit; print(openff.toolkit.__file__)"
             python -c "import openeye; print(openeye.oechem.OEChemIsLicensed())"
           fi
 
           PYTEST_ARGS=" -r fE --tb=short"
-          PYTEST_ARGS+=" --ignore=openforcefield/tests/test_links.py"
-          pytest $PYTEST_ARGS openforcefield
+          PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_links.py"
+          pytest $PYTEST_ARGS openff

.github/workflows/installer.yml

@@ -54,7 +54,7 @@ jobs:
 
         # Find the tag of the last release (excluding RCs)
         # TODO: Make this a variable that can be passed through from trigger and/or allow RC
-        export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openforcefield.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
+        export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
 
         echo $LATEST_TAG
 
@@ -76,7 +76,7 @@ jobs:
       uses: actions/upload-artifact@v2
       with:
         name: ${{ matrix.os }}_py${{ matrix.python-version }}.sh  
-        path: toolkit-installer-constructor/build/openforcefield*/openforcefield*.sh
+        path: toolkit-installer-constructor/build/openff-toolkit*/openff-toolkit*.sh
 
     - name: Install from installer
       shell: bash -l {0}
@@ -86,18 +86,18 @@ jobs:
         ls
         ls toolkit-installer-constructor
         ls toolkit-installer-constructor/build
-        ls toolkit-installer-constructor/build/openforcefield-*/
+        ls toolkit-installer-constructor/build/openff-toolkit-*/
 
         mkdir scratch
         cd scratch
-        echo $HOME/constructor_install/ | bash ../toolkit-installer-constructor/build/openforcefield-*/openforcefield-*.sh
+        echo $HOME/constructor_install/ | bash ../toolkit-installer-constructor/build/openff-toolkit-*/openff-toolkit-*.sh
 
         conda activate $HOME/constructor_install/
         conda info
         conda list
 
-        export FOUND_VER=$(python -c "import openforcefield; print(openforcefield.__version__)")
-        export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openforcefield.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
+        export FOUND_VER=$(python -c "import openff.toolkit; print(openff.toolkit.__version__)")
+        export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -v "rc" | tail -1 | sed 's/refs\/tags\///')
 
         echo $LATEST_TAG
         echo $FOUND_VER
@@ -108,9 +108,9 @@ jobs:
         fi
 
         PYTEST_ARGS=" -r fE --tb=short"
-        PYTEST_ARGS+=" --ignore=openforcefield/tests/test_links.py"
+        PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_links.py"
 
         # This should work if run directly at release time, but a safer approach would be
         # to `git checkout` the corresponding tag of the release, see PR #577
-        pytest $PYTEST_ARGS ../openforcefield/tests/
+        pytest $PYTEST_ARGS ../openff/toolkit/tests/
 

.github/workflows/lint.yml

@@ -22,8 +22,8 @@ jobs:
 
       - name: Run black
         run: |
-          black --check openforcefield
+          black --check openff
 
       - name: Run isort
         run: |
-          isort --check openforcefield
+          isort --check openff

FAQ.md

@@ -51,7 +51,7 @@ Essentially, anything which provides the full identity of what you want to simul
 
 We recommend that you install the toolkit in a fresh conda environment, explicitly passing the channels to be used, in-order:
 
-    conda create -n <my_new_env> -c conda-forge -c omnia openforcefield
+    conda create -n <my_new_env> -c conda-forge openff-toolkit
     conda activate <my_new_env>
 
 Installing into a new environment avoids forcing conda to satisfy the dependencies of both the toolkit and all existing packages in that environment.

MANIFEST.in

@@ -1,2 +1,6 @@
+include LICENSE
+include MANIFEST.in
 include versioneer.py
-include openforcefield/_version.py
+
+graft openff
+global-exclude *.py[cod] __pycache__ *.so