Allow pytest 8 in deployment tests

.github/workflows/CI.yml

@@ -1,14 +1,6 @@
 name: CI
 
 on:
-  push:
-    branches:
-      - "main"
-      - "maintenance/.*"
-  pull_request:
-    branches:
-      - "main"
-      - "maintenance/.*"
   schedule:
     # Nightly tests run on main by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
@@ -41,7 +33,6 @@ jobs:
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openff
       PYTEST_ARGS: -r fE --tb=short -nauto
       COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml
 

.github/workflows/conda.yml

@@ -1,6 +1,7 @@
 name: Conda latest
 
 on:
+  push:
   release:
     types:
       - released
@@ -20,59 +21,43 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10"]
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
         openeye: ["true", "false"]
 
     env:
-      CI_OS: ${{ matrix.os }}
       OPENEYE: ${{ matrix.openeye }}
-      PYVER: ${{ matrix.python-version }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openff-toolkit
+      PYTEST_ARGS: -r fE --tb=short
 
     steps:
-      - uses: actions/checkout@v4
-
       - name: Vanilla install from conda
         uses: mamba-org/setup-micromamba@v1
-        if: ${{ matrix.openeye == 'false' }}
-        with:
-          environment-file: devtools/conda-envs/conda.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
-      - name: Install from conda with OpenEye
-        uses: mamba-org/setup-micromamba@v1
-        if: ${{ matrix.openeye == 'true' }}
         with:
-          environment-file: devtools/conda-envs/conda_oe.yaml
+          environment-name: latest-deployment
           create-args: >-
             python=${{ matrix.python-version }}
+            openff-toolkit-examples
+            pytest-xdist
+            pytest-rerunfailures
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
+      - name: Install OpenEye Toolkits
+        if: ${{ matrix.openeye == 'true' }}
+        run: micromamba install openeye-toolkits -c openeye
 
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
+        if: ${{ matrix.openeye == 'true' }}
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
         run: |
           echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
       - name: Environment Information
-        run: |
-          conda info
-          conda list
+        run: micromamba info && micromamba list
 
       - name: Check installed toolkits
         run: |
-          # Checkout the state of the repo as of the last release (including RCs)
           export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -E "([0-9]+)\.([0-9]+)\.([0-9]+)$" | sort --version-sort | tail -1 | sed 's/refs\/tags\///')
-          git fetch --tags
-          git checkout tags/$LATEST_TAG
-          git log -1 | cat
 
           if [[ "$OPENEYE" == true ]]; then
             python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
@@ -86,9 +71,6 @@ jobs:
 
       - name: Check that correct OFFTK version was installed
         run: |
-          # Go up one directory to ensure that we don't just load the OFFTK from the checked-out repo
-          cd ../
-
           export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -E "([0-9]+)\.([0-9]+)\.([0-9]+)$" | sort --version-sort | tail -1 | sed 's/refs\/tags\///')
           export FOUND_VER=$(python -c "import openff.toolkit; print(openff.toolkit.__version__)")
 
@@ -102,20 +84,14 @@ jobs:
             exit 1
           fi
 
-          cd openff-toolkit
-
       - name: Test the package
         run: |
-          python -m pip install utilities/test_plugins
-
-          pwd
-          ls
-
           if [[ "$OPENEYE" == true ]]; then
             python -c "import openff.toolkit; print(openff.toolkit.__file__)"
             python -c "import openeye; print(openeye.oechem.OEChemIsLicensed())"
           fi
 
-          PYTEST_ARGS=" -r fE --tb=short --runslow openff/toolkit/_tests/conftest.py"
-          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
-          pytest $PYTEST_ARGS openff
+          # PYTEST_ARGS+=" --runslow -x"
+          # PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
+
+          python -m pytest --pyargs "openff.toolkit" $PYTEST_ARGS $COV --trace-config

.github/workflows/examples.yml

@@ -1,14 +1,6 @@
 name: Examples
 
 on:
-  push:
-    branches:
-      - "main"
-      - "maintenance/.+"
-  pull_request:
-    branches:
-      - "main"
-      - "maintenance/.+"
   schedule:
     - cron: "0 0 * * *"
 
@@ -66,24 +58,13 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-        run: |
-          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+        run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
       - name: Install package
-        run: |
-          # Maybe remove the packaged openff-toolkit, installed as a dependency of openmmforcefields
-          # and/or Interchange
-          micromamba remove --force openff-toolkit-base
-          python -m pip install .
+        run: python -m pip install .
 
       - name: Remove undesired toolkits
         run: |
@@ -92,7 +73,7 @@ jobs:
           # so don't remove it.
           if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
             for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do
-              if [[ $(conda list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
+              if [[ $(micromamba list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
             done
           fi
 
@@ -119,10 +100,11 @@ jobs:
               python -c "from openff.toolkit.utils.toolkits import ${TK}_AVAILABLE; assert not ${TK}_AVAILABLE, '${TK} available'"
             done
           fi
+
       - name: Environment Information
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Run example scripts
         run: |

openff/toolkit/_tests/test_forcefield.py

@@ -6,6 +6,7 @@
 import copy
 import itertools
 import os
+import re
 from tempfile import NamedTemporaryFile
 
 import numpy as np
@@ -899,31 +900,33 @@ def test_create_forcefield_from_file(self, force_field):
         assert force_field.aromaticity_model == "OEAroModel_MDL"
 
     def test_load_bad_string(self):
-        with pytest.raises(IOError) as exception_info:
+        # This exception is a multi-line string, and `.*` by default doesn't
+        # consider newlines, so need to copmile with re.DOTALL flag
+        with pytest.raises(
+            IOError,
+            match=re.compile(
+                "Source '1234' could not be read.*"
+                "openforcefield.*"
+                "SMIRNOFFParseError.*"
+                "syntax error",
+                flags=re.DOTALL,
+            ),
+        ):
             ForceField("1234")
 
-        # This may need to be updated if the `openforcefields` package changes name;
-        # searching through `site-packages/` and other paths is probably unrelaiable
-        for match in [
-            "Source '1234' could not be read",
-            "SMIRNOFFParseError",
-            "syntax error",
-            "openforcefields",
-        ]:
-            assert match in str(exception_info.value)
-
     def test_load_bad_bytes(self):
-        with pytest.raises(IOError) as exception_info:
+        with pytest.raises(
+            IOError,
+            match=re.compile(
+                "Source 'b'the holy grail.*"
+                "could not be read.*"
+                "SMIRNOFFParseError.*"
+                "syntax error.*",
+                flags=re.DOTALL,
+            ),
+        ) as exception_info:
             ForceField(b"the holy grail of computational chemistry")
 
-        for match in [
-            "Source 'b'the holy grail",
-            "could not be read",
-            "SMIRNOFFParseError",
-            "syntax error",
-        ]:
-            assert match in str(exception_info.value)
-
         # See note in test_load_bad_string
         assert "openforcefields" not in str(exception_info.value)
 
@@ -933,13 +936,12 @@ def test_load_filelike_object(self):
 
     def test_load_bad_filelike_object(self):
         with open(get_data_file_path("test_forcefields/mangled.offxml")) as f:
-            with pytest.raises(IOError) as exception_info:
+            with pytest.raises(
+                IOError,
+                match="while trying to parse source as an object",
+            ):
                 ForceField(f)
 
-            assert "while trying to parse source as an object" in str(
-                exception_info.value
-            )
-
     def test_create_forcefield_from_xml_string(self):
         forcefield = ForceField(xml_simple_ff)
         assert len(forcefield._parameter_handlers["Bonds"]._parameters) == 3

openff/toolkit/typing/engines/smirnoff/forcefield.py

@@ -797,9 +797,12 @@ def parse_sources(self, sources, allow_cosmetic_attributes=True):
         # TODO: If a non-first source fails here, the force field might be partially modified
         for source in sources:
             smirnoff_data = self.parse_smirnoff_from_source(source)
-            self._load_smirnoff_data(
-                smirnoff_data, allow_cosmetic_attributes=allow_cosmetic_attributes
-            )
+            try:
+                self._load_smirnoff_data(
+                    smirnoff_data, allow_cosmetic_attributes=allow_cosmetic_attributes
+                )
+            except Exception as error:
+                raise TypeError(f"{smirnoff_data=}\n{source=}\n{sources=}\n") from error
 
     def _to_smirnoff_data(self, discard_cosmetic_attributes=False) -> dict:
         """