Switch version handling to versioningit (#1968)

* Switch version handling to `versioningit` * Do not use shallow fetch * Fix * Fix * Add `pip list` * Debug docs builds * Cleanup/simplify diff
openforcefield · Dec 10, 2024 · ec5ce32 · ec5ce32
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diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -48,7 +48,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 2
+          fetch-depth: 0
 
       - name: Set environment variables
         run: |
@@ -133,6 +133,7 @@ jobs:
         run: |
           micromamba info
           micromamba list
+          pip list
 
       - name: Check links
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}

diff --git a/.github/workflows/beta_rc.yaml b/.github/workflows/beta_rc.yaml
@@ -29,7 +29,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 2
+          fetch-depth: 0
 
       - name: Install environment with ${{ env.JOBNAME }}
         uses: mamba-org/setup-micromamba@v1

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -43,7 +43,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 2
+          fetch-depth: 0
 
       - name: Set environment variables
         run: |

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,17 +1,21 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
-sphinx:
-  configuration: docs/conf.py
-  fail_on_warning: true
+
 build:
   os: ubuntu-20.04
   tools:
     python: "mambaforge-4.10"
+
 python:
   install:
-  - method: setuptools
-    path: .
+    - method: pip
+      path: .
+
 conda:
   environment: docs/environment.yml
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
 formats:
 - pdf
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,6 +1,5 @@
 include LICENSE
 include MANIFEST.in
-include versioneer.py
 
 graft openff
-global-exclude *.py[cod] __pycache__ *.so
+global-exclude *.py[cod] __pycache__ *.so
diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
@@ -5,7 +5,7 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic
+  - versioningit
   - packaging
   - numpy
   - networkx

diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
@@ -5,7 +5,7 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic
+  - versioningit
   - packaging
   - numpy
   - networkx
@@ -34,6 +34,7 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - pydantic
   - qcelemental
   - qcportal >=0.50
   - qcengine

diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
@@ -4,7 +4,7 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic
+  - versioningit
   - packaging
   - numpy
   - networkx

diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
@@ -4,7 +4,7 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic
+  - versioningit
   - packaging
   - numpy
   - networkx
@@ -35,6 +35,7 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - pydantic
   - qcelemental
   - qcportal >=0.50
   - qcengine

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -5,6 +5,7 @@ channels:
 dependencies:
     # Base depends
   - python
+  - versioningit
   - packaging
   - numpy
   - networkx
@@ -40,6 +41,7 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - pydantic
   - qcelemental
   - qcportal >=0.50
   - qcengine
@@ -50,7 +52,6 @@ dependencies:
   - nomkl
   - mypy
   - typing_extensions
-  - pydantic
   - pip:
     - types-setuptools
     - types-toml

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -13,7 +13,7 @@ dependencies:
     - sphinx-notfound-page
     - sphinx=6
     # conda build dependencies
-    - python
+    - python <3.13
     - setuptools
     - numpy
     - openmm

diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -14,18 +14,22 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ### Behavior changes
 
 ### Bugfixes
-- [PR #1971](https://github.com/openforcefield/openff-toolkit/pull/1971): Fixes bug where OpenEyeToolkitWrapper would write coordinate-less PDB atoms if insertion_code or chain_id was an empty string ([Issue #1967](https://github.com/openforcefield/openff-toolkit/issues/1967))     
-
+- [PR #1971](https://github.com/openforcefield/openff-toolkit/pull/1971): Fixes bug where OpenEyeToolkitWrapper would write coordinate-less PDB atoms if insertion_code or chain_id was an empty string ([Issue #1967](https://github.com/openforcefield/openff-toolkit/issues/1967))
 
 ### New features
 
 ### Improved documentation and warnings
 
 ### Tests updated
 
-- [PR #1965](https://github.com/openforcefield/openff-toolkit/pull/1965): Fixes slight difference in GBSA energy reported in [Issue #1964](https://github.com/openforcefield/openff-toolkit/issues/1964) by forcing the use of the Reference platform in OpenMM for both calculations.   
-- [PR #1965](https://github.com/openforcefield/openff-toolkit/pull/1965): Disables testing of parmed-dependent notebook in `external` examples, since ParmEd 3 is no longer compatible with our upstreams and ParmEd 4 raises an error for our use cases.     
-- [PR #1965](https://github.com/openforcefield/openff-toolkit/pull/1965): Uses a different molecule in test_nagl's test_unsupported_molecule_bond to avoid having molecule handled successfully by nagl's new lookup table. 
+- [PR #1965](https://github.com/openforcefield/openff-toolkit/pull/1965): Fixes slight difference in GBSA energy reported in [Issue #1964](https://github.com/openforcefield/openff-toolkit/issues/1964) by forcing the use of the Reference platform in OpenMM for both calculations.
+- [PR #1965](https://github.com/openforcefield/openff-toolkit/pull/1965): Disables testing of parmed-dependent notebook in `external` examples, since ParmEd 3 is no longer compatible with our upstreams and ParmEd 4 raises an error for our use cases.
+- [PR #1965](https://github.com/openforcefield/openff-toolkit/pull/1965): Uses a different molecule in test_nagl's test_unsupported_molecule_bond to avoid having molecule handled successfully by nagl's new lookup table.
+
+### Miscellaneous
+
+- [PR #1970](https://github.com/openforcefield/openff-toolkit/pull/1970): Consolidates config files into `pyproject.toml`.
+- [PR #1968](https://github.com/openforcefield/openff-toolkit/pull/1968): Switches version handling to `versioningit`.
 
 ## 0.16.6
 
@@ -49,7 +53,6 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ### Tests updated
 - [PR #1942](https://github.com/openforcefield/openff-toolkit/pull/1942): Update tests for newer versions of RDKit, while stepping around recent RDKit conda-forge packages that fail when run natively on osx-arm64.
 
-
 ## 0.16.5
 
 ### Improved documentation and warnings

diff --git a/openff/toolkit/__init__.py b/openff/toolkit/__init__.py
@@ -4,10 +4,9 @@
 """
 
 import importlib
+from importlib.metadata import version
 from typing import TYPE_CHECKING
 
-from openff.toolkit._version import get_versions
-
 if TYPE_CHECKING:
     # These types are imported lazily at runtime, but we need to tell type
     # checkers what they are
@@ -27,7 +26,7 @@
         ToolkitRegistry,
     )
 
-__version__ = get_versions()["version"]
+__version__ = version("openff.toolkit")
 
 __all__ = [
     "GLOBAL_TOOLKIT_REGISTRY",