Add new InterIntraMD Calculator to IPSuite

.github/workflows/build.yaml

@@ -7,51 +7,51 @@
 # To get a newer version, you will need to update the SHA.
 # You can also reference a tag or branch, but the action may change without warning.
 
-name: Publish Docker image
-
-on:
-  workflow_dispatch:
-  release:
-    types: [published]
-
-jobs:
-  push_to_registry:
-    name: Push Docker image to Docker Hub
-    runs-on: self-hosted
-    permissions:
-      packages: write
-      contents: read
-      attestations: write
-      id-token: write
-    steps:
-      - name: Check out the repo
-        uses: actions/checkout@v4
-
-      - name: Log in to Docker Hub
-        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
-        with:
-          images: pythonf/ipsuite
-
-      - name: Build and push Docker image
-        id: push
-        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
-        with:
-          context: .
-          file: ./Dockerfile
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-
-      - name: Generate artifact attestation
-        uses: actions/attest-build-provenance@v1
-        with:
-          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
-          subject-digest: ${{ steps.push.outputs.digest }}
-          push-to-registry: true
+# name: Publish Docker image
+
+# on:
+#   workflow_dispatch:
+#   release:
+#     types: [published]
+
+# jobs:
+#   push_to_registry:
+#     name: Push Docker image to Docker Hub
+#     runs-on: self-hosted
+#     permissions:
+#       packages: write
+#       contents: read
+#       attestations: write
+#       id-token: write
+#     steps:
+#       - name: Check out the repo
+#         uses: actions/checkout@v4
+
+#       - name: Log in to Docker Hub
+#         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+#         with:
+#           username: ${{ secrets.DOCKER_USERNAME }}
+#           password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
+
+#       - name: Extract metadata (tags, labels) for Docker
+#         id: meta
+#         uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+#         with:
+#           images: pythonf/ipsuite
+
+#       - name: Build and push Docker image
+#         id: push
+#         uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+#         with:
+#           context: .
+#           file: ./Dockerfile
+#           push: true
+#           tags: ${{ steps.meta.outputs.tags }}
+#           labels: ${{ steps.meta.outputs.labels }}
+
+#       - name: Generate artifact attestation
+#         uses: actions/attest-build-provenance@v1
+#         with:
+#           subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+#           subject-digest: ${{ steps.push.outputs.digest }}
+#           push-to-registry: true

.github/workflows/publish.yaml

@@ -1,31 +1,19 @@
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-# GitHub recommends pinning actions to a commit SHA.
-# To get a newer version, you will need to update the SHA.
-# You can also reference a tag or branch, but the action may change without warning.
-
-name: Publish PyPi package
-
+name: Release
 on:
   release:
-    types: [published]
+    types:
+      - created
 
 jobs:
-  publish-pypi:
+  publish:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
       - name: Publish
         env:
           PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
         run: |
-          poetry config pypi-token.pypi $PYPI_TOKEN
-          poetry publish --build
+          uv build
+          uv publish --token $PYPI_TOKEN

.github/workflows/tests.yaml

@@ -18,31 +18,36 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.10"
+          - "3.11"
         os:
           - ubuntu-latest
 
     steps:
       - uses: actions/checkout@v2
-      - name: Install Poetry
-        run: |
-          pipx install poetry
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'poetry'
+      - name: Install the project
+        run: uv sync --all-extras --dev --group=gap
       - name: Setup git user
         run: |
           git config --global user.name "John Doe"
           git config --global user.email johndoe@example.com
           git config --global init.defaultBranch "main"
-      - name: Install package
-        run: |
-          poetry install --all-extras
       - name: Pytest
         run: |
-          poetry run pytest . -vv
+          uv run python --version
+          uv run pytest -vv --cov --junitxml=junit.xml -o junit_family=legacy
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   # examples:
   #   runs-on: ${{ matrix.os }}

.pre-commit-config.yaml

@@ -2,44 +2,31 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
       - id: check-docstring-first
       - id: check-executables-have-shebangs
-      - id: check-json
+      # - id: check-json
       - id: check-merge-conflict
-        args: ['--assume-in-merge']
+        args: ["--assume-in-merge"]
       - id: check-toml
       - id: check-yaml
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
-        args: ['--fix=lf']
+        args: ["--fix=lf"]
       - id: sort-simple-yaml
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies: ["tomli"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.9
+    rev: v0.11.9
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
-  - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
-    hooks:
-    - id: mdformat
-      args: ["--wrap=80"]

.python-version

@@ -0,0 +1 @@
+3.11

.readthedocs.yaml

@@ -4,22 +4,19 @@
 
 version: 2
 
+submodules:
+  include: all
+
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
   jobs:
-    post_create_environment:
-      # Install poetry
-      # https://python-poetry.org/docs/#installing-manually
-      - pip install poetry
     post_install:
-      # Install dependencies with 'docs' dependency group
-      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
-      # VIRTUAL_ENV needs to be set manually for now.
-      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+      # see https://github.com/astral-sh/uv/issues/10074
+      - pip install uv
+      - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --all-extras --link-mode=copy --group=docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG.md

@@ -21,3 +21,5 @@
 - add `density` to `RescaleBoxModifier`
 - add `fraction_traceless` parameter to `NPTThermostat`
 - add `TorchD3NL` calculator
+- add `HookeanConstraint` calculator
+- add `FixedBondLengthConstraint` calculator

docs/source/_get_started/quickstart.rst

@@ -61,7 +61,7 @@ The goal is to place water molecules inside a box at a specified density.
         mol = ips.Smiles2Atoms(smiles="O")
         # Duplicate water molecules
         packmol = ips.Packmol(
-            data=[mol.atoms], count=[10], density=876
+            data=[mol.frames], count=[10], density=876
             )
 
     project.build()