Ghostly: Initial commit.

Author: lohedges

.github/workflows/main.yaml

@@ -0,0 +1,67 @@
+name: Build and test
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - "**"
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+  pre_job:
+    runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@v5
+        with:
+          concurrent_skipping: 'same_content_newer'
+  build:
+    needs: pre_job
+    if: needs.pre_job.outputs.should_skip != 'true'
+    name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
+    runs-on: ${{ matrix.platform.os }}
+    strategy:
+      max-parallel: 9
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]
+        platform:
+          #- { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
+          - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+    defaults:
+      run:
+        shell: ${{ matrix.platform.shell }}
+    steps:
+#
+      - name: Checkout the repository (commit)
+        uses: actions/checkout@v4
+        if: github.event_name != 'pull_request'
+#
+      - name: Checkout the repository (PR)
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+        if: github.event_name == 'pull_request'
+#
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: somd2
+          environment-file: environment.yaml
+          miniforge-version: latest
+          run-post: ${{ matrix.platform.name != 'windows' }}
+#
+      - name: Install pytest
+        run: conda install pytest
+#
+      - name: Install the package
+        run: pip install .
+#
+      - name: Run the tests
+        run: python -m pytest -svvv --color=yes tests

.gitignore

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+# Byte-compiled / optimized / DLL files.
+__pycache__/
+*.py[cod]
+
+# C extensions.
+*.so
+
+# Pytest directories.
+.pytest_cache/
+
+# macOS folder attributes.
+.DS_Store
+
+# Jupyter notebook checkpoints.
+.ipynb_checkpoints/
+
+# Build artifacts.
+setup.out
+setup.err
+dist/
+build/
+ghostly.egg-info
+src/ghostly/_version.py
+
+# Test output.
+output.yaml
+
+# Trajectory artifacts.
+*_offsets.npz
+*.lock
+
+# Scratch space.
+.idea/
+
+# VSCode config
+.vscode/
+
+# Conda recipe (it is auto-generated)
+recipes/ghostly/meta.yaml
+
+# Sire cache files.
+cache/