Add codspeed benchmarks

.github/workflows/test_and_deploy.yml

@@ -38,7 +38,7 @@ jobs:
       - name: Install wheel
         run: pip install .//dist//*.whl
       - name: Test wheel
-        run: pytest --assert=plain
+        run: pytest --assert=plain tests
       - uses: actions/upload-artifact@v3
         with:
           path: .//dist//*.whl
@@ -62,17 +62,30 @@ jobs:
       - name: Install source distribution
         run: pip install .//dist//*.tar.gz
       - name: Test source distribution
-        run: pytest --assert=plain
+        run: pytest --assert=plain tests
       - uses: actions/upload-artifact@v3
         with:
           path: dist//*.tar.gz
 
+  benchmarks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: pip install .[test]
+      - name: Run benchmarks
+        uses: CodSpeedHQ/action@v3
+        with:
+          run: pytest --codspeed benchmarks
 
   upload:
     name: Upload to GitHub Releases & PyPI
     permissions:
       contents: write
-    needs: [wheels, sdist]
+    needs: [wheels, sdist, benchmarks]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/download-artifact@v3

benchmarks/conftest.py

@@ -0,0 +1,13 @@
+from pathlib import Path
+import pytest
+import fastpdb
+
+
+@pytest.fixture
+def pdb_file_path():
+    return Path(__file__).parents[1] / "tests" / "data" / "1aki.pdb"
+
+
+@pytest.fixture
+def pdb_file(pdb_file_path):
+    return fastpdb.PDBFile.read(pdb_file_path)

benchmarks/test_get.py

@@ -0,0 +1,27 @@
+import pytest
+import fastpdb
+
+
+@pytest.mark.benchmark
+def test_read(pdb_file_path):
+    fastpdb.PDBFile.read(pdb_file_path)
+
+
+@pytest.mark.benchmark
+def test_get_coord(pdb_file):
+    pdb_file.get_coord(model=1)
+
+
+@pytest.mark.benchmark
+def test_get_structure(pdb_file):
+    pdb_file.get_structure(model=1)
+
+
+@pytest.mark.benchmark
+def test_get_structure_with_bonds(pdb_file):
+    pdb_file.get_structure(model=1, include_bonds=True)
+
+
+@pytest.mark.benchmark
+def test_get_remark(pdb_file):
+    pdb_file.get_remark(350)

benchmarks/test_set.py

@@ -0,0 +1,23 @@
+import pytest
+import fastpdb
+
+
+@pytest.fixture
+def atoms(pdb_file):
+    return pdb_file.get_structure(model=1, include_bonds=True)
+
+
+@pytest.fixture
+def empty_pdb_file():
+    return fastpdb.PDBFile()
+
+
+@pytest.mark.benchmark
+def test_set_structure(atoms, empty_pdb_file):
+    atoms.bonds = None
+    empty_pdb_file.set_structure(atoms)
+
+
+@pytest.mark.benchmark
+def test_set_structure_with_bonds(atoms, empty_pdb_file):
+    empty_pdb_file.set_structure(atoms)

pyproject.toml

@@ -25,7 +25,14 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [
-  "biotite >= 0.39"
+  "biotite >= 0.39",
+]
+
+[project.optional-dependencies]
+# development dependency groups
+test = [
+    "pytest",
+    "pytest-codspeed",
 ]
 
 [project.urls]