chore: migrate from black to ruff format

Author: elkins

.github/workflows/test.yml

@@ -83,8 +83,8 @@ jobs:
     - name: Lint with ruff
       run: ruff check .
 
-    - name: Check formatting (Black)
-      run: black --check .
+    - name: Check formatting (Ruff)
+      run: ruff format --check .
 
     - name: Static type check (Mypy)
       run: mypy . --explicit-package-bases

.pre-commit-config.yaml

@@ -14,11 +14,7 @@ repos:
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
-
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-      - id: black
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.15.0

examples/quickstart_ensemble.ipynb

@@ -23,7 +23,7 @@
     "import sys\n",
     "\n",
     "if \"google.colab\" in sys.modules:\n",
-    "    !pip install -q diff-ensemble matplotlib\n"
+    "    !pip install -q diff-ensemble matplotlib"
    ]
   },
   {
@@ -64,7 +64,7 @@
     "\n",
     "# Initialize model parameters\n",
     "params = model.init(init_rng, dummy_x, init_rng)\n",
-    "print(f\"Model initialized! Ready to generate ensembles of {ensemble_size} structures.\")\n"
+    "print(f\"Model initialized! Ready to generate ensembles of {ensemble_size} structures.\")"
    ]
   },
   {
@@ -91,7 +91,7 @@
     "coords = model.generate_coordinates(torsions)\n",
     "\n",
     "print(f\"Generated Coordinates Shape: {coords.shape}\")\n",
-    "print(\"(ensemble_size, seq_len * 3 atoms, 3 dimensions)\")\n"
+    "print(\"(ensemble_size, seq_len * 3 atoms, 3 dimensions)\")"
    ]
   },
   {
@@ -117,20 +117,20 @@
     "coords_np = np.array(coords)\n",
     "\n",
     "fig = plt.figure(figsize=(10, 8))\n",
-    "ax = fig.add_subplot(111, projection='3d')\n",
+    "ax = fig.add_subplot(111, projection=\"3d\")\n",
     "\n",
     "# Plot the backbone trace of the first 5 structures\n",
     "for i in range(5):\n",
     "    # Extract only the C-alpha atoms (every 3rd atom starting at index 1: N, CA, C)\n",
     "    ca_coords = coords_np[i, 1::3, :]\n",
-    "    ax.plot(ca_coords[:, 0], ca_coords[:, 1], ca_coords[:, 2], marker='o', label=f'Conf {i+1}')\n",
+    "    ax.plot(ca_coords[:, 0], ca_coords[:, 1], ca_coords[:, 2], marker=\"o\", label=f\"Conf {i + 1}\")\n",
     "\n",
     "ax.set_title(\"3D Overlay of Sampled IDP Conformations\")\n",
     "ax.set_xlabel(\"X (Å)\")\n",
     "ax.set_ylabel(\"Y (Å)\")\n",
     "ax.set_zlabel(\"Z (Å)\")\n",
     "ax.legend()\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   },
   {
@@ -154,23 +154,30 @@
     "    # Center of mass (assuming equal mass for simplicity)\n",
     "    com = np.mean(coords, axis=0)\n",
     "    # Mean squared distance from COM\n",
-    "    sq_dist = np.sum((coords - com)**2, axis=1)\n",
+    "    sq_dist = np.sum((coords - com) ** 2, axis=1)\n",
     "    return np.sqrt(np.mean(sq_dist))\n",
     "\n",
+    "\n",
     "# Calculate Rg for all 100 structures (using C-alpha atoms only)\n",
     "ca_ensemble = coords_np[:, 1::3, :]\n",
     "rg_values = [calculate_rg(ca_ensemble[i]) for i in range(ensemble_size)]\n",
     "\n",
     "# Plot the distribution\n",
     "plt.figure(figsize=(8, 5))\n",
-    "plt.hist(rg_values, bins=15, color='skyblue', edgecolor='black', alpha=0.7)\n",
-    "plt.axvline(np.mean(rg_values), color='red', linestyle='dashed', linewidth=2, label=f'Mean Rg: {np.mean(rg_values):.2f} Å')\n",
+    "plt.hist(rg_values, bins=15, color=\"skyblue\", edgecolor=\"black\", alpha=0.7)\n",
+    "plt.axvline(\n",
+    "    np.mean(rg_values),\n",
+    "    color=\"red\",\n",
+    "    linestyle=\"dashed\",\n",
+    "    linewidth=2,\n",
+    "    label=f\"Mean Rg: {np.mean(rg_values):.2f} Å\",\n",
+    ")\n",
     "plt.title(\"Distribution of Radius of Gyration ($R_g$) across the Ensemble\")\n",
     "plt.xlabel(\"Radius of Gyration (Å)\")\n",
     "plt.ylabel(\"Frequency\")\n",
     "plt.legend()\n",
-    "plt.grid(axis='y', alpha=0.3)\n",
-    "plt.show()\n"
+    "plt.grid(axis=\"y\", alpha=0.3)\n",
+    "plt.show()"
    ]
   },
   {
@@ -197,23 +204,23 @@
     "\n",
     "# Create a Ramachandran plot\n",
     "plt.figure(figsize=(7, 7))\n",
-    "plt.scatter(phi_angles, psi_angles, alpha=0.3, s=10, color='indigo')\n",
+    "plt.scatter(phi_angles, psi_angles, alpha=0.3, s=10, color=\"indigo\")\n",
     "\n",
     "# Draw typical Ramachandran region boundaries\n",
-    "plt.axhline(0, color='black', lw=1)\n",
-    "plt.axvline(0, color='black', lw=1)\n",
+    "plt.axhline(0, color=\"black\", lw=1)\n",
+    "plt.axvline(0, color=\"black\", lw=1)\n",
     "plt.xlim(-180, 180)\n",
     "plt.ylim(-180, 180)\n",
     "\n",
     "# Formatting\n",
-    "plt.xlabel(r'$\\phi$ (degrees)', fontsize=14)\n",
-    "plt.ylabel(r'$\\psi$ (degrees)', fontsize=14)\n",
-    "plt.title('Ramachandran Plot of Generated Ensemble', fontsize=16)\n",
-    "plt.grid(True, linestyle='--', alpha=0.5)\n",
+    "plt.xlabel(r\"$\\phi$ (degrees)\", fontsize=14)\n",
+    "plt.ylabel(r\"$\\psi$ (degrees)\", fontsize=14)\n",
+    "plt.title(\"Ramachandran Plot of Generated Ensemble\", fontsize=16)\n",
+    "plt.grid(True, linestyle=\"--\", alpha=0.5)\n",
     "plt.xticks(np.arange(-180, 181, 60))\n",
     "plt.yticks(np.arange(-180, 181, 60))\n",
     "\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   }
  ],

examples/quickstart_ensemble.nbconvert.ipynb

@@ -30,7 +30,7 @@
     "import sys\n",
     "\n",
     "if \"google.colab\" in sys.modules:\n",
-    "    !pip install -q diff-ensemble matplotlib\n"
+    "    !pip install -q diff-ensemble matplotlib"
    ]
   },
   {
@@ -86,7 +86,7 @@
     "\n",
     "# Initialize model parameters\n",
     "params = model.init(init_rng, dummy_x, init_rng)\n",
-    "print(f\"Model initialized! Ready to generate ensembles of {ensemble_size} structures.\")\n"
+    "print(f\"Model initialized! Ready to generate ensembles of {ensemble_size} structures.\")"
    ]
   },
   {
@@ -129,7 +129,7 @@
     "coords = model.generate_coordinates(torsions)\n",
     "\n",
     "print(f\"Generated Coordinates Shape: {coords.shape}\")\n",
-    "print(\"(ensemble_size, seq_len * 3 atoms, 3 dimensions)\")\n"
+    "print(\"(ensemble_size, seq_len * 3 atoms, 3 dimensions)\")"
    ]
   },
   {
@@ -173,20 +173,20 @@
     "coords_np = np.array(coords)\n",
     "\n",
     "fig = plt.figure(figsize=(10, 8))\n",
-    "ax = fig.add_subplot(111, projection='3d')\n",
+    "ax = fig.add_subplot(111, projection=\"3d\")\n",
     "\n",
     "# Plot the backbone trace of the first 5 structures\n",
     "for i in range(5):\n",
     "    # Extract only the C-alpha atoms (every 3rd atom starting at index 1: N, CA, C)\n",
     "    ca_coords = coords_np[i, 1::3, :]\n",
-    "    ax.plot(ca_coords[:, 0], ca_coords[:, 1], ca_coords[:, 2], marker='o', label=f'Conf {i+1}')\n",
+    "    ax.plot(ca_coords[:, 0], ca_coords[:, 1], ca_coords[:, 2], marker=\"o\", label=f\"Conf {i + 1}\")\n",
     "\n",
     "ax.set_title(\"3D Overlay of Sampled IDP Conformations\")\n",
     "ax.set_xlabel(\"X (Å)\")\n",
     "ax.set_ylabel(\"Y (Å)\")\n",
     "ax.set_zlabel(\"Z (Å)\")\n",
     "ax.legend()\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   },
   {
@@ -228,23 +228,30 @@
     "    # Center of mass (assuming equal mass for simplicity)\n",
     "    com = np.mean(coords, axis=0)\n",
     "    # Mean squared distance from COM\n",
-    "    sq_dist = np.sum((coords - com)**2, axis=1)\n",
+    "    sq_dist = np.sum((coords - com) ** 2, axis=1)\n",
     "    return np.sqrt(np.mean(sq_dist))\n",
     "\n",
+    "\n",
     "# Calculate Rg for all 100 structures (using C-alpha atoms only)\n",
     "ca_ensemble = coords_np[:, 1::3, :]\n",
     "rg_values = [calculate_rg(ca_ensemble[i]) for i in range(ensemble_size)]\n",
     "\n",
     "# Plot the distribution\n",
     "plt.figure(figsize=(8, 5))\n",
-    "plt.hist(rg_values, bins=15, color='skyblue', edgecolor='black', alpha=0.7)\n",
-    "plt.axvline(np.mean(rg_values), color='red', linestyle='dashed', linewidth=2, label=f'Mean Rg: {np.mean(rg_values):.2f} Å')\n",
+    "plt.hist(rg_values, bins=15, color=\"skyblue\", edgecolor=\"black\", alpha=0.7)\n",
+    "plt.axvline(\n",
+    "    np.mean(rg_values),\n",
+    "    color=\"red\",\n",
+    "    linestyle=\"dashed\",\n",
+    "    linewidth=2,\n",
+    "    label=f\"Mean Rg: {np.mean(rg_values):.2f} Å\",\n",
+    ")\n",
     "plt.title(\"Distribution of Radius of Gyration ($R_g$) across the Ensemble\")\n",
     "plt.xlabel(\"Radius of Gyration (Å)\")\n",
     "plt.ylabel(\"Frequency\")\n",
     "plt.legend()\n",
-    "plt.grid(axis='y', alpha=0.3)\n",
-    "plt.show()\n"
+    "plt.grid(axis=\"y\", alpha=0.3)\n",
+    "plt.show()"
    ]
   },
   {
@@ -303,23 +310,23 @@
     "\n",
     "# Create a Ramachandran plot\n",
     "plt.figure(figsize=(7, 7))\n",
-    "plt.scatter(phi_angles, psi_angles, alpha=0.3, s=10, color='indigo')\n",
+    "plt.scatter(phi_angles, psi_angles, alpha=0.3, s=10, color=\"indigo\")\n",
     "\n",
     "# Draw typical Ramachandran region boundaries\n",
-    "plt.axhline(0, color='black', lw=1)\n",
-    "plt.axvline(0, color='black', lw=1)\n",
+    "plt.axhline(0, color=\"black\", lw=1)\n",
+    "plt.axvline(0, color=\"black\", lw=1)\n",
     "plt.xlim(-180, 180)\n",
     "plt.ylim(-180, 180)\n",
     "\n",
     "# Formatting\n",
-    "plt.xlabel(r'$\\phi$ (degrees)', fontsize=14)\n",
-    "plt.ylabel(r'$\\psi$ (degrees)', fontsize=14)\n",
-    "plt.title('Ramachandran Plot of Generated Ensemble', fontsize=16)\n",
-    "plt.grid(True, linestyle='--', alpha=0.5)\n",
+    "plt.xlabel(r\"$\\phi$ (degrees)\", fontsize=14)\n",
+    "plt.ylabel(r\"$\\psi$ (degrees)\", fontsize=14)\n",
+    "plt.title(\"Ramachandran Plot of Generated Ensemble\", fontsize=16)\n",
+    "plt.grid(True, linestyle=\"--\", alpha=0.5)\n",
     "plt.xticks(np.arange(-180, 181, 60))\n",
     "plt.yticks(np.arange(-180, 181, 60))\n",
     "\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   }
  ],

pyproject.toml

@@ -32,9 +32,6 @@ ignore_missing_imports = true
 line-length = 100
 target-version = "py310"
 
-[tool.black]
-line-length = 100
-target-version = ['py310']
 
 [tool.ruff.format]
 quote-style = "double"
@@ -113,7 +110,7 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "pytest",
-    "black",
+    "pytest-cov",
     "ruff",
     "mypy",
     "pre-commit",

tests/test_io.py

@@ -58,9 +58,9 @@ def test_save_ensemble_to_pdb_default_res_names(tmp_path):
     stack = pdb_file.get_structure()
 
     # Every residue name should be the ALA default
-    assert all(
-        name == "ALA" for name in stack.res_name
-    ), f"Expected all 'ALA', got: {set(stack.res_name)}"
+    assert all(name == "ALA" for name in stack.res_name), (
+        f"Expected all 'ALA', got: {set(stack.res_name)}"
+    )
 
 
 def test_save_ensemble_to_pdb_mismatched_res_names(tmp_path):