[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
ComPWA · Sep 27, 2023 · ac34984 · ac34984
1 parent 7ccaffe
commit ac34984
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -53,9 +53,6 @@ repos:
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.7.0
     hooks:
-      - id: nbqa-black
-        additional_dependencies:
-          - black>=22.1.0
       - id: nbqa-pyupgrade
         args:
           - --py37-plus
@@ -67,6 +64,11 @@ repos:
     rev: 23.9.1
     hooks:
       - id: black
+      - id: black-jupyter
+        args:
+          - --line-length=85
+        types_or:
+          - jupyter
 
   - repo: https://github.com/asottile/blacken-docs
     rev: 1.16.0
@@ -122,6 +124,7 @@ repos:
             cell.attachments
             cell.metadata.code_folding
             cell.metadata.id
+            cell.metadata.pycharm
             cell.metadata.user_expressions
             metadata.celltoolbar
             metadata.colab.name

diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -25,6 +25,7 @@
   ],
   "unwantedRecommendations": [
     "bungcip.better-toml",
+    "davidanson.vscode-markdownlint",
     "ms-python.flake8",
     "ms-python.isort",
     "ms-python.mypy-type-checker",

diff --git a/docs/adr/001/sympy.ipynb b/docs/adr/001/sympy.ipynb
@@ -510,9 +510,7 @@
     "\n",
     "import sympy as sp\n",
     "\n",
-    "x, A1, mu1, sigma1, A2, mu2, sigma2 = sp.symbols(\n",
-    "    \"x, A1, mu1, sigma1, A2, mu2, sigma2\"\n",
-    ")\n",
+    "x, A1, mu1, sigma1, A2, mu2, sigma2 = sp.symbols(\"x, A1, mu1, sigma1, A2, mu2, sigma2\")\n",
     "gaussian1 = (\n",
     "    A1 / (sigma1 * sp.sqrt(2.0 * math.pi)) * sp.exp(-((x - mu1) ** 2) / (2 * sigma1))\n",
     ")\n",
@@ -595,9 +593,7 @@
     }
    ],
    "source": [
-    "numpy_gauss_sum = sp.lambdify(\n",
-    "    (x, A1, mu1, sigma1, A2, mu2, sigma2), gauss_sum, \"numpy\"\n",
-    ")\n",
+    "numpy_gauss_sum = sp.lambdify((x, A1, mu1, sigma1, A2, mu2, sigma2), gauss_sum, \"numpy\")\n",
     "print(inspect.getsource(numpy_gauss_sum))"
    ]
   },
@@ -687,9 +683,7 @@
     "\n",
     "\n",
     "def native_jax_gauss_sum(x_, A1_, mu1_, sigma1_, A2_, mu2_, sigma2_):\n",
-    "    return jax_gaussian(x_, A1_, mu1_, sigma1_) + jax_gaussian(\n",
-    "        x_, A2_, mu2_, sigma2_\n",
-    "    )"
+    "    return jax_gaussian(x_, A1_, mu1_, sigma1_) + jax_gaussian(x_, A2_, mu2_, sigma2_)"
    ]
   },
   {

diff --git a/docs/adr/002/composition.ipynb b/docs/adr/002/composition.ipynb
@@ -133,9 +133,7 @@
     "    ff02 = blatt_weisskopf(q0_squared, meson_radius, angular_momentum)\n",
     "    width = gamma0 * (mass0 / mass) * (ff2 / ff02)\n",
     "    width = width * sp.sqrt(q_squared / q0_squared)\n",
-    "    return (\n",
-    "        relativistic_breit_wigner(mass, mass0, width) * mass0 * gamma0 * sp.sqrt(ff2)\n",
-    "    )"
+    "    return relativistic_breit_wigner(mass, mass0, width) * mass0 * gamma0 * sp.sqrt(ff2)"
    ]
   },
   {
@@ -364,9 +362,7 @@
    "outputs": [],
    "source": [
     "class DynamicsBuilder(Protocol):\n",
-    "    def __call__(\n",
-    "        self, graph: StateTransitionGraph, edge_id: int\n",
-    "    ) -> DynamicsExpression:\n",
+    "    def __call__(self, graph: StateTransitionGraph, edge_id: int) -> DynamicsExpression:\n",
     "        ..."
    ]
   },

diff --git a/docs/adr/002/function.ipynb b/docs/adr/002/function.ipynb
@@ -153,10 +153,7 @@
     "        width = width * sp.sqrt(q_squared / q0_squared)\n",
     "        # Expression\n",
     "        return (\n",
-    "            RelativisticBreitWigner(mass, mass0, width)\n",
-    "            * mass0\n",
-    "            * gamma0\n",
-    "            * sp.sqrt(ff2)\n",
+    "            RelativisticBreitWigner(mass, mass0, width) * mass0 * gamma0 * sp.sqrt(ff2)\n",
     "        )\n",
     "\n",
     "    @classmethod\n",

diff --git a/docs/report/001.ipynb b/docs/report/001.ipynb
@@ -474,8 +474,7 @@
     "        arg = expr.args[0]\n",
     "        x = self._print(arg)\n",
     "        return (\n",
-    "            f\"select([less({x}, 0), True], [1j * sqrt(-{x}), sqrt({x})],\"\n",
-    "            \" default=nan,)\"\n",
+    "            f\"select([less({x}, 0), True], [1j * sqrt(-{x}), sqrt({x})], default=nan,)\"\n",
     "        )"
    ]
   },

diff --git a/docs/report/002.ipynb b/docs/report/002.ipynb
@@ -836,9 +836,7 @@
     "intensity = LambdifiedFunction(sympy_model, backend=\"jax\")\n",
     "data_converter = HelicityTransformer(model.adapter)\n",
     "rng = TFUniformRealNumberGenerator(seed=0)\n",
-    "phsp_sample = generate_phsp(\n",
-    "    10_000, model.adapter.reaction_info, random_generator=rng\n",
-    ")\n",
+    "phsp_sample = generate_phsp(10_000, model.adapter.reaction_info, random_generator=rng)\n",
     "phsp_set = data_converter.transform(phsp_sample)"
    ]
   },

diff --git a/docs/report/003.ipynb b/docs/report/003.ipynb
@@ -448,8 +448,7 @@
     "\n",
     "iplt.plot(\n",
     "    plot_domain,\n",
-    "    lambda *args, **kwargs: y_factor\n",
-    "    * np_chew_mandelstam_s_wave(*args, **kwargs).real,\n",
+    "    lambda *args, **kwargs: y_factor * np_chew_mandelstam_s_wave(*args, **kwargs).real,\n",
     "    controls=controls,\n",
     "    ylim=ylim,\n",
     "    alpha=0.7,\n",
@@ -458,8 +457,7 @@
     ")\n",
     "iplt.plot(\n",
     "    plot_domain,\n",
-    "    lambda *args, **kwargs: y_factor\n",
-    "    * np_chew_mandelstam_s_wave(*args, **kwargs).imag,\n",
+    "    lambda *args, **kwargs: y_factor * np_chew_mandelstam_s_wave(*args, **kwargs).imag,\n",
     "    controls=controls,\n",
     "    ylim=ylim,\n",
     "    alpha=0.7,\n",
@@ -739,8 +737,7 @@
    "outputs": [],
    "source": [
     "sigma = {\n",
-    "    l_val: (s_domain - s_thr_val) / np.pi * integral_values[l_val]\n",
-    "    for l_val in l_values\n",
+    "    l_val: (s_domain - s_thr_val) / np.pi * integral_values[l_val] for l_val in l_values\n",
     "}\n",
     "sigma_scaled = {l_val: 16 * np.pi * sigma[l_val] for l_val in l_values}"
    ]
@@ -1064,9 +1061,7 @@
     "s_values = np.linspace(-0.15, 1.4, num=200)\n",
     "fig, axes = plt.subplots(nrows=2, figsize=(6, 7), sharex=True)\n",
     "ax1, ax2 = axes\n",
-    "fig.suptitle(\n",
-    "    f\"Symbolic dispersion integrals for $m_1={m1_val:.2f}, m_2={m2_val:.2f}$\"\n",
-    ")\n",
+    "fig.suptitle(f\"Symbolic dispersion integrals for $m_1={m1_val:.2f}, m_2={m2_val:.2f}$\")\n",
     "for ax in axes:\n",
     "    ax.axhline(0, linewidth=0.5, c=\"black\")\n",
     "    ax.axvline(s_thr_val, **threshold_style)\n",

diff --git a/docs/report/005.ipynb b/docs/report/005.ipynb
@@ -453,9 +453,7 @@
    ],
    "source": [
     "K_symbol = sp.IndexedBase(\"K\", shape=(n_channels, n_channels))\n",
-    "K = sp.Matrix(\n",
-    "    [[K_symbol[i, j] for j in range(n_channels)] for i in range(n_channels)]\n",
-    ")\n",
+    "K = sp.Matrix([[K_symbol[i, j] for j in range(n_channels)] for i in range(n_channels)])\n",
     "display(K_symbol[i, j], K)"
    ]
   },

diff --git a/docs/report/008.ipynb b/docs/report/008.ipynb
@@ -244,11 +244,7 @@
    "source": [
     "def replace_indexed_symbols(expression: sp.Expr) -> sp.Expr:\n",
     "    return expression.subs(\n",
-    "        {\n",
-    "            s: to_symbol(s)\n",
-    "            for s in expression.free_symbols\n",
-    "            if isinstance(s, sp.Indexed)\n",
-    "        }\n",
+    "        {s: to_symbol(s) for s in expression.free_symbols if isinstance(s, sp.Indexed)}\n",
     "    )"
    ]
   },

diff --git a/docs/report/009.ipynb b/docs/report/009.ipynb
@@ -921,9 +921,7 @@
     "                    c=color,\n",
     "                    rotation=+90,\n",
     "                )\n",
-    "                threshold_indicators.append(\n",
-    "                    (line_thr, line_diff, text_thr, text_diff)\n",
-    "                )\n",
+    "                threshold_indicators.append((line_thr, line_diff, text_thr, text_diff))\n",
     "        for i, (_, line_diff, _, text_diff) in enumerate(threshold_indicators):\n",
     "            m_a = kwargs[f\"m_a{i}\"]\n",
     "            m_b = kwargs[f\"m_b{i}\"]\n",

diff --git a/docs/report/010.ipynb b/docs/report/010.ipynb
@@ -478,9 +478,9 @@
     "    m = sp.Symbol(\"m\", real=True)\n",
     "    epsilon = sp.Symbol(\"epsilon\", real=True)\n",
     "    i = sp.Symbol(\"i\", integer=True, negative=False)\n",
-    "    expr = f_vector(\n",
-    "        n_resonances, n_channels, angular_momentum=angular_momentum\n",
-    "    ).doit()[i, 0]\n",
+    "    expr = f_vector(n_resonances, n_channels, angular_momentum=angular_momentum).doit()[\n",
+    "        i, 0\n",
+    "    ]\n",
     "    expr = symplot.substitute_indexed_symbols(expr)\n",
     "    expr = expr.subs(m, m + epsilon * sp.I)\n",
     "    np_expr, sliders = symplot.prepare_sliders(expr, m)\n",

diff --git a/docs/report/013.ipynb b/docs/report/013.ipynb
@@ -487,9 +487,7 @@
     "    intensity_func = create_function(substituted_expression, backend=\"jax\")\n",
     "    intensities_all = np.array(intensity_func(phsp).real)\n",
     "    intensities_k = compute_sub_intensities(model, \"K^*\", phsp, full_expression)\n",
-    "    intensities_delta = compute_sub_intensities(\n",
-    "        model, \"Delta^*\", phsp, full_expression\n",
-    "    )\n",
+    "    intensities_delta = compute_sub_intensities(model, \"Delta^*\", phsp, full_expression)\n",
     "    intensities_lambda = compute_sub_intensities(\n",
     "        model, \"Lambda^*\", phsp, full_expression\n",
     "    )\n",

diff --git a/docs/report/014.ipynb b/docs/report/014.ipynb
@@ -853,9 +853,7 @@
     "display(\n",
     "    *[\n",
     "        graphviz.Source(\n",
-    "            qrules.io.asdot(\n",
-    "                g, collapse_graphs=True, size=4, render_resonance_id=True\n",
-    "            )\n",
+    "            qrules.io.asdot(g, collapse_graphs=True, size=4, render_resonance_id=True)\n",
     "        )\n",
     "        for g in reaction_two_resonances.transition_groups\n",
     "    ]\n",

diff --git a/docs/report/015.ipynb b/docs/report/015.ipynb
@@ -561,9 +561,7 @@
     "        particle_name = state.particle.latex\n",
     "        s = sp.Rational(state.particle.spin)\n",
     "        m = sp.Rational(state.spin_projection)\n",
-    "        display(\n",
-    "            Math(Rf\"|s_{i},m_{i}\\rangle=|{s},{m}\\rangle \\quad ({particle_name})\")\n",
-    "        )\n",
+    "        display(Math(Rf\"|s_{i},m_{i}\\rangle=|{s},{m}\\rangle \\quad ({particle_name})\"))\n",
     "        if functor is formulate_rotation_chain:\n",
     "            args = (transition, i)\n",
     "        else:\n",

diff --git a/docs/report/017.ipynb b/docs/report/017.ipynb
@@ -210,9 +210,7 @@
     "@implement_doit_method\n",
     "class Kibble(UnevaluatedExpression):\n",
     "    def __new__(cls, sigma1, sigma2, sigma3, m0, m1, m2, m3, **hints) -> Kibble:\n",
-    "        return create_expression(\n",
-    "            cls, sigma1, sigma2, sigma3, m0, m1, m2, m3, **hints\n",
-    "        )\n",
+    "        return create_expression(cls, sigma1, sigma2, sigma3, m0, m1, m2, m3, **hints)\n",
     "\n",
     "    def evaluate(self) -> sp.Expr:\n",
     "        sigma1, sigma2, sigma3, m0, m1, m2, m3 = self.args\n",

diff --git a/docs/report/018.ipynb b/docs/report/018.ipynb
@@ -217,9 +217,7 @@
     "    initial_state_mass=reaction.initial_state[-1].mass,\n",
     "    final_state_masses={i: p.mass for i, p in reaction.final_state.items()},\n",
     ")\n",
-    "transformer = SympyDataTransformer.from_sympy(\n",
-    "    model.kinematic_variables, backend=\"jax\"\n",
-    ")\n",
+    "transformer = SympyDataTransformer.from_sympy(model.kinematic_variables, backend=\"jax\")\n",
     "phsp = phsp_generator.generate(1_000_000, rng)\n",
     "phsp = transformer(phsp)"
    ]
@@ -354,9 +352,7 @@
     "\n",
     "    Z_weights = griddata(np.transpose([x, y]), weights, (X, Y))\n",
     "    Z_unweighted, x_edges, y_edges = jnp.histogram2d(x, y, bins=n_bins)\n",
-    "    Z_weighted, x_edges, y_edges = jnp.histogram2d(\n",
-    "        x, y, bins=n_bins, weights=weights\n",
-    "    )\n",
+    "    Z_weighted, x_edges, y_edges = jnp.histogram2d(x, y, bins=n_bins, weights=weights)\n",
     "    # https://numpy.org/doc/stable/reference/generated/numpy.histogram2d.html\n",
     "    Z_unweighted = Z_unweighted.T\n",
     "    Z_weighted = Z_weighted.T\n",

diff --git a/docs/report/020.ipynb b/docs/report/020.ipynb
@@ -812,9 +812,7 @@
    ],
    "source": [
     "minuit2 = Minuit2()\n",
-    "fit_result_with_caching = minuit2.optimize(\n",
-    "    estimator_with_caching, initial_parameters\n",
-    ")\n",
+    "fit_result_with_caching = minuit2.optimize(estimator_with_caching, initial_parameters)\n",
     "fit_result_with_caching"
    ]
   },

diff --git a/docs/report/021.ipynb b/docs/report/021.ipynb
@@ -445,8 +445,7 @@
     "    child1, child2 = decay_products[chain_id]\n",
     "    for resonance in resonance_list:\n",
     "        src += create_html_table_row(\n",
-    "            Rf\"\\({resonance.particle.latex} \\to\"\n",
-    "            Rf\" {child1.latex} {child2.latex}\\)\",\n",
+    "            Rf\"\\({resonance.particle.latex} \\to {child1.latex} {child2.latex}\\)\",\n",
     "            jp(resonance.particle),\n",
     "            int(1e3 * resonance.particle.mass),\n",
     "            int(1e3 * resonance.particle.width),\n",
@@ -512,9 +511,7 @@
     "    _ν = sp.Symbol(R\"\\nu^{\\prime}\", rational=True)\n",
     "    _λ = sp.Symbol(R\"\\lambda^{\\prime}\", rational=True)\n",
     "    return PoolSum(\n",
-    "        A_K[_ν, _λ]\n",
-    "        * Wigner.d(half, λ_Λc, _ν, ζ_0_11)\n",
-    "        * Wigner.d(half, _λ, λ_p, ζ_1_11)\n",
+    "        A_K[_ν, _λ] * Wigner.d(half, λ_Λc, _ν, ζ_0_11) * Wigner.d(half, _λ, λ_p, ζ_1_11)\n",
     "        + A_Λ[_ν, _λ]\n",
     "        * Wigner.d(half, λ_Λc, _ν, ζ_0_21)\n",
     "        * Wigner.d(half, _λ, λ_p, ζ_1_21)\n",
@@ -2424,16 +2421,8 @@
     "for res_list in resonance_particles.values():\n",
     "    for res in res_list:\n",
     "        coupling_sliders[res.name] = (\n",
-    "            [\n",
-    "                s\n",
-    "                for n, s in sliders.items()\n",
-    "                if n.endswith(\"_real\") and res.latex in n\n",
-    "            ],\n",
-    "            [\n",
-    "                s\n",
-    "                for n, s in sliders.items()\n",
-    "                if n.endswith(\"_imag\") and res.latex in n\n",
-    "            ],\n",
+    "            [s for n, s in sliders.items() if n.endswith(\"_real\") and res.latex in n],\n",
+    "            [s for n, s in sliders.items() if n.endswith(\"_imag\") and res.latex in n],\n",
     "            [\n",
     "                HTMLMath(f\"${latex[n[:-5]]}$\")\n",
     "                for n in sliders\n",
@@ -2513,9 +2502,7 @@
     "    else:\n",
     "        mesh.set_array(intensity)\n",
     "    if quiver is None:\n",
-    "        quiver = ax2.quiver(\n",
-    "            Xα, Yα, αx, αz, abs_α, cmap=plt.cm.viridis_r, clim=(0, 1)\n",
-    "        )\n",
+    "        quiver = ax2.quiver(Xα, Yα, αx, αz, abs_α, cmap=plt.cm.viridis_r, clim=(0, 1))\n",
     "        c_bar = fig.colorbar(quiver, ax=ax2, pad=0.01, fraction=0.0473)\n",
     "        c_bar.ax.set_ylabel(R\"$\\left|\\vec\\alpha\\right|$\")\n",
     "    else:\n",

diff --git a/docs/report/022.ipynb b/docs/report/022.ipynb
@@ -423,9 +423,7 @@
     }
    ],
    "source": [
-    "B_arrays = jnp.array(\n",
-    "    [[B_funcs[τ, ρ](GRID_SAMPLE) for ρ in range(4)] for τ in range(4)]\n",
-    ")\n",
+    "B_arrays = jnp.array([[B_funcs[τ, ρ](GRID_SAMPLE) for ρ in range(4)] for τ in range(4)])\n",
     "B_norm = B_arrays / B_arrays[0, 0]\n",
     "B_arrays.shape"
    ]

diff --git a/pyproject.toml b/pyproject.toml
@@ -33,7 +33,6 @@ target-version = [
 ]
 
 [tool.nbqa.addopts]
-black = ["--line-length=85"]
 ruff = [
     "--extend-ignore=A003",
     "--extend-ignore=B008",