Merge pull request #8 from kkovary/fix-int32-out-of-bounds

fix int32 out of bounds

Author: daenuprobst

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Python Package using Conda
+name: Python Package using uv
 
 on: [push]
 
@@ -9,26 +9,22 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: 3.7
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
     - name: Install dependencies
       run: |
-        conda env update --file environment.yml --name base
-    - name: Lint with flake8
+        uv sync
+    - name: Run pre-commit
       run: |
-        conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        uv run pre-commit run --all-files
     - name: Test with tox
       run: |
-        pip install -e .[testing]
-        tox
+        uv run tox

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.3
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest
+        entry: uv run pytest
+        language: system
+        types: [python]
+        pass_filenames: false
+        always_run: true

environment.yml

@@ -31,7 +31,7 @@
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
     "from sklearn.decomposition import PCA\n",
-    "from drfp import DrfpEncoder\n"
+    "from drfp import DrfpEncoder"
    ]
   },
   {
@@ -288,7 +288,7 @@
     "pca = PCA(n_components=2)\n",
     "X = pca.fit(fps).transform(fps)\n",
     "\n",
-    "plt.scatter(X[:,0], X[:,1], alpha=0.8)\n",
+    "plt.scatter(X[:, 0], X[:, 1], alpha=0.8)\n",
     "plt.title(\"PCA of 100 drfp-encoded reactions\")"
    ]
   },

notebooks/01_fingerprinting.ipynb

@@ -277,7 +277,7 @@
     }
    ],
    "source": [
-    "shap.force_plot(explainer.expected_value, shap_values[0,:], matplotlib=True)"
+    "shap.force_plot(explainer.expected_value, shap_values[0, :], matplotlib=True)"
    ]
   },
   {
@@ -321,7 +321,7 @@
     }
    ],
    "source": [
-    "shap.force_plot(explainer.expected_value, shap_values[42,:], matplotlib=True)"
+    "shap.force_plot(explainer.expected_value, shap_values[42, :], matplotlib=True)"
    ]
   },
   {

notebooks/02_model_explainability.ipynb

@@ -90,7 +90,6 @@
     }
    ],
    "source": [
-    "\n",
     "%pip install theia-pypi xgboost matplotlib faerun-notebook --upgrade\n",
     "import pickle\n",
     "from pathlib import Path\n",
@@ -321,6 +320,7 @@
     "!pip uninstall ipywidgets -y\n",
     "!pip install ipywidgets==7.7.1\n",
     "import ipywidgets\n",
+    "\n",
     "ipywidgets.version_info"
    ]
   },
@@ -375,11 +375,9 @@
     "mapping = split[\"test\"][\"mapping\"]\n",
     "dataset = InferenceReactionDataset([rxn])\n",
     "\n",
-    "expl = explain_regression(\n",
-    "    dataset, explainer, mapping\n",
-    ")\n",
+    "expl = explain_regression(dataset, explainer, mapping)\n",
     "\n",
-    "w = { \"reactants\": expl.reactant_weights, \"products\": expl.product_weights}\n",
+    "w = {\"reactants\": expl.reactant_weights, \"products\": expl.product_weights}\n",
     "\n",
     "SmilesDrawer(value=[(\"Example\", rxn)], weights=[w], output=\"img\", theme=\"solarized\")"
    ]

notebooks/03_more_model_explainability.ipynb

@@ -42,11 +42,7 @@
     "\n",
     "pd.options.mode.chained_assignment = None\n",
     "\n",
-    "modern_cmap = LinearSegmentedColormap.from_list(\n",
-    "    \"modern_cmap\", \n",
-    "    [\"#ffffff\", \"#003f5c\"], \n",
-    "    N=256\n",
-    ")\n",
+    "modern_cmap = LinearSegmentedColormap.from_list(\"modern_cmap\", [\"#ffffff\", \"#003f5c\"], N=256)\n",
     "\n",
     "schneider_class_names = [\n",
     "    \"Alductive amination\",\n",
@@ -124,9 +120,7 @@
     }
    ],
    "source": [
-    "df = pd.read_csv(\"yield_prediction_results.csv\", names=[\n",
-    "    \"data_set\", \"split\", \"filename\", \"ground_truth\", \"prediction\"\n",
-    "])\n",
+    "df = pd.read_csv(\"yield_prediction_results.csv\", names=[\"data_set\", \"split\", \"filename\", \"ground_truth\", \"prediction\"])\n",
     "\n",
     "df[\"error\"] = df.prediction - df.ground_truth\n",
     "\n",
@@ -181,6 +175,7 @@
     "            fontfamily=font_family,\n",
     "        )\n",
     "\n",
+    "\n",
     "def calc_r2(df, verbose=True):\n",
     "    result = []\n",
     "    result_raw = []\n",
@@ -196,34 +191,31 @@
     "            r2 = r2_score(df_tmp.ground_truth, df_tmp.prediction)\n",
     "            result_raw.append({\"r2\": r2, \"split\": split})\n",
     "            r2s.append(r2)\n",
-    "        \n",
+    "\n",
     "        if verbose:\n",
     "            print(f\"r2 mean={round(sum(r2s) / len(r2s), 5)}, r2 std={round(stdev(r2s), 5)}\")\n",
     "        result.append((sum(r2s) / len(r2s), stdev(r2s)))\n",
     "\n",
     "    return (result, pd.DataFrame(result_raw))\n",
     "\n",
+    "\n",
     "def scatter(df, ax, title):\n",
     "    sns.kdeplot(\n",
-    "        data=df, \n",
-    "        x=\"ground_truth\", y=\"prediction\", clip=((0, 100), (None, None)),\n",
-    "        color=\"#003f5c\", levels=6, zorder=2, ax=ax\n",
+    "        data=df, x=\"ground_truth\", y=\"prediction\", clip=((0, 100), (None, None)), color=\"#003f5c\", levels=6, zorder=2, ax=ax\n",
     "    )\n",
     "\n",
     "    ax.plot(\n",
-    "        [0, 100], [0, 100], linewidth=2, \n",
-    "        color=\"#bc5090\", linestyle=\"dashed\",\n",
+    "        [0, 100],\n",
+    "        [0, 100],\n",
+    "        linewidth=2,\n",
+    "        color=\"#bc5090\",\n",
+    "        linestyle=\"dashed\",\n",
     "        zorder=1,\n",
     "    )\n",
     "\n",
-    "    sns.scatterplot(\n",
-    "        data=df, \n",
-    "        x=\"ground_truth\", y=\"prediction\",\n",
-    "        color=\"#cccccc\", linewidth=0,\n",
-    "        alpha=0.125, zorder=0, ax=ax\n",
-    "    )\n",
+    "    sns.scatterplot(data=df, x=\"ground_truth\", y=\"prediction\", color=\"#cccccc\", linewidth=0, alpha=0.125, zorder=0, ax=ax)\n",
     "\n",
-    "    ax.set(xlabel=\"Ground Truth\", ylabel='Prediction')\n",
+    "    ax.set(xlabel=\"Ground Truth\", ylabel=\"Prediction\")\n",
     "    ax.set_title(title)"
    ]
   },
@@ -329,36 +321,28 @@
     "splits = [98, 197, 395, 791, 1186, 1977, 2766]\n",
     "\n",
     "for i in range(7):\n",
-    "    scatter(\n",
-    "        df_buchwald_hartwig_cv[df_buchwald_hartwig_cv.split == splits[i]],\n",
-    "        axs.flat[i], titles[i]\n",
-    "    )\n",
+    "    scatter(df_buchwald_hartwig_cv[df_buchwald_hartwig_cv.split == splits[i]], axs.flat[i], titles[i])\n",
     "\n",
     "_, df_results = calc_r2(df_buchwald_hartwig_cv, verbose=False)\n",
     "\n",
     "sns.stripplot(\n",
-    "    x=\"split\", y=\"r2\", data=df_results, linewidth=1, ax=axs.flat[7],\n",
-    "    palette=[\"#003f5c\", \"#374c80\", \"#7a5195\", \"#bc5090\", \"#ef5675\", \"#ff764a\", \"#ffa600\"]\n",
+    "    x=\"split\",\n",
+    "    y=\"r2\",\n",
+    "    data=df_results,\n",
+    "    linewidth=1,\n",
+    "    ax=axs.flat[7],\n",
+    "    palette=[\"#003f5c\", \"#374c80\", \"#7a5195\", \"#bc5090\", \"#ef5675\", \"#ff764a\", \"#ffa600\"],\n",
     ")\n",
     "axs.flat[7].set_xticklabels([\"a\", \"b\", \"c\", \"d\", \"e\", \"f\", \"g\"])\n",
     "axs.flat[7].set(xlabel=\"Split\", ylabel=\"Accuracy\")\n",
     "\n",
-    "titles = [\n",
-    "    \"Out-of-sample Split 1\", \"Out-of-sample Split 2\", \n",
-    "    \"Out-of-sample Split 3\", \"Out-of-sample Split 4\"\n",
-    "]\n",
+    "titles = [\"Out-of-sample Split 1\", \"Out-of-sample Split 2\", \"Out-of-sample Split 3\", \"Out-of-sample Split 4\"]\n",
     "\n",
-    "splits = [\n",
-    "    \"Test1-2048-3-true.pkl\", \"Test2-2048-3-true.pkl\", \n",
-    "    \"Test3-2048-3-true.pkl\", \"Test4-2048-3-true.pkl\"\n",
-    "]\n",
+    "splits = [\"Test1-2048-3-true.pkl\", \"Test2-2048-3-true.pkl\", \"Test3-2048-3-true.pkl\", \"Test4-2048-3-true.pkl\"]\n",
     "\n",
     "j = 0\n",
     "for i in range(8, 12):\n",
-    "    scatter(\n",
-    "        df_buchwald_hartwig_tests[df_buchwald_hartwig_tests.split == splits[j]],\n",
-    "        axs.flat[i], titles[j]\n",
-    "    )\n",
+    "    scatter(df_buchwald_hartwig_tests[df_buchwald_hartwig_tests.split == splits[j]], axs.flat[i], titles[j])\n",
     "    j += 1\n",
     "\n",
     "index_subplots(axs.flat, font_size=14, y=1.17)\n",
@@ -401,7 +385,7 @@
     "\n",
     "plt_cm = []\n",
     "for i in cm.classes:\n",
-    "    row=[]\n",
+    "    row = []\n",
     "    for j in cm.classes:\n",
     "        row.append(cm.table[i][j])\n",
     "    plt_cm.append(row)\n",
@@ -414,9 +398,7 @@
     "\n",
     "\n",
     "sns.heatmap(\n",
-    "    plt_cm, cmap=\"RdPu\", linewidths=.1, linecolor=\"#eeeeee\", square=True, \n",
-    "    cbar_kws={\"shrink\": 0.5}, norm=LogNorm(),\n",
-    "    ax=ax\n",
+    "    plt_cm, cmap=\"RdPu\", linewidths=0.1, linecolor=\"#eeeeee\", square=True, cbar_kws={\"shrink\": 0.5}, norm=LogNorm(), ax=ax\n",
     ")\n",
     "\n",
     "cax = plt.gcf().axes[-1]\n",
@@ -491,8 +473,17 @@
     "y.extend(y_train)\n",
     "y.extend(y_test)\n",
     "\n",
-    "labels = {\"1\": \"Heteroatom alkylation and arylation\", \"2\": \"Acylation and related processes\", \"3\": \"C-C bond formation\", \"5\": \"Protections\", \"6\": \"Deprotections\",\n",
-    "    \"7\": \"Reductions\", \"8\": \"Oxidations\", \"9\": \"Functional group interconversion (FGI)\", \"10\": \"Functional group addition (FGA)\"}\n",
+    "labels = {\n",
+    "    \"1\": \"Heteroatom alkylation and arylation\",\n",
+    "    \"2\": \"Acylation and related processes\",\n",
+    "    \"3\": \"C-C bond formation\",\n",
+    "    \"5\": \"Protections\",\n",
+    "    \"6\": \"Deprotections\",\n",
+    "    \"7\": \"Reductions\",\n",
+    "    \"8\": \"Oxidations\",\n",
+    "    \"9\": \"Functional group interconversion (FGI)\",\n",
+    "    \"10\": \"Functional group addition (FGA)\",\n",
+    "}\n",
     "\n",
     "y_values = [labels[ytem.split(\".\")[0]] for ytem in y]\n",
     "\n",
@@ -535,24 +526,16 @@
     "    \"#595959\",\n",
     "    \"#5f9ed1\",\n",
     "    \"#c85300\",\n",
-    "    #\"#898989\",\n",
+    "    # \"#898989\",\n",
     "    \"#a2c8ec\",\n",
     "    \"#ffbc79\",\n",
-    "    \"#cfcfcf\"\n",
+    "    \"#cfcfcf\",\n",
     "]\n",
     "\n",
     "df_tmap = pd.DataFrame({\"x\": x, \"y\": y, \"c\": y_values})\n",
     "sns.scatterplot(x=\"x\", y=\"y\", hue=\"c\", data=df_tmap, s=5.0, palette=palette, ax=ax, zorder=2)\n",
     "\n",
-    "legend = ax.legend(\n",
-    "    loc=\"center left\", \n",
-    "    bbox_to_anchor=(1, 0.5),\n",
-    "    fancybox=False, \n",
-    "    shadow=False, \n",
-    "    frameon=False,\n",
-    "    ncol=1,\n",
-    "    fontsize=7\n",
-    ")\n",
+    "legend = ax.legend(loc=\"center left\", bbox_to_anchor=(1, 0.5), fancybox=False, shadow=False, frameon=False, ncol=1, fontsize=7)\n",
     "\n",
     "for handle in legend.legendHandles:\n",
     "    handle.set_sizes([12.0])\n",