maintenance: relax & organize dependencies, simplify function signatures

.github/workflows/quality.yml → .github/workflows/linting.yml

@@ -1,9 +1,9 @@
-name: Code Quality
+name: Linting
 
 on: [push, pull_request]
 
 jobs:
-  qualitycheck:
+  lint:
     runs-on: ubuntu-latest
 
     steps:
@@ -37,19 +37,13 @@ jobs:
         echo "$PWD/.venv/bin" >> $GITHUB_PATH
 
     - name: Install dependencies
-      run: uv pip install -e ".[dev]"
+      run: uv sync
 
     - name: Run ruff (linter)
       run: ruff check
 
     - name: Run ruff (formatter)
       run: ruff format --check
 
-    - name: Run isort
-      run: isort --check --profile black .
-
     - name: Run mypy
-      run: mypy .
-
-    - name: Run tests
-      run: pytest -v
+      run: mypy .

.github/workflows/testing.yml

@@ -0,0 +1,42 @@
+name: Tests
+
+on: [pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.13'
+
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+    - name: Cache dependencies
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/uv
+          ~/.uv
+          .venv
+        key: ${{ runner.os }}-uv-${{ hashFiles('pyproject.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-uv-
+
+    - name: Create and activate virtual environment
+      run: |
+        uv venv
+        echo "$PWD/.venv/bin" >> $GITHUB_PATH
+
+    - name: Install dependencies
+      run: uv sync
+
+    - name: Run tests
+      run: pytest -v 

.pre-commit-config.yaml

@@ -16,15 +16,10 @@ repos:
         language: python
         types: [python]
 
-      - id: isort
-        name: isort
-        entry: isort
-        language: python
-        types: [python]
-        args: [--profile=black]
-
       - id: mypy
         name: mypy
         entry: mypy
         language: system
-        types: [python]
+        types: [python]
+        exclude: ^(tests/)
+        args: ["--config-file=pyproject.toml"]

data/process.py

@@ -33,7 +33,8 @@ class PaRoutesDataset:
     def __init__(self, data_path: Path, filename: str, verbose: bool = True) -> None:
         self.data_path = data_path
         self.filename = filename
-        self.dataset = json.load(open(data_path.joinpath(filename), "r"))
+        with open(data_path.joinpath(filename)) as f:
+            self.dataset = json.load(f)
 
         self.verbose = verbose
 
@@ -94,18 +95,16 @@ def prepare_final_dataset_v2(
                         if n_sms is not None and sm_count + 1 >= n_sms:
                             break
         print(f"Created dataset with {len(products)} entries")
-        pickle.dump(
-            (products, starting_materials, path_strings, n_steps_list),
-            open(save_path, "wb"),
-        )
+        with open(save_path, "wb") as f:
+            pickle.dump((products, starting_materials, path_strings, n_steps_list), f)
         return non_permuted_paths
 
 
 # ------- Dataset Processing -------
 print("--- Processing of the PaRoutes dataset begins!")
 print("-- starting to canonicalize n1 and n5 stocks")
-n1_stock = open(data_path / "n1-stock.txt").read().splitlines()
-n5_stock = open(data_path / "n5-stock.txt").read().splitlines()
+n1_stock = open(data_path / "n1-stock.txt").read().splitlines()  # noqa: SIM115
+n5_stock = open(data_path / "n5-stock.txt").read().splitlines()  # noqa: SIM115
 
 n1_stock_canon = [canonicalize_smiles(smi) for smi in n1_stock]
 n5_stock_canon = [canonicalize_smiles(smi) for smi in n5_stock]
@@ -128,17 +127,17 @@ def prepare_final_dataset_v2(
     n_perms=n_perms,
     n_sms=n_sms,
 )
-pickle.dump(n1_path_set, open(save_path / f"n1_nperms={perm_suffix}_nsms={sm_suffix}_path_set.pkl", "wb"))
+pickle.dump(n1_path_set, open(save_path / f"n1_nperms={perm_suffix}_nsms={sm_suffix}_path_set.pkl", "wb"))  # noqa: SIM115
 
 print("-- starting to process n5 Routes")
 n5_routes_obj = PaRoutesDataset(data_path, "n5-routes.json")
 n5_path_set = n5_routes_obj.prepare_final_dataset_v2(
     save_path / f"n5_dataset_nperms={perm_suffix}_nsms={sm_suffix}.pkl", n_perms=n_perms, n_sms=n_sms
 )
-pickle.dump(n5_path_set, open(save_path / f"n5_nperms={perm_suffix}_nsms={sm_suffix}_path_set.pkl", "wb"))
+pickle.dump(n5_path_set, open(save_path / f"n5_nperms={perm_suffix}_nsms={sm_suffix}_path_set.pkl", "wb"))  # noqa: SIM115
 
-n1_path_set = pickle.load(open(save_path / "n1_nperms=all_nsms=1_path_set.pkl", "rb"))
-n5_path_set = pickle.load(open(save_path / "n5_nperms=all_nsms=1_path_set.pkl", "rb"))
+n1_path_set = pickle.load(open(save_path / "n1_nperms=all_nsms=1_path_set.pkl", "rb"))  # noqa: SIM115
+n5_path_set = pickle.load(open(save_path / "n5_nperms=all_nsms=1_path_set.pkl", "rb"))  # noqa: SIM115
 
 print("-- starting to process All Routes")
 all_routes_obj = PaRoutesDataset(data_path, "all_routes.json")
@@ -188,8 +187,8 @@ def prepare_final_dataset_v2(
 
 
 def remove_sm_from_ds(load_path: Path, save_path: Path) -> None:
-    products, _, path_strings, n_steps_lists = pickle.load(open(load_path, "rb"))
-    pickle.dump((products, path_strings, n_steps_lists), open(save_path, "wb"))
+    products, _, path_strings, n_steps_lists = pickle.load(open(load_path, "rb"))  # noqa: SIM115
+    pickle.dump((products, path_strings, n_steps_lists), open(save_path, "wb"))  # noqa: SIM115
 
 
 remove_sm_from_ds(
@@ -219,5 +218,5 @@ def remove_sm_from_ds(load_path: Path, save_path: Path) -> None:
 train_ds_dict = convert_list_of_dicts_to_dict_of_lists(train_ds)
 val_ds_dict = convert_list_of_dicts_to_dict_of_lists(val_ds)
 
-save_dataset_sm(train_ds_dict, save_path / f"{train_fname.split('.')[0]}_train={1-val_frac}.pkl")
+save_dataset_sm(train_ds_dict, save_path / f"{train_fname.split('.')[0]}_train={1 - val_frac}.pkl")
 save_dataset_sm(val_ds_dict, save_path / f"{train_fname.split('.')[0]}_val={val_frac}.pkl")

pyproject.toml

@@ -3,19 +3,13 @@ name = "directmultistep"
 version = "1.1.2"
 requires-python = ">=3.11"
 dependencies = [
-    "numpy==1.26.4",
-    "pandas==1.5.3",
-    "pdoc3==0.11.5",
-    "plotly==5.24.1",
-    "lightning==2.2.5",
-    "pyyaml==6.0.1",
-    "rdkit==2023.9.3",
-    "torch==2.3.0",
-    "torchmetrics==1.6.0",
-    "tqdm==4.67.1",
-    "svgwrite==1.4.3",
-    "svglib==1.5.1",
-    "tomli>=2.2.1",
+    "numpy>=1.26.4",
+    "lightning>=2.2.5",
+    "pyyaml>=6.0.1",
+    "rdkit>=2023.9.3",
+    "torch>=2.3.0",
+    "tqdm>=4.67.1",
+
 ]
 authors = [
     { name = "Anton Morgunov", email = "anton@ischemist.com" },
@@ -28,32 +22,44 @@ readme = "README.md"
 Homepage = "https://github.com/batistagroup/DirectMultiStep"
 Issues = "https://github.com/batistagroup/DirectMultiStep/issues"
 
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
 [tool.setuptools]
 package-dir = { "" = "src" }
 
+[tool.setuptools.package-data]
+"directmultistep.model.default_configs" = ["*.yaml"]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "ipykernel>=6.29.5",
     "nbformat>=5.10.4",
     "rich>=13.9.4",
     "kaleido==0.2.1",
-    "pre-commit==4.0.1",
-    "mkdocs==1.6.1",
-    "mkdocstrings-python==1.12.2",
-    "mkdocs-material==9.5.49",
+    "pre-commit>=4.0.1",
+    "mkdocs>=1.6.1",
+    "mkdocstrings-python>=1.12.2",
+    "mkdocs-material>=9.5.49",
     "material-plausible-plugin>=0.3.0",
-    "pytest==8.3.4",
-    "ruff==0.4.7",
-    "mypy==1.13.0",
-    "isort==5.13.2",
-    "typing-extensions==4.12.2",
-    "mypy-extensions==1.0.0",
+    "pytest>=8.3.4",
+    "ruff>=0.12.5",
+    "mypy>=1.17.0",
+    "typing-extensions>=4.12.2",
+    "mypy-extensions>=1.0.0",
     "types-pyyaml",
     "types-tqdm",
     "types-requests",
 ]
 
+[project.optional-dependencies]
+vis = [
+"svgwrite>=1.4.3",
+    "svglib>=1.5.1",
+    "plotly>=5.24.1",
+]
+
 [tool.mypy]
 strict = true
 ignore_missing_imports = true
@@ -66,4 +72,14 @@ ignore_errors = true
 
 [tool.ruff]
 line-length = 120
+lint.select = [
+    "E",   # pycodestyle
+    "F",   # Pyflakes
+    "UP",  # pyupgrade
+    "B",   # flake8-bugbear
+    "SIM", # flake8-simplify
+    "I",   # isort
+]
+lint.ignore = ["E501"] 
+
 

scripts/solve_compounds.py

@@ -42,22 +42,22 @@
 
     logger.info("Loading targets and stock compounds")
     if target_name == "uspto_190":
-        with open(COMPOUND_PATH / "uspto_190.txt", "r") as f:
+        with open(COMPOUND_PATH / "uspto_190.txt") as f:
             targets = f.read().splitlines()
     elif target_name == "chembl":
-        with open(COMPOUND_PATH / "chembl_targets.json", "r") as f:
+        with open(COMPOUND_PATH / "chembl_targets.json") as f:
             targets = json.load(f)
     else:
         logger.error(f"{target_name} is not a valid target name")
         raise Exception("Not valid target_name")
 
     # eMols is available at https://github.com/binghong-ml/retro_star
     # make sure to canonicalize the SMILES strings before using them
-    with open(COMPOUND_PATH / "eMolecules.txt", "r") as f:
+    with open(COMPOUND_PATH / "eMolecules.txt") as f:
         emol_stock_set = set(f.read().splitlines())
     # buyables-stock is available at https://github.com/jihye-roh/higherlev_retro
     # make sure to canonicalize the SMILES strings before using them
-    with open(COMPOUND_PATH / "buyables-stock.txt", "r") as f:
+    with open(COMPOUND_PATH / "buyables-stock.txt") as f:
         buyables_stock_set = set(f.read().splitlines())
 
     chunk_size = len(targets) // num_part

src/directmultistep/analysis/paper/linear_vs_convergent.py

@@ -330,15 +330,15 @@ def create_comparative_bar_plots(
 
         colors = style.colors_blue + style.colors_purple + style.colors_red
 
-        for cat, pos in zip(categories, positions):
+        for cat, pos in zip(categories, positions, strict=True):
             x = list(results[0][cat].keys())
             x.sort(key=lambda k: int(k.split()[-1]))
 
             if k_vals is not None:
                 k_vals_str = [f"Top {k}" for k in k_vals]
                 x = [k for k in x if k in k_vals_str]
 
-            for i, (result, name) in enumerate(zip(results, trace_names)):
+            for i, (result, name) in enumerate(zip(results, trace_names, strict=True)):
                 y = [float(result[cat][k].strip('%')) for k in x]
 
                 fig.add_trace(
@@ -408,7 +408,7 @@ def create_accuracy_by_length_plot(
         cset = style.publication_colors
         colors = [cset["primary_blue"], cset["dark_blue"], cset["purple"], cset["dark_purple"]]
 
-        for i, (path, dataset, config) in enumerate(zip(result_paths, datasets, configs)):
+        for i, (path, dataset, config) in enumerate(zip(result_paths, datasets, configs, strict=True)):
             paths_name = config.processed_paths_name
 
             with open(path / paths_name, "rb") as f:
@@ -469,7 +469,7 @@ def create_accuracy_by_length_subplots(
         cset = style.publication_colors
         colors = [cset["primary_blue"], cset["dark_blue"], cset["purple"], cset["dark_purple"]]
 
-        for i, (path, dataset, config) in enumerate(zip(result_paths, datasets, configs)):
+        for i, (path, dataset, config) in enumerate(zip(result_paths, datasets, configs, strict=True)):
             paths_name = config.processed_paths_name
 
             with open(path / paths_name, "rb") as f:
@@ -482,7 +482,7 @@ def create_accuracy_by_length_subplots(
                 "non_convergent": (analyzer.convergent_idxs, 3),
             }
 
-            for route_type, (ignore_ids, row) in route_types.items():
+            for _route_type, (ignore_ids, row) in route_types.items():
                 lengths, step_stats = RouteAnalyzer._calculate_accuracy_by_length_data(
                     predicted_routes, dataset, k_vals, ignore_ids=ignore_ids
                 )
@@ -552,7 +552,7 @@ def get_predictions_by_type(routes: PathsProcessedType) -> tuple[list[int], list
         # Create subplot titles
         def create_subtitle(stage: str, predictions: list[int]) -> str:
             mean, median, mean_f, median_f = calculate_prediction_stats(predictions)
-            base = f"{stage}<br><span style=\"font-size:{FONT_SIZES['subplot_title']-4}px\">"
+            base = f'{stage}<br><span style="font-size:{FONT_SIZES["subplot_title"] - 4}px">'
             stats = f"mean={mean:.1f}, median={median:.1f}"
             if show_filtered_stats:
                 stats += f" (μ*={mean_f:.1f}, m*={median_f:.1f})"