Migrate to pyproject.toml (#25)

* initial commit * lint cleanup * workflow cleanup * disable 3.12 * fix lint * lock `torch` in workflow
arangoml · Nov 15, 2023 · ce6e1d1 · ce6e1d1
1 parent dbee0fc
commit ce6e1d1
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Showing 8 changed files with 109 additions and 103 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: ["3.8", "3.9", "3.10", "3.11"]
+        python: ["3.8", "3.9", "3.10", "3.11"] # "3.12"
     name: Python ${{ matrix.python }}
     steps:
       - uses: actions/checkout@v4
@@ -32,7 +32,7 @@ jobs:
 
       - name: Install packages
         run: |
-          pip install torch
+          pip install torch==2.1.0
           pip install torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-$(python -c 'import torch; print(torch.__version__.split("+")[0])')+cpu.html
           pip install -e .[dev]
 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -68,12 +68,12 @@ jobs:
         run: gitchangelog ${{env.VERSION}} > CHANGELOG.md
 
       - name: Make commit for auto-generated changelog
-        uses: EndBug/add-and-commit@v7
+        uses: EndBug/add-and-commit@v9
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           add: "CHANGELOG.md"
-          branch: actions/changelog
+          new_branch: actions/changelog
           message: "!gitchangelog"
 
       - name: Create pull request for the auto generated changelog

diff --git a/adbpyg_adapter/adapter.py b/adbpyg_adapter/adapter.py
@@ -437,8 +437,8 @@ def arangodb_graph_to_pyg(
         :raise adbpyg_adapter.exceptions.ADBMetagraphError: If invalid metagraph.
         """
         graph = self.__db.graph(name)
-        v_cols: Set[str] = graph.vertex_collections()  # type: ignore
-        edge_definitions: List[Json] = graph.edge_definitions()  # type: ignore
+        v_cols: Set[str] = graph.vertex_collections()
+        edge_definitions: List[Json] = graph.edge_definitions()
         e_cols: Set[str] = {c["edge_collection"] for c in edge_definitions}
 
         return self.arangodb_collections_to_pyg(
@@ -731,12 +731,12 @@ def get_aql_return_value(
                 )
             """
 
-        col_size: int = self.__db.collection(col).count()  # type: ignore
+        col_size: int = self.__db.collection(col).count()
 
         with get_export_spinner_progress(f"ADB Export: '{col}' ({col_size})") as p:
             p.add_task(col)
 
-            cursor: Cursor = self.__db.aql.execute(  # type: ignore
+            cursor: Cursor = self.__db.aql.execute(
                 f"FOR doc IN @@col RETURN {get_aql_return_value(meta)}",
                 bind_vars={"@col": col},
                 **{**adb_export_kwargs, **{"stream": True}},
@@ -785,7 +785,7 @@ def __process_adb_cursor(
         with Live(Group(progress)):
             i = 0
             while not cursor.empty():
-                cursor_batch = len(cursor.batch())  # type: ignore
+                cursor_batch = len(cursor.batch())
                 df = DataFrame([cursor.pop() for _ in range(cursor_batch)])
 
                 i = process_adb_df(i, df, col, adb_map, meta, preserve_key, **kwargs)
@@ -1180,7 +1180,7 @@ def __create_adb_graph(
         edge_definitions = self.__etypes_to_edefinitions(edge_types)
         orphan_collections = self.__ntypes_to_ocollections(node_types, edge_types)
 
-        return self.__db.create_graph(  # type: ignore[return-value]
+        return self.__db.create_graph(
             name,
             edge_definitions,
             orphan_collections,
@@ -1239,8 +1239,7 @@ def __process_pyg_node_batch(
 
         # 3. Apply the ArangoDB Node Controller (if provided)
         if is_custom_controller:
-            f = lambda n: self.__cntrl._prepare_pyg_node(n, n_type)
-            df = df.apply(f, axis=1)
+            df = df.apply(lambda n: self.__cntrl._prepare_pyg_node(n, n_type), axis=1)
 
         return df
 
@@ -1313,8 +1312,7 @@ def __process_pyg_edge_batch(
 
         # 5. Apply the ArangoDB Edge Controller (if provided)
         if is_custom_controller:
-            f = lambda e: self.__cntrl._prepare_pyg_edge(e, e_type)
-            df = df.apply(f, axis=1)
+            df = df.apply(lambda e: self.__cntrl._prepare_pyg_edge(e, e_type), axis=1)
 
         return df
 

diff --git a/adbpyg_adapter/utils.py b/adbpyg_adapter/utils.py
@@ -23,9 +23,7 @@
 logger.addHandler(handler)
 
 
-def get_export_spinner_progress(
-    text: str,
-) -> Progress:
+def get_export_spinner_progress(text: str) -> Progress:
     return Progress(
         TextColumn(text),
         SpinnerColumn("aesthetic", "#5BC0DE"),

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,17 +1,92 @@
 [build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
+requires = ["setuptools>=45", "wheel", "setuptools_scm"]
 build-backend = "setuptools.build_meta"
 
-[tool.coverage.run]
-omit = [
-    "adbpyg_adapter/version.py",
-    "setup.py",
+[tool.setuptools_scm]
+normalize = true
+
+[project]
+name = "adbpyg_adapter"
+description = "Convert ArangoDB graphs to PyG & vice-versa."
+keywords = ["arangodb", "pyg", "pytorch", "pytorch geometric", "adapter"]
+readme = "README.md"
+dynamic = ["version"]
+license = {file = "LICENSE"}
+requires-python = ">=3.8"
+
+authors = [{name = "Anthony Mahanna", email = "[email protected]"}]
+
+classifiers = [
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    # "Programming Language :: Python :: 3.12",
+    "Topic :: Utilities",
+    "Typing :: Typed",
+]
+
+dependencies = [
+    "requests>=2.27.1",
+    "rich>=12.5.1",
+    "pandas>=1.3.5",
+    "python-arango~=7.6",
+    "torch>=1.12.0",
+    "torch-sparse>=0.6.14",
+    "torch-scatter>=2.0.9",
+    "torch-geometric>=2.0.4",
+    "setuptools>=45"
+]
+
+[project.optional-dependencies]
+dev = [
+    "black==23.3.0",
+    "flake8==6.0.0",
+    "Flake8-pyproject",
+    "isort==5.12.0",
+    "mypy==1.4.1",
+    "pytest>=6.0.0",
+    "pytest-cov>=2.0.0",
+    "coveralls>=3.3.1",
+    "types-setuptools>=57.4.9",
+    "types-requests>=2.27.11",
+    "networkx>=2.5.1",
 ]
 
+[project.urls]
+"Homepage" = "https://github.com/arangoml/pyg-adapter"
+
+[tool.setuptools]
+packages = ["adbpyg_adapter"]
+
 [tool.pytest.ini_options]
 addopts = "-s -vv"
 minversion = "6.0"
 testpaths = ["tests"]
 
-[tool.setuptools_scm]
-write_to = "adbpyg_adapter/version.py"
+[tool.coverage.report]
+omit = ["*tests*"]
+
+[tool.coverage.run]
+omit = ["*tests*"]
+
+[tool.isort]
+profile = "black"
+
+[tool.flake8]
+max-line-length = 88
+extend-ignore = ["E203", "W503", "E251"]
+exclude = [".git", ".idea", ".*_cache", "dist", "venv"]
+
+[tool.mypy]
+strict = true
+ignore_missing_imports = true
+implicit_reexport = true
+scripts_are_modules = true
+follow_imports = "skip"
+disallow_subclassing_any = false
+disallow_untyped_decorators = false
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
@@ -1,56 +1,3 @@
 from setuptools import setup
 
-with open("./README.md") as fp:
-    long_description = fp.read()
-
-setup(
-    name="adbpyg_adapter",
-    author="Anthony Mahanna",
-    author_email="[email protected]",
-    description="Convert ArangoDB graphs to PyG & vice-versa.",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/arangoml/pyg-adapter",
-    keywords=["arangodb", "pyg", "pytorch", "pytorch geometric", "adapter"],
-    packages=["adbpyg_adapter"],
-    include_package_data=True,
-    python_requires=">=3.8",
-    license="Apache Software License",
-    install_requires=[
-        "requests>=2.27.1",
-        "rich>=12.5.1",
-        "pandas>=1.3.5",
-        "python-arango~=7.6",
-        "torch>=1.12.0",
-        "torch-sparse>=0.6.14",
-        "torch-scatter>=2.0.9",
-        "torch-geometric>=2.0.4",
-        "setuptools>=45",
-    ],
-    extras_require={
-        "dev": [
-            "black==23.3.0",
-            "flake8==6.0.0",
-            "isort==5.12.0",
-            "mypy==1.4.1",
-            "pytest>=6.0.0",
-            "pytest-cov>=2.0.0",
-            "coveralls>=3.3.1",
-            "types-setuptools>=57.4.9",
-            "types-requests>=2.27.11",
-            "networkx>=2.5.1",
-        ],
-    },
-    classifiers=[
-        "Intended Audience :: Developers",
-        "License :: OSI Approved :: Apache Software License",
-        "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Topic :: Utilities",
-        "Typing :: Typed",
-    ],
-)
+setup()
diff --git a/tests/test_adapter.py b/tests/test_adapter.py
@@ -50,10 +50,10 @@ class Bad_ADBPyG_Controller:
         pass
 
     with pytest.raises(TypeError):
-        ADBPyG_Adapter(bad_db)  # type: ignore
+        ADBPyG_Adapter(bad_db)
 
     with pytest.raises(TypeError):
-        ADBPyG_Adapter(db, Bad_ADBPyG_Controller())  # type: ignore
+        ADBPyG_Adapter(db, Bad_ADBPyG_Controller())  # type:ignore[arg-type]
 
 
 @pytest.mark.parametrize(
@@ -395,11 +395,11 @@ def test_pyg_to_arangodb_with_controller() -> None:
 
     ADBPyG_Adapter(db, Custom_ADBPyG_Controller()).pyg_to_arangodb(name, data)
 
-    for doc in db.collection(f"{name}_N"):  # type: ignore
+    for doc in db.collection(f"{name}_N"):
         assert "foo" in doc
         assert doc["foo"] == "bar"
 
-    for edge in db.collection(f"{name}_E"):  # type: ignore
+    for edge in db.collection(f"{name}_E"):
         assert "bar" in edge
         assert edge["bar"] == "foo"
 
@@ -649,8 +649,8 @@ def test_adb_graph_to_pyg(
     pyg_g_new = adapter.arangodb_graph_to_pyg(name)
 
     graph = db.graph(name)
-    v_cols: Set[str] = graph.vertex_collections()  # type: ignore
-    edge_definitions: List[Json] = graph.edge_definitions()  # type: ignore
+    v_cols: Set[str] = graph.vertex_collections()
+    edge_definitions: List[Json] = graph.edge_definitions()
     e_cols: Set[str] = {c["edge_collection"] for c in edge_definitions}
 
     # Manually set the number of nodes (since nodes are feature-less)
@@ -683,8 +683,8 @@ def test_adb_graph_to_pyg_to_arangodb_with_missing_document_and_strict(
     ADBPyG_Adapter(db).pyg_to_arangodb(name, data)
 
     graph = db.graph(name)
-    v_cols: Set[str] = graph.vertex_collections()  # type: ignore
-    edge_definitions: List[Json] = graph.edge_definitions()  # type: ignore
+    v_cols: Set[str] = graph.vertex_collections()
+    edge_definitions: List[Json] = graph.edge_definitions()
     e_cols: Set[str] = {c["edge_collection"] for c in edge_definitions}
 
     for v_col in v_cols:
@@ -713,8 +713,8 @@ def test_adb_graph_to_pyg_to_arangodb_with_missing_document_and_permissive(
     ADBPyG_Adapter(db).pyg_to_arangodb(name, data)
 
     graph = db.graph(name)
-    v_cols: Set[str] = graph.vertex_collections()  # type: ignore
-    edge_definitions: List[Json] = graph.edge_definitions()  # type: ignore
+    v_cols: Set[str] = graph.vertex_collections()
+    edge_definitions: List[Json] = graph.edge_definitions()
     e_cols: Set[str] = {c["edge_collection"] for c in edge_definitions}
 
     for v_col in v_cols:
@@ -728,7 +728,7 @@ def test_adb_graph_to_pyg_to_arangodb_with_missing_document_and_permissive(
 
     data = adapter.arangodb_to_pyg(name, metagraph=metagraph, strict=False)
 
-    collection_count: int = db.collection(list(e_cols)[0]).count()  # type: ignore
+    collection_count: int = db.collection(list(e_cols)[0]).count()
     assert len(data.edge_index[0]) < collection_count
 
     db.delete_graph(name, drop_collections=True)
@@ -799,8 +799,8 @@ def test_full_cycle_homogeneous_with_preserve_adb_keys() -> None:
     pyg_g = adbpyg_adapter.arangodb_graph_to_pyg(name, preserve_adb_keys=True)
 
     graph = db.graph(name)
-    v_cols: Set[str] = graph.vertex_collections()  # type: ignore
-    edge_definitions: List[Json] = graph.edge_definitions()  # type: ignore
+    v_cols: Set[str] = graph.vertex_collections()
+    edge_definitions: List[Json] = graph.edge_definitions()
     e_cols: Set[str] = {c["edge_collection"] for c in edge_definitions}
 
     metagraph: ADBMetagraph = {