Switch quivr to pdm dependency management

Author: akoumjian

.github/workflows/build-lint-test-coverage.yml

@@ -1,4 +1,4 @@
-name: Build Lint Test
+name: Build Lint Test and Coverage
 
 on:
   push:
@@ -8,10 +8,9 @@ on:
 
 jobs:
   build-lint-test-coverage:
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [ubuntu-latest]
         python-version: ["3.10", "3.11"]
     defaults:
       run:
@@ -22,15 +21,41 @@ jobs:
         uses: actions/checkout@v3
       - name: Get git tags
         run:  git fetch --prune --unshallow --tags
-      - uses: actions/setup-python@v4
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v4
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip' # caching pip dependencies
-      - name: Install hatch, the build tool
-        run: pip install hatch
-      - name: Build
-        run: hatch build
+          cache: true
+          cache-dependency-path: ./pyproject.toml
+      - name: Install Testing Dependencies
+        run: |
+          pdm install -G test
       - name: Lint
-        run: hatch run dev:lint
-      - name: Test
-        run: hatch run test:all
+        run: pdm run lint
+      - name: Test with coverage
+        run: pdm run test
+      - name: Run benchmarks
+        run: |
+          pdm run benchmark --benchmark-json bench.json
+      - name: Store main benchmark result
+        if: github.ref == 'refs/heads/main'
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: Python Benchmark
+          tool: 'pytest'
+          output-file-path: bench.json
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          auto-push: true
+          gh-pages-branch: gh-pages
+      - name: Compare benchmarks
+        if: github.event_name == 'pull_request'
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: Python Benchmark
+          tool: 'pytest'
+          output-file-path: bench.json
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          comment-always: true
+          fail-threshold: '200%'
+          alert-threshold: '150%'
+          auto-push: false

.gitignore

@@ -1,4 +1,6 @@
 dist/
 *~
 .mypy_cache
-.dir-locals.el
+.dir-locals.el
+pdm.lock
+.pdm-python

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
 
 [project]
 name = "quivr"
@@ -17,7 +17,10 @@ dependencies = [
   "mmh3",
   "typing_extensions>=4.0.0"
 ]
-dynamic = [ "version" ]
+dynamic = ["version"]
+
+[project.urls]
+Source = "https://github.com/B612-Asteroid-Institute/quivr"
 
 [project.optional-dependencies]
 docs = [
@@ -28,19 +31,16 @@ docs = [
   "furo==2023.08.17",
 ]
 
-[project.urls]
-Source = "https://github.com/spenczar/quivr"
-
-[tool.hatch.build.targets.sdist]
-include = [
-  "/quivr",
-]
+[tool.pdm.build]
+includes = ["quivr"]
 
-[tool.hatch.version]
-path = "quivr/__version__.py"
+[tool.pdm.version]
+source = "scm"
+write_to = "quivr/__version__.py"
+write_template = "__version__ = '{}'"
 
-[tool.hatch.envs.dev]
-dependencies = [
+[dependency-groups]
+dev = [
   "black",
   "isort",
   "mypy",
@@ -51,39 +51,7 @@ dependencies = [
   "ipython"
 ]
 
-[tool.hatch.envs.dev.scripts]
-check = [
-  "lint",
-  "typecheck",
-  "test",
-]
-fix = [
-  "ruff ./quivr ./test --fix"
-]
-lint = [
-  "ruff check ./quivr ./test",
-  "black --check ./quivr ./test",
-  "isort --check-only ./quivr ./test"
-]
-format = [
-  "black ./quivr ./test",
-  "isort ./quivr ./test"
-]
-typecheck = [
-  "mypy --strict ./quivr ./examples ./test/typing_tests",
-]
 test = [
-  "pytest --benchmark-disable ./test {args}",
-]
-doctest = [
-  "pytest --doctest-modules ./quivr {args}"
-]
-benchmark = [
-  "pytest --benchmark-only ./test {args}"
-]
-
-[tool.hatch.envs.test]
-dependencies = [
   "black",
   "isort",
   "mypy",
@@ -93,49 +61,27 @@ dependencies = [
   "ruff",
 ]
 
-[[tool.hatch.envs.test.matrix]]
-python = ["3.10", "3.11"]
-
-[tool.hatch.envs.test.scripts]
-all = [
+[tool.pdm.scripts]
+check = { composite = ["lint", "typecheck", "test"] }
+fix = "ruff check ./quivr ./test --fix"
+lint = { composite = [
   "ruff check ./quivr ./test",
   "black --check ./quivr ./test",
-  "isort --check-only ./quivr ./test",
-  "mypy --strict ./quivr ./examples ./test/typing_tests",
-  "pytest --benchmark-disable ./test {args}",
-  "pytest --doctest-modules ./quivr",  
-]
-
-benchmark = [
-  "pytest --benchmark-only ./test"
-]
-
-[tool.hatch.envs.docs]
-dependencies = [
-  "sphinx==7.2.2",
-  "sphinx-autodoc-typehints",
-  "sphinx-copybutton",
-  "sphinx-toolbox",
-  "furo==2023.08.17",
-]
-
-[tool.hatch.envs.docs.scripts]
-make-html = [
-  "make -C docs html"
-]
-
-open-html = [
-  "open docs/build/html/index.html"
-]
-
-clean = [
-  "make -C docs clean"
-]
-
-rebuild = [
-  "make -C docs clean",
-  "make -C docs html"
-]
+  "isort --check-only ./quivr ./test"
+] }
+format = { composite = [
+  "black ./quivr ./test",
+  "isort ./quivr ./test"
+] }
+typecheck = "mypy --strict ./quivr ./examples ./test/typing_tests"
+test = "pytest --benchmark-disable ./test {args}"
+doctest = "pytest --doctest-modules ./quivr {args}"
+benchmark = "pytest --benchmark-only ./test {args}"
+
+docs-html = "make -C docs html"
+docs-open = "open docs/build/html/index.html"
+docs-clean = "make -C docs clean"
+docs-rebuild = { composite = ["docs-clean", "docs-html"] }
 
 [tool.black]
 line-length = 110

quivr/__init__.py

@@ -1,4 +1,8 @@
-from .__version__ import __version__
+try:
+    from .__version__ import __version__
+except ImportError:
+    __version__ = "unknown"
+
 from .attributes import FloatAttribute, IntAttribute, StringAttribute
 from .columns import (
     BinaryColumn,

quivr/__version__.py

@@ -1 +1 @@
-__version__ = "0.7.5"
+__version__ = "unknown"

quivr/linkage.py

@@ -448,7 +448,7 @@ def _concatenate_linkage_components(
 
 
 def combine_multilinkages(
-    links: Iterable[MultiKeyLinkage[LeftTable, RightTable]]
+    links: Iterable[MultiKeyLinkage[LeftTable, RightTable]],
 ) -> MultiKeyLinkage[LeftTable, RightTable]:
     """Combine a list of MultiKeyLinkages into a single MultiKeyLinkage.
 

quivr/tables.py

@@ -274,13 +274,14 @@ def from_kwargs(
                 arrays.append(None)
                 continue
 
+            assert hasattr(array, "__len__"), f"Cannot determine length of {type(array).__name__}"
             if size is None:
                 size = len(array)
                 size_col = column_name
             elif len(array) != size:
                 raise errors.InvalidColumnDataError(
                     column,
-                    f"wrong length {len(value)} (expected {size} based on column {size_col})",
+                    f"wrong length {len(array)} (expected {size} based on column {size_col})",
                 )
 
             arrays.append(array)
@@ -1036,7 +1037,7 @@ def nulls(cls, size: int, **kwargs: AttributeValueType) -> Self:
         for all columns, while also setting the Table's attributes.
         """
         null_array = pa.repeat(None, size)
-        data = [null_array for _ in range(len(cls.schema))]  # type: ignore
+        data = [null_array for _ in range(len(cls.schema))]
         null_table = pa.table(data, schema=cls.schema)
         return cls.from_pyarrow(table=null_table, validate=False, permit_nulls=True, **kwargs)