Test against mindeps

.azure-pipelines.yml

@@ -5,7 +5,9 @@ variables:
   PIP_CACHE_DIR: $(Pipeline.Workspace)/.pip
   RUN_COVERAGE: no
   PYTEST_ADDOPTS: --color=yes --junitxml=test-data/test-results.xml
-  PRERELEASE_DEPENDENCIES: no
+  # PRERELEASE_DEPENDENCIES: no
+  DEPENDENCIES_VERSION: "latest"
+  TEST_TYPE: "standard"
 
 jobs:
   - job: PyTest
@@ -16,11 +18,16 @@ jobs:
         Python3.11:
           python.version: "3.11"
           RUN_COVERAGE: yes
+          TEST_TYPE: "coverage"
         Python3.9:
           python.version: "3.9"
         PreRelease:
           python.version: "3.11"
-          PRERELEASE_DEPENDENCIES: yes
+          DEPENDENCIES_VERSION: "pre-release"
+          TEST_TYPE: "strict-warning"
+        MinDeps:
+          python.version: "3.9"
+          DEPENDENCIES_VERSION: "minimum"
     steps:
       - task: UsePythonVersion@0
         inputs:
@@ -40,13 +47,20 @@ jobs:
           python -m pip install --upgrade pip wheel
           pip install .[dev,test]
         displayName: "Install dependencies"
-        condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'no')
+        condition: eq(variables['DEPENDENCIES_VERSION'], 'latest')
+
+      - script: |
+          python -m pip install pip wheel tomli packaging
+          pip install `python3 ci/scripts/min-deps.py pyproject.toml --extra dev test`
+          pip install --no-deps .
+        displayName: "Install minimum dependencies"
+        condition: eq(variables['DEPENDENCIES_VERSION'], 'minimum')
 
       - script: |
           python -m pip install --pre --upgrade pip wheel
           pip install --pre .[dev,test]
         displayName: "Install dependencies release candidates"
-        condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'yes')
+        condition: eq(variables['DEPENDENCIES_VERSION'], 'pre-release')
 
       - script: |
           pip list
@@ -55,23 +69,27 @@ jobs:
       - script: |
           pytest
         displayName: "PyTest"
-        condition: and(eq(variables['RUN_COVERAGE'], 'no'), eq(variables['PRERELEASE_DEPENDENCIES'], 'no'))
+        condition: eq(variables['TEST_TYPE'], 'standard')
+        # and(eq(variables['RUN_COVERAGE'], 'no'), eq(variables['PRERELEASE_DEPENDENCIES'], 'no'))
 
       - script: |
           pytest --cov --cov-report=xml --cov-context=test
         displayName: "PyTest (coverage)"
-        condition: and(eq(variables['RUN_COVERAGE'], 'yes'), eq(variables['PRERELEASE_DEPENDENCIES'], 'no'))
+        condition: eq(variables['TEST_TYPE'], 'coverage')
+        # condition: and(eq(variables['RUN_COVERAGE'], 'yes'), eq(variables['PRERELEASE_DEPENDENCIES'], 'no'))
 
       - script: |
           pytest --strict-warnings
         displayName: "PyTest (treat warnings as errors)"
-        condition: and(eq(variables['RUN_COVERAGE'], 'no'), eq(variables['PRERELEASE_DEPENDENCIES'], 'yes'))
+        condition: eq(variables['TEST_TYPE'], 'strict-warning')
+        # condition: and(eq(variables['RUN_COVERAGE'], 'no'), eq(variables['PRERELEASE_DEPENDENCIES'], 'yes'))
 
       - task: PublishCodeCoverageResults@1
         inputs:
           codeCoverageTool: Cobertura
           summaryFileLocation: "test-data/coverage.xml"
-        condition: eq(variables['RUN_COVERAGE'], 'yes')
+        condition: eq(variables['TEST_TYPE'], 'coverage')
+        # eq(variables['RUN_COVERAGE'], 'yes')
 
       - task: PublishTestResults@2
         condition: succeededOrFailed()
@@ -82,7 +100,8 @@ jobs:
 
       - script: bash <(curl -s https://codecov.io/bash)
         displayName: "Upload to codecov.io"
-        condition: eq(variables['RUN_COVERAGE'], 'yes')
+        condition: eq(variables['TEST_TYPE'], 'coverage')
+        # eq(variables['RUN_COVERAGE'], 'yes')
 
   - job: CheckBuild
     pool:

ci/scripts/min-deps.py

@@ -0,0 +1,72 @@
+#!python3
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+import tomli
+from packaging.requirements import Requirement
+from packaging.version import Version
+
+
+def min_dep(req: Requirement) -> str:
+    """
+    Given a requirement, return the minimum version specifier.
+
+    Example
+    -------
+
+    >>> min_dep(Requirement("numpy>=1.0"))
+    "numpy==1.0"
+    """
+    req_name = req.name
+    if req.extras:
+        req_name = f"{req_name}[{','.join(req.extras)}]"
+
+    # TODO: Should this be allowed?
+    if not req.specifier:
+        return req_name
+
+    min_version = Version("0.0.0.a1")
+    for spec in req.specifier:
+        if spec.operator in [">", ">=", "~-"]:
+            min_version = max(min_version, Version(spec.version))
+
+    # TODO: should this return `~=` or `==`?
+    return f"{req_name}=={min_version}.*"
+
+
+def extract_min_deps(dependencies: list[str]) -> list[str]:
+    return [min_dep(Requirement(dep)) for dep in dependencies]
+
+
+def main():
+    # TODO: Allow optional dependencies
+    parser = argparse.ArgumentParser(
+        prog="min-deps",
+        description="""Parse a pyproject.toml file and output a list of minimum dependencies.
+
+        Output is directly passable to `pip install`.""",
+        usage="pip install `python min-deps.py pyproject.toml`",
+    )
+    parser.add_argument(
+        "path", type=Path, help="pyproject.toml to parse minimum dependencies from"
+    )
+    parser.add_argument("--extras", type=str, nargs="*", help="extras to install")
+
+    args = parser.parse_args()
+
+    pyproject = tomli.loads(args.path.read_text())
+
+    deps = pyproject["project"]["dependencies"]
+
+    for extra in args.extras:
+        deps += pyproject["project"]["optional-dependencies"][extra]
+
+    min_deps = extract_min_deps(deps)
+
+    print(" ".join(min_deps))
+
+
+if __name__ == "__main__":
+    main()

ci/scripts/run-min-deps.sh

@@ -0,0 +1,18 @@
+# conda deactivate
+
+mamba env remove -yn anndata-min-deps-test
+mamba create -yn anndata-min-deps-test "python=3.9"
+
+PACKAGES=`python3 ci/scripts/min-deps.py pyproject.toml --extra dev test`
+
+# conda activate anndata-min-deps-test
+# conda run -n anndata-min-deps-test pip install cupy-cuda12x
+
+
+echo Installing $PACKAGES
+conda run -n anndata-min-deps-test pip install $PACKAGES
+conda run -n anndata-min-deps-test pip install pytest-xdist # cupy-cuda12x
+conda run -n anndata-min-deps-test pip install -e . --no-deps
+conda run -n anndata-min-deps-test pytest -n auto
+
+conda list -n anndata-min-deps-tests

pyproject.toml

@@ -36,16 +36,15 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
-    # pandas <1.1.1 has pandas/issues/35446
+    # pandas <1.4 has pandas/issues/35446
     # pandas 2.1.0rc0 has pandas/issues/54622
-    # pandas 2.1.2 has pandas/issues/52927
-    "pandas >=1.1.1, !=2.1.0rc0, !=2.1.2",
-    "numpy>=1.16.5",                         # required by pandas 1.x
-    "scipy>1.4",
-    "h5py>=3",
+    "pandas >=1.4, !=2.1.0rc0, !=2.1.2",
+    "numpy>=1.23",
+    "scipy>1.8",
+    "h5py>=3.1",
     "exceptiongroup; python_version<'3.11'",
     "natsort",
-    "packaging>=20",
+    "packaging>=20.0",
     "array_api_compat",
 ]
 dynamic = ["version"]
@@ -81,7 +80,7 @@ doc = [
 ]
 test = [
     "loompy>=3.0.5",
-    "pytest >=6.0",
+    "pytest>=7.3",
     "pytest-cov>=2.10",
     "zarr",
     "matplotlib",
@@ -91,7 +90,7 @@ test = [
     "boltons",
     "scanpy",
     "httpx", # For data downloading
-    "dask[array,distributed]",
+    "dask[array,distributed]>=2022.01",
     "awkward>=2.3, !=2.5.2",
     "pyarrow",
     "pytest_memray",