scverse · flying-sheep · Apr 9, 2024 · Sep 8, 2023 · Sep 8, 2023 · Oct 2, 2023
diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml
@@ -4,7 +4,8 @@ trigger:
 
 variables:
   RUN_COVERAGE: no
-  PYTEST_ADDOPTS: --color=yes --junitxml=test-data/test-results.xml
+  # TODO: remove paths after moving tests to test dir
+  PYTEST_ADDOPTS: --color=yes --junitxml=test-data/test-results.xml anndata ./src/anndata/tests ./docs/concatenation.rst
   DEPENDENCIES_VERSION: "latest" # |"pre-release" | "minimum-version"
   TEST_TYPE: "standard" # | "coverage"
 
@@ -41,10 +42,10 @@ jobs:
 
       - task: Cache@2
         inputs:
-          key: '"python $(python.version)" | "$(Agent.OS)" | pyproject.toml'
+          key: '2 | "python $(python.version)" | "$(Agent.OS)" | pyproject.toml'
           restoreKeys: |
-            python | "$(Agent.OS)"
-            python
+            2 | python | "$(Agent.OS)"
+            2 | python
           path: $(uv_cache_dir)
         displayName: Cache pip packages
 

diff --git a/.gitignore b/.gitignore
@@ -10,7 +10,7 @@ __pycache__/
 
 # Distribution / packaging
 /dist/
-/anndata/_version.py
+/src/anndata/_version.py
 /requirements*.lock
 /.python-version
 /hatch.toml

diff --git a/pyproject.toml b/pyproject.toml
@@ -83,7 +83,7 @@ doc = [
 ]
 test = [
     "loompy>=3.0.5",
-    "pytest>=7.3",
+    "pytest>=8.1",
     "pytest-cov>=2.10",
     "zarr",
     "matplotlib",
@@ -102,15 +102,21 @@ test = [
 gpu = ["cupy"]
 
 [tool.hatch.build]
-exclude = ["anndata/tests/test_*.py", "anndata/tests/data"]
+exclude = [
+    "src/anndata/tests/conftest.py",
+    "src/anndata/tests/test_*.py",
+    "src/anndata/tests/data",
+]
 [tool.hatch.version]
 source = "vcs"
 [tool.hatch.build.hooks.vcs]
-version-file = "anndata/_version.py"
+version-file = "src/anndata/_version.py"
 
 [tool.coverage.run]
-source = ["anndata"]
-omit = ["anndata/_version.py", "**/test_*.py"]
+source_pkgs = ["anndata"]
+omit = ["src/anndata/_version.py", "**/test_*.py"]
+[tool.coverage.paths]
+source = ["./src", "**/site-packages"]
 
 [tool.coverage.report]
 exclude_also = [
@@ -119,8 +125,10 @@ exclude_also = [
 
 [tool.pytest.ini_options]
 addopts = [
+    # "--import-mode=importlib",  # TODO: enable
     "--strict-markers",
     "--doctest-modules",
+    "--pyargs",
 ]
 filterwarnings = [
     'ignore:Support for Awkward Arrays is currently experimental',
@@ -137,11 +145,17 @@ filterwarnings_when_strict = [
     "default::dask.array.core.PerformanceWarning",
 ]
 python_files = "test_*.py"
-testpaths = ["anndata", "docs/concatenation.rst"]
+testpaths = [
+    "anndata", # docstrings and unit tests (module name due to --pyargs)
+    "./docs/concatenation.rst", # further doctests
+]
 # For some reason this effects how logging is shown when tests are run
 xfail_strict = true
 markers = ["gpu: mark test to run on GPU"]
 
+[tool.ruff]
+src = ["src"]
+
 [tool.ruff.format]
 docstring-code-format = true
 
@@ -166,7 +180,7 @@ ignore = [
 ]
 [tool.ruff.lint.per-file-ignores]
 # E721 comparing types, but we specifically are checking that we aren't getting subtypes (views)
-"anndata/tests/test_readwrite.py" = ["E721"]
+"src/anndata/tests/test_readwrite.py" = ["E721"]
 [tool.ruff.lint.isort]
 known-first-party = ["anndata"]
 required-imports = ["from __future__ import annotations"]

diff --git a/anndata/__init__.py → src/anndata/__init__.py b/anndata/__init__.py → src/anndata/__init__.py
@@ -5,7 +5,7 @@
 try:  # See https://github.com/maresb/hatch-vcs-footgun-example
     from setuptools_scm import get_version
 
-    __version__ = get_version(root="..", relative_to=__file__)
+    __version__ = get_version(root="../..", relative_to=__file__)
 except (ImportError, LookupError):
     try:
         from ._version import __version__

diff --git a/anndata/_core/__init__.py → src/anndata/_core/__init__.py b/anndata/_core/__init__.py → src/anndata/_core/__init__.py
diff --git a/anndata/_core/access.py → src/anndata/_core/access.py b/anndata/_core/access.py → src/anndata/_core/access.py
diff --git a/anndata/_core/aligned_df.py → src/anndata/_core/aligned_df.py b/anndata/_core/aligned_df.py → src/anndata/_core/aligned_df.py
diff --git a/anndata/_core/aligned_mapping.py → src/anndata/_core/aligned_mapping.py b/anndata/_core/aligned_mapping.py → src/anndata/_core/aligned_mapping.py
diff --git a/anndata/_core/anndata.py → src/anndata/_core/anndata.py b/anndata/_core/anndata.py → src/anndata/_core/anndata.py
diff --git a/anndata/_core/file_backing.py → src/anndata/_core/file_backing.py b/anndata/_core/file_backing.py → src/anndata/_core/file_backing.py
diff --git a/anndata/_core/index.py → src/anndata/_core/index.py b/anndata/_core/index.py → src/anndata/_core/index.py
diff --git a/anndata/_core/merge.py → src/anndata/_core/merge.py b/anndata/_core/merge.py → src/anndata/_core/merge.py
diff --git a/anndata/_core/raw.py → src/anndata/_core/raw.py b/anndata/_core/raw.py → src/anndata/_core/raw.py
diff --git a/anndata/_core/sparse_dataset.py → src/anndata/_core/sparse_dataset.py b/anndata/_core/sparse_dataset.py → src/anndata/_core/sparse_dataset.py
diff --git a/anndata/_core/views.py → src/anndata/_core/views.py b/anndata/_core/views.py → src/anndata/_core/views.py
diff --git a/anndata/_io/__init__.py → src/anndata/_io/__init__.py b/anndata/_io/__init__.py → src/anndata/_io/__init__.py
diff --git a/anndata/_io/h5ad.py → src/anndata/_io/h5ad.py b/anndata/_io/h5ad.py → src/anndata/_io/h5ad.py
diff --git a/anndata/_io/read.py → src/anndata/_io/read.py b/anndata/_io/read.py → src/anndata/_io/read.py
diff --git a/anndata/_io/specs/__init__.py → src/anndata/_io/specs/__init__.py b/anndata/_io/specs/__init__.py → src/anndata/_io/specs/__init__.py
diff --git a/anndata/_io/specs/methods.py → src/anndata/_io/specs/methods.py b/anndata/_io/specs/methods.py → src/anndata/_io/specs/methods.py
diff --git a/anndata/_io/specs/registry.py → src/anndata/_io/specs/registry.py b/anndata/_io/specs/registry.py → src/anndata/_io/specs/registry.py
diff --git a/anndata/_io/utils.py → src/anndata/_io/utils.py b/anndata/_io/utils.py → src/anndata/_io/utils.py
diff --git a/anndata/_io/write.py → src/anndata/_io/write.py b/anndata/_io/write.py → src/anndata/_io/write.py
diff --git a/anndata/_io/zarr.py → src/anndata/_io/zarr.py b/anndata/_io/zarr.py → src/anndata/_io/zarr.py
diff --git a/anndata/_settings.py → src/anndata/_settings.py b/anndata/_settings.py → src/anndata/_settings.py
diff --git a/anndata/_types.py → src/anndata/_types.py b/anndata/_types.py → src/anndata/_types.py
diff --git a/anndata/_warnings.py → src/anndata/_warnings.py b/anndata/_warnings.py → src/anndata/_warnings.py
diff --git a/anndata/compat/__init__.py → src/anndata/compat/__init__.py b/anndata/compat/__init__.py → src/anndata/compat/__init__.py
diff --git a/anndata/compat/exceptiongroups.py → src/anndata/compat/exceptiongroups.py b/anndata/compat/exceptiongroups.py → src/anndata/compat/exceptiongroups.py
diff --git a/anndata/experimental/__init__.py → src/anndata/experimental/__init__.py b/anndata/experimental/__init__.py → src/anndata/experimental/__init__.py
diff --git a/anndata/experimental/_dispatch_io.py → src/anndata/experimental/_dispatch_io.py b/anndata/experimental/_dispatch_io.py → src/anndata/experimental/_dispatch_io.py
diff --git a/anndata/experimental/merge.py → src/anndata/experimental/merge.py b/anndata/experimental/merge.py → src/anndata/experimental/merge.py
diff --git a/anndata/experimental/multi_files/__init__.py → ...data/experimental/multi_files/__init__.py b/anndata/experimental/multi_files/__init__.py → ...data/experimental/multi_files/__init__.py
diff --git a/...xperimental/multi_files/_anncollection.py → ...xperimental/multi_files/_anncollection.py b/...xperimental/multi_files/_anncollection.py → ...xperimental/multi_files/_anncollection.py
diff --git a/anndata/experimental/pytorch/__init__.py → src/anndata/experimental/pytorch/__init__.py b/anndata/experimental/pytorch/__init__.py → src/anndata/experimental/pytorch/__init__.py
diff --git a/anndata/experimental/pytorch/_annloader.py → ...nndata/experimental/pytorch/_annloader.py b/anndata/experimental/pytorch/_annloader.py → ...nndata/experimental/pytorch/_annloader.py
diff --git a/anndata/logging.py → src/anndata/logging.py b/anndata/logging.py → src/anndata/logging.py
diff --git a/anndata/tests/adata-comments.tsv → src/anndata/tests/adata-comments.tsv b/anndata/tests/adata-comments.tsv → src/anndata/tests/adata-comments.tsv
diff --git a/anndata/tests/adata.csv → src/anndata/tests/adata.csv b/anndata/tests/adata.csv → src/anndata/tests/adata.csv
diff --git a/anndata/tests/conftest.py → src/anndata/tests/conftest.py b/anndata/tests/conftest.py → src/anndata/tests/conftest.py
@@ -10,6 +10,9 @@
 # TODO: Should be done in pyproject.toml, see anndata/conftest.py
 warnings.filterwarnings("ignore", category=anndata.OldFormatWarning)
 
+# TODO: remove once we extricated test utils and tests
+collect_ignore = ["helpers.py"]
+
 
 @pytest.fixture
 def backing_h5ad(tmp_path):

diff --git a/anndata/tests/data/archives/readme.md → src/anndata/tests/data/archives/readme.md b/anndata/tests/data/archives/readme.md → src/anndata/tests/data/archives/readme.md
diff --git a/...ata/tests/data/archives/v0.7.0/adata.h5ad → ...ata/tests/data/archives/v0.7.0/adata.h5ad b/...ata/tests/data/archives/v0.7.0/adata.h5ad → ...ata/tests/data/archives/v0.7.0/adata.h5ad
diff --git a/...tests/data/archives/v0.7.0/adata.zarr.zip → ...tests/data/archives/v0.7.0/adata.zarr.zip b/...tests/data/archives/v0.7.0/adata.zarr.zip → ...tests/data/archives/v0.7.0/adata.zarr.zip
diff --git a/...ata/tests/data/archives/v0.7.8/adata.h5ad → ...ata/tests/data/archives/v0.7.8/adata.h5ad b/...ata/tests/data/archives/v0.7.8/adata.h5ad → ...ata/tests/data/archives/v0.7.8/adata.h5ad
diff --git a/...tests/data/archives/v0.7.8/adata.zarr.zip → ...tests/data/archives/v0.7.8/adata.zarr.zip b/...tests/data/archives/v0.7.8/adata.zarr.zip → ...tests/data/archives/v0.7.8/adata.zarr.zip
diff --git a/anndata/tests/data/excel.xlsx → src/anndata/tests/data/excel.xlsx b/anndata/tests/data/excel.xlsx → src/anndata/tests/data/excel.xlsx
diff --git a/anndata/tests/data/umi_tools.tsv.gz → src/anndata/tests/data/umi_tools.tsv.gz b/anndata/tests/data/umi_tools.tsv.gz → src/anndata/tests/data/umi_tools.tsv.gz
diff --git a/anndata/tests/helpers.py → src/anndata/tests/helpers.py b/anndata/tests/helpers.py → src/anndata/tests/helpers.py
diff --git a/anndata/tests/test_anncollection.py → src/anndata/tests/test_anncollection.py b/anndata/tests/test_anncollection.py → src/anndata/tests/test_anncollection.py
diff --git a/anndata/tests/test_annot.py → src/anndata/tests/test_annot.py b/anndata/tests/test_annot.py → src/anndata/tests/test_annot.py
diff --git a/anndata/tests/test_awkward.py → src/anndata/tests/test_awkward.py b/anndata/tests/test_awkward.py → src/anndata/tests/test_awkward.py
diff --git a/anndata/tests/test_backed_sparse.py → src/anndata/tests/test_backed_sparse.py b/anndata/tests/test_backed_sparse.py → src/anndata/tests/test_backed_sparse.py
diff --git a/anndata/tests/test_base.py → src/anndata/tests/test_base.py b/anndata/tests/test_base.py → src/anndata/tests/test_base.py
diff --git a/anndata/tests/test_concatenate.py → src/anndata/tests/test_concatenate.py b/anndata/tests/test_concatenate.py → src/anndata/tests/test_concatenate.py
diff --git a/anndata/tests/test_concatenate_disk.py → src/anndata/tests/test_concatenate_disk.py b/anndata/tests/test_concatenate_disk.py → src/anndata/tests/test_concatenate_disk.py
diff --git a/anndata/tests/test_dask.py → src/anndata/tests/test_dask.py b/anndata/tests/test_dask.py → src/anndata/tests/test_dask.py
diff --git a/anndata/tests/test_dask_view_mem.py → src/anndata/tests/test_dask_view_mem.py b/anndata/tests/test_dask_view_mem.py → src/anndata/tests/test_dask_view_mem.py
diff --git a/anndata/tests/test_deprecations.py → src/anndata/tests/test_deprecations.py b/anndata/tests/test_deprecations.py → src/anndata/tests/test_deprecations.py
diff --git a/anndata/tests/test_get_vector.py → src/anndata/tests/test_get_vector.py b/anndata/tests/test_get_vector.py → src/anndata/tests/test_get_vector.py
diff --git a/anndata/tests/test_gpu.py → src/anndata/tests/test_gpu.py b/anndata/tests/test_gpu.py → src/anndata/tests/test_gpu.py
diff --git a/anndata/tests/test_hdf5_backing.py → src/anndata/tests/test_hdf5_backing.py b/anndata/tests/test_hdf5_backing.py → src/anndata/tests/test_hdf5_backing.py
diff --git a/anndata/tests/test_helpers.py → src/anndata/tests/test_helpers.py b/anndata/tests/test_helpers.py → src/anndata/tests/test_helpers.py
diff --git a/anndata/tests/test_inplace_subset.py → src/anndata/tests/test_inplace_subset.py b/anndata/tests/test_inplace_subset.py → src/anndata/tests/test_inplace_subset.py
diff --git a/anndata/tests/test_io_backwards_compat.py → ...anndata/tests/test_io_backwards_compat.py b/anndata/tests/test_io_backwards_compat.py → ...anndata/tests/test_io_backwards_compat.py
diff --git a/anndata/tests/test_io_conversion.py → src/anndata/tests/test_io_conversion.py b/anndata/tests/test_io_conversion.py → src/anndata/tests/test_io_conversion.py
diff --git a/anndata/tests/test_io_dispatched.py → src/anndata/tests/test_io_dispatched.py b/anndata/tests/test_io_dispatched.py → src/anndata/tests/test_io_dispatched.py
diff --git a/anndata/tests/test_io_elementwise.py → src/anndata/tests/test_io_elementwise.py b/anndata/tests/test_io_elementwise.py → src/anndata/tests/test_io_elementwise.py
diff --git a/anndata/tests/test_io_partial.py → src/anndata/tests/test_io_partial.py b/anndata/tests/test_io_partial.py → src/anndata/tests/test_io_partial.py
diff --git a/anndata/tests/test_io_utils.py → src/anndata/tests/test_io_utils.py b/anndata/tests/test_io_utils.py → src/anndata/tests/test_io_utils.py
diff --git a/anndata/tests/test_io_warnings.py → src/anndata/tests/test_io_warnings.py b/anndata/tests/test_io_warnings.py → src/anndata/tests/test_io_warnings.py
diff --git a/anndata/tests/test_layers.py → src/anndata/tests/test_layers.py b/anndata/tests/test_layers.py → src/anndata/tests/test_layers.py
diff --git a/anndata/tests/test_obsmvarm.py → src/anndata/tests/test_obsmvarm.py b/anndata/tests/test_obsmvarm.py → src/anndata/tests/test_obsmvarm.py
diff --git a/anndata/tests/test_obspvarp.py → src/anndata/tests/test_obspvarp.py b/anndata/tests/test_obspvarp.py → src/anndata/tests/test_obspvarp.py
diff --git a/anndata/tests/test_raw.py → src/anndata/tests/test_raw.py b/anndata/tests/test_raw.py → src/anndata/tests/test_raw.py
diff --git a/anndata/tests/test_readwrite.py → src/anndata/tests/test_readwrite.py b/anndata/tests/test_readwrite.py → src/anndata/tests/test_readwrite.py
diff --git a/anndata/tests/test_repr.py → src/anndata/tests/test_repr.py b/anndata/tests/test_repr.py → src/anndata/tests/test_repr.py
diff --git a/anndata/tests/test_settings.py → src/anndata/tests/test_settings.py b/anndata/tests/test_settings.py → src/anndata/tests/test_settings.py
diff --git a/anndata/tests/test_structured_arrays.py → src/anndata/tests/test_structured_arrays.py b/anndata/tests/test_structured_arrays.py → src/anndata/tests/test_structured_arrays.py
diff --git a/anndata/tests/test_transpose.py → src/anndata/tests/test_transpose.py b/anndata/tests/test_transpose.py → src/anndata/tests/test_transpose.py
diff --git a/anndata/tests/test_uns.py → src/anndata/tests/test_uns.py b/anndata/tests/test_uns.py → src/anndata/tests/test_uns.py
diff --git a/anndata/tests/test_utils.py → src/anndata/tests/test_utils.py b/anndata/tests/test_utils.py → src/anndata/tests/test_utils.py
diff --git a/anndata/tests/test_views.py → src/anndata/tests/test_views.py b/anndata/tests/test_views.py → src/anndata/tests/test_views.py
diff --git a/anndata/tests/test_x.py → src/anndata/tests/test_x.py b/anndata/tests/test_x.py → src/anndata/tests/test_x.py
diff --git a/anndata/utils.py → src/anndata/utils.py b/anndata/utils.py → src/anndata/utils.py