Separate static analysis, move tests out of the package

.azure-pipelines.yml

@@ -28,25 +28,32 @@ jobs:
   - script: |
       python -m pip install --upgrade pip
       pip install pytest-azurepipelines wheel
-      pip install -e .[dev,doc,test,louvain,leiden,magic,scvi,harmony]
+      pip install .[dev,doc,test,louvain,leiden,magic,scvi,harmony]
     displayName: 'Install dependencies'
 
-  - script: |
-      pip install -v git+https://github.com/theislab/anndata
+  - script: pip install -v git+https://github.com/theislab/anndata
     displayName: 'Install development anndata'
     condition: eq(variables['ANNDATA_DEV'], 'yes')
 
+  - script: pytest --ignore=tests/_images
+    displayName: 'PyTest'
+
+- job: static_analysis
+  pool:
+    vmImage: 'ubuntu-16.04'
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.8'
+    displayName: 'Use Python 3.8'
+
+  - script: pip install black docutils
+    displayName: 'Install dependencies'
+
   - script: |
-      pip install black
       black . --check --diff
-      python -m scanpy.tests.blackdiff 10
+      python -m tests.blackdiff 10
     displayName: 'Black'
 
-  - script: |
-      pytest --ignore=scanpy/tests/_images
-    displayName: 'PyTest'
-
-  - script: |
-      python setup.py check --restructuredtext --strict
-      rst2html.py --halt=2 README.rst >/dev/null
+  - script: rst2html.py --halt=2 README.rst >/dev/null
     displayName: 'rst2html'

.travis.yml

@@ -11,7 +11,7 @@ matrix:
     - pip install .[dev,doc]
     script:
     - black . --check --diff
-    - python -m scanpy.tests.blackdiff 10
+    - python -m tests.blackdiff 10
     - python setup.py check --restructuredtext --strict
     - rst2html.py --halt=2 README.rst >/dev/null
     after_success: skip
@@ -33,4 +33,4 @@ install:
 env:
 - MPLBACKEND=Agg
 script:
-- pytest --ignore=scanpy/tests/_images
+- pytest --ignore=tests/_images

pyproject.toml

@@ -14,7 +14,7 @@ author-email = '[email protected], [email protected]'
 
 [tool.pytest.ini_options]
 python_files = 'test_*.py'
-testpaths = 'scanpy/tests/'
+testpaths = 'tests/'
 xfail_strict = true
 markers = [
     'internet: tests which rely on internet resources (enable with `--internet-tests`)',
@@ -60,16 +60,4 @@ exclude = '''
         |palettes
         |_tools/(__init__|paga)
     )
-    |tests/(
-        test_get
-        |test_neighbors
-        |test_readwrite
-        |test_clustering
-        |test_preprocessing
-        |test_rank_genes_groups
-        |test_marker_gene_overlap
-        |test_highly_variable_genes
-        |test_rank_genes_groups_logreg
-        |notebooks/(test_paga_paul15_subsampled|test_pbmc3k)
-    )
 ).py'''

tests/conftest.py

@@ -0,0 +1,140 @@
+import sys
+from pathlib import Path
+
+import matplotlib as mpl
+import numpy as np
+from anndata import AnnData
+from scipy import sparse
+from anndata.tests.helpers import asarray, assert_equal
+
+mpl.use('agg')
+from matplotlib import pyplot
+from matplotlib.testing.compare import compare_images
+import pytest
+
+import scanpy
+
+scanpy.settings.verbosity = "hint"
+
+# define this after importing scanpy but before running tests
+IMPORTED = frozenset(sys.modules.keys())
+
+
+@pytest.fixture
+def imported_modules():
+    return IMPORTED
+
+
+def make_comparer(path_expected: Path, path_actual: Path, *, tol: int):
+    def save_and_compare(basename, tolerance=None):
+        path_actual.mkdir(parents=True, exist_ok=True)
+        out_path = path_actual / f'{basename}.png'
+        pyplot.savefig(out_path, dpi=40)
+        pyplot.close()
+        if tolerance is None:
+            tolerance = tol
+        res = compare_images(
+            str(path_expected / f'{basename}.png'), str(out_path), tolerance
+        )
+        assert res is None, res
+
+    return save_and_compare
+
+
+@pytest.fixture
+def image_comparer():
+    return make_comparer
+
+
+@pytest.fixture
+def plt():
+    return pyplot
+
+
+@pytest.fixture(
+    params=[sparse.csr_matrix, sparse.csc_matrix, asarray],
+    ids=["scipy-csr", "scipy-csc", "np-ndarray"],
+)
+def array_type(request):
+    """Function which converts passed array to one of the common array types."""
+    return request.param
+
+
+@pytest.fixture(params=[np.float64, np.float32])
+def float_dtype(request):
+    return request.param
+
+
+###########################
+# Representation choice
+###########################
+# These functions can be used to check that functions are correctly using arugments
+# like `layers`, `obsm`, etc.
+
+
+@pytest.fixture(scope='session')
+def check_rep_mutation():
+    def check_rep_mutation(func, X, **kwargs):
+        """Check that only the array meant to be modified is modified."""
+        adata = AnnData(
+            X=X.copy(),
+            layers={"layer": X.copy()},
+            obsm={"obsm": X.copy()},
+            dtype=X.dtype,
+        )
+        adata_X = func(adata, copy=True, **kwargs)
+        adata_layer = func(adata, layer="layer", copy=True, **kwargs)
+        adata_obsm = func(adata, obsm="obsm", copy=True, **kwargs)
+
+        assert np.array_equal(asarray(adata_X.X), asarray(adata_layer.layers["layer"]))
+        assert np.array_equal(asarray(adata_X.X), asarray(adata_obsm.obsm["obsm"]))
+
+        assert np.array_equal(asarray(adata_layer.X), asarray(adata_layer.obsm["obsm"]))
+        assert np.array_equal(
+            asarray(adata_obsm.X), asarray(adata_obsm.layers["layer"])
+        )
+        assert np.array_equal(
+            asarray(adata_X.layers["layer"]), asarray(adata_X.obsm["obsm"])
+        )
+
+    return check_rep_mutation
+
+
+@pytest.fixture(scope='session')
+def check_rep_results():
+    def check_rep_results(func, X, **kwargs):
+        """Checks that the results of a computation add values/
+        mutate the anndata object in a consistent way.
+        """
+        # Gen data
+        adata_X = AnnData(
+            X=X.copy(),
+            layers={"layer": np.zeros(shape=X.shape, dtype=X.dtype)},
+            obsm={"obsm": np.zeros(shape=X.shape, dtype=X.dtype)},
+        )
+        adata_layer = AnnData(
+            X=np.zeros(shape=X.shape, dtype=X.dtype),
+            layers={"layer": X.copy()},
+            obsm={"obsm": np.zeros(shape=X.shape, dtype=X.dtype)},
+        )
+        adata_obsm = AnnData(
+            X=np.zeros(shape=X.shape, dtype=X.dtype),
+            layers={"layer": np.zeros(shape=X.shape, dtype=X.dtype)},
+            obsm={"obsm": X.copy()},
+        )
+
+        # Apply function
+        func(adata_X, **kwargs)
+        func(adata_layer, layer="layer", **kwargs)
+        func(adata_obsm, obsm="obsm", **kwargs)
+
+        # Reset X
+        adata_X.X = np.zeros(shape=X.shape, dtype=X.dtype)
+        adata_layer.layers["layer"] = np.zeros(shape=X.shape, dtype=X.dtype)
+        adata_obsm.obsm["obsm"] = np.zeros(shape=X.shape, dtype=X.dtype)
+
+        # Check equality
+        assert_equal(adata_X, adata_layer)
+        assert_equal(adata_X, adata_obsm)
+
+    return check_rep_results