add moran from scanpy (#317)

* add moran from scanpy * add abs to pvalue * fix pvalues * add standard approx from perm pvalue (pysal dep return) * change req * update tests and req * add gearys' and unify function * add analytic pvalues * fix tests and docstring * explicilty add leiden * explicilty add leiden * Fix tests * resolve comments * more fixes * Add CI job * Pass mode instead of function * Force restore tox cache, fix not passing env var * Pass backend as env * Fix doc linting condition * remove pysal from setup * remaining comments, modify return excluding nan * fix tests * Fix docs, mypy, and some pet peeves * Fix wrong requirement * [ci skip] Remove doc linting Co-authored-by: Michal Klein <michal.klein@protonmail.com>
scverse · Apr 9, 2021 · d8c20d7 · d8c20d7
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commit d8c20d7
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Showing 22 changed files with 299 additions and 127 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -112,14 +112,12 @@ jobs:
             with:
                 path: .tox
                 key: tox-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/tox.ini') }}
-                restore-keys: |
-                    tox-${{ runner.os }}-${{ env.pythonLocation }}-
-                    tox-${{ runner.os }}-
 
         -   name: Testing
             run: |
                 tox -vv
             env:
+                MPLBACKEND: agg
                 PLATFORM: ${{ matrix.os }}
                 DISPLAY: :42
 

diff --git a/.mypy.ini b/.mypy.ini
@@ -14,7 +14,7 @@ disallow_any_generics = True
 strict_optional = True
 strict_equality = True
 warn_return_any = True
-warn_unreachable = True
+warn_unreachable = False
 check_untyped_defs = True
 ; because of docrep
 allow_untyped_decorators = True

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.800
+    rev: v0.812
     hooks:
     -   id: mypy
         additional_dependencies: [numpy, scipy, pandas]
@@ -17,7 +17,7 @@ repos:
     -   id: black
         additional_dependencies: [toml]
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.7.0
+    rev: 5.8.0
     hooks:
     -   id: isort
         additional_dependencies: [toml]
@@ -61,12 +61,12 @@ repos:
     -   id: autoflake
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+    rev: 3.9.0
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-mock, flake8-string-format]
 -   repo: https://github.com/jumanjihouse/pre-commit-hooks
-    rev: 2.1.4
+    rev: 2.1.5
     hooks:
     -   id: script-must-have-extension
         name: Check executable files use .sh extension
@@ -77,7 +77,7 @@ repos:
     hooks:
     -   id: rstcheck
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.9.2
+    rev: v1.10.0
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==20.8b1]
@@ -87,7 +87,7 @@ repos:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.7.0
+    rev: v1.8.0
     hooks:
     -   id: python-no-eval
     -   id: python-use-type-annotations

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -19,7 +19,7 @@ Graph
     gr.centrality_scores
     gr.interaction_matrix
     gr.ligrec
-    gr.moran
+    gr.spatial_autocorr
     gr.ripley_k
     gr.co_occurrence
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -67,7 +67,7 @@
     pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
     anndata=("https://anndata.readthedocs.io/en/stable/", None),
     scanpy=("https://scanpy.readthedocs.io/en/stable/", None),
-    matplotlib=("https://matplotlib.org/", None),
+    matplotlib=("https://matplotlib.org/stable/", None),
     seaborn=("https://seaborn.pydata.org/", None),
     joblib=("https://joblib.readthedocs.io/en/latest/", None),
     networkx=("https://networkx.org/documentation/stable/", None),

diff --git a/docs/source/utils.py b/docs/source/utils.py
@@ -93,6 +93,10 @@ def _download_dir(url: str, *, path: Union[str, Path], depth: int) -> Tuple[bool
 
 
 def _download_notebooks(org: str, repo: str, raise_exc: bool = False) -> None:
+    if not int(os.environ.get("SQUIDPY_DOWNLOAD_NOTEBOOKS", 1)):
+        info("Not downloading notebooks because a flag is set")
+        return
+
     ep = ENDPOINT_FMT.format(org=org, repo=repo)
     for path in [FIXED_TUTORIALS_DIR, TUTORIALS_DIR, EXAMPLES_DIR, GENMOD_DIR]:
         ok, reason = _download_dir(urljoin(ep, path), path=path, depth=DEPTH)

diff --git a/requirements.txt b/requirements.txt
@@ -2,10 +2,11 @@ anndata>=0.7.4
 dask>=2.30
 docrep>=0.3.1
 ipywidgets>=7.5.1  # progress bar
+leidenalg>=0.8.2
 omnipath>=1.0.4
 pandas>=1.2.0
 rasterio>=1.1.8
-scanpy[leiden]>=1.7.0
+scanpy @ git+https://github.com/theislab/scanpy@master # scanpy[leiden]>=1.7.0
 scikit-image>=0.17.1
 statsmodels>=0.12.0
 tifffile>=2020.10.1

diff --git a/setup.py b/setup.py
@@ -45,7 +45,7 @@
             if not l.startswith("-r")
         ],
         interactive=["PyQt5>=5.15.0", "napari>=0.4.2"],
-        all=["PyQt5>=5.15.0", "napari>=0.4.2", "esda>=2.3.1", "libpysal>=4.3.0", "astropy>=4.1"],
+        all=["PyQt5>=5.15.0", "napari>=0.4.2", "astropy>=4.1"],
     ),
     classifiers=[
         "Development Status :: 5 - Production/Stable",

diff --git a/squidpy/_constants/_constants.py b/squidpy/_constants/_constants.py
@@ -88,3 +88,9 @@ class DendrogramAxis(ModeEnum):  # noqa: D101
 class Symbol(ModeEnum):  # noqa: D101
     DISC = "disc"
     SQUARE = "square"
+
+
+@unique
+class SpatialAutocorr(ModeEnum):  # noqa: D101
+    MORAN = "moran"
+    GEARY = "geary"
diff --git a/squidpy/_utils.py b/squidpy/_utils.py
@@ -57,7 +57,7 @@ def _unique_order_preserving(iterable: Iterable[Hashable]) -> Tuple[List[Hashabl
 
 
 class Signal(Enum):
-    """Signalling values when informing parallelizer."""
+    """Signaling values when informing parallelizer."""
 
     NONE = 0
     UPDATE = 1

diff --git a/squidpy/gr/__init__.py b/squidpy/gr/__init__.py
@@ -2,4 +2,4 @@
 from squidpy.gr._build import spatial_neighbors
 from squidpy.gr._nhood import nhood_enrichment, centrality_scores, interaction_matrix
 from squidpy.gr._ligrec import ligrec
-from squidpy.gr._ppatterns import moran, ripley_k, co_occurrence
+from squidpy.gr._ppatterns import ripley_k, co_occurrence, spatial_autocorr