Remove references to numba_scipy

it's now vendored in

conda/recipe-meta/meta.yaml

@@ -21,7 +21,6 @@ requirements:
   run:
     - python >=3.7
     - {{ pin_compatible('hdc-algo-core', max_pin='x.x.x') }}
-    - numba-scipy >=0.3.1
     - scipy
 
 test:

dev-env.yml

@@ -1,23 +1,22 @@
 # Setup instructions:
 #   > mamba env create -f dev-env.yml
-#   > conda activate vam-hdc-algo
+#   > conda activate hdc-algo
 #   > pip install -e .
 #   > pytest -s tests/
 name: hdc-algo
 channels:
   - conda-forge
 
 dependencies:
-  - python =3.9
-  - pip =20
+  - python =3.10
+  - pip =23
 
   # hdc-algo dependencies
   - xarray
   - numpy
   - numba
   - dask[array]
   - scipy
-  - numba-scipy >=0.3.0
 
   # tests and dev
   ## to use from jupyter-lab: `python -m ipykernel install --user --name vam-seasmon`
@@ -33,10 +32,6 @@ dependencies:
   - pycodestyle
   - pylint
   - docutils
-  ### shed dependencies
-  - pyyaml
-  - pyupgrade
-  - libcst
 
   ## test
   - pytest

hdc/algo/ops/stats.py

@@ -2,12 +2,14 @@
 from math import erf, log, sqrt
 
 import numba
-import numba_scipy  # pylint: disable=unused-import
 import numpy as np
 import scipy.special as sc
 
+from ..vendor.numba_scipy import _init_extension
 from ._helper import lazycompile
 
+_init_extension()
+
 
 @numba.njit
 def brentq(xa, xb, s):

pyproject.toml

@@ -26,12 +26,21 @@ exclude = '''
   | _build
   | build
   | dist
+  | hdc/algo/vendor
 )/
 '''
 
 [tool.isort]
 profile = "black"
 
+[tool.pylint.main]
+ignore-paths = [
+   "hdc/algo/vendor/*"
+]
+extension-pkg-allow-list = [
+  "scipy.special"
+]
+
 [tool.pylint.messages_control]
 max-line-length = 99
 
@@ -48,4 +57,7 @@ disable = [
   "fixme",
   "wrong-import-order",
   "unnecessary-lambda-assignment",
-]
+]
+
+[tool.pydocstyle]
+match-dir = "(?!vendor).*"

requirements.txt

@@ -1,7 +1,5 @@
-numba-scipy==0.3.1
-scipy==1.7.3
-numba==0.57.0
-numpy==1.22.4
-xarray==2023.5.0
-
+scipy
+numba
+numpy
+xarray
 dask[array]

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-name =hdc-algo 
+name = hdc-algo
 description = xarray tools for seasonal monitor
 version = attr: hdc.algo._version.__version__
 author = WFP-VAM
@@ -43,7 +43,6 @@ test =
     pytest
 stats =
     scipy
-    numba-scipy
 
 [options.packages.find]
 include =
@@ -52,3 +51,7 @@ include =
 [aliases]
 # Define setup.py command aliases here
 test = pytest
+
+[options.entry_points]
+numba_extensions =
+  init = hdc.algo.vendor.numba_scipy:_init_extension