Replace cyfunc with native cython ufuncs. (#28)

* Add workflow dispatch trigger.

* Update actions and Python version.

* Add `.readthedocs.yaml` config and `index.rst` symlink.

* Fix Python version identifier.

* Preinstall cython and cyfunc.

* Remove compiled cython for `clean` target.

* Update requirements and replace cyfunc with `cython.ufunc`.

* Update cython installation.

* Add pyproject.toml for build dependencies.

* Remove Cython pre-install step.

.github/workflows/main.yml

@@ -5,6 +5,7 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
+  workflow_dispatch:
 
 jobs:
   build:
@@ -13,11 +14,11 @@ jobs:
         command: [make build, make inference_test]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8.x
+        python-version: "3.10"
     - name: Install dependencies
       run: pip install -r requirements.txt
     - name: Build docs, lint, and test

.readthedocs.yaml

@@ -0,0 +1,9 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+python:
+  install:
+  - requirements: requirements.txt

Makefile

@@ -18,6 +18,7 @@ docs : doctests
 
 clean :
 	rm -rf docs/_build PolyChordLite
+	rm -f shedding/*.so shedding/*.c
 
 clean-results:
 	rm -rf workspace figures results.html

conf.py

@@ -105,7 +105,6 @@ def setup(app):
 project = 'shedding'
 copyright = '2020, Till Hoffmann'
 author = 'Till Hoffmann'
-master_doc = 'README'
 
 
 # -- General configuration ---------------------------------------------------

index.rst

@@ -0,0 +1 @@
+README.rst

pyproject.toml

@@ -0,0 +1,11 @@
+[build-system]
+requires = ["setuptools", "wheel", "Cython", "numpy", "scipy"]
+
+[project]
+name = 'shedding'
+version = '0.1'
+authors = [{ name = 'Till Hoffmann' }]
+dependencies = ['numpy', 'scipy']
+
+[tool.setuptools]
+packages = ['shedding']

requirements.in

@@ -1,5 +1,14 @@
--e file:.[tests,docs]
+-e file:.
+cython
+flake8
+jinja2
+jsonschema
 jupyter
+linuxdoc @ git+http://github.com/return42/linuxdoc.git
 localscope
+matplotlib
 pandas
+pytest
+pytest-cov
+sphinx
 tqdm