Merge pull request #34 from yqiqichen/devel

Adding GitHub actions

.github/workflows/publish.yml

@@ -0,0 +1,48 @@
+name: Publish Python distributions to PyPI
+on: push
+
+jobs:
+    build-n-publish:
+        name: Build and publish Python distributions to PyPI
+        runs-on: ubuntu-latest
+        permissions:
+          contents: read
+          id-token: write
+        environment: release
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                python-version: "3.x"
+
+            - name: Install pypa/build
+              run: >-
+                python3 -m
+                pip install
+                --upgrade 
+                build
+
+            - name: Initialize submodules
+              run: |
+                git submodule update --init
+
+            - name: Build SDist and wheel
+              run: python3 -m build
+
+            - uses: actions/upload-artifact@v3
+              with:
+                path: dist/*
+
+            - name: Check metadata
+              run: pipx run twine check dist/*
+
+            - uses: actions/download-artifact@v3
+              with:
+                name: artifact
+                path: dist
+
+            - name: Publish distribution to PyPI
+              if: startsWith(github.ref, 'refs/tags')
+              uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

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+name: Evaluate code syntax and correctness
+on: [push, pull_request]
+
+jobs:
+    pre-commit_and_pytest:
+        name: Run pre-commit and pytest
+        strategy:
+          matrix:
+            os: [ubuntu-latest, Windows-latest, macos-latest]
+        runs-on: ${{ matrix.os }}
+        permissions:
+            contents: read
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                python-version: "3.11.x"
+
+            - uses: pre-commit/[email protected]
+              name: Run pre-commit
+
+            - name: Install pypa/build
+              run: >-
+                python3 -m
+                pip install
+                --upgrade 
+                build
+            
+            - name: Initialize submodules
+              run: |
+                  git submodule update --init
+  
+            - name: Build SDist and wheel
+              run: python3 -m build
+
+            - name: Install AlphaPeel
+              run: pip install dist/AlphaPeel-1.1.3-py3-none-any.whl
+
+            - name: Install pytest
+              run: |
+                pip install pytest
+                pip install pytest-benchmark
+            
+            - name: Run pytest
+              run: |
+                pytest

pyproject.toml

@@ -0,0 +1,35 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "AlphaImpute2"
+version = "0.0.3"
+authors = [
+  { name="Andrew Whalen", email="[email protected]" },
+]
+description = "An imputation software for massive livestock populations."
+# readme corresponds to the long_description
+# "*.md" specifies the long_description_content_type
+readme = "README.md"
+license = {file = "MIT_License.txt"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+# correspond to install_requires
+dependencies = [
+    "numpy>=1.19",
+    "numba>=0.49.0"
+]
+
+[project.scripts]
+# correspond to entry_points
+AlphaImpute2 = "alphaimpute2.alphaimpute2:main"
+
+[project.urls]
+"Homepage" = "https://github.com/AlphaGenes/AlphaImpute2"
+"Bug Tracker" = "https://github.com/AlphaGenes/AlphaImpute2/issues"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+packages = ["alphaimpute2", "alphaimpute2.tinyhouse", "alphaimpute2.Imputation"]