Merge pull request #88 from wells-wood-research/bug/CYTHON-86

Bug/cython-86

.github/workflows/python-build.yml

@@ -0,0 +1,38 @@
+name: Python Build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install .
+        pip install -r dev-requirements.txt
+    - name: Lint with flake8
+      run: |
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest
+    - name: Build wheel
+      run: |
+        pip install wheel
+        python setup.py bdist_wheel

Dockerfile

@@ -20,4 +20,4 @@ RUN pip install --upgrade pip && pip install Cython
 # Install build dependencies from pyproject.toml and runtime dependencies from setup.py
 RUN pip install .
 
-RUN pip install -r requirements.txt
+RUN pip install -r dev-requirements.txt

README.md

@@ -26,15 +26,9 @@ pip install aposteriori
 Change directory to the aposteriori folder if you have not done so already:
 
 ```sh
+git clone https://github.com/wells-wood-research/aposteriori/tree/master
 cd aposteriori/
 ```
-
-Install requirements:
-
-```sh
-pip install -r requirements.txt
-```
-
 Install aposteriori
 
 ```sh
@@ -261,7 +255,7 @@ cd aposteriori/
 Install dependencies:
 
 ```sh
-pip install -r requirements.txt
+pip install -r dev-requirements.txt
 ```
 
 Install aposteriori:
@@ -282,15 +276,14 @@ pytest tests/
 ```
 
 
-### Conda and Pip
+### Pip (only)
 
 Alternatively you can install the repository with pip:
 
-
 ```shell
 git clone https://github.com/wells-wood-research/aposteriori.git
 cd aposteriori/
-pip install -r requirements.txt
+pip install -r dev-requirements.txt
 ```
 
 Install aposteriori:

requirements.txt → dev-requirements.txt

@@ -1,6 +1,8 @@
-ampal==1.5.0
+ampal==1.5.1
+click==8.1.7
 h5py==3.8.0
 hypothesis==6.91.0
-numpy==1.22
+numpy
 pytest==6.2.5
 setuptools==67.8.0
+flake8

make_wheels.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+set -e -u -x
+
+function repair_wheel {
+    wheel="$1"
+    if ! auditwheel show "$wheel"; then
+        echo "Skipping non-platform wheel $wheel"
+    else
+        auditwheel repair "$wheel" --plat "$PLAT" -w /io/wheelhouse/
+    fi
+}
+
+
+# Install a system package required by our library
+yum install -y atlas-devel
+
+# Compile wheels
+for PYBIN in /opt/python/*/bin; do
+    "${PYBIN}/pip" install -r /io/dev-requirements.txt
+    "${PYBIN}/pip" wheel /io/ --no-deps -w wheelhouse/
+done
+
+# Bundle external shared libraries into the wheels
+for whl in wheelhouse/*.whl; do
+    repair_wheel "$whl"
+done
+
+# Install packages and test
+for PYBIN in /opt/python/*/bin/; do
+    "${PYBIN}/pip" install python-manylinux-demo --no-index -f /io/wheelhouse
+    (cd "$HOME"; "${PYBIN}/nosetests" pymanylinuxdemo)
+done

pyproject.toml

@@ -1,3 +1,16 @@
 [build-system]
-requires = ["setuptools>=40.6.0", "wheel", "Cython"]
+requires = ["setuptools", "wheel", "Cython"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "Aposteriori"
+version = "2.1.2"
+requires-python = ">= 3.8"
+readme = "README.md"
+dependencies = [
+    "ampal==1.5.1",
+    "click==8.1.7",
+    "h5py==3.8.0",
+    "numpy",
+    "flake8"
+    ]

setup.py

@@ -1,11 +1,11 @@
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
 setup(
     name="aposteriori",
-    version="2.1.1",
+    version="2.1.2",
     author="Wells Wood Research Group",
     author_email="[email protected]",
     description="A library for the voxelization of protein structures for protein design.",
@@ -20,9 +20,17 @@
     python_requires=">=3.8",
     packages=find_packages("src"),
     package_dir={"": "src"},
+    setup_requires=[
+        "Cython",
+    ],
+    entry_points={
+        "console_scripts": [
+            "make-frame-dataset=aposteriori.data_prep.cli:cli",
+        ],
+    },
     install_requires=[
-        "ampal==1.5.0",
+        "ampal==1.5.1",
+        "click==8.1.7",
         "h5py==3.8.0",
-        "numpy==1.22",
     ],
 )