Simplify the build (#9)

* test simpler setup.py

* Remove "python setup.py develop"

* add requests to pyprojects' build dependency

* update pre-commit config

* add setuptools_scm to pyproject.toml

* test wheel build

* Resurrect find_packages & add manual pb11 installation

* - Resurrect branch policy for wheels.yml
- rename doctests' job name

.github/workflows/doctest.yml

@@ -1,7 +1,7 @@
 name: Doctest
 on: [push]
 jobs:
-  run_pytest_upload_coverage:
+  test_readme_and_sphinx_docs:
     runs-on: ubuntu-latest
     env:
       OS: ubuntu-latest
@@ -17,7 +17,7 @@ jobs:
         run: |
           pip install --upgrade pip
           pip install numpy scipy pandas scikit-learn
-          python setup.py install
+          pip install .
           curl http://files.grouplens.org/datasets/movielens/ml-100k.zip -o ~/.ml-100k.zip
       - name: Run pytest
         run: |

.github/workflows/pre-commit.yml

@@ -10,4 +10,4 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
-    - uses: pre-commit/[email protected].0
+    - uses: pre-commit/[email protected].3

.github/workflows/run-test.yml

@@ -18,7 +18,7 @@ jobs:
           pip install --upgrade pip
           pip install numpy scipy pandas
           sudo apt-get install lcov
-          TEST_BUILD=true python setup.py develop
+          CXXFLAGS="-O0 -g -coverage" pip install -e .
       - name: Run pytest
         run: |
           pip install pytest pytest-cov pytest-mock

.github/workflows/wheels.yml

@@ -19,9 +19,9 @@ jobs:
       - uses: actions/setup-python@v2
         name: Install Python
         with:
-          python-version: '3.7'
+          python-version: "3.7"
       - name: Build sdist
-        run: python setup.py sdist
+        run: pip install pybind11 && python setup.py sdist
       - uses: actions/upload-artifact@v2
         with:
           path: dist/*.tar.gz
@@ -126,7 +126,6 @@ jobs:
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
 
-
       - uses: actions/upload-artifact@v2
         with:
           path: ./wheelhouse/*.whl

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
       - id: isort
         name: isort
   - repo: https://github.com/psf/black
-    rev: 20.8b1 # Replace by any tag/version: https://github.com/psf/black/tags
+    rev: 22.3.0
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.6+

pyproject.toml

@@ -1,3 +1,14 @@
+[build-system]
+requires = [
+  "setuptools>=42",
+  "wheel",
+  "pybind11>=2.8.0",
+  "requests",
+  "setuptools_scm[toml]>=6.2",
+]
+
+build-backend = "setuptools.build_meta"
+
 [tool.black]
 ensure_newline_before_comments = true
 force_grid_wrap = 0
@@ -10,6 +21,7 @@ use_parentheses = true
 ensure_newline_before_comments = true
 force_grid_wrap = 0
 include_trailing_comma = true
+known_third_party = ["pybind11"]
 line_length = 88
 multi_line_output = 3
 use_parentheses = true

setup.py

@@ -1,16 +1,9 @@
-# Taken from
-# https://github.com/wichert/pybind11-example/blob/master/setup.py
-# and modified.
-
 import os
-import sys
-from distutils.ccompiler import CCompiler
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any
 
-import setuptools
-from setuptools import Extension, find_packages, setup
-from setuptools.command.build_ext import build_ext
+from pybind11.setup_helpers import Pybind11Extension, build_ext
+from setuptools import find_packages, setup
 
 install_requires = [
     "numpy>=1.11",
@@ -19,10 +12,7 @@
     "pandas>=1.0.0",
     "typing-extensions>=4.0.0",
 ]
-setup_requires = ["pybind11>=2.5", "requests", "setuptools_scm"]
-
 
-eigen_include_dir = os.environ.get("EIGEN3_INCLUDE_DIR", None)
 
 TEST_BUILD = os.environ.get("TEST_BUILD", None) is not None
 
@@ -32,7 +22,7 @@ class get_eigen_include(object):
     EIGEN3_DIRNAME = "eigen-3.4.0"
 
     def __str__(self) -> str:
-
+        eigen_include_dir = os.environ.get("EIGEN3_INCLUDE_DIR", None)
         if eigen_include_dir is not None:
             return eigen_include_dir
 
@@ -59,22 +49,6 @@ def __str__(self) -> str:
         return str(target_dir)
 
 
-class get_pybind_include:
-    """Helper class to determine the pybind11 include path
-    The purpose of this class is to postpone importing pybind11
-    until it is actually installed, so that the ``get_include()``
-    method can be invoked."""
-
-    def __init__(self, user: bool = False):
-        self.user = user
-
-    def __str__(self) -> str:
-        import pybind11
-
-        include_dir: str = pybind11.get_include(self.user)
-        return include_dir
-
-
 headers = [
     "include/myfm/definitions.hpp",
     "include/myfm/util.hpp",
@@ -90,93 +64,18 @@ def __str__(self) -> str:
 
 
 ext_modules = [
-    Extension(
+    Pybind11Extension(
         "myfm._myfm",
         ["cpp_source/bind.cpp", "cpp_source/Faddeeva.cc"],
         include_dirs=[
             # Path to pybind11 headers
-            get_pybind_include(),
-            get_pybind_include(user=True),
             get_eigen_include(),
             "include",
         ],
-        language="c++",
     ),
 ]
 
 
-def has_flag(compiler: CCompiler, flagname: str) -> bool:
-    """Return a boolean indicating whether a flag name is supported on
-    the specified compiler.
-    """
-    import tempfile
-
-    with tempfile.NamedTemporaryFile("w", suffix=".cpp") as f:
-        f.write("int main (int argc, char **argv) { return 0; }")
-        try:
-            compiler.compile([f.name], extra_postargs=[flagname])
-        except setuptools.distutils.errors.CompileError:
-            return False
-    return True
-
-
-def cpp_flag(compiler: CCompiler) -> str:
-    """Return the -std=c++[11/14/17] compiler flag.
-    The newer version is prefered over c++11 (when it is available).
-    """
-    flags = ["-std=c++11"]
-
-    for flag in flags:
-        if has_flag(compiler, flag):
-            return flag
-
-    raise RuntimeError("Unsupported compiler -- at least C++11 support is needed!")
-
-
-class BuildExt(build_ext):
-    """A custom build extension for adding compiler-specific options."""
-
-    if TEST_BUILD:
-        c_opts: Dict[str, List[str]] = {
-            "msvc": ["/EHsc"],
-            "unix": ["-O0", "-coverage", "-g"],
-        }
-        l_opts: Dict[str, List[str]] = {
-            "msvc": [],
-            "unix": ["-coverage"],
-        }
-    else:
-        c_opts = {
-            "msvc": ["/EHsc"],
-            "unix": [],
-        }
-        l_opts = {
-            "msvc": [],
-            "unix": [],
-        }
-
-    if sys.platform == "darwin":
-        darwin_opts = ["-stdlib=libc++", "-mmacosx-version-min=10.7"]
-        c_opts["unix"] += darwin_opts
-        l_opts["unix"] += darwin_opts
-
-    def build_extensions(self) -> None:
-        ct = self.compiler.compiler_type
-        opts = self.c_opts.get(ct, [])
-        link_opts = self.l_opts.get(ct, [])
-        if ct == "unix":
-            opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
-            opts.append(cpp_flag(self.compiler))
-            if has_flag(self.compiler, "-fvisibility=hidden"):
-                opts.append("-fvisibility=hidden")
-        elif ct == "msvc":
-            opts.append('/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version())
-        for ext in self.extensions:
-            ext.extra_compile_args = opts
-            ext.extra_link_args = link_opts
-        build_ext.build_extensions(self)
-
-
 def local_scheme(version: Any) -> str:
     return ""
 
@@ -186,17 +85,16 @@ def local_scheme(version: Any) -> str:
     use_scm_version={"local_scheme": local_scheme},
     author="Tomoki Ohtsuki",
     url="https://github.com/tohtsky/myfm",
-    author_email="tomoki.[email protected]",
-    description="Yet another factorization machine",
+    author_email="tomoki.[email protected]",
+    description="Yet another Bayesian factorization machines.",
     long_description="",
     ext_modules=ext_modules,
     install_requires=install_requires,
-    setup_requires=setup_requires,
-    cmdclass={"build_ext": BuildExt},
-    packages=find_packages("src"),
+    cmdclass={"build_ext": build_ext},
     package_dir={"": "src"},
     zip_safe=False,
     headers=headers,
-    python_requires=">=3.6.0",
+    python_requires=">=3.6",
+    packages=find_packages("src"),
     package_data={"myfm": ["*.pyi"]},
 )

src/myfm/utils/dummy_data.py

@@ -20,7 +20,7 @@ def gen_dummy_rating_df(
     user_indices_all = np.arange(max(int(size / 3), 10))
     item_indices_all = np.arange(max(int(size / 2), 10))
     user_factor = rns.normal(
-        0, 1 / factor_rank ** 0.5, size=(user_indices_all.shape[0], factor_rank)
+        0, 1 / factor_rank**0.5, size=(user_indices_all.shape[0], factor_rank)
     )
     item_factor = rns.normal(0, 1, size=(item_indices_all.shape[0], factor_rank))
 

tests/regression/test_block.py

@@ -29,17 +29,17 @@ def test_block_vfm() -> None:
         [tm_column, user_block[user_indices], item_block[item_indices]]
     )
     X_flatten_squread = X_flatten.copy()
-    X_flatten_squread.data = X_flatten_squread.data ** 2
+    X_flatten_squread.data = X_flatten_squread.data**2
     factor = rns.randn(X_flatten.shape[1], 3)
-    f2 = (factor ** 2).sum(axis=1)
+    f2 = (factor**2).sum(axis=1)
     Xf = X_flatten.dot(factor)
 
     gb = 3.0
     linear_weights = rns.randn(X_flatten.shape[1])
     y = (
         gb
         + X_flatten.dot(linear_weights)
-        + 0.5 * ((Xf ** 2).sum(axis=1) - X_flatten_squread.dot(f2))
+        + 0.5 * ((Xf**2).sum(axis=1) - X_flatten_squread.dot(f2))
         + rns.normal(1.0, size=X_flatten.shape[0])
     )
 
@@ -111,12 +111,12 @@ def test_block() -> None:
         [tm_column, user_block[user_indices], item_block[item_indices]]
     )
     X_flatten_squread = X_flatten.copy()
-    X_flatten_squread.data = X_flatten_squread.data ** 2
+    X_flatten_squread.data = X_flatten_squread.data**2
 
     weights = rns.randn(3, X_flatten.shape[1])
     Xw = X_flatten.dot(weights.T)
-    X2w2 = X_flatten_squread.dot((weights ** 2).sum(axis=0))
-    y = 0.5 * ((Xw ** 2).sum(axis=1) - X2w2) + rns.randn(N_train)
+    X2w2 = X_flatten_squread.dot((weights**2).sum(axis=0))
+    y = 0.5 * ((Xw**2).sum(axis=1) - X2w2) + rns.randn(N_train)
 
     blocks = [
         RelationBlock(user_indices, user_block),

tests/regression/test_fit.py

@@ -31,8 +31,8 @@ def test_middle_reg(
     vfm_weights = vfm.predictor_.weights()
     hp_trance = fm.get_hyper_trace()
     last_alphs = hp_trance["alpha"].iloc[-20:].values
-    assert np.all(last_alphs > ((1 / alpha_inv ** 2) / 2))
-    assert np.all(last_alphs < ((1 / alpha_inv ** 2) * 2))
+    assert np.all(last_alphs > ((1 / alpha_inv**2) / 2))
+    assert np.all(last_alphs < ((1 / alpha_inv**2) * 2))
 
     last_samples = fm.predictor_.samples[-20:]
     assert np.all([s.w0 < stub_weight.global_bias + 0.5 for s in last_samples])

tests/test_utils.py

@@ -15,11 +15,11 @@ class FMWeights(NamedTuple):
 
 def prediction(X: sps.csr_matrix, weight: FMWeights) -> np.ndarray:
     X2 = X.copy()
-    X2.data[:] = X2.data ** 2
+    X2.data[:] = X2.data**2
     result = np.zeros(X.shape[0], dtype=np.float64)
     result[:] = weight.global_bias
     result += X.dot(weight.weight)
-    w2 = (weight.factors ** 2).sum(axis=0)
+    w2 = (weight.factors**2).sum(axis=0)
     Xw = X.dot(weight.factors.T)
-    result += ((Xw ** 2).sum(axis=1) - (X2.dot(w2))) * 0.5
+    result += ((Xw**2).sum(axis=1) - (X2.dot(w2))) * 0.5
     return result