Simplify setup.py and tests (#2336)

.github/workflows/build-and-test.yml

@@ -9,37 +9,40 @@ on:
 jobs:
   build-and-test-python:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ["3.8"]
+        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
       fail-fast: false
 
     steps:
-    - name: "Get OS version (Linux)"
-      if: startsWith(runner.os, 'Linux')
+    - name: "Set environment variables (Windows)"
+      if: startsWith(runner.os, 'Windows')
+      shell: pwsh
       run: |
-        echo "OS_VERSION=`lsb_release -sr`" >> $GITHUB_ENV
-        echo "PIP_DEFAULT_CACHE=$HOME/.cache/pip" >> $GITHUB_ENV
-        echo "DEFAULT_HOME=$HOME" >> $GITHUB_ENV
-    - uses: actions/checkout@v2
+        (Get-ItemProperty "HKLM:System\CurrentControlSet\Control\FileSystem").LongPathsEnabled
+        $os_version = (Get-CimInstance Win32_OperatingSystem).version
+        Echo "OS_VERSION=$os_version" >> $env:GITHUB_ENV
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: "Restore pip cache"
-      id: cache-pip
-      uses: actions/cache@v2
+        cache: pip
+        cache-dependency-path: "**/python/pyproject.toml"
+    - name: "Restore RTools40"
+      if: startsWith(runner.os, 'Windows')
+      id: cache-rtools
+      uses: actions/cache@v3
       with:
-        path: ${{ env.PIP_DEFAULT_CACHE }}
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/python/requirements.txt') }}-v1
-        restore-keys: |
-          ${{ runner.os }}-pip-
+        path: C:/rtools40
+        key: ${{ runner.os }}-${{ env.OS_VERSION }}-rtools-v1
     - name: Install and test
       run: |
-        pip install -U -r python/requirements.txt dask[dataframe] distributed
         cd python
-        python setup.py develop test
+        python -m pip install -U --editable ".[dev,parallel]"
+        python -m pytest prophet/tests/
 
   build-and-test-r:
 
@@ -55,7 +58,7 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up R
       uses: r-lib/actions/setup-r@v2
       with:
@@ -71,7 +74,7 @@ jobs:
       shell: Rscript {0}
     - name: Restore R package cache
       if: runner.os != 'Windows'
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

Dockerfile

@@ -2,17 +2,12 @@ FROM python:3.7-stretch
 
 RUN apt-get -y install libc-dev
 
-RUN pip install pip==19.1.1
-
-COPY python/requirements.txt .
-RUN pip install -r requirements.txt
-RUN pip install ipython==7.5.0
+RUN pip install pip==22.3.1
 
 COPY . .
 
 WORKDIR python
 
-RUN python setup.py install
+RUN python -m pip install -e \".[dev, parallel]\"
 
 WORKDIR /
-

README.md

@@ -88,14 +88,13 @@ To get the latest code changes as they are merged, you can clone this repo and b
 ```bash
 git clone https://github.com/facebook/prophet.git
 cd prophet/python
-python -m pip install -r requirements.txt
-python setup.py develop
+python -m pip install -e .
 ```
 
 By default, Prophet will use a fixed version of `cmdstan` (downloading and installing it if necessary) to compile the model executables. If this is undesired and you would like to use your own existing `cmdstan` installation, you can set the environment variable `PROPHET_REPACKAGE_CMDSTAN` to `False`:
 
 ```bash
-export PROPHET_REPACKAGE_CMDSTAN=False; python setup.py develop
+export PROPHET_REPACKAGE_CMDSTAN=False; python -m pip install -e .
 ```
 
 ### Linux

docs/_docs/contributing.md

@@ -46,12 +46,10 @@ $ cd python
 # with Anaconda
 $ conda create -n prophet
 $ conda activate prophet
-$ pip install -r requirements.txt
 
 # with venv
 $ python3 -m venv prophet
 $ source prophet/bin/activate
-$ pip install -r requirements.txt
 ```
 
 ### R
@@ -86,7 +84,7 @@ The next step is to build and install the development version of prophet in the
 ### Python
 
 ```bash
-$ python setup.py develop
+$ python -m pip install -e ".[dev,parallel]"
 ```
 
 You should be able to import *prophet* from your locally built version:
@@ -95,7 +93,7 @@ You should be able to import *prophet* from your locally built version:
 $ python  # start an interpreter
 >>> import prophet
 >>> prophet.__version__
-'1.0'  # whatever the current github version is
+'1.1.2'  # whatever the current github version is
 ```
 
 This will create the new environment, and not touch any of your existing environments,
@@ -154,11 +152,11 @@ Adding tests is one of the most common requests after code is pushed to prophet.
 
 ### Python
 
-Prophet uses the ``unittest`` package for running tests in Python and ``testthat`` package for testing in R. All tests should go into the tests subdirectory in either the Python or R folders.
+Prophet uses the ``pytest`` package for running tests in Python and ``testthat`` package for testing in R. All tests should go into the tests subdirectory in either the Python or R folders.
 
 The entire test suite can be run by typing:
 ```bash
-$ python setup.py test
+$ python -m pytest prophet/tests/
 ```
 
 ### R

python/MANIFEST.in

@@ -1,6 +1,6 @@
 include stan/*.stan
 include LICENSE
-include requirements.txt
+include pyproject.toml
 
 # Ensure in-place built models do not get included in the source dist.
 prune prophet/stan_model

python/README.md

@@ -30,7 +30,7 @@ See [Installation in Python - Development version](https://github.com/facebook/p
 
 Simply type `make build` and if everything is fine you should be able to `make shell` or alternative jump directly to `make py-shell`.
 
-To run the tests, inside the container `cd python/prophet` and then `python -m unittest`
+To run the tests, inside the container `cd python/prophet` and then `python -m pytest prophet/tests/`
 
 ### Example usage
 

python/prophet/__version__.py

@@ -1,7 +1 @@
-__title__ = "prophet"
-__description__ = "Automatic Forecasting Procedure"
-__url__ = "https://facebook.github.io/prophet/"
-__version__ = "1.1.1"
-__author__ = "Sean J. Taylor <sjtz@pm.me>, Ben Letham <bletham@fb.com>"
-__author_email__ = "sjtz@pm.me"
-__license__ = "MIT"
+__version__ = "1.1.2"

python/prophet/tests/conftest.py

@@ -0,0 +1,18 @@
+import pytest
+
+
+def pytest_configure(config):
+    config.addinivalue_line("markers", "slow: mark tests as slow (include in run with --test-slow)")
+
+
+def pytest_addoption(parser):
+    parser.addoption("--test-slow", action="store_true", default=False, help="Run slow tests")
+
+
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--test-slow"):
+        return
+    skip_slow = pytest.mark.skip(reason="Skipped due to the lack of '--test-slow' argument")
+    for item in items:
+        if "slow" in item.keywords:
+            item.add_marker(skip_slow)

python/prophet/tests/test_prophet.py

@@ -9,11 +9,11 @@ from __future__ import print_function
 from __future__ import unicode_literals
 
 import os
-import sys
-from unittest import TestCase, skipUnless
+from unittest import TestCase
 
 import numpy as np
 import pandas as pd
+import pytest
 from prophet import Prophet
 from prophet.utilities import warm_start_params
 
@@ -66,7 +66,7 @@ class TestProphet(TestCase):
         res = self.rmse(future['yhat'], test['y'])
         self.assertAlmostEqual(res, 23.44, places=2, msg="backend: {}".format(forecaster.stan_backend))
 
-    @skipUnless("--test-slow" in sys.argv, "Skipped due to the lack of '--test-slow' argument")
+    @pytest.mark.slow
     def test_fit_sampling_predict(self):
         days = 30
         N = DATA.shape[0]
@@ -106,7 +106,7 @@ class TestProphet(TestCase):
         forecaster.fit(train)
         forecaster.predict(future)
 
-    @skipUnless("--test-slow" in sys.argv, "Skipped due to the lack of '--test-slow' argument")
+    @pytest.mark.slow
     def test_fit_predict_no_changepoints_mcmc(self):
         N = DATA.shape[0]
         train = DATA.head(N // 2)

python/pyproject.toml

@@ -1,7 +1,61 @@
 [build-system]
 requires = [
-    "setuptools>=42",
-    "wheel",
-    "cmdstanpy>=1.0.4",
+  "setuptools>=64",
+  "wheel",
+  "cmdstanpy>=1.0.4",
 ]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "prophet"
+dynamic = ["version"]
+description = "Automatic Forecasting Procedure"
+readme = "README.md"
+requires-python = ">=3.7"
+dependencies = [
+  "cmdstanpy>=1.0.4",
+  "numpy>=1.15.4",
+  "matplotlib>=2.0.0",
+  "pandas>=1.0.4",
+  "LunarCalendar>=0.0.9",
+  "convertdate>=2.1.2",
+  "holidays>=0.14.2",
+  "python-dateutil>=2.8.0",
+  "tqdm>=4.36.1",
+]
+authors = [
+  {name = "Sean J. Taylor", email = "sjtz@pm.me"},
+  {name = "Ben Letham", email = "bletham@fb.com"},
+]
+maintainers = [
+  {name = "Cuong Duong", email = "cuong.duong242@gmail.com"},
+]
+license = {text = "MIT"}
+classifiers = [
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+]
+
+[project.optional-dependencies]
+dev = [
+  "setuptools>=64",
+  "wheel",
+  "pytest",
+  "jupyterlab",
+  "nbconvert",
+  "plotly",
+]
+parallel = [
+  "dask[dataframe]",
+  "distributed",
+]
+
+[project.urls]
+homepage = "https://facebook.github.io/prophet/"
+documentation = "https://facebook.github.io/prophet/"
+repository = "https://github.com/facebook/prophet"

python/requirements.txt

@@ -1,12 +0,0 @@
-cmdstanpy>=1.0.4
-numpy>=1.15.4
-pandas>=1.0.4
-matplotlib>=2.0.0
-LunarCalendar>=0.0.9
-convertdate>=2.1.2
-holidays>=0.14.2
-setuptools>=42
-setuptools-git>=1.2
-python-dateutil>=2.8.0
-tqdm>=4.36.1
-wheel>=0.37.0

python/setup.py

@@ -4,18 +4,15 @@
 # LICENSE file in the root directory of this source tree.
 
 import os
-import sys
 import platform
 from pathlib import Path
 from shutil import copy, copytree, rmtree
 from typing import List
 
-from pkg_resources import add_activation_listener, normalize_path, require, working_set
 from setuptools import find_packages, setup, Extension
 from setuptools.command.build_ext import build_ext
 from setuptools.command.build_py import build_py
-from setuptools.command.develop import develop
-from setuptools.command.test import test as test_command
+from setuptools.command.editable_wheel import editable_wheel
 
 
 MODEL_DIR = "stan"
@@ -52,6 +49,7 @@ def prune_cmdstan(cmdstan_dir: str) -> None:
     rmtree(original_dir)
     temp_dir.rename(original_dir)
 
+
 def repackage_cmdstan():
     return os.environ.get("PROPHET_REPACKAGE_CMDSTAN", "").lower() not in ["false", "0"]
 
@@ -59,6 +57,7 @@ def repackage_cmdstan():
 def maybe_install_cmdstan_toolchain():
     """Install C++ compilers required to build stan models on Windows machines."""
     import cmdstanpy
+
     try:
         cmdstanpy.utils.cxx_toolchain_path()
     except Exception:
@@ -122,7 +121,6 @@ def build_cmdstan_model(target_dir):
         prune_cmdstan(cmdstan_dir)
 
 
-
 def get_backends_from_env() -> List[str]:
     return os.environ.get("STAN_BACKEND", "CMDSTANPY").split(",")
 
@@ -131,9 +129,10 @@ def build_models(target_dir):
     print("Compiling cmdstanpy model")
     build_cmdstan_model(target_dir)
 
-    if 'PYSTAN' in get_backends_from_env():
+    if "PYSTAN" in get_backends_from_env():
         raise ValueError("PyStan backend is not supported for Prophet >= 1.1")
 
+
 class BuildPyCommand(build_py):
     """Custom build command to pre-compile Stan models."""
 
@@ -153,117 +152,33 @@ class BuildExtCommand(build_ext):
         pass
 
 
-class DevelopCommand(develop):
+class EditableWheel(editable_wheel):
     """Custom develop command to pre-compile Stan models in-place."""
 
     def run(self):
         if not self.dry_run:
-            target_dir = os.path.join(self.setup_path, MODEL_TARGET_DIR)
+            target_dir = os.path.join(self.project_dir, MODEL_TARGET_DIR)
             self.mkpath(target_dir)
             build_models(target_dir)
 
-        develop.run(self)
+        editable_wheel.run(self)
 
 
-class TestCommand(test_command):
-    user_options = [
-        ("test-module=", "m", "Run 'test_suite' in specified module"),
-        (
-            "test-suite=",
-            "s",
-            "Run single test, case or suite (e.g. 'module.test_suite')",
-        ),
-        ("test-runner=", "r", "Test runner to use"),
-        ("test-slow", "w", "Test slow suites (default off)"),
-    ]
-    test_slow = None
-
-    def initialize_options(self):
-        super(TestCommand, self).initialize_options()
-        self.test_slow = False
-
-    def finalize_options(self):
-        super(TestCommand, self).finalize_options()
-        if self.test_slow is None:
-            self.test_slow = getattr(self.distribution, "test_slow", False)
-
-    """We must run tests on the build directory, not source."""
-
-    def with_project_on_sys_path(self, func):
-        # Ensure metadata is up-to-date
-        self.reinitialize_command("build_py", inplace=0)
-        self.run_command("build_py")
-        bpy_cmd = self.get_finalized_command("build_py")
-        build_path = normalize_path(bpy_cmd.build_lib)
-
-        # Build extensions
-        self.reinitialize_command("egg_info", egg_base=build_path)
-        self.run_command("egg_info")
-
-        self.reinitialize_command("build_ext", inplace=0)
-        self.run_command("build_ext")
-
-        ei_cmd = self.get_finalized_command("egg_info")
-
-        old_path = sys.path[:]
-        old_modules = sys.modules.copy()
-
-        try:
-            sys.path.insert(0, normalize_path(ei_cmd.egg_base))
-            working_set.__init__()
-            add_activation_listener(lambda dist: dist.activate())
-            require("%s==%s" % (ei_cmd.egg_name, ei_cmd.egg_version))
-            func()
-        finally:
-            sys.path[:] = old_path
-            sys.modules.clear()
-            sys.modules.update(old_modules)
-            working_set.__init__()
-
-
-with open("README.md", "r", encoding="utf-8") as f:
-    long_description = f.read()
-
-with open("requirements.txt", "r") as f:
-    install_requires = f.read().splitlines()
-
 about = {}
 here = Path(__file__).parent.resolve()
-with open(here / "prophet" /  "__version__.py", "r") as f:
+with open(here / "prophet" / "__version__.py", "r") as f:
     exec(f.read(), about)
 
 setup(
-    name=about["__title__"],
     version=about["__version__"],
-    description=about["__description__"],
-    url=about["__url__"],
-    project_urls={
-        "Source": "https://github.com/facebook/prophet",
-    },
-    author=about["__author__"],
-    author_email=about["__author_email__"],
-    license=about["__license__"],
     packages=find_packages(),
-    install_requires=install_requires,
-    python_requires=">=3.7",
     zip_safe=False,
     include_package_data=True,
     ext_modules=[Extension("prophet.stan_model", [])],
     cmdclass={
         "build_ext": BuildExtCommand,
         "build_py": BuildPyCommand,
-        "develop": DevelopCommand,
-        "test": TestCommand,
+        "editable_wheel": EditableWheel,
     },
     test_suite="prophet.tests",
-    classifiers=[
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-    ],
-    long_description=long_description,
-    long_description_content_type="text/markdown",
 )