More modern package layout (#1025)

.github/workflows/benchmark_default_branch.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt -r test-requirements.txt
+          pip install ".[testing]"
       - name: Run benchmark
         run: |
           cd tests

.github/workflows/deploy.yml

@@ -14,6 +14,7 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: "3.8"
+          cache: 'pip' # caching pip dependencies
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/test.yml

@@ -14,77 +14,21 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.7, 3.8, 3.9]
-        installation: ["lowest", "highest"]
-        include:
-          - python-version: 3.7
-            installation: "lowest"
-
-            NUMPY: "1.15.1"
-            PANDAS: "1.0.5" # see https://github.com/numpy/numpy/issues/18355
-            SCIKITLEARN: "0.22.0"
-            DASK: "2.9.0"
-            DISTRIBUTED: "2.11.0"
-            SCIPY: "1.2.0"
-            STATSMODELS: "0.13.0"
-
-          - python-version: 3.8
-            installation: "lowest"
-
-            # only starting from these version, there is a wheel
-            NUMPY: "1.17.3"
-            PANDAS: "1.0.5"
-            SCIKITLEARN: "0.22.0"
-            DASK: "2.9.0"
-            DISTRIBUTED: "2.11.0"
-            # 1.2.0 is not installable with python 3.8...
-            SCIPY: "1.4.0"
-            STATSMODELS: "0.13.0"
-
-          - python-version: 3.9
-            installation: "lowest"
-
-            # only starting from these version, there is a wheel
-            NUMPY: "1.20.3"
-            PANDAS: "1.3.5"
-            SCIKITLEARN: "1.0.1"
-            DASK: "2021.12.0"
-            DISTRIBUTED: "2021.12.0"
-            SCIPY: "1.7.3"
-            STATSMODELS: "0.13.0"
-
     steps:
       - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('test-requirements.txt') }}-${{ matrix.python-version }}-${{ matrix.installation }}
-          restore-keys: |
-            ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('test-requirements.txt') }}-${{ matrix.python-version }}-${{ matrix.installation }}
+          cache: 'pip' # caching pip dependencies
 
       - name: Install dependencies
         run: |
           # Do all the installations
           python -m pip install --upgrade pip wheel setuptools
 
-          # Now downgrade packages if required by environment variables
-          [ -z "${{matrix.NUMPY}}" ] || pip install numpy==${{matrix.NUMPY}}
-          [ -z "${{matrix.PANDAS}}" ] || pip install pandas==${{matrix.PANDAS}}
-          [ -z "${{matrix.SCIKITLEARN}}" ] || pip install scikit-learn==${{matrix.SCIKITLEARN}}
-          [ -z "${{matrix.STATSMODELS}}" ] || pip install statsmodels==${{matrix.STATSMODELS}}
-          [ -z "${{matrix.DASK}}" ] || pip install dask==${{matrix.DASK}}
-          [ -z "${{matrix.DISTRIBUTED}}" ] || pip install distributed==${{matrix.DISTRIBUTED}}
-          # need to downgrade tornado manually
-          [ -z "${{matrix.SCIPY}}" ] || pip install scipy==${{matrix.SCIPY}}
-
-          pip install -r requirements.txt -r test-requirements.txt
-          pip install .
+          pip install .[testing]
 
           # Print out the pip versions for debugging
           pip list

.github/workflows/test_all.yml

@@ -12,26 +12,17 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.7
+    - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
-
-    - name: Cache pip
-      uses: actions/cache@v2
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('test-requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('test-requirements.txt') }}
+        python-version: 3.9
+        cache: 'pip' # caching pip dependencies
 
     - name: Install dependencies
       run: |
         # Do all the installations
         python -m pip install --upgrade pip wheel setuptools
-        pip uninstall tsfresh
-        pip install -r requirements.txt -r test-requirements.txt
-        pip install .
+        pip install .[testing]
 
         # Print out the pip versions for debugging
         pip list

.readthedocs.yml

@@ -20,4 +20,5 @@ python:
   install:
    - method: pip
      path: .
-   - requirements: rdocs-requirements.txt
+     extra_requirements:
+        - docs

binder/requirements.txt

@@ -1,3 +1 @@
--e .  # relative to cwd
--r ../requirements.txt  # relative to here
--r ../test-requirements.txt  # relative to here
+-e .[testing]

docs/text/how_to_contribute.rst

@@ -47,11 +47,8 @@ Install all the relevant python packages with
 .. code::
 
     cd /path/to/tsfresh
-    pip install -r requirements.txt
-    pip install -r rdocs-requirements.txt
-    pip install -r test-requirements.txt
+    pip install -e ".[testing]"
     pre-commit install
-    pip install -e .
 
 
 The last command will dynamically link the tsfresh package which means that changes to the code will directly show up
@@ -67,7 +64,7 @@ you have to:
 
 .. code::
 
-    pytest tests/
+    pytest
 
 
 Documentation
@@ -78,8 +75,9 @@ Build the documentation after installing as described above with
 
 .. code::
 
-    python setup.py docs
-
+    pip install -e ".[docs]"
+    cd docs
+    make html
 
 The finished documentation can be found in the docs/_build/html folder.
 

setup.cfg

@@ -1,10 +1,13 @@
+# This file is used to configure your project.
+# Read more about the various options under:
+# http://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files
 [metadata]
 name = tsfresh
 summary = tsfresh extracts relevant characteristics from time series
 author = Maximilian Christ, Nils Braun, Julius Neuffer, Andreas W. Kempa-Liehr
-author-email = max.christ@me.com
+author_email = max.christ@me.com
 license = MIT
-home-page = https://github.com/blue-yonder/tsfresh
+home_page = https://github.com/blue-yonder/tsfresh
 # Add here all kinds of additional classifiers as defined under
 # https://pypi.python.org/pypi?%3Aaction=list_classifiers
 classifier =
@@ -23,50 +26,91 @@ classifier =
     Topic :: Scientific/Engineering
     Topic :: Software Development
 
+
 [options]
+packages = find:
+# DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
+setup_requires =
+   pyscaffold>=3.3a0,<4
+# Add here dependencies of your project (semicolon/line-separated), e.g.
+install_requires =
+    requests>=2.9.1
+    numpy >=1.15.1, <1.24
+    pandas>=0.25.0, <2.0.0
+    scipy>=1.2.0
+    statsmodels>=0.13
+    patsy>=0.4.1
+    scikit-learn>=0.22.0
+    tqdm>=4.10.0
+    dask[dataframe]>=2.9.0
+    distributed>=2.11.0
+    stumpy>=1.7.2
+    cloudpickle
+
+# Require a specific Python version, e.g. Python 2.7 or >= 3.4
 python_requires = >= 3.7
 
-[entry_points]
-# Add here console scripts like:
-# console_scripts =
-#     script_name = tsfresh.module:function
-# For example:
-# console_scripts =
-#     fibonacci = tsfresh.skeleton:run
-# as well as other entry_points.
+[options.packages.find]
+where = .
+exclude =
+    tests*
+
+[options.extras_require]
+matrixprofile =
+    matrixprofile>=1.1.10,<2.0.0
+
+docs =
+    Sphinx>=6.1.3
+    sphinx_rtd_theme>=1.2.0
+    b2luigi
+    docutils>=0.18.1
+
+# Add here test requirements (semicolon/line-separated)
+testing =
+    pytest>=4.4.0
+    pytest-cov>=2.6.1
+    pytest-xdist>=1.26.1
+    pytest-benchmark>=3.0.0
+    mock>=2.0.0
+    matplotlib>=2.0.0
+    seaborn>=0.7.1
+    ipython>=5.3.0
+    notebook>=4.4.1
+    pandas-datareader>=0.5.0
+    pre-commit
+
+[options.entry_points]
 console_scripts =
     run_tsfresh = tsfresh.scripts.run_tsfresh:main
 
 
-[files]
-# Add here 'data_files', 'packages' or 'namespace_packages'.
-# Additional data files are defined as key value pairs of source and target:
-packages =
-    tsfresh
-# data_files =
-#    share/tsfresh_docs = docs/*
+[easy_install]
+find_links = https://pypi.org/
+index_url = https://pypi.org/simple
 
-[extras]
-# Add here additional requirements for extra features, like:
-# PDF =
-#    ReportLab>=1.2
-#    RXP
+[test]
+# py.test options when running `python setup.py test`
+# addopts = --verbose
+extras = True
 
 [tool:pytest]
 # Options for py.test:
 # Specify command line options as you would do when invoking py.test directly.
 # e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
 # in order to write a coverage file that can be read by Jenkins.
+junit_family = xunit2
 addopts =
     --cov tsfresh --cov-report term-missing
     --verbose
     -n auto
+testpaths = tests
+filterwarnings =
 
 [aliases]
+dists = bdist_wheel
 docs = build_sphinx
 
 [bdist_wheel]
-# Use this option if your package is pure-python
 universal = 1
 
 [build_sphinx]
@@ -76,12 +120,6 @@ build_dir = docs/_build
 [pbr]
 # Let pbr run sphinx-apidoc
 autodoc_tree_index_modules = True
-# autodoc_tree_excludes = ...
-# Let pbr itself generate the apidoc
-# autodoc_index_modules = True
-# autodoc_exclude_modules = ...
-# Convert warnings to errors
-# warnerrors = True
 
 [devpi:upload]
 # Options for the devpi: PyPI server and packaging tool
@@ -93,3 +131,9 @@ with-docs = 0
 
 [pycodestyle]
 max-line-length = 120
+
+[pyscaffold]
+# PyScaffold's parameters when the project was created.
+# This will be used when updating. Do not change!
+version = 3.2.3
+package = tsfresh

setup.py

@@ -1,32 +1,23 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
     Setup file for tsfresh.
+    Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 2.5.6, a tool that easily
-    puts up a scaffold for your new Python project. Learn more under:
-    http://pyscaffold.readthedocs.org/
+    This file was generated with PyScaffold 3.2.3.
+    PyScaffold helps you to put up the scaffold of your new Python project.
+    Learn more under: https://pyscaffold.org/
 """
-
 import sys
 
-from setuptools import find_packages, setup
-
-with open("README.md") as f:
-    long_description = f.read()
+from pkg_resources import VersionConflict, require
+from setuptools import setup
 
-with open("requirements.txt") as f:
-    requirements = [line for line in f if not line.startswith("#")]
+try:
+    require("setuptools>=38.3")
+except VersionConflict:
+    print("Error: version of setuptools is too old (<38.3)!")
+    sys.exit(1)
 
-needs_sphinx = {"build_sphinx", "upload_docs"}.intersection(sys.argv)
-sphinx = ["sphinx", "sphinx_rtd_theme"] if needs_sphinx else []
 
-setup(
-    use_scm_version=True,
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    setup_requires=["setuptools_scm"] + sphinx,
-    packages=find_packages(exclude=["tests.*", "tests"]),
-    install_requires=requirements,
-    extras_require={"matrixprofile": ["matrixprofile>=1.1.10,<2.0.0"]},
-)
+if __name__ == "__main__":
+    setup(use_pyscaffold=True)