PyTorch 181 and some minor updates (skorch-dev#755)

* Add PyTorch 1.8.1 to CI, docs Also: - remove PyTorch 1.4. - bump to cuda_toolkit 11.1. - add Python 3.9 - remove mention of Python 3.5 - Add more common file types to .gitignore - No longer mention nolearn in doc intro - Update environment.yml using --from-history - Add dirty worktree check to deploy.sh - Add README rendering check to deploy.sh - Add flake8 section to setup.cfg - Add python_requires >= 3.6 to setup.py
sthagen · Apr 23, 2021 · 6e5df5b · 6e5df5b
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diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -15,9 +15,16 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python_version: ['3.6', '3.7', '3.8']
-        torch_version: ['1.4.0+cpu', '1.5.1+cpu', '1.6.0+cpu', '1.7.1+cpu']
+        python_version: ['3.6', '3.7', '3.8', '3.9']
+        torch_version: ['1.5.1+cpu', '1.6.0+cpu', '1.7.1+cpu', '1.8.1+cpu']
         os: [ubuntu-latest]
+        exclude:
+          - python_version: '3.9'
+            torch_version: '1.5.1+cpu'
+          - python_version: '3.9'
+            torch_version: '1.6.0+cpu'
+          - python_version: '3.9'
+            torch_version: '1.7.1+cpu'
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.gitignore b/.gitignore
@@ -21,4 +21,8 @@ data/
 *.w2v
 *prof
 *.py~
-*.pt
+*.pt
+*.pth
+*.pickle
+*.mat
+*.ipynb
diff --git a/README.rst b/README.rst
@@ -132,7 +132,7 @@ skorch also provides many convenient features, among others:
 Installation
 ============
 
-skorch requires Python 3.5 or higher.
+skorch requires Python 3.6 or higher.
 
 conda installation
 ==================
@@ -234,22 +234,22 @@ instructions for PyTorch, visit the `PyTorch website
 <http://pytorch.org/>`__. skorch officially supports the last four
 minor PyTorch versions, which currently are:
 
-- 1.4.0
 - 1.5.1
 - 1.6.0
 - 1.7.1
+- 1.8.1
 
 However, that doesn't mean that older versions don't work, just that
 they aren't tested. Since skorch mostly relies on the stable part of
 the PyTorch API, older PyTorch versions should work fine.
 
 In general, running this to install PyTorch should work (assuming CUDA
-10.2):
+11.1):
 
 .. code:: bash
 
     # using conda:
-    conda install pytorch cudatoolkit==10.2 -c pytorch
+    conda install pytorch cudatoolkit==11.1 -c pytorch
     # using pip
     pip install torch
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -9,9 +9,7 @@ Introduction
 
 The goal of skorch is to make it possible to use PyTorch_ with
 sklearn_. This is achieved by providing a wrapper around
-PyTorch that has an sklearn interface. In that sense,
-skorch is the spiritual successor to nolearn_, but instead of
-using Lasagne and Theano, it uses PyTorch.
+PyTorch that has an sklearn interface.
 
 skorch does not re-invent the wheel, instead getting as much out
 of your way as possible. If you are familiar with sklearn and
@@ -84,6 +82,5 @@ Indices and tables
 * :ref:`search`
 
 
-.. _nolearn: https://github.com/dnouri/nolearn
 .. _pytorch: http://pytorch.org/
 .. _sklearn: http://scikit-learn.org/
diff --git a/docs/user/installation.rst b/docs/user/installation.rst
@@ -90,21 +90,21 @@ instructions for PyTorch, visit the `PyTorch website
 <http://pytorch.org/>`__. skorch officially supports the last four
 minor PyTorch versions, which currently are:
 
-- 1.4.0
 - 1.5.1
 - 1.6.0
 - 1.7.1
+- 1.8.1
 
 However, that doesn't mean that older versions don't work, just that
 they aren't tested. Since skorch mostly relies on the stable part of
 the PyTorch API, older PyTorch versions should work fine.
 
 In general, running this to install PyTorch should work (assuming CUDA
-10.2):
+11.1):
 
 .. code:: bash
 
     # using conda:
-    conda install pytorch cudatoolkit==10.2 -c pytorch
+    conda install pytorch cudatoolkit==11.1 -c pytorch
     # using pip
     pip install torch
diff --git a/environment.yml b/environment.yml
@@ -4,36 +4,130 @@ channels:
   - pytorch
   - conda-forge
 dependencies:
+  - zlib=1.2.11
+  - sphinxcontrib-serializinghtml=1.1.4
+  - mkl-service=2.3.0
+  - click=7.1.2
+  - importlib-metadata=3.10.0
+  - tensorboard[version='>=1.14.0']
+  - google-auth-oauthlib=0.4.2
+  - libgcc-ng=9.1.0
+  - sqlite=3.35.4
+  - ca-certificates
+  - lazy-object-proxy=1.6.0
+  - pytorch=1.8.1
+  - packaging=20.9
+  - babel=2.9.0
+  - python=3.9.4
+  - pyjwt=2.0.1
+  - chardet=3.0.4
+  - numpydoc
+  - certifi
+  - blinker=1.4
+  - tensorboard-plugin-wit=1.6.0
+  - astroid=2.5
+  - attrs=20.3.0
+  - threadpoolctl=2.1.0
+  - google-auth=1.28.1
+  - tzdata=2020f
+  - libstdcxx-ng=9.1.0
+  - scipy=1.6.2
+  - wrapt=1.12.1
+  - absl-py=0.12.0
+  - more-itertools=8.7.0
+  - intel-openmp=2020.2
+  - libgfortran-ng=7.3.0
+  - werkzeug=1.0.1
+  - numpy-base=1.19.2
+  - imagesize=1.2.0
+  - wheel=0.36.2
+  - scikit-learn=0.24.1
+  - pluggy=0.13.1
+  - typing-extensions=3.7.4.3
+  - aiohttp=3.7.4
+  - pyasn1-modules=0.2.8
+  - sphinxcontrib-htmlhelp=1.0.3
+  - yarl=1.6.3
   - _libgcc_mutex=0.1
+  - rsa=4.7.2
+  - protobuf=3.14.0
+  - c-ares=1.17.1
+  - tqdm=4.59.0
+  - docutils=0.17
+  - tabulate=0.8.9
+  - cryptography=2.9.2
+  - idna=2.10
+  - oauthlib=3.1.0
+  - alabaster=0.7.12
+  - zipp=3.4.1
+  - ninja=1.10.2
+  - sphinxcontrib-qthelp=1.0.3
+  - pytest-cov
   - blas=1.0
-  - fire=0.3.1
-  - flaky=3.6.1
-  - future=0.18.2
-  - joblib=0.14.1
-  - jupyter=1.0.0
-  - matplotlib=3.1.3
-  - neptune-client=0.4.110
-  - numpy=1.18.1
-  - numpy-base=1.18.1
-  - numpydoc=0.9.2
-  - openpyxl=3.0.3
-  - pandas=1.0.3
-  - pillow=5.3.0
-  - pip=20.0.2
-  - pylint=2.4.4
-  - pytest=5.4.1
-  - pytest-cov=2.8.1
-  - python=3.7.7
-  - pytorch=1.4.0
-  - scikit-learn=0.22.1
-  - scipy=1.4.1
-  - setuptools=46.1.3
-  - six=1.14.0
-  - sphinx=3.0.1
-  - sphinx_rtd_theme=0.4.3
-  - tabulate=0.8.3
-  - tensorboard=1.15.0
-  - tqdm=4.44.1
-  - wheel=0.34.2
+  - isort=5.8.0
+  - jinja2=2.11.3
+  - markupsafe=1.1.1
+  - cachetools=4.2.1
+  - python-dateutil=2.8.1
+  - colorama=0.4.4
+  - libuv=1.40.0
+  - sphinxcontrib-applehelp=1.0.2
+  - pyasn1=0.4.8
+  - toml=0.10.2
+  - pyopenssl=20.0.1
+  - requests-oauthlib=1.3.0
+  - async-timeout=3.0.1
+  - flaky
+  - pycparser=2.20
+  - multidict=5.1.0
+  - libffi=3.3
+  - snowballstemmer=2.1.0
+  - pytz=2021.1
+  - cffi=1.14.5
+  - mccabe=0.6.1
+  - grpcio=1.36.1
+  - openssl
+  - six=1.15.0
+  - setuptools=52.0.0
+  - numpy=1.19.2
+  - ld_impl_linux-64=2.33.1
+  - requests=2.25.1
+  - iniconfig=1.1.1
+  - pysocks=1.7.1
+  - pylint
+  - urllib3=1.26.4
+  - coverage=5.5
+  - cudatoolkit=10.2.89
+  - pip=21.0.1
+  - pyparsing=2.4.7
+  - markdown=3.3.4
+  - pytest[version='>=3.4']
+  - sphinxcontrib-jsmath=1.0.1
+  - readline=8.1
+  - tk=8.6.10
+  - pygments=2.8.1
+  - cython=0.29.23
+  - ncurses=6.2
+  - mkl_random=1.0.2
+  - brotlipy=0.7.0
+  - pandas
+  - libprotobuf=3.14.0
+  - mkl_fft=1.3.0
+  - xz=5.2.5
+  - mkl=2020.2
+  - py=1.10.0
+  - typing_extensions=3.7.4.3
+  - joblib=1.0.1
+  - sphinx
+  - sphinxcontrib-devhelp=1.0.2
+  - neptune-client[version='>=0.4.103']
+  - pillow
+  - fire
+  - openpyxl
+  - sphinx_rtd_theme
+  - wandb[version='>=0.8.30']
+  - future[version='>=0.17.1']
+  - matplotlib[version='>=2.0.2']
+  - jupyter
   - pip:
-    - wandb>=0.8.30
+    - sacred==0.8.2
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -4,14 +4,14 @@ future>=0.17.1
 jupyter
 matplotlib>=2.0.2
 neptune-client>=0.4.103
-sacred
 numpydoc
 openpyxl
 pandas
 pillow
 pylint
 pytest>=3.4
 pytest-cov
+sacred
 sphinx
 sphinx_rtd_theme
 tensorboard>=1.14.0

diff --git a/scripts/deploy.sh b/scripts/deploy.sh
@@ -17,6 +17,9 @@ if [ -z "$PYTORCH_VERSION" ]; then
 	exit 1
 fi
 
+# check if worktree is not dirty, see https://stackoverflow.com/a/5737794
+test -z "$(git status --porcelain --untracked-files=no)"
+
 conda update -q -y conda
 
 # Remove previous deploy environment
@@ -46,6 +49,10 @@ python setup.py install
 
 pytest -x
 
+# check if README can be rendered correctly on PyPI
+pip install readme-renderer
+python -m readme_renderer README.rst > /dev/null
+
 python setup.py sdist bdist_wheel
 
 if [[ $1 == "live" ]]; then

diff --git a/setup.cfg b/setup.cfg
@@ -8,3 +8,8 @@ python_files = test*py
 
 [metadata]
 description-file = README.rst
+
+[flake8]
+max-line-length = 88
+docstring-convention = numpy
+ignore = D204,D401
diff --git a/setup.py b/setup.py
@@ -9,6 +9,9 @@
 with open('requirements.txt') as f:
     install_requires = [l.strip() for l in f]
 
+
+python_requires = '>=3.6'
+
 tests_require = [
     'pytest',
     'pytest-cov',
@@ -26,10 +29,6 @@
 except IOError:
     README = ''
 
-try:
-    CHANGES = open(os.path.join(here, 'CHANGES.txt')).read()
-except IOError:
-    CHANGES = ''
 
 setup(
     name='skorch',
@@ -41,6 +40,7 @@
     include_package_data=True,
     url="https://github.com/skorch-dev/skorch",
     zip_safe=False,
+    python_requires=python_requires,
     install_requires=install_requires,
     extras_require={
         'testing': tests_require,
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,4 +21,8 @@ data/ @@
     *.w2v
     *prof
     *.py~
-    *.pt
+    *.pt
+    *.pth
+    *.pickle
+    *.mat
+    *.ipynb