Upper bound dependencies and dependabot support (#349)

* Upper bound dependencies and dependabot support * Update CI config to use new requirement files * Remove dependency section from readme to avoid going out of sync * Relax dependency bounds * Fix typo * Fix more typos * Update ray upper bound, fix some mroe typos
SeldonIO · Feb 15, 2021 · 656a5eb · 656a5eb
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,9 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+  open-pull-requests-limit: 10
+  reviewers:
+    - "jklaise"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
         run: |
           sudo apt-get install pandoc
           pip install --upgrade pip setuptools
-          pip install -r requirements/requirements_all.txt
+          pip install -r requirements/dev.txt -r requirements/docs.txt
           python -m spacy download en_core_web_md
           pip install -e .
           pip freeze

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -9,7 +9,7 @@ When you contribute code, you affirm that the contribution is your original work
 The easiest way to get started is to install all the development dependencies
 in a separate virtual environment:
 ```
-pip install -r requirements/requirements_all.txt
+pip install -r requirements/dev.txt -r requirements/docs.txt
 ```
 This will install everything needed to run alibi and all the dev tools
 (docs builder, testing, linting etc.)

diff --git a/README.md b/README.md
@@ -209,29 +209,6 @@ Key:
     [Iris dataset](https://docs.seldon.io/projects/alibi/en/latest/examples/linearity_measure_iris.html),
     [fashion MNIST](https://docs.seldon.io/projects/alibi/en/latest/examples/linearity_measure_fashion_mnist.html)
 
-## Dependencies
-```bash
-  attrs
-  beautifulsoup4
-  matplotlib
-  numpy
-  Pillow
-  pandas
-  requests
-  scikit-learn
-  scikit-image!=0.17.1
-  scipy
-  shap>=0.36
-  spacy[lookups]
-  tensorflow>=2.0
-  typing-extensions>=3.7.2
-```
-
-Dependencies for distributed computation of explanations:
-```bash
-ray
-```
-
 ## Citations
 If you use alibi in your research, please consider citing it.
 

diff --git a/doc/README.md b/doc/README.md
@@ -10,7 +10,7 @@ docstrings.
 ## Building documentation locally
 To build the documentation, first we need to install Python requirements:
 
-`pip install -r ../requirements/requirements_ci.txt -r ../requirements/requirements.txt`
+`pip install -r ../requirements/docs.txt`
 
 We also need `pandoc` for parsing Jupyter notebooks, the easiest way
 to install this is using conda:

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -71,7 +71,7 @@
 
 # mock imports
 autodoc_mock_imports = ['sklearn', 'skimage', 'requests',
-                        'cv2', 'bs4', 'keras', 'seaborn', 'PIL', 'tensorflow', 'spacy']
+                        'cv2', 'bs4', 'keras', 'seaborn', 'PIL', 'tensorflow', 'spacy', 'catboost']
 
 # Napoleon settings
 napoleon_google_docstring = True

diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -0,0 +1,18 @@
+# development dependencies (see docs.txt for documentation building dependencies)
+# linting and static type-checking
+flake8>=3.7.7, <4.0.0
+mypy>=0.670, <0.900
+# testing
+pytest>=5.3.5, <7.0.0
+pytest-cov>=2.6.1, <3.0.0
+pytest-xdist>=1.28.0, <3.0.0 # for distributed testing, currently unused (see setup.cfg)s
+pytest-lazy-fixture>=0.6.3, <0.7.0
+codecov>=2.0.15, <3.0.0
+catboost>=0.23.0, <0.25.0
+Keras>=2.2.4, <2.4.0 # Keras 2.4 specifies tensorflow>=2.2
+alibi-testing @ git+git://github.com/SeldonIO/alibi-testing@master#egg=alibi-testing # pre-trained models for testing
+ray>=0.8.7, <2.0.0
+# other
+pre-commit>=1.20.0, <3.0.0
+tox>=3.21.0, <4.0.0 # used to generate licence info via `make licenses`
+twine>3.2.0, <4.0.0
diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -0,0 +1,16 @@
+# dependencies for building docs, separate from dev.txt as this is also used for builds on readthedocs.org
+# core dependencies
+sphinx>=2.1.2, <3.0.0 # m2r breaks with sphinx 3.0
+sphinx-autodoc-typehints>=1.6.0, <1.11.0 # later versions depend on sphinx 3.0
+sphinx-rtd-theme>=0.4.3, <0.6.0
+m2r>=0.2.1, <0.3.0 # TODO: unmaintained, deprecate (currently useful for `mdinclude` directive)
+sphinxcontrib-apidoc>=0.3.0, <0.4.0
+nbsphinx>=0.4.2, <0.9.0
+nbsphinx-link>=1.2.0, <2.0.0
+ipykernel>=5.1.0, <6.0.0 # required for executing notebooks via nbsphinx
+ipython>=7.2.0, <8.0.0 # required for executing notebooks nbsphinx
+# dependencies required for imports to work and docs to render properly (as mocking doesn't work well)
+# these should be identical to the ones in `setup.py` or `dev.txt`
+shap>=0.36.0, !=0.38.1, <0.39 # https://github.com/SeldonIO/alibi/issues/333
+# pandoc
+# pandoc==1.16.02 # NB: as this is not a Python library, it should be installed manually on the system or via a package manager such as `conda`
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
diff --git a/requirements/requirements_all.txt b/requirements/requirements_all.txt
diff --git a/requirements/requirements_ci.txt b/requirements/requirements_ci.txt
diff --git a/requirements/requirements_examples.txt b/requirements/requirements_examples.txt
diff --git a/setup.cfg b/setup.cfg
@@ -30,9 +30,6 @@ ignore_errors = True
 # tox test environment for generating licenses
 [tox:tox]
 
-[testenv]
-deps = -r{toxinidir}/requirements/reqruirements-ci.txt
-
 [testenv:licenses]
 basepython = python
 deps =

diff --git a/setup.py b/setup.py
@@ -10,8 +10,8 @@ def readme():
 exec(open('alibi/version.py').read())
 
 extras_require = {
-    'examples': ['seaborn', 'xgboost'],
-    'ray': ['ray'],
+    'examples': ['seaborn>=0.9.0', 'xgboost>=0.90'],
+    'ray': ['ray>=0.8.7, <2.0.0'],  # from requirements/dev.txt
 }
 
 setup(name='alibi',
@@ -26,21 +26,22 @@ def readme():
       packages=find_packages(),
       include_package_data=True,
       python_requires='>=3.6',
+      # lower bounds based on Debian Stable versions where available
       install_requires=[
-          'attrs',
-          'beautifulsoup4',
-          'matplotlib',
-          'numpy',
-          'Pillow',
-          'pandas',
-          'requests',
-          'scikit-learn',
-          'spacy[lookups]',
-          'scikit-image!=0.17.1',  # https://github.com/SeldonIO/alibi/issues/215
-          'tensorflow>=2.0',
-          'shap>=0.36,!=0.38.1',  # https://github.com/SeldonIO/alibi/issues/333
-          'scipy',
-          'typing-extensions>=3.7.2'
+          'numpy>=1.16.2, <2.0.0',
+          'pandas>=0.23.3, <2.0.0',
+          'scikit-learn>=0.20.2, <0.25.0',
+          'spacy[lookups]>=2.0.0, <4.0.0',
+          'scikit-image>=0.14.2, !=0.17.1, <0.19',  # https://github.com/SeldonIO/alibi/issues/215
+          'requests>=2.21.0, <3.0.0',
+          'Pillow>=5.4.1, <9.0',
+          'beautifulsoup4>=4.7.1, <5.0.0',
+          'tensorflow>=2.0.0, <2.5.0',
+          'attrs>=19.2.0, <21.0.0',
+          'shap>=0.36.0, !=0.38.1, <0.39.0',  # https://github.com/SeldonIO/alibi/issues/333
+          'scipy>=1.1.0, <2.0.0',
+          'matplotlib>=3.0.0, <4.0.0',
+          'typing-extensions>=3.7.2; python_version < "3.8"',  # https://github.com/SeldonIO/alibi/pull/248
       ],
       extras_require=extras_require,
       test_suite='tests',