Merge pull request #2 from FINRAOS/config-updates

Config updates

Author: matthewgillett

.circleci/config.yml

@@ -1,50 +1,54 @@
-# Use the latest 2.1 version of CircleCI pipeline process engine.
-# See: https://circleci.com/docs/2.0/configuration-reference
 version: 2.1
 
-# Orbs are reusable packages of CircleCI configuration that you may share across projects, enabling you to create encapsulated, parameterized commands, jobs, and executors that can be used across multiple projects.
-# See: https://circleci.com/docs/2.0/orb-intro/
-orbs:
-  # The python orb contains a set of prepackaged CircleCI configuration you can use repeatedly in your configuration files
-  # Orb commands and jobs help you with common scripting around a language/tool
-  # so you dont have to copy and paste it everywhere.
-  # See the orb documentation here: https://circleci.com/developer/orbs/orb/circleci/python
-  python: circleci/[email protected]
-
-# Define a job to be invoked later in a workflow.
-# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
-  build-and-test: # This is the name of the job, feel free to change it to better match what you're trying to do!
-    # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/
-    # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub
-    # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
-    # The executor is the environment in which the steps below will be executed - below will use a python 3.8 container
-    # Change the version below to your required version of python
+  test:
+    docker:
+      - image: circleci/python:3.8
+    steps:
+      - checkout
+      - run: sudo apt-get install pandoc  
+      - run: sudo pip install tox
+      - run: tox
+      - run: ls -la docs
+      - persist_to_workspace:
+          root: docs
+          paths: html
+  docs-deploy:
     docker:
-      - image: cimg/python:3.8
-    # Checkout the code as the first step. This is a dedicated CircleCI step.
-    # The python orb's install-packages step will install the dependencies from a Pipfile via Pipenv by default.
-    # Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
-    # Then run your tests!
-    # CircleCI will report the results back to your VCS provider.
+      - image: node:16.14.2
     steps:
       - checkout
-      - python/install-packages:
-          pkg-manager: pip-dist
-          pip-dependency-file: 
+      - attach_workspace:
+          at: docs
+      - run: mkdir -p website/docs && mv docs/html website/docs/
       - run:
-          name: Run pre-commit
-          command: pip install pre-commit && pre-commit run --all
+          name: Disable jekyll builds
+          command: touch website/.nojekyll
+      - run: mkdir -p website/.circleci
+      - run: cp .circleci/config.yml website/.circleci/config.yml
       - run:
-          name: Run tests
-          # This assumes pytest is installed via the install-package step above
-          no_output_timeout: 30m
-          command: pip install pytest && pytest tests
-
-# Invoke jobs via workflows
-# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
+          name: Install and configure dependencies
+          command: |
+            npm install -g --silent [email protected]
+            git config user.email "$(git log --format=%ae -n 1)"
+            git config user.name "$(git log --format=%an -n 1)"
+      - add_ssh_keys:
+          fingerprints:
+            - "4e:e4:68:5b:4b:62:62:47:73:47:d5:b4:99:23:98:b1"
+      - run:
+          name: Deploy docs to gh-pages branch
+          command: gh-pages -b website --dotfiles --message "$(git log --format=%B -n 1)" --dist website
 workflows:
-  sample: # This is the name of the workflow, feel free to change it to better match your workflow.
-    # Inside the workflow, you define the jobs you want to run.
+  version: 2
+  build:
     jobs:
-      - build-and-test
+      - test:
+          filters:
+            branches:
+              ignore: website
+      - docs-deploy:
+          requires:
+            - test
+          filters:
+            branches:
+              only: main

.pre-commit-config.yaml

@@ -10,19 +10,19 @@
 repos:
 
 - repo: https://github.com/ambv/black
-  rev: 21.7b0
+  rev: 22.3.0
   hooks:
   - id: black
     language_version: python3.8
     args: [--line-length=88, tests, mvtk]
 
 - repo: https://gitlab.com/pycqa/flake8
-  rev: '3.9.2'
+  rev: 4.0.1
   hooks:
   - id: flake8
     args: [--max-line-length=88, '--per-file-ignores=__init__.py:F401,F403', tests, mvtk]
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v0.910'
+  rev: v0.942
   hooks:
   - id: mypy
     files: mvtk/

README.md

@@ -20,7 +20,8 @@ Check out this repository and `cd` into the directory.
 
 Run `pip install -e ".[doc]"`.
 
-The `[doc]` is used to install dependencies for building documentation.
+The `[doc]` is used to install dependencies for building documentation. You
+will need [pandoc](https://pandoc.org/) installed.
 
 # Submodules
 You can import:
@@ -29,7 +30,7 @@ You can import:
 - `mvtk.interprenet` for building interpretable neural nets.
 - `mvtk.thresholding` for adaptive thresholding.
 - `mvtk.sobol` for Sobol sensitivity analysis
-- `mvtk.supervisor` for divergence anlysis
+- `mvtk.supervisor` for divergence analysis
 - `mvtk.metrics` for specialised metrics
 
 # Documentation

docs/conf.py

@@ -87,3 +87,5 @@
     ".txt": "markdown",
     ".md": "markdown",
 }
+
+user_agent = "Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0"

docs/contributing.md

@@ -6,7 +6,7 @@ Everyone can contribute to Model Validation Toolkit, and we value everyone's con
 ways to contribute, including:
 
 
-- Answering questions on Model Validation Toolkit's [discussions page](https://github.com/FINRAOS/model-validation-toolkit/discussions)
+- Answering questions on Model Validation Toolkit's [Gitter channel](https://gitter.im/FINRAOS/model-validation-toolkit)
 - Improving or expanding Model Validation Toolkit's [documentation](https://finraos.github.io/model-validation-toolkit/docs/html/index.html)
 - Contributing to Model Validation Toolkit's [code-base](https://github.com/FINRAOS/model-validation-toolkit/)
 
@@ -18,7 +18,8 @@ We welcome pull requests, in particular for those issues marked with
 
 For other proposals, we ask that you first open a GitHub
 [Issue](https://github.com/FINRAOS/model-validation-toolkit/issues/new/choose) or
-[Discussion](https://github.com/FINRAOS/model-validation-toolkit/discussions)
+[Gitter channel](https://gitter.im/FINRAOS/model-validation-toolkit)
+
 to seek feedback on your planned contribution.
 
 ## Contributing code using pull requests
@@ -80,7 +81,7 @@ Follow these steps to contribute code:
    git commit -s -m "Your commit message"
    ```
 
-   Please be sure to sign off your work when you commit it with the `-s` or, equivalently `--sign-off` flag to agree to our [DCO](https://raw.githubusercontent.com/FINRAOS/model-validation-toolkit/main/DCO.txt).
+   Please be sure to sign off your work when you commit it with the `-s` or, equivalently `--sign-off` flag to agree to our [DCO](https://raw.githubusercontent.com/FINRAOS/model-validation-toolkit/main/DCO).
 
    Then sync your code with the main repo:
 
@@ -98,7 +99,7 @@ Follow these steps to contribute code:
 
 8. Create a pull request from the Model Validation Toolkit repository and send it for review.
    Check the {ref}`pr-checklist` for considerations when preparing your PR, and
-   consult [GitHub Help](https://help.github.com/articles/about-pull-requests/)
+   consult [GitHub Help](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests)
    if you need more information on using pull requests.
 
 ## Model Validation Toolkit pull request checklist
@@ -107,7 +108,7 @@ As you prepare a Model Validation Toolkit pull request, here are a few things to
 
 ### DCO
 
-By contributing to this project, you agree to our [DCO](https://raw.githubusercontent.com/FINRAOS/model-validation-toolkit/main/DCO.txt).
+By contributing to this project, you agree to our [DCO](https://raw.githubusercontent.com/FINRAOS/model-validation-toolkit/main/DCO).
 
 ### Single-change commits and pull requests
 

docs/index.rst

@@ -33,6 +33,8 @@ The Model Validation Toolkit is a library for model validation, metaanalysis, an
     notebooks/divergence/Airlines
     notebooks/divergence/DivergenceFunctions
     notebooks/divergence/CategoricalColumns
+    notebooks/divergence/BugDetection
+    notebooks/divergence/TrainingDatasetDrift
 
 .. toctree::
     :maxdepth: 1

docs/interprenet_user_guide.rst

@@ -14,10 +14,11 @@ and return a scalar value is generally limited to various measures of feature
 importance. This can be problematic as what makes a feature "important" can
 vary between use cases.
 
-Rather than interpret a neural network as a black box, we seek to constrain
-neural network in ways we consider useful and interpretable. In particular, The
-`interprenet <interprenet.html>`_ module currently have two such constraints
-implemented:
+Rather than interpret a neural network as a black
+box, we seek to constrain neural network in ways we
+consider useful and interpretable. In particular,
+The interprenet module currently has two such
+constraints implemented:
 
 * Monotonicity
 * Lipschitz constraint