Merge pull request #1 from neurodata/staging

Pulled updates from Staging
neurodata · Feb 8, 2021 · 7cfbffd · 7cfbffd
2 parents 1ffe82c + 2148ff3
commit 7cfbffd
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -0,0 +1,133 @@
+version: 2.1
+
+orbs:
+  codecov: codecov/[email protected]
+
+jobs:
+  build:
+    parameters:
+      version:
+        type: string
+    docker:
+      - image: cimg/python:<< parameters.version >>
+    steps:
+      - checkout
+      - restore_cache:
+          key: v1-<< parameters.version >>-min-dependency-cache-{{ checksum "dev-requirements.txt" }}
+      - run:
+          name: install python dependencies
+          command: |
+            python3 -m venv venv
+            . venv/bin/activate
+            pip install --upgrade pip
+            pip install -r dev-requirements.txt
+      - save_cache:
+          key: v1-<< parameters.version >>-min-dependency-cache-{{ checksum "dev-requirements.txt" }}
+          paths:
+            - "venv"
+      - run:
+          name: test if package installs
+          command: |
+            . venv/bin/activate
+            python3 setup.py install
+  test-module:
+    parameters:
+      module:
+        type: string
+    docker:
+      - image: cimg/python:3.8
+    steps:
+      - checkout
+      - restore_cache:
+          key: v1-3.8-dependency-cache-{{ checksum "dev-requirements.txt" }}
+      - run:
+          name: install python dependencies
+          command: |
+            python3 -m venv venv
+            . venv/bin/activate
+            pip install -r dev-requirements.txt
+            pip install -e .
+      - save_cache:
+          key: v1-3.8-dependency-cache-{{ checksum "dev-requirements.txt" }}
+          paths:
+            - "venv"
+      - run:
+          name: run code linting
+          command: |
+            . venv/bin/activate
+            black --check --diff ./<< parameters.module >>
+      - run:
+          name: run tests and coverage
+          command: |
+            . venv/bin/activate
+            pytest --junitxml=test-reports/junit.xml --cov-report=xml --cov=./<< parameters.module >> ./<< parameters.module >>
+      - store_test_results:
+          path: test-reports
+      - store_artifacts:
+          path: test-reports
+      - codecov/upload:
+          file: "coverage.xml"
+  deploy:
+    docker:
+      - image: cimg/python:3.8
+    steps:
+      - checkout
+      - restore_cache:
+          key: v1-3.8-dependency-cache-{{ checksum "dev-requirements.txt" }}
+      - run:
+          name: install python dependencies
+          command: |
+            python3 -m venv venv
+            . venv/bin/activate
+            pip install -r dev-requirements.txt
+            pip install -e .
+      - save_cache:
+          key: v1-3.8-dependency-cache-{{ checksum "dev-requirements.txt" }}
+          paths:
+            - "venv"
+      - run:
+          name: verify git tag vs. version
+          command: |
+            python3 -m venv venv
+            . venv/bin/activate
+            python setup.py verify
+      - run:
+          name: init .pypirc
+          command: |
+            echo -e "[pypi]" >> ~/.pypirc
+            echo -e "username = $PYPI_USERNAME" >> ~/.pypirc
+            echo -e "password = $PYPI_PASSWORD" >> ~/.pypirc
+      - run:
+          name: create packages
+          command: |
+            python setup.py sdist
+      - run:
+          name: upload to pypi
+          command: |
+            . venv/bin/activate
+            twine upload dist/*
+workflows:
+  build-test-deploy:
+    jobs:
+      - build:
+          name: "v3.6"
+          version: "3.6"
+      - build:
+          name: "v3.7"
+          version: "3.7"
+      - build:
+          name: "v3.8"
+          version: "3.8"
+      - test-module:
+          name: "proglearn"
+          module: "proglearn"
+          requires:
+            - "v3.8"
+      - deploy:
+          requires:
+            - "proglearn"
+          filters:
+            tags:
+              only: /[0-9]+(\.[0-9]+)*/
+            branches:
+              ignore: /.*/
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # ProgLearn
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4276573.svg)](https://doi.org/10.5281/zenodo.4276573)
-[![Build Status](https://travis-ci.org/neurodata/ProgLearn.svg?branch=main)](https://travis-ci.org/neurodata/ProgLearn)
+[![Build Status](https://circleci.com/gh/neurodata/ProgLearn/tree/main.svg?style=shield&circle-token=:circle-token)](https://app.circleci.com/pipelines/github/neurodata/ProgLearn)
 [![Codecov](https://codecov.io/gh/neurodata/ProgLearn/branches/main/graph/badge.svg)](https://codecov.io/gh/neurodata/ProgLearn)
 [![PyPI version](https://img.shields.io/pypi/v/proglearn.svg)](https://pypi.org/project/proglearn/)
 [![arXiv](https://img.shields.io/badge/arXiv-2004.12908-red.svg?style=flat)](https://arxiv.org/abs/2004.12908)

diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -0,0 +1,6 @@
+-r requirements.txt
+pytest
+coverage
+pytest-cov
+codecov
+black
diff --git a/docs/index.rst b/docs/index.rst
@@ -9,8 +9,8 @@ Overview of ProgLearn_
 
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4276573.svg
    :target: https://doi.org/10.5281/zenodo.4276573
-.. image:: https://travis-ci.org/neurodata/ProgLearn.svg?branch=main
-   :target: https://travis-ci.org/neurodata/ProgLearn
+.. image:: https://circleci.com/gh/neurodata/ProgLearn/tree/main.svg?style=shield&circle-token=:circle-token
+   :target: https://app.circleci.com/pipelines/github/neurodata/ProgLearn
 .. image:: https://codecov.io/gh/neurodata/ProgLearn/branches/main/graph/badge.svg
    :target: https://codecov.io/gh/neurodata/ProgLearn
 .. image:: https://img.shields.io/pypi/v/proglearn.svg

diff --git a/docs/install.rst b/docs/install.rst
@@ -53,8 +53,8 @@ Python package dependencies
 - tensorflow>=1.19.0
 - scikit-learn>=0.22.0
 - scipy==1.4.1
-- numpy<1.19
 - joblib>=0.14.1
+- numpy==1.19.2
 
 Hardware requirements
 ---------------------
@@ -65,7 +65,7 @@ tensorflow's backend.
 OS Requirements
 ---------------
 This package is supported for all major operating systems. The following
-versions of operating systems was tested on Travis CI:
+versions of operating systems was tested on CircleCI:
 
 - **Linux**: Ubuntu 16.04
 - **macOS**: Mojave (10.14.1)

diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -14,8 +14,6 @@ The following tutorials highlight what one can do with the ``ProgLearn`` package
     tutorials/random_class_exp
     tutorials/rotation_cifar
     tutorials/spiral_exp
-    tutorials/sporf_datasets
-    tutorials/sporf_decision_boundaries
     tutorials/uncertaintyforest_running_example
     tutorials/uncertaintyforest_posteriorestimates
     tutorials/uncertaintyforest_conditionalentropyestimates
@@ -24,4 +22,3 @@ The following tutorials highlight what one can do with the ``ProgLearn`` package
     tutorials/xor_rxor_exp
     tutorials/xor_rxor_with_cpd
     tutorials/xor_rxor_with_icp
-
diff --git a/docs/tutorials/functions/sporf_datasets_functions.py b/docs/tutorials/functions/sporf_datasets_functions.py