Initial setup of repository (#6)

- Adds all the CI stuff
- Adds the developer workflow copied and pasted
- Changes the name of directory to `pywhy_stats` to keep in line w/ the
Python convention that `-` is turned to `_` in package names -> import
names

---------

Signed-off-by: Adam Li <[email protected]>

.circleci/config.yml

@@ -0,0 +1,247 @@
+version: 2.1
+
+orbs:
+  python: circleci/[email protected]
+
+jobs:
+  build_doc:
+    executor: python/default
+    steps:
+      - restore_cache:
+          name: Restore .git
+          keys:
+            - source-cache-graphs
+      - checkout
+      - run:
+          name: Complete checkout
+          command: |
+            if ! git remote -v | grep upstream; then
+              git remote add upstream https://github.com/py-why/pywhy-stats.git
+            fi
+            git remote set-url upstream https://github.com/py-why/pywhy-stats.git
+            git fetch upstream
+      - save_cache:
+          name: Save .git
+          key: source-cache-graphs
+          paths:
+            - ".git"
+      - run:
+          name: Check-skip
+          command: |
+            set -e
+            export COMMIT_MESSAGE=$(git log --format=oneline -n 1);
+            if [[ -v CIRCLE_PULL_REQUEST ]] && ([[ "$COMMIT_MESSAGE" == *"[skip circle]"* ]] || [[ "$COMMIT_MESSAGE" == *"[circle skip]"* ]]); then
+              echo "Skip detected, exiting job ${CIRCLE_JOB} for PR ${CIRCLE_PULL_REQUEST}."
+              circleci-agent step halt;
+            fi
+      - run:
+          name: Merge with upstream
+          command: |
+            echo $(git log -1 --pretty=%B) | tee gitlog.txt
+            echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+            if [[ $(cat merge.txt) != "" ]]; then
+              echo "Merging $(cat merge.txt)";
+              git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+            fi
+      - run:
+          name: Install the latest version of Poetry
+          command: |
+            curl -sSL https://install.python-poetry.org | python3 - --version 1.3.0
+            poetry --version
+      - run:
+          name: Set BASH_ENV
+          command: |
+            set -e
+            sudo apt update
+            sudo apt-get update
+            echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
+            echo "BASH_ENV:"
+            cat $BASH_ENV
+      - run:
+          name: Install pysal dependencies
+          command: |
+            sudo apt install libspatialindex-dev xdg-utils
+      - python/install-packages:
+          pkg-manager: poetry
+          args: "-E graph_func -E viz --with docs"
+          cache-version: "v1" # change to clear cache
+      - run:
+          name: Check poetry package versions
+          command: |
+            poetry --version
+            poetry show
+      - run:
+          name: Setup pandoc
+          command: sudo apt update && sudo apt install -y pandoc optipng
+      - run:
+          name: Check installation
+          command: |
+            poetry run python -c "import pywhy_stats;"
+            poetry run python -c "import numpy; numpy.show_config()"
+            LIBGL_DEBUG=verbose poetry run python -c "import matplotlib.pyplot as plt; plt.figure()"
+      - run:
+          name: Build documentation
+          command: |
+            cd doc
+            poetry run make html
+      # Save the example test results
+      - store_test_results:
+          path: doc/_build/test-results
+      - store_artifacts:
+          path: doc/_build/test-results
+          destination: test-results
+      # Save the SG RST
+      - store_artifacts:
+          path: doc/auto_examples.zip
+      - store_artifacts:
+          path: doc/generated.zip
+      # Save the outputs
+      - store_artifacts:
+          path: doc/_build/html/
+          destination: dev
+      - store_artifacts:
+          path: doc/_build/html_stable/
+          destination: stable
+      - persist_to_workspace:
+          root: doc/_build
+          paths:
+            - html
+            - html_stable
+
+  linkcheck:
+    parameters:
+      scheduled:
+        type: string
+        default: "false"
+    executor: python/default
+    steps:
+      - restore_cache:
+          keys:
+            - source-cache-graphs
+      - checkout
+      - run:
+          name: Check-skip
+          command: |
+            export COMMIT_MESSAGE=$(git log --format=oneline -n 1);
+            if [[ "$COMMIT_MESSAGE" != *"[circle linkcheck]"* ]] && [ "<< parameters.scheduled >>" != "true" ]; then
+              echo "Skip detected, exiting job ${CIRCLE_JOB}."
+              circleci-agent step halt;
+            fi
+      - run:
+          name: Set BASH_ENV
+          command: |
+            set -e
+            echo "set -e" >> $BASH_ENV
+            echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
+      - python/install-packages:
+          pkg-manager: poetry
+          cache-version: "v1" # change to clear cache
+          args: "--with docs"
+      - run:
+          name: Check poetry package versions
+          command: |
+            poetry --version
+            poetry show
+      - run:
+          name: make linkcheck
+          command: |
+            make -C doc linkcheck
+      - run:
+          name: make linkcheck-grep
+          when: always
+          command: |
+            make -C doc linkcheck-grep
+      - store_artifacts:
+          path: doc/_build/linkcheck
+          destination: linkcheck
+
+  deploy:
+    docker:
+      - image: cimg/node:lts
+    steps:
+      - checkout
+
+      - attach_workspace:
+          at: doc/_build
+      - run:
+          name: Set BASH_ENV
+          command: |
+            set -e
+            echo "set -e" >> $BASH_ENV
+      # Don't try to deploy if nothing is there or not on the right branch
+      - run:
+          name: Check docs
+          command: |
+            if [ ! -f doc/_build/html/index.html ] && [ ! -f doc/_build/html_stable/index.html ]; then
+              echo "No files found to upload (build: ${CIRCLE_BRANCH}).";
+              circleci-agent step halt;
+            fi;
+      - run:
+          name: Install and configure dependencies
+          # do not update gh-pages above 3.0.0
+          # see: https://github.com/tschaub/gh-pages/issues/354
+          command: |
+            npm install [email protected]
+            git config --global user.email "[email protected]"
+            git config --global user.name "Circle Ci"
+      - add_ssh_keys:
+          fingerprints:
+            - "2d:4e:14:8e:32:00:68:e5:f9:dd:64:17:07:3e:2c:9e"
+      - run:
+          # push built doc into the `dev` directory on the `gh-pages` branch
+          name: Deploy doc to gh-pages branch
+          command: |
+            if [ "${CIRCLE_BRANCH}" == "main" ]; then
+              echo "Deploying dev doc for ${CIRCLE_BRANCH}.";
+              node_modules/gh-pages/bin/gh-pages.js --dotfiles --message "doc updates [skip ci]" --dist doc/_build/html --dest ./dev
+            else
+              echo "Deploying stable doc for ${CIRCLE_BRANCH}.";
+              node_modules/gh-pages/bin/gh-pages.js --dotfiles --message "doc updates [skip ci]" --dist doc/_build/html_stable --dest ./stable
+            fi;
+
+workflows:
+  default:
+    jobs:
+      - build_doc:
+          name: build_doc
+      - linkcheck:
+          name: linkcheck
+      - deploy:
+          requires:
+            - build_doc
+          filters:
+            branches:
+              only:
+                - main
+
+  main:
+    jobs:
+      - build_doc:
+          name: build_doc_main
+      - deploy:
+          name: deploy_main
+          requires:
+            - build_doc_main
+    triggers:
+      - schedule:
+          # "At 00:00" (once a day) should be enough "0 0 * * *",
+          # But for testing at first, let's do once an hour (6 AM GMT)
+          cron: "0 6 * * *"
+          filters:
+            branches:
+              only:
+                - main
+
+  weekly:
+    jobs:
+      - linkcheck:
+          name: linkcheck_weekly
+          scheduled: "true"
+    triggers:
+      - schedule:
+          # "At 00:00 on Sunday" should be often enough
+          cron: "0 0 * * 0"
+          filters:
+            branches:
+              only:
+                - main

.codespellignore

@@ -0,0 +1,2 @@
+raison
+wee

.flake8

@@ -0,0 +1,26 @@
+[flake8]
+max-line-length = 100
+
+ignore =
+    # these rules don't play well with black
+    # whitespace before ':'
+    E203
+    # line break before binary operator
+    W503
+    E241,E305,W504,W605,E731
+
+exclude =
+    .git
+    .github
+    .venv
+    .mypy_cache
+    .pytest_cache
+    .circleci
+    paper
+    setup.py
+    doc
+
+per-file-ignores =
+    # __init__.py files are allowed to have unused imports
+    */__init__.py:F401
+    */**/__init__.py:F401

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,84 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+<!--
+Please fill this template entirely and do not erase any of it.
+We reserve the right to close without a response bug reports which are incomplete.
+-->
+
+## Checklist
+
+<!-- To check an item on the list replace [ ] with [x]. -->
+
+- [ ] I have verified that the issue exists against the `main` branch.
+- [ ] I have read the relevant section in the [contribution guide](https://github.com/py-why/pywhy-stats/blob/main/CONTRIBUTING.md#bug-reports-and-feature-requests) on reporting bugs.
+- [ ] I have checked the [issues list](https://github.com/py-why/pywhy-stats/issues) for similar or identical bug reports.
+- [ ] I have checked the [pull requests list](https://github.com/py-why/pywhy-stats/pulls) for existing proposed fixes.
+- [ ] I have checked the [CHANGELOG](https://github.com/py-why/pywhy-stats/blob/main/CHANGELOG.md) and the [commit log](https://github.com/py-why/pywhy-stats/commits/main) to find out if the bug was already fixed in the main branch.
+- [ ] I have included in the "Description" section below a traceback from any exceptions related to this bug.
+- [ ] I have included in the "Related issues or possible duplicates" section beloew all related issues and possible duplicate issues (If there are none, check this box anyway).
+- [ ] I have included in the "Environment" section below the name of the operating system and Python version that I was using when I discovered this bug.
+- [ ] I have included in the "Environment" section below the output of `pip freeze`.
+- [ ] I have included in the "Steps to reproduce" section below a minimally reproducible example.
+
+
+## Description
+
+<!-- Please provide a clear and concise description of what the bug is here. -->
+
+<details>
+<summary><b>Python traceback:</b></summary>
+<p>
+
+<!-- Paste the traceback from any exception (if there was one) in between the next two lines below -->
+```
+```
+
+</p>
+</details>
+
+
+## Related issues or possible duplicates
+
+- None
+
+
+## Environment
+
+<!-- Provide the name of operating system below (e.g. OS X, Linux) -->
+OS:
+
+<!-- Provide the Python version you were using (e.g. 3.7.1) -->
+Python version:
+
+<details>
+<summary><b>Output of <code>pip freeze</code>:</b></summary>
+<p>
+
+<!-- Paste the output of `pip freeze` in between the next two lines below -->
+```
+```
+
+</p>
+</details>
+
+
+## Steps to reproduce
+
+
+<details>
+<summary><b>Example source:</b></summary>
+<p>
+
+<!-- Add a fully runnable example in between the next two lines below that will reproduce the bug -->
+```
+```
+
+</p>
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: 'Feature request'
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"