[CI] Enable CI and setup all logistics

.circleci/config.yml

@@ -1,26 +1,264 @@
-# Use the latest 2.1 version of CircleCI pipeline process engine.
-# See: https://circleci.com/docs/2.0/configuration-reference
 version: 2.1
 
-# Define a job to be invoked later in a workflow.
-# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
-  say-hello:
-    # Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
-    # See: https://circleci.com/docs/2.0/configuration-reference/#docker-machine-macos-windows-executor
-    docker:
-      - image: cimg/base:stable
-    # Add steps to the job
-    # See: https://circleci.com/docs/2.0/configuration-reference/#steps
-    steps:
-      - checkout
-      - run:
-          name: "Say hello"
-          command: "echo Hello, World!"
+    build_doc:
+      docker:
+        - image: cimg/base:stable-20.04
+      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/dodiscover.git
+              fi
+              git remote set-url upstream https://github.com/py-why/dodiscover.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: Set BASH_ENV
+            command: |
+              set -e
+              sudo apt install -qq graphviz optipng python3.8-venv python3-venv libxft2
+              python3.8 -m venv ~/python_env
+              echo "set -e" >> $BASH_ENV
+              echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
+              echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci" >> $BASH_ENV
+              echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
+              echo "export DISPLAY=:99" >> $BASH_ENV
+              echo "source ~/python_env/bin/activate" >> $BASH_ENV
+              mkdir -p ~/.local/bin
+              ln -s ~/python_env/bin/python ~/.local/bin/python
+              echo "BASH_ENV:"
+              cat $BASH_ENV
+        - run:
+            name: Setup pandoc
+            command: sudo apt update && sudo apt install -y pandoc optipng
+        - restore_cache:
+            name: Restore pip cache
+            keys:
+              - pip-cache
+        - restore_cache:
+            name: Restore install-bin-cache
+            keys:
+              - user-install-bin-cache
+        - run:
+            name: Get Python running and install dependencies
+            command: |
+              python -m pip install --progress-bar off --upgrade pip setuptools wheel poetry
+              python -m poetry install --extras docs --quiet
+        - save_cache:
+            name: Save pip cache
+            key: pip-cache
+            paths:
+              - ~/.cache/pip
+        - save_cache:
+            name: Save install-bin-cache
+            key: user-install-bin-cache
+            paths:
+              - ~/.local/lib/python3.8/site-packages
+              - ~/.local/bin
+        - run:
+            name: Check poetry package versions
+            command: |
+               poetry --version
+               poetry show
+        - run:
+            name: Check installation
+            command: |
+               LIBGL_DEBUG=verbose python -c "import matplotlib.pyplot as plt; plt.figure()"
+               python -c "import dodiscover;"
+               python -c "import numpy; numpy.show_config()"
+        - run:
+            name: Build documentation
+            command: |
+              cd doc
+              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"
+      docker:
+        - image: cimg/python:3.9.2
+      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
+        - restore_cache:
+            keys:
+              - pip-cache
+        - run:
+            name: Get Python running
+            command: |
+              python -m pip install --progress-bar off --upgrade pip setuptools wheel
+              python -m pip install --progress-bar off .[doc]
+        - 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: ${CIRCLE_BRANCH}).";
+                  circleci-agent step halt;
+                fi;
+          - run:
+              name: Install and configure dependencies
+              # do not update gh-pages above 3.0.0
+              # see: https://github.com/tschaub/gh-pages/issues/354
+              command: |
+                npm install [email protected]
+                git config --global user.email "[email protected]"
+                git config --global user.name "Circle Ci"
+          - add_ssh_keys:
+              fingerprints:
+                - "b5:1e:a1:6d:8d:48:f2:8f:dd:bd:2d:66:a9:30:fe:b9"
+          - run:
+              # push built doc into the `dev` directory on the `gh-pages` branch
+              name: Deploy doc to gh-pages branch
+              command: |
+                if [ "${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;
 
-# Invoke jobs via workflows
-# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
 workflows:
-  say-hello-workflow:
+  default:
+    jobs:
+      - build_doc:
+          name: build_doc
+      - linkcheck:
+          name: linkcheck
+      - deploy:
+          requires:
+            - build_doc
+          filters:
+            branches:
+              only:
+                - main
+                - maint/0.2
+
+  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:
-      - say-hello
+      - 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 @@
+raison

.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
+    docs
+
+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/dodiscover/blob/main/CONTRIBUTING.md#bug-reports-and-feature-requests) on reporting bugs.
+- [ ] I have checked the [issues list](https://github.com/py-why/dodiscover/issues) for similar or identical bug reports.
+- [ ] I have checked the [pull requests list](https://github.com/py-why/dodiscover/pulls) for existing proposed fixes.
+- [ ] I have checked the [CHANGELOG](https://github.com/py-why/dodiscover/blob/main/CHANGELOG.md) and the [commit log](https://github.com/py-why/dodiscover/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>