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Signed-off-by: Adam Li <adam2392@gmail.com>
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‎.circleci/config.yml

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# Use the latest 2.1 version of CircleCI pipeline process engine.
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# See: https://circleci.com/docs/2.0/configuration-reference
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version: 2.1
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# Define a job to be invoked later in a workflow.
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# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
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jobs:
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say-hello:
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# Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
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# See: https://circleci.com/docs/2.0/configuration-reference/#docker-machine-macos-windows-executor
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docker:
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- image: cimg/base:stable
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# Add steps to the job
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# See: https://circleci.com/docs/2.0/configuration-reference/#steps
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steps:
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- checkout
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- run:
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name: "Say hello"
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command: "echo Hello, World!"
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build_doc:
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docker:
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- image: cimg/base:stable-20.04
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steps:
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- restore_cache:
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name: Restore .git
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keys:
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- source-cache-graphs
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- checkout
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- run:
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name: Complete checkout
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command: |
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if ! git remote -v | grep upstream; then
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git remote add upstream https://github.com/py-why/dodiscover.git
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fi
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git remote set-url upstream https://github.com/py-why/dodiscover.git
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git fetch upstream
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- save_cache:
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name: Save .git
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key: source-cache-graphs
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paths:
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- ".git"
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- run:
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name: Check-skip
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command: |
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set -e
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export COMMIT_MESSAGE=$(git log --format=oneline -n 1);
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if [[ -v CIRCLE_PULL_REQUEST ]] && ([[ "$COMMIT_MESSAGE" == *"[skip circle]"* ]] || [[ "$COMMIT_MESSAGE" == *"[circle skip]"* ]]); then
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echo "Skip detected, exiting job ${CIRCLE_JOB} for PR ${CIRCLE_PULL_REQUEST}."
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circleci-agent step halt;
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fi
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- run:
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name: Merge with upstream
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command: |
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echo $(git log -1 --pretty=%B) | tee gitlog.txt
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echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
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if [[ $(cat merge.txt) != "" ]]; then
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echo "Merging $(cat merge.txt)";
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git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
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fi
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- run:
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name: Set BASH_ENV
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command: |
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set -e
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sudo apt install -qq graphviz optipng python3.8-venv python3-venv libxft2
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python3.8 -m venv ~/python_env
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echo "set -e" >> $BASH_ENV
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echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
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echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci" >> $BASH_ENV
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echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
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echo "export DISPLAY=:99" >> $BASH_ENV
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echo "source ~/python_env/bin/activate" >> $BASH_ENV
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mkdir -p ~/.local/bin
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ln -s ~/python_env/bin/python ~/.local/bin/python
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echo "BASH_ENV:"
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cat $BASH_ENV
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- run:
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name: Setup pandoc
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command: sudo apt update && sudo apt install -y pandoc optipng
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- restore_cache:
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name: Restore pip cache
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keys:
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- pip-cache
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- restore_cache:
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name: Restore install-bin-cache
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keys:
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- user-install-bin-cache
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- run:
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name: Get Python running and install dependencies
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command: |
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python -m pip install --progress-bar off --upgrade pip setuptools wheel poetry
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poetry install
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- save_cache:
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name: Save pip cache
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key: pip-cache
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paths:
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- ~/.cache/pip
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- save_cache:
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name: Save install-bin-cache
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key: user-install-bin-cache
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paths:
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- ~/.local/lib/python3.8/site-packages
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- ~/.local/bin
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- run:
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name: Check pip package versions
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command: pip freeze
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- run:
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name: Check installation
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command: |
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LIBGL_DEBUG=verbose python -c "import matplotlib.pyplot as plt; plt.figure()"
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python -c "import dodiscover;"
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python -c "import numpy; numpy.show_config()"
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- run:
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name: Build documentation
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command: |
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cd doc
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make html
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# Save the example test results
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- store_test_results:
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path: doc/_build/test-results
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- store_artifacts:
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path: doc/_build/test-results
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destination: test-results
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# Save the SG RST
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- store_artifacts:
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path: doc/auto_examples.zip
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- store_artifacts:
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path: doc/generated.zip
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# Save the outputs
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- store_artifacts:
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path: doc/_build/html/
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destination: dev
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- store_artifacts:
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path: doc/_build/html_stable/
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destination: stable
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- persist_to_workspace:
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root: doc/_build
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paths:
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- html
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- html_stable
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linkcheck:
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parameters:
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scheduled:
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type: string
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default: "false"
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docker:
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- image: cimg/python:3.9.2
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steps:
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- restore_cache:
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keys:
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- source-cache-graphs
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- checkout
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- run:
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name: Check-skip
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command: |
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export COMMIT_MESSAGE=$(git log --format=oneline -n 1);
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if [[ "$COMMIT_MESSAGE" != *"[circle linkcheck]"* ]] && [ "<< parameters.scheduled >>" != "true" ]; then
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echo "Skip detected, exiting job ${CIRCLE_JOB}."
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circleci-agent step halt;
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fi
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- run:
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name: Set BASH_ENV
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command: |
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set -e
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echo "set -e" >> $BASH_ENV
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echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
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- restore_cache:
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keys:
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- pip-cache
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- run:
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name: Get Python running
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command: |
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python -m pip install --progress-bar off --upgrade pip setuptools wheel
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python -m pip install --progress-bar off .[doc]
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- run:
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name: make linkcheck
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command: |
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make -C doc linkcheck
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- run:
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name: make linkcheck-grep
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when: always
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command: |
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make -C doc linkcheck-grep
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- store_artifacts:
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path: doc/_build/linkcheck
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destination: linkcheck
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deploy:
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docker:
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- image: cimg/node:lts
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steps:
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- checkout
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- attach_workspace:
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at: doc/_build
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- run:
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name: Set BASH_ENV
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command: |
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set -e
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echo "set -e" >> $BASH_ENV
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# Don't try to deploy if nothing is there or not on the right branch
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- run:
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name: Check docs
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command: |
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if [ ! -f doc/_build/html/index.html ] && [ ! -f doc/_build/html_stable/index.html ]; then
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echo "No files found to upload (build: ${CIRCLE_BRANCH}).";
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circleci-agent step halt;
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fi;
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- run:
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name: Install and configure dependencies
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# do not update gh-pages above 3.0.0
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# see: https://github.com/tschaub/gh-pages/issues/354
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command: |
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npm install gh-pages@3.0
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git config --global user.email "circle@pywhy.com"
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git config --global user.name "Circle Ci"
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- add_ssh_keys:
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fingerprints:
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- "b5:1e:a1:6d:8d:48:f2:8f:dd:bd:2d:66:a9:30:fe:b9"
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- run:
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# push built doc into the `dev` directory on the `gh-pages` branch
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name: Deploy doc to gh-pages branch
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command: |
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if [ "${CIRCLE_BRANCH}" == "main" ]; then
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echo "Deploying dev doc for ${CIRCLE_BRANCH}.";
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node_modules/gh-pages/bin/gh-pages.js --dotfiles --message "doc updates [skip ci]" --dist doc/_build/html --dest ./dev
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else
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echo "Deploying stable doc for ${CIRCLE_BRANCH}.";
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node_modules/gh-pages/bin/gh-pages.js --dotfiles --message "doc updates [skip ci]" --dist doc/_build/html_stable --dest ./stable
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fi;
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# Invoke jobs via workflows
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# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
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workflows:
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say-hello-workflow:
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default:
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jobs:
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- build_doc:
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name: build_doc
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- linkcheck:
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name: linkcheck
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- deploy:
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requires:
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- build_doc
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filters:
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branches:
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only:
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- main
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- maint/0.2
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main:
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jobs:
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- build_doc:
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name: build_doc_main
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- deploy:
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name: deploy_main
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requires:
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- build_doc_main
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triggers:
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- schedule:
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# "At 00:00" (once a day) should be enough "0 0 * * *",
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# But for testing at first, let's do once an hour (6 AM GMT)
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cron: "0 6 * * *"
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filters:
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branches:
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only:
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- main
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weekly:
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jobs:
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- say-hello
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- linkcheck:
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name: linkcheck_weekly
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scheduled: "true"
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triggers:
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- schedule:
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# "At 00:00 on Sunday" should be often enough
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cron: "0 0 * * 0"
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filters:
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branches:
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only:
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- main

‎.codespellignore

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raison

‎.flake8

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

‎.github/ISSUE_TEMPLATE/bug_report.md

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

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