From f2c3cb982b0de543a30905789bfe78c45f4fe82a Mon Sep 17 00:00:00 2001
From: peter <petrel.harp@gmail.com>
Date: Sat, 11 Dec 2021 10:33:06 -0800
Subject: [PATCH 1/2] removed circleci

---
 .circleci/config.yml | 85 --------------------------------------------
 1 file changed, 85 deletions(-)
 delete mode 100644 .circleci/config.yml

diff --git a/.circleci/config.yml b/.circleci/config.yml
deleted file mode 100644
index ea65694c..00000000
--- a/.circleci/config.yml
+++ /dev/null
@@ -1,85 +0,0 @@
-version: 2.1
-jobs:
-  build:
-    docker:
-      - image: circleci/python:3.7-stretch
-    working_directory: /home/circleci/pyslim
-    steps:
-      - checkout
-      - run: sudo chown -R circleci:circleci *
-      - restore_cache:
-          # It's sometimes necessary to nuke the cache, and the simplest
-          # way to do it is to change the key. We can increment this
-          # version number when we want to do this.
-          key: pyslim-{{ .Branch }}-v1
-      - run:
-          name: Install dependencies and set path
-          command: |
-            sudo apt-get install libgsl-dev doxygen
-            pip install --user -r requirements/CI/pip-requirements.txt
-            pip install --user -r requirements/CI/conda-requirements.txt
-            pip install twine --user
-            echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
-
-      - run:
-          name: Build and install SLiM
-          command: |
-            sudo apt-get install cmake
-            git clone https://github.com/MesserLab/SLiM.git
-            cd SLiM
-            if [ ! -e /home/circleci/.local/SLiM.hash ]; then
-              git rev-parse HEAD > /home/circleci/.local/SLiM.hash
-            fi
-            if [ $(git rev-list HEAD...$(cat /home/circleci/.local/SLiM.hash) --count) -gt 0 -o ! -e /home/circleci/.local/bin/slim ]; then
-              mkdir -p build
-              cd build
-              cmake ..
-              make
-              cp slim /home/circleci/.local/bin/
-            else
-              echo "Restoring SLiM from cache:"
-            fi
-            slim -v
-            git rev-parse HEAD > /home/circleci/.local/SLiM.hash
-
-      - save_cache:
-          key: pyslim-{{ .Branch }}-v1
-          paths:
-            - "/home/circleci/.local"
-
-      - run:
-          name: Build docs
-          command: |
-            # don't re-generate these which require tricky prerequisites (inkscape, xmlstarlet)
-            touch docs/_static/{pedigree0.svg,pedigree1.svg,pedigree2.svg,pedigree_recapitate.svg,pedigree_simplify.svg,pedigree_mutate.svg}
-            touch docs/_static/{pedigree01.png,pedigree0.png,pedigree1.png,pedigree2.png,pedigree_recapitate.png,pedigree_simplify.png,pedigree_mutate.png}
-            cd docs && make
-
-      - run:
-          name: Run Python tests
-          command: |
-            PYTHONPATH=python pytest --cov=pyslim --cov-report=xml --cov-branch \
-              -n 1 tests
-
-      - run:
-          name: Upload Python coverage
-          command: |
-            bash <(curl -s https://codecov.io/bash) -X gcov -n python_tests
-            # Clean up reports so we don't upload them twice.
-            rm -f coverage.xml
-
-      - run:
-          name: Build Python package
-          command: |
-            rm -fR build
-            python setup.py sdist
-            python setup.py check
-            python -m twine check dist/*.tar.gz
-            python -m venv venv
-            source venv/bin/activate
-            pip install --upgrade setuptools pip wheel
-            python setup.py build_ext
-            python setup.py egg_info
-            python setup.py bdist_wheel
-            pip install dist/*.tar.gz
-            python3 -c "import pyslim; print(pyslim.__version__)"

From d5510fdff6113d04c79c0ed33c9c5a7ae6a55deb Mon Sep 17 00:00:00 2001
From: peter <petrel.harp@gmail.com>
Date: Sat, 11 Dec 2021 10:41:19 -0800
Subject: [PATCH 2/2] citation.cff (closes #188)

---
 CITATION.cff | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 00000000..3938dd43
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,8 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Ralph
+    given-names: Peter
+    orcid: https://orcid.org/0000-0002-9459-6866
+title: "pyslim: Python tools for SLiM tree sequences"
+url: https://tskit.dev/pyslim