Merge pull request #39 from GertjanBisschop/circleci

setup circleci

.circleci/config.yml

@@ -0,0 +1,62 @@
+version: 2.1
+orbs:
+  codecov: codecov/[email protected]
+
+jobs:
+  build:
+    docker:
+      - image: cimg/python:3.7
+    working_directory: /home/circleci/tstrait
+    steps:
+      - checkout
+      - run: sudo chown -R circleci:circleci *
+      - restore_cache:
+          # Note: we put a v{x} suffix at the end of the cache key so that
+          # we can invalidate the cache when we need to. Note that we need
+          # to update the key in the ``save_cache`` block below also when
+          # doing that.
+          key: tstrait-{{ .Branch }}-v4
+      - run:
+          name: Install dependencies and set path
+          command: |
+            pip install --user -r requirements/CI-complete/requirements.txt
+            pip install --user build twine
+            # way to set path persistently https://circleci.com/docs/2.0/env-vars/#setting-path
+            echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
+      - save_cache:
+          key: tstrait-{{ .Branch }}-v4
+          paths:
+            - "/home/circleci/.local"
+
+      - run:
+          name: Run highlevel tests
+          # Run tests without background threads
+          command: |
+            pytest --cov=tstrait --cov-report=xml --cov-branch -n 0 tests
+
+      - codecov/upload:
+          flags: python
+          token: CODECOV_TOKEN
+
+      - run:
+            name: Delete coverage
+            command: |
+              rm .coverage
+
+      - run:
+          name: Make sure we can build a distribution.
+          command: |
+            python setup.py sdist
+            python setup.py check
+            python -m twine check dist/*.tar.gz --strict
+            rm dist/*
+            python -m build
+
+      - run:
+          name: Install from the distribution tarball
+          command: |
+            python -m venv venv
+            source venv/bin/activate
+            pip install --upgrade setuptools pip
+            pip install dist/*.tar.gz
+            python -c 'import tstrait'

.codecov.yaml

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+coverage:
+  status:
+    project:
+      python:
+        target: 95%
+        flags: python
+
+    patch:
+      python:
+        target: 90%
+        flags: python

requirements/CI-complete/requirements.txt

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+msprime
+numba
+numpy
+pytest==6.2.5
+pytest-cov==3.0.0
+tskit==0.5.3