Add upstream CI

Author: ravwojdyla

.github/scripts/upstream_install.py

@@ -0,0 +1,49 @@
+import subprocess
+import sys
+from pathlib import Path
+
+
+def install_deps() -> None:
+    # NOTE: need to use legacy-resolver due to https://github.com/dask/community/issues/124
+    install_cmd = (
+        sys.executable,
+        "-m",
+        "pip",
+        "install",
+        "--use-deprecated=legacy-resolver",
+        "--upgrade",
+    )
+    upstream_deps = (
+        "git+https://github.com/dask/dask.git#egg=dask[array]",
+        "git+https://github.com/dask/distributed.git#egg=distributed",
+        "git+https://github.com/dask/dask-ml.git#egg=dask-ml",
+        "git+https://github.com/pydata/xarray.git#egg=xarray",
+        "git+https://github.com/zarr-developers/zarr-python.git#egg=zarr",
+    )
+    full_cmd_upstream = install_cmd + upstream_deps
+    print(f"Install upstream dependencies via: {full_cmd_upstream}")
+    subprocess.check_call(full_cmd_upstream)
+    req_deps = set(Path("requirements.txt").read_text().splitlines())
+    req_upstream = [x.split("egg=")[-1].strip() for x in upstream_deps]
+    req_left = tuple(x for x in req_deps if not any(y in x for y in req_upstream))
+    full_cmd_left_over = install_cmd + req_left
+    print(f"Install left over dependencies via: {full_cmd_left_over}")
+    subprocess.check_call(full_cmd_left_over)
+
+
+def install_self() -> None:
+    install_cmd = (
+        sys.executable,
+        "-m",
+        "pip",
+        "install",
+        "--no-deps",
+        "-e" ".",
+    )
+    print(f"Install sgkit via: `{install_cmd}`")
+    subprocess.check_call(install_cmd)
+
+
+if __name__ == "__main__":
+    install_deps()
+    install_self()

.github/workflows/upstream.yml

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+name: Upstream
+
+on:
+  push:
+  schedule:
+    - cron: "0 1 * * *"
+  # manual trigger
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'pystatgen'
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install deps and sgkit
+      run: |
+        sudo apt update -y
+        sudo apt install libgsl-dev   # Needed for msprime < 1.0. Binary wheels include GSL for >= 1.0
+        python -m pip install --upgrade pip
+        python .github/scripts/upstream_install.py
+        python -m pip install -r requirements-dev.txt
+
+    - name: Test with pytest
+      run: |
+        python -m pip freeze
+        pytest -v