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base repository: camlab-bioml/starling
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base: a6f870d1abd458d123354c19d011a3d91d466d4b
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head repository: camlab-bioml/starling
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compare: f8e4cdc51e1b08492f23701edbfdf22d81faf4ce
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Showing with 1 addition and 1,964 deletions.
  1. +1 −21 .github/dependabot.yml
  2. +0 −153 .github/workflows/tests.yml
  3. +0 −1,709 poetry.lock
  4. +0 −81 pyproject.toml
22 changes: 1 addition & 21 deletions .github/dependabot.yml
Original file line number Diff line number Diff line change
@@ -1,21 +1 @@
version: 2
updates:
- package-ecosystem: github-actions
directory: "/"
schedule:
interval: daily
- package-ecosystem: pip
directory: "/.github/workflows"
schedule:
interval: daily
- package-ecosystem: pip
directory: "/docs"
schedule:
interval: daily
- package-ecosystem: pip
directory: "/"
schedule:
interval: daily
versioning-strategy: lockfile-only
allow:
- dependency-type: "all"

153 changes: 0 additions & 153 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
@@ -1,154 +1 @@
name: Tests

on:
- push
- pull_request

jobs:
tests:
name: ${{ matrix.session }} ${{ matrix.python }} / ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
include:
- { python: "3.10", os: "ubuntu-latest", session: "pre-commit" }
- { python: "3.10", os: "ubuntu-latest", session: "safety" }
- { python: "3.10", os: "ubuntu-latest", session: "mypy" }
- { python: "3.9", os: "ubuntu-latest", session: "mypy" }
- { python: "3.8", os: "ubuntu-latest", session: "mypy" }
- { python: "3.7", os: "ubuntu-latest", session: "mypy" }
- { python: "3.10", os: "ubuntu-latest", session: "tests" }
- { python: "3.9", os: "ubuntu-latest", session: "tests" }
- { python: "3.8", os: "ubuntu-latest", session: "tests" }
- { python: "3.7", os: "ubuntu-latest", session: "tests" }
- { python: "3.10", os: "windows-latest", session: "tests" }
- { python: "3.10", os: "macos-latest", session: "tests" }
- { python: "3.10", os: "ubuntu-latest", session: "typeguard" }
- { python: "3.10", os: "ubuntu-latest", session: "xdoctest" }
- { python: "3.10", os: "ubuntu-latest", session: "docs-build" }

env:
NOXSESSION: ${{ matrix.session }}
FORCE_COLOR: "1"
PRE_COMMIT_COLOR: "always"

steps:
- name: Check out the repository
uses: actions/checkout@v3

- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python }}

- name: Upgrade pip
run: |
pip install --constraint=.github/workflows/constraints.txt pip
pip --version
- name: Upgrade pip in virtual environments
shell: python
run: |
import os
import pip
with open(os.environ["GITHUB_ENV"], mode="a") as io:
print(f"VIRTUALENV_PIP={pip.__version__}", file=io)
- name: Install Poetry
run: |
pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
poetry --version
- name: Install Nox
run: |
pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox
pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry
nox --version
- name: Compute pre-commit cache key
if: matrix.session == 'pre-commit'
id: pre-commit-cache
shell: python
run: |
import hashlib
import sys
python = "py{}.{}".format(*sys.version_info[:2])
payload = sys.version.encode() + sys.executable.encode()
digest = hashlib.sha256(payload).hexdigest()
result = "${{ runner.os }}-{}-{}-pre-commit".format(python, digest[:8])
print("::set-output name=result::{}".format(result))
- name: Restore pre-commit cache
uses: actions/cache@v3
if: matrix.session == 'pre-commit'
with:
path: ~/.cache/pre-commit
key: ${{ steps.pre-commit-cache.outputs.result }}-${{ hashFiles('.pre-commit-config.yaml') }}
restore-keys: |
${{ steps.pre-commit-cache.outputs.result }}-
- name: Run Nox
run: |
nox --python=${{ matrix.python }}
- name: Upload coverage data
if: always() && matrix.session == 'tests'
uses: "actions/upload-artifact@v3"
with:
name: coverage-data
path: ".coverage.*"

- name: Upload documentation
if: matrix.session == 'docs-build'
uses: actions/upload-artifact@v3
with:
name: docs
path: docs/_build

coverage:
runs-on: ubuntu-latest
needs: tests
steps:
- name: Check out the repository
uses: actions/checkout@v3

- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.10"

- name: Upgrade pip
run: |
pip install --constraint=.github/workflows/constraints.txt pip
pip --version
- name: Install Poetry
run: |
pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
poetry --version
- name: Install Nox
run: |
pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox
pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry
nox --version
- name: Download coverage data
uses: actions/download-artifact@v3
with:
name: coverage-data

- name: Combine coverage data and display human readable report
run: |
nox --session=coverage
- name: Create coverage report
run: |
nox --session=coverage -- xml
- name: Upload coverage report
uses: codecov/codecov-action@v3.1.0
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