Merge pull request #26 from wtsi-hgi/develop

merge from develop

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @altaf-ali

.github/workflows/dev.yml

@@ -8,7 +8,7 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, develop ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -60,7 +60,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: spack/spack
-          ref: 0707ffd4e466402bf19dff1add59eaf2b6d9154e
+          ref: e8658d6493887ef702dd38f0e9ee5870a1651c1e
           path: spack
 
       - name: Update PATH

README.md

@@ -26,6 +26,20 @@ SoftPack Core - GraphQL backend service
 
 ## Installation
 
+### External dependencies
+
+SoftPack Core requires Python version 3.11 or greater.
+
+This project also relies on Spack. Install that first:
+
+``` console
+$ git clone -c feature.manyFiles=true --depth 1 https://github.com/spack/spack.git
+$ source spack/share/spack/setup-env.sh
+```
+
+To start the service, you will also need to configure a git repository to store
+artifacts.
+
 ### Stable release
 
 To install SoftPack Core, run this command in your
@@ -90,6 +104,48 @@ Run tests with [Tox][]
 poetry run tox
 ```
 
+To run integration tests, you need a git repository set up with token access and
+a branch named after your git repo username (stripped of any @domain if your
+username is an email address).
+
+Make sure the artifacts/repo section of ~/.softpack/core/config.yml is
+configured correctly:
+
+```
+artifacts:
+  repo:
+    url: https://github.com/[your-org]/development-softpack-artifacts.git
+    username: [your-username]
+    author: [your-name]
+    email: [your-email]
+    writer: [your-token]
+```
+
+Then enable the integration tests by suppling --repo to `poetry run pytest`, or
+to tox like this:
+
+```
+poetry run tox -- -- --repo
+```
+
+To discover all tests and run them (skipping integration tests with no --repo):
+
+``` console
+poetry run pytest tests -sv
+```
+
+To run just the integration tests:
+
+``` console
+poetry run pytest tests/integration -sv --repo
+```
+
+To run an individual test:
+
+``` console
+poetry run pytest tests/integration/test_artifacts.py::test_clone -sv --repo
+```
+
 Run [MkDocs] server to view documentation:
 
 ``` console

pyproject.toml

@@ -13,8 +13,6 @@ classifiers=[
     'License :: OSI Approved :: MIT License',
     'Natural Language :: English',
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.9',
-    'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
 ]
 packages = [
@@ -48,6 +46,9 @@ singleton-decorator = "^1.0.0"
 sqlalchemy = "1.4.45"
 strawberry-graphql = "^0.177.1"
 typer = "^0.9.0"
+pytest-mock = "^3.11.1"
+pytest-asyncio = "^0.21.1"
+python-multipart = "^0.0.6"
 
 [tool.poetry.group.dev]
 optional = true
@@ -132,11 +133,13 @@ skip_gitignore = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true
 ignore_missing_imports = true
+plugins = "strawberry.ext.mypy_plugin"
 
 [tool.pytest.ini_options]
 filterwarnings = [
     "ignore::DeprecationWarning:starlette"
 ]
+markers = "repo: mark test as altering a real git repo"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]