feat(update): jinja2 (#4068) (major)

### Changed

- Standardize to python project instead of Poetry
- Remove cache to allow updates to be installed
- Update several packages

.github/workflows/tests_and_coverage.yml

@@ -24,16 +24,8 @@ jobs:
         with:
           virtualenvs-create: false
 
-      - name: Cache dependencies
-        uses: actions/cache@v4
-        id: cache
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }}
-
       - name: Install Dependencies
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction
+        run: poetry install --no-interaction --all-extras
 
       - name: Test with Pytest & Coveralls
         run: |

pyproject.toml

@@ -2,12 +2,11 @@
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
-[tool.poetry]
+[project]
 name = "cg"
 version = "65.0.16"
 description = "Clinical Genomics command center"
-authors = ["Clinical Genomics <[email protected]>"]
-readme = "README.md"
+readme = {file = "README.md", content-type = "text/markdown"}
 homepage = "https://github.com/Clinical-Genomics/cg"
 repository = "https://github.com/Clinical-Genomics/cg"
 classifiers = [
@@ -20,72 +19,62 @@ include = [
   "cg/**/*",
   "tests/**/*"
 ]
+requires-python = ">=3.9,<3.13"
+dependencies = [
+"alembic",
+"SQLAlchemy",
+"PyMySQL",
+"click",
+"blinker",
+"CacheControl",
+"Flask-Admin",
+"Flask-CORS",
+"Flask-Dance",
+"Flask",
+"Flask-WTF",
+"WTForms",
+"google-auth",
+"gunicorn",
+"requests",
+"werkzeug",
+"cachetools",
+"cryptography",
+"coloredlogs",
+"Jinja2",
+"lxml",
+"marshmallow",
+"MarkupSafe",
+"openpyxl",
+"packaging",
+"pandas",
+"paramiko",
+"petname",
+"psutil",
+"pydantic == 2.7.4",
+"python-dateutil",
+"PyYAML",
+"tabulate",
+"typing_extensions",
+"urllib3",
+"genologics",
+"housekeeper>=4.11.3",
+"pydantic-settings>=2.3.3",
+"email-validator>=2.2.0",
+"rich-click>=1.8.4",
+  ]
+[project.optional-dependencies]
+coveralls = ["coveralls"]
+mock = ["mock"]
+pre-commit = ["pre-commit"]
+pytest-cov = ["pytest-cov"]
+pytest-mock = ["pytest-mock"]
+pytest = ["pytest"]
+ruff = ["ruff"]
+pytest-xdist = ["pytest-xdist"]
 
-[tool.poetry.dependencies]
-python = ">=3.9,<3.13"
 
-# Database
-alembic = "*"
-SQLAlchemy = "*"
-PyMySQL = "*"
 
-# CLI
-click = "*"
-
-# Server
-blinker = "*"
-CacheControl = "*"
-Flask-Admin = "*"
-Flask-CORS = "*"
-Flask-Dance = "*"
-Flask = "*"
-Flask-WTF = "*"
-WTForms = "*"
-google-auth = "*"
-gunicorn = "*"
-requests = "*"
-werkzeug = "*"
-
-# Utils
-cachetools = "*"
-cryptography = "*"
-coloredlogs = "*"
-Jinja2 = ">=3.1.3"
-lxml = "*"
-marshmallow = "*"
-MarkupSafe = "*"
-openpyxl = "*"
-packaging = "*"
-pandas = "*"
-paramiko = "*"
-petname = "*"
-psutil = "*"
-pydantic = "*"
-python-dateutil = "*"
-PyYAML = "*"
-tabulate = "*"
-typing_extensions = "*"
-urllib3 = "*"
-
-# Apps
-genologics = "*"
-housekeeper = ">=4.11.3"
-pydantic-settings = "^2.3.3"
-email-validator = "^2.2.0"
-rich-click = "^1.8.4"
-
-
-[tool.poetry.dev-dependencies]
-coveralls = "*"
-mock = "*"
-pre-commit = "*"
-pytest-cov = "*"
-pytest-mock = "*"
-pytest = "*"
-ruff = "*"
-pytest-xdist = "*"
-
-[tool.poetry.scripts]
+[project.scripts]
 cg = "cg.cli.base:base"
 
 

tests/cli/store/test_store.py

@@ -133,9 +133,10 @@ def test_store_flow_cell(
     assert sample
 
     # GIVEN samples objects on a flow cell
-    with mocker.patch.object(
-        Store, "get_samples_by_illumina_flow_cell", return_value=[sample]
-    ), mocker.patch.object(CompressAPI, "add_decompressed_fastq", return_value=True):
+    with (
+        mocker.patch.object(Store, "get_samples_by_illumina_flow_cell", return_value=[sample]),
+        mocker.patch.object(CompressAPI, "add_decompressed_fastq", return_value=True),
+    ):
         # WHEN running the store flow cell command
         res = cli_runner.invoke(
             store_illumina_run,