more consistent

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/elixir-cloud-aai/cookiecutter-python",
-  "commit": "dc0f027857b60851e3cb40663f662add4343ef5a",
+  "commit": "5c50248527fc91252e31cb971aad02a455f64e1c",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/code_quality.yaml

@@ -22,8 +22,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--only=lint --no-root"
-          poetry-export-options: "--only=lint"
+          poetry-install-options: "--only=code_quality --no-root"
+          poetry-export-options: "--only=code_quality --no-root"
 
       - name: Check code style
         run: poetry run ruff format --check
@@ -40,8 +40,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--only=lint --no-root"
-          poetry-export-options: "--only=lint"
+          poetry-install-options: "--only=code_quality --no-root"
+          poetry-export-options: "--only=code_quality"
 
       - name: Check code quality
         run: poetry run ruff check .
@@ -58,8 +58,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--only=lint --no-root"
-          poetry-export-options: "--only=lint"
+          poetry-install-options: "--only=code_quality --no-root"
+          poetry-export-options: "--only=code_quality"
 
       - name: Check spellings
         run: poetry run typos .
@@ -76,8 +76,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--with=types --no-root"
-          poetry-export-options: "--with=types"
+          poetry-install-options: "--with=code_quality,types --no-root"
+          poetry-export-options: "--with=code_quality,types"
 
       - name: Check types
         run: poetry run mypy tus_storagehandler/

.github/workflows/docs.yaml

@@ -22,8 +22,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--with=docs"
-          poetry-export-options: "--with=docs"
+          poetry-install-options: "--with=docs,types --no-root"
+          poetry-export-options: "--with=docs,types"
 
       - name: Generate API docs
         run: |

.github/workflows/update.yaml

@@ -17,8 +17,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--with=misc --no-root"
-          poetry-export-options: "--with=misc"
+          poetry-install-options: "--only=misc --no-root"
+          poetry-export-options: "--only=misc"
 
       - name: Update project structure
         run: |

.github/workflows/vulnerability.yaml

@@ -22,8 +22,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--only=security --no-root"
-          poetry-export-options: "--only=security"
+          poetry-install-options: "--only=vulnerability --no-root"
+          poetry-export-options: "--only=vulnerability"
 
       - name: Check code vulnerabilities with bandit
         run: poetry run bandit -c pyproject.toml -r tus_storagehandler/
@@ -40,8 +40,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--only=security --no-root"
-          poetry-export-options: "--only=security"
+          poetry-install-options: "--only=vulnerability --no-root"
+          poetry-export-options: "--only=vulnerability"
 
       - name: Check dependency vulnerabilities with safety
         run: poetry run safety check --full-report

README.md

@@ -47,12 +47,31 @@ Here are certain commands that you might find useful:
 make v
 ```
 
-- Installing dependencies
+- Installing all dependencies including optional dependencies
 
 ```sh
 make i
 ```
 
+> **Note**: This project uses optional dependency groups such as `types`,
+> `code_quality`, `docs`, `vulnerability`, `test`, and `misc`. To install stubs
+> or types for the dependencies, you **must** use the following command:
+>
+> ```sh
+> poetry add types-foo --group types
+> ```
+>
+> Replace `types-foo` with the name of the package for the types. All runtime
+> dependencies should be added to the `default` group. For example, to install
+> `requests` and its type stubs, run:
+>
+> ```sh
+> poetry add requests
+> poetry add types-requests --group types
+> ```
+>
+> This ensures that the type checker functions correctly.
+
 - Running tests
 
 ```sh

pyproject.toml

@@ -25,6 +25,17 @@ version = "0.1.0"
 [tool.poetry.dependencies]
 python = ">=3.11"
 
+[tool.poetry.group.code_quality]
+optional = true
+
+[tool.poetry.group.code_quality.dependencies]
+mypy = ">=1.10.0,<2.0.0"
+ruff = ">=0.4.10,<1.0.0"
+typos = ">=1.22.8,<2.0.0"
+
+[tool.poetry.group.docs]
+optional = true
+
 [tool.poetry.group.docs.dependencies]
 added-value = ">=0.24.0,<1.0.0"
 docutils = "0.20.1"
@@ -34,25 +45,27 @@ sphinx = "^7.3.7"
 sphinx-autodoc-typehints = "^2.1.0"
 tomli = ">=2.0.1,<3.0.0"
 
-[tool.poetry.group.lint.dependencies]
-ruff = ">=0.4.10,<1.0.0"
-typos = ">=1.22.8,<2.0.0"
+[tool.poetry.group.misc]
+optional = true
 
 [tool.poetry.group.misc.dependencies]
 cruft = ">=2.15.0,<3.0.0"
 jello = ">=1.6.0,<2.0.0"
 pre-commit = ">=3.7.1,<4.0.0"
 
-[tool.poetry.group.security.dependencies]
-bandit = ">=1.7.8,<2.0.0"
-safety = ">=3.2.0,<4.0.0"
+[tool.poetry.group.test]
+optional = true
 
 [tool.poetry.group.test.dependencies]
 pytest = ">=8.2.2,<9.0.0"
 pytest-cov = ">=5.0.0,<=6.0.0"
 
-[tool.poetry.group.types.dependencies]
-mypy = ">=1.10.0,<2.0.0"
+[tool.poetry.group.vulnerability]
+optional = true
+
+[tool.poetry.group.vulnerability.dependencies]
+bandit = ">=1.7.8,<2.0.0"
+safety = ">=3.2.0,<4.0.0"
 
 [tool.ruff]
 indent-width = 4