PEP 735 compliance

Author: DimitriPapadopoulos

.github/workflows/docker_build.jinja

@@ -38,7 +38,7 @@ jobs:
           python-version: "3.11"
 
       - name: Install neurodocker
-        run: python -m pip install --editable .[dev]
+        run: python -m pip install --editable  --group [dev]
 
       - name: Generate Dockerfile
         run: |

.github/workflows/docs.yml

@@ -15,7 +15,7 @@ jobs:
             with:
                 python-version: '3.10'
         -   name: Install neurodocker
-            run: python -m pip install --editable .[all]
+            run: python -m pip install --editable . --group all
         -   name: build docs
             run: |
                 make -C docs cli

.github/workflows/pull-request.yml

@@ -38,7 +38,7 @@ jobs:
                 python-version: ${{ matrix.python-version }}
                 allow-prereleases: true
         -   name: Install neurodocker
-            run: python -m pip install --editable .[dev]
+            run: python -m pip install --editable . --group dev
         -   name: Run python tests
             run: pytest --numprocesses auto
         -   name: Get code coverage

README.md

@@ -52,7 +52,7 @@ Clone the repository and install in editable mode.
 ```
 git clone https://github.com/ReproNim/neurodocker
 cd neurodocker
-python -m pip install --no-cache-dir --editable .[all]
+python -m pip install --no-cache-dir --editable . --group all
 ```
 
 Before committing changes, initialize `pre-commit` with `pre-commit install`. This will format code with each commit to keep the style consistent. _Neurodocker_ uses `black` for formatting.

pyproject.toml

@@ -37,10 +37,14 @@ name = "neurodocker"
 readme = "README.md"
 requires-python = ">=3.10"
 
-[project.optional-dependencies]
-all = ["neurodocker[minify,dev,doc]"]
+[dependency-groups]
+all = [
+    {include-group = "dev"},
+    {include-group = "doc"},
+    {include-group = "minify"}
+]
 dev = [
-    "neurodocker[minify]",
+    {include-group = "minify"},
     "codecov",
     "coverage[toml]",
     "mypy",