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

@@ -2,6 +2,33 @@
 build-backend = "hatchling.build"
 requires = ["hatchling>=1.27.0", "hatch-vcs"]
 
+[dependency-groups]
+all = [
+    {include-group = "dev"},
+    {include-group = "doc"},
+    {include-group = "minify"}
+]
+dev = [
+    {include-group = "minify"},
+    "codecov",
+    "coverage[toml]",
+    "mypy",
+    "pre-commit",
+    "pytest >= 6.0",
+    "pytest-cov >= 2.0.0",
+    "pytest-reportlog >= 0.1.2",
+    "pytest-xdist >= 2.2.0",
+    "types-PyYAML"
+]
+doc = [
+    "sphinx <7",
+    "pydata-sphinx-theme >= 0.13",
+    "sphinxcontrib.apidoc >= 0.3"
+]
+minify = [
+    "docker >= 4.4.1"
+]
+
 [project]
 authors = [{name = "Neurodocker Developers"}]
 classifiers = [
@@ -37,29 +64,6 @@ name = "neurodocker"
 readme = "README.md"
 requires-python = ">=3.10"
 
-[project.optional-dependencies]
-all = ["neurodocker[minify,dev,doc]"]
-dev = [
-    "neurodocker[minify]",
-    "codecov",
-    "coverage[toml]",
-    "mypy",
-    "pre-commit",
-    "pytest >= 6.0",
-    "pytest-cov >= 2.0.0",
-    "pytest-reportlog >= 0.1.2",
-    "pytest-xdist >= 2.2.0",
-    "types-PyYAML"
-]
-doc = [
-    "sphinx <7",
-    "pydata-sphinx-theme >= 0.13",
-    "sphinxcontrib.apidoc >= 0.3"
-]
-minify = [
-    "docker >= 4.4.1"
-]
-
 [project.scripts]
 neurodocker = "neurodocker.cli.cli:cli"