chore: remove optional dependencies used for internal development

.github/workflows/release.yml

@@ -35,9 +35,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           pip install --upgrade pip
-          pip install build twine
-          pip install .
-          pip install ".[lint, test]"
+          pip install . --group test --group build twine
 
       - name: Update version
         id: version

DEVELOPER.md

@@ -23,11 +23,16 @@ Python3.11+. This project has historically aimed to support several recent versi
 
 ## Installation
 
-To get started, first fork and clone this repository. Then install the project and core packages as well as linting and testing dependencies:
+To get started, first fork and clone this repository. Then install the project in "editable" mode, along with all of the dependencies needed for running and development:
 
 ```shell
-pip install .
-pip install ".[lint, test]"
+pip install -e . --group dev
+```
+
+Developers that use a `uv` environment can "sync" the project to install the project with all dependencies:
+
+```shell
+uv sync
 ```
 
 ## Testing

README.md

@@ -43,10 +43,10 @@ Python development tools for MODFLOW 6 and related projects.
 
 Python3.11+, dependency-free by default.
 
-Two main dependency groups are available, oriented around specific use cases:
+Two optional dependencies are available, oriented around specific use cases:
 
-- `test`: pytest fixtures, markers, and extensions
 - `ecosystem`: program/model management, definition file utilities
+- `pytest`: pytest fixtures, markers, and extensions
 
 ## Installation
 
@@ -56,10 +56,10 @@ Two main dependency groups are available, oriented around specific use cases:
 pip install modflow-devtools
 ```
 
-To install an optional dependency group:
+To install the optional dependencies (choose one or more):
 
 ```shell
-pip install "modflow-devtools[test]"
+pip install "modflow-devtools[ecosystem,pytest]"
 ```
 
 To install from source and set up a development environment please see the [developer documentation](DEVELOPER.md).

docs/md/install.md

@@ -8,6 +8,17 @@ Packages are [available on PyPi](https://pypi.org/project/modflow-devtools/) and
 pip install modflow-devtools
 ```
 
+Two optional dependencies are available, oriented around specific use cases:
+
+- `ecosystem`: program/model management, definition file utilities
+- `pytest`: pytest fixtures, markers, and extensions
+
+To install the optional dependencies (choose one or more):
+
+```shell
+pip install modflow-devtools[ecosystem,pytest]
+```
+
 ## Installing `modflow-devtools` from source
 
 To set up a `modflow-devtools` development environment, first clone the repository:
@@ -16,11 +27,10 @@ To set up a `modflow-devtools` development environment, first clone the reposito
 git clone https://github.com/MODFLOW-ORG/modflow-devtools.git
 ```
 
-Then install the local copy as well as testing, linting, and docs dependencies:
+Then install the local copy in "editable" mode, as well as dependencies needed for testing, linting, and build docs:
 
-```
-pip install .
-pip install ".[lint, test, docs]"
+```shell
+pip install -e . --group dev
 ```
 
 ## Using `modflow-devtools` as a `pytest` plugin

pyproject.toml

@@ -39,47 +39,7 @@ requires-python = ">=3.11"
 dynamic = ["version"]
 
 [project.optional-dependencies]
-build = [
-    "build",
-    "twine"
-]
-lint = [
-    "codespell[toml]",
-    "ruff",
-    "mypy"
-]
-test = [
-    "modflow-devtools[lint]",
-    "coverage",
-    "flaky",
-    "filelock",
-    "meson!=0.63.0",
-    "ninja",
-    "numpy",
-    "pandas",
-    "pytest!=8.1.0",
-    "pytest-cov",
-    "pytest-dotenv",
-    "pytest-xdist",
-    "PyYaml",
-    "syrupy <5.0.0"
-]
-docs = [
-    "sphinx",
-    "sphinx-rtd-theme",
-    "myst-parser"
-]
-# deprecated
-dfn = [
-    "boltons",
-    "pooch",
-    "pyaml",
-    "pydantic",
-    "tomli",
-    "tomli-w"
-]
-# deprecated
-models = [
+ecosystem = [
     "boltons",
     "filelock",
     "pooch",
@@ -88,9 +48,17 @@ models = [
     "tomli",
     "tomli-w"
 ]
-# prefer ecosystem to dfn/models separately
-ecosystem = ["modflow-devtools[dfn,models]"]
-dev = ["modflow-devtools[lint,test,docs,dfn,models]"]
+pytest = [
+    "numpy",
+    "pytest!=8.1.0",
+    "syrupy <5.0.0",
+]
+# optional dependencies listed below are deprecated, to be removed in version 2.x
+# deprecated - prefer "ecosystem" to "dfn"/"models" separately
+dfn = ["modflow-devtools[ecosystem]"]
+models = ["modflow-devtools[ecosystem]"]
+# deprecated - prefer "pytest" to "test" (to be kept only as a dependency-group)
+test = ["modflow-devtools[pytest]"]
 
 [dependency-groups]
 build = [
@@ -103,10 +71,9 @@ lint = [
     "mypy",
 ]
 test = [
-    "modflow-devtools[lint]",
+    "modflow-devtools[ecosystem,pytest]",  # self-reference to project.optional-dependencies
     "coverage",
     "flaky",
-    "filelock",
     "meson!=0.63.0",
     "ninja",
     "numpy",
@@ -116,44 +83,19 @@ test = [
     "pytest-dotenv",
     "pytest-xdist",
     "PyYaml",
-    "syrupy <5.0.0"
+    "syrupy <5.0.0",
+    {include-group = "lint"},
 ]
 docs = [
     "sphinx",
     "sphinx-rtd-theme",
     "myst-parser"
 ]
-# deprecated
-dfn = [
-    "boltons",
-    "pooch",
-    "pyaml",
-    "pydantic",
-    "tomli",
-    "tomli-w"
-]
-# deprecated
-models = [
-    "boltons",
-    "filelock",
-    "pooch",
-    "pyaml",
-    "pydantic",
-    "tomli",
-    "tomli-w"
-]
-# prefer ecosystem to dfn/models separately
-ecosystem = [
-    {include-group = "dfn"},
-    {include-group = "models"},
-]
 dev = [
+    "modflow-devtools[ecosystem,pytest]",  # self-reference to project.optional-dependencies
     {include-group = "build"},
     {include-group = "lint"},
     {include-group = "test"},
-    {include-group = "docs"},
-    {include-group = "dfn"},
-    {include-group = "models"},
 ]
 
 [project.urls]