Packaging: Use of pyproject.toml and move to minimal setup.py for modernization

.github/workflows/fv3_translate_tests.yaml

@@ -6,5 +6,5 @@ jobs:
   fv3_translate_tests:
     uses: NOAA-GFDL/pyFV3/.github/workflows/translate.yaml@develop
     with:
-      component_trigger:  true
+      component_trigger: true
       component_name: NDSL

.github/workflows/lint.yaml

@@ -11,18 +11,18 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-        - name: Checkout repository
-          uses: actions/checkout@v4
-          with:
-            submodules: 'recursive'
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
 
-        - name: Setup Python 3.11
-          uses: actions/setup-python@v5
-          with:
-            python-version: '3.11'
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
 
-        - name: Install pre-commit
-          run: pip install pre-commit
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-        - name: Run lint via pre-commit
-          run: pre-commit run --all-files
+      - name: Run lint via pre-commit
+        run: pre-commit run --all-files

.github/workflows/pace_tests.yaml

@@ -6,5 +6,5 @@ jobs:
   pace_main_tests:
     uses: NOAA-GFDL/pace/.github/workflows/main_unit_tests.yaml@develop
     with:
-      component_trigger:  true
+      component_trigger: true
       component_name: NDSL

.github/workflows/shield_tests.yaml

@@ -6,5 +6,5 @@ jobs:
   shield_translate_tests:
     uses: NOAA-GFDL/pySHiELD/.github/workflows/translate.yaml@develop
     with:
-      component_trigger:  true
+      component_trigger: true
       component_name: NDSL

.github/workflows/unit_tests.yaml

@@ -14,21 +14,21 @@ jobs:
       image: ghcr.io/noaa-gfdl/miniforge:mpich
     steps:
 
-        - name: Checkout repository
-          uses: actions/checkout@v4
-          with:
-            submodules: 'recursive'
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
 
-        - name: Install Python packages
-          run: pip3 install .[test]
+      - name: Install Python packages
+        run: pip3 install .[test]
 
-        - name: Run serial-cpu tests
-          run: coverage run --rcfile=setup.cfg -m pytest tests
+      - name: Run serial-cpu tests
+        run: coverage run --rcfile=pyproject.toml -m pytest tests
 
-        - name: Run parallel-cpu tests
-          run: mpiexec -np 6 --oversubscribe coverage run --rcfile=setup.cfg -m mpi4py -m pytest tests/mpi
+      - name: Run parallel-cpu tests
+        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest tests/mpi
 
-        - name: Output code coverage
-          run: |
-            coverage combine
-            coverage report
+      - name: Output code coverage
+        run: |
+          coverage combine
+          coverage report

.pre-commit-config.yaml

@@ -2,50 +2,59 @@ default_language_version:
   python: python3
 
 repos:
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 25.1.0
     hooks:
-    - id: black
-      additional_dependencies: ["click==8.0.4"]
+      - id: black
+        additional_dependencies: ["click==8.0.4"]
 
--   repo: https://github.com/pre-commit/mirrors-isort
+  - repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
-    - id: isort
-      args: ["--profile", "black"]
+      - id: isort
+        args: ["--profile", "black"]
 
--   repo: https://github.com/pre-commit/mirrors-mypy
+  - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.16.1
     hooks:
-    - id: mypy
-      name: mypy-ndsl
-      args: [--config-file, setup.cfg]
-      additional_dependencies: [types-PyYAML]
-      files: ndsl
-      exclude: |
-        (?x)^(
-        ndsl/ndsl/gt4py_utils.py |
-        )$
--   repo: https://github.com/pre-commit/pre-commit-hooks
+      - id: mypy
+        name: mypy-ndsl
+        args: ["--config-file", "pyproject.toml"]
+        additional_dependencies: [types-PyYAML]
+        files: ndsl
+        exclude: |
+          (?x)^(
+          ndsl/ndsl/gt4py_utils.py |
+          )$
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-    - id: check-toml
-    - id: check-yaml
-    - id: end-of-file-fixer
-    - id: trailing-whitespace
--   repo: https://github.com/pycqa/flake8
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pycqa/flake8
     rev: 7.3.0
     hooks:
-    - id: flake8
-      name: flake8
-      language_version: python3
-      args: [--config, setup.cfg]
-      exclude: |
-        (?x)^(
-        .*/__init__.py |
-        )$
-    - id: flake8
-      name: flake8 __init__.py files
-      files: "__init__.py"
-      # ignore unused import error in __init__.py files
-      args: ["--ignore=F401,E203", --config, setup.cfg]
+      - id: flake8
+        name: flake8
+        language_version: python3
+        additional_dependencies: [Flake8-pyproject]
+        exclude: |
+          (?x)^(
+          .*/__init__.py |
+          )$
+      - id: flake8
+        additional_dependencies: [Flake8-pyproject]
+        name: flake8 __init__.py files
+        files: "__init__.py"
+
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.15.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix, --indent, "2"]
+      - id: pretty-format-yaml
+        args: [--autofix, --preserve-quotes, --indent, "2", --offset, "2"]

README.md

@@ -23,7 +23,7 @@ cd NDSL/
 python -m venv .venv/
 source ./venv/bin/activate
 
-# Choose pip install -e .[develop] if you'd like to contribute
+# Choose pip install -e .[dev] if you'd like to contribute
 pip install .[demos]
 ```
 
@@ -57,11 +57,11 @@ See [quickstart](#quickstart) above on how to pull and setup a virtual environme
 - `ndsl[test]`: extra dependencies to run tests (based on `pytest`)
 - `ndsl[demos]`: extra dependencies to run [NDSL examples](./examples/NDSL/)
 - `ndsl[docs]`: extra dependencies to build the docs
-- `ndsl[develop]`: installs tools for development, docs, and tests.
+- `ndsl[dev]`: installs tools for development, docs, and tests.
 
 ### Running tests
 
-Tests are available via `pytest` (don't forget to install the `test` or `develop` extras).
+Tests are available via `pytest` (don't forget to install the `test` or `dev` extras).
 
 To run serial tests on CPU (GPU tests also run if `cupy` is available)
 
@@ -79,15 +79,15 @@ mpirun -np 6 pytest tests/mpi
 
 ### Code/contribution guidelines
 
-1. Code quality is enforced by `pre-commit` (which is part of the "develop" extra). Run `pre-commit install`  to install the pre-commit hooks locally or make sure to run `pre-commit run -a`  before submitting a pull request.
+1. Code quality is enforced by `pre-commit` (which is part of the "dev" extra). Run `pre-commit install`  to install the pre-commit hooks locally or make sure to run `pre-commit run -a`  before submitting a pull request.
 2. While we don't strictly enforce type hints, we add them on new code.
 3. Pull requests have to merged as "squash merge" to keep the `git` history clean.
 
 ### Documentation
 
 We are using [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/), which allows us to write the docs in Markdown files and optionally serve it as a static site.
 
-To view the documentation, install NDSL with the `docs` or `develop` extras. Then  run the following:
+To view the documentation, install NDSL with the `docs` or `dev` extras. Then  run the following:
 
 ```bash
 mkdocs serve

mkdocs.yml

@@ -11,12 +11,12 @@ nav:
   - Home: index.md
   - User documentation: user/index.md
   - Porting:
-    - General Concepts: porting/index.md
-    - Testing Infrastructure: porting/translate/index.md
+      - General Concepts: porting/index.md
+      - Testing Infrastructure: porting/translate/index.md
   - Under the hood:
-    - Technical Documentation: dev/index.md
-    - DaCe: dev/dace.md
-    - GT4Py: dev/gt4py.md
+      - Technical Documentation: dev/index.md
+      - DaCe: dev/dace.md
+      - GT4Py: dev/gt4py.md
 
 
 markdown_extensions:
@@ -39,9 +39,9 @@ markdown_extensions:
   - pymdownx.superfences:
       custom_fences:
       # support for mermaid graphs
-      - name: mermaid
-        class: mermaid
-        format: python/name:pymdownx.superfences.fence_code_format
+        - name: mermaid
+          class: mermaid
+          format: python/name:pymdownx.superfences.fence_code_format
   # image inclusion
 
 plugins: