build(ci,packaging): migrate to pyproject.toml, adopt src layout, and streamline workflows (#104)

build(ci,packaging): migrate to pyproject.toml, adopt src layout, and streamline workflows

* Switch to PEP 621-compatible `pyproject.toml` for metadata and builds  
* Move package into `src/` layout  
* Remove legacy Conda workflow and rename CI files  
* Update GitHub Actions and pull-request template  

ref: #105

Author: MAfarrag

.flake8

@@ -5,6 +5,7 @@
 - List any dependencies that are required for this change.
 
 
+# Issues
 - Fixes # (issue)
 ## Type of change
 
@@ -14,6 +15,7 @@ Check relevant points.
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
 - [ ] This change requires a documentation update
+- [ ] Dev changes (CI/pyproject.toml/docs/examples/testing)
 
 # How Has This Been Tested?
 
@@ -26,8 +28,7 @@ Check relevant points.
 
 # Checklist:
 
-- [ ] updated version number in setup.py/pyproject.toml
-- [ ] updated environment.yml and the lock file
+- [ ] updated version number in pyproject.toml
 - [ ] added changes to History.rst
 - [ ] updated the latest version in README file
 - [ ] I have added tests that prove my fix is effective or that my feature works

.github/pull_request_template.md

@@ -24,10 +24,10 @@ jobs:
         - name: Install tools
           run: |
               python -m pip install --upgrade pip
-              pip install setuptools wheel twine
+              pip install wheel twine build
         - name: Build and publish
           run: |
-              python setup.py sdist bdist_wheel
+              python -m build  --sdist --wheel
               twine upload dist/*
           env:
               TWINE_USERNAME: ${{ secrets.PYPI_USERS }}

.github/workflows/conda-deployment.yml

@@ -1,23 +1,20 @@
-name: pypi-deployment
+name: tests
+
+on: [push]
 
-on:
-    push:
-        branches:
-            - main
-    pull_request:
-        branches:
-            - main
 jobs:
-  Run:
+  main-package:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest] # , macos-latest
-        python-version: ["3.10", "3.11", "3.12"]
+        os: [ubuntu-latest]
+        python-version: ["3.11", "3.12", "3.13"]
+    env:
+      OS: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }} ${{ matrix.os }}
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -27,9 +24,13 @@ jobs:
         run: |
             pip install .[dev]
 
-      - name: Generate coverage report
+      - name: Run Tests
         run: |
-          python -m pytest -vvv --cov=statista --cov-report=xml
+          pytest -vvv --cov=statista --cov-report=xml
 
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v3
+
+      - name: test Jupyter notebook
+        run: |
+          pytest --nbval --nbval-lax --verbose

.github/workflows/pypi-release.yml

@@ -1,16 +1,21 @@
 fail_fast: true
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
+      - id: check-toml
+        name: "[py -  check] check toml"
       - id: end-of-file-fixer
         name: "[py -  check] validate yaml"
+      - id: no-commit-to-branch
+        name: "[git -  check] no commit to branch"
+        args: [ --branch=main ]
       - id: trailing-whitespace
         name: "[file - format] trim trailing whitespace"
         args: [ --markdown-linebreak-ext=md ]
       - id: check-added-large-files
         name: "[file -  check] large file"
-        args: [ --maxkb=5000 ]
+        args: [ --maxkb=2000 ]
       - id: check-docstring-first
         name: "[py   -  check] docstring first"
         files: /examples
@@ -38,50 +43,45 @@ repos:
         name: "[reqs - format] fix requirements.txt"
       - id: check-yaml
         name: "[yaml -  check] validate yaml"
-#  - repo: https://github.com/pre-commit/mirrors-isort
-#    rev: v5.10.1
-#    hooks:
-#      - id: isort
-#        name: "[py   - format] isort"
-#  - repo: https://github.com/PyCQA/docformatter
-#    rev: v1.4
-#    hooks:
-#      - id: docformatter
-#        name: "[py   - format] docformatter"
-#        args: [ -i, --wrap-summaries, "0" ]
-
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.3.0
-    hooks:
-      - id: pydocstyle
-        name: "[py   - check] pydocstyle"
-        files: ^Hapi/
-
+        exclude: '^mkdocs\.yml$'
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.0
+    rev: 7.2.0
     hooks:
       - id: flake8
+        additional_dependencies: [Flake8-pyproject]
         name: "[py   - check] flake8"
-#        language_version: python3.9
         exclude: ^(examples/|tests/)
-
-  #- repo: https://github.com/psf/black
-  #  rev: 22.8.0
-  #  hooks:
-  #    - id: black
-  - repo: https://github.com/ambv/black
-    rev: 24.8.0
+#   - repo: https://github.com/pycqa/docformatter
+#     rev: v1.4
+#     hooks:
+#      - id: docformatter
+#        name: "[py   - format] docformatter"
+#        description: 'Formats docstrings to follow PEP 257.'
+#        entry: docformatter
+#        args: [-i]
+#        language: python
+#        types: [python]
+#   - repo: https://github.com/pycqa/pydocstyle
+#     rev: 6.3.0
+#     hooks:
+#       - id: pydocstyle
+#         name: "[py   - check] pydocstyle"
+#         files: ^hydrolib/.*\.py$
+  - repo: https://github.com/pycqa/isort
+    rev: 6.0.1
+    hooks:
+      - id: isort
+        name: "[py   - format] isort"
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
     hooks:
       - id: black
-        name: "[py   - format] black"
-#        language_version: python3.9
   - repo: https://github.com/lovesegfault/beautysh
     rev: v6.2.1
     hooks:
       - id: beautysh
         name: "[bash - format] beautysh"
 
-  # pre-commit-shell: Checks shell scripts against shellcheck.
   - repo: https://github.com/detailyang/pre-commit-shell
     rev: 1.0.5
     hooks:
@@ -104,27 +104,69 @@ repos:
       - id: check-summary-punctuation
         name: "[bash -   format] check-summary-punctuation"
 
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.8.3
+    hooks:
+      - id: bandit
+        args: ["--skip=B101"]
+
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.25.1
+    hooks:
+      - id: gitleaks
+
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.5.0
+    hooks:
+      - id: detect-secrets
+  - repo: https://github.com/bridgecrewio/checkov
+    rev: 3.2.416
+    hooks:
+      - id: checkov
+
+  - repo: https://github.com/trufflesecurity/truffleHog
+    rev: v3.88.29
+    hooks:
+      - id: trufflehog
+
+#   - repo: local
+#     hooks:
+#       - id: safety
+#         name: Safety Check
+#         entry: safety scan --full-report
+#         language: system
+#         types: [python]
+#         pass_filenames: false
+
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v4.6.3
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+
   - repo: local
     hooks:
       - id: pytest-check
         name: pytest-check
-        entry: pytest -vvv --cov=statista
+        entry: pytest -v --cov=src/statista --cov-report term-missing
         language: system
         pass_filenames: false
         always_run: true
 
   - repo: local
     hooks:
-      - id: examples-notebook-check
+      - id: notebook-check
         name: nbval
-        entry: pytest --nbval
+        entry: pytest --nbval-lax
         language: system
         files: \.ipynb$
+        always_run: true
 
   - repo: local
     hooks:
       - id: doctest
         name: doctest
-        entry: pytest --doctest-modules
+        entry: python -c "import matplotlib; matplotlib.use('Agg'); import pytest; pytest.main(['--doctest-modules'])"
         language: system
-        files: statista\.py$
+        files: ^src/statista/.*\.py$
+        always_run: true

.github/workflows/pypi-deployment.yml .github/workflows/tests.yml.github/workflows/pypi-deployment.yml renamed to .github/workflows/tests.yml

@@ -74,3 +74,9 @@ distributions
 descriptors
 """""""""""
 * rename the `metrics` module to `descriptors`.
+
+0.6.1 (2025-06-**)
+------------------
+Dev
+"""
+* replace the setup.py with pyproject.toml.