ENH: Modernize package setup (#56)

* ENH: Modernize package setup

Modernize packate setup:
- Adopt PEP621 to store project metadata in `pyproject.toml`. Remove the
  `setup.py` file.
- Adopt PEP518 to specify the build system requirements for the
  package.
- Adopt PEP631 to specify the package dependencies in the
  `pyproject.toml` file, and remove the `requirements,txt`.
- Transition to `setuptools_scm` dynamic versioning system.

Change the GHA package test workflow file accordingly.

Add the `_version.py` file to the `.gitignore` file list.

Documentation:
https://peps.python.org/pep-0621/
https://packaging.python.org/en/latest/specifications/pyproject-toml/#pyproject-toml-spec
https://peps.python.org/pep-0518/
https://peps.python.org/pep-0631/
https://setuptools.pypa.io/en/latest/index.html
https://setuptools-scm.readthedocs.io/en/latest/

* ENH: Require a more recent version of `NumPy`

Require a more recent version of `NumPy`: require any version greater or
equal to 1.19.5 but lower than 2.0.0. `NumPy` 1.19.5 was the first
release supporting Python 3.9.

Fixes:
```
    from distutils.msvccompiler import get_build_version as get_build_msvc_version
ModuleNotFoundError: No module named 'distutils.msvccompiler'
```

raised for example at:
https://github.com/demianw/tract_querier/actions/runs/12145326696/job/33866697673#step:5:806

Author: jhlegarreta

.github/workflows/test_package.yaml

@@ -36,7 +36,7 @@ jobs:
     - name: Set min. dependencies
       if: matrix.requires == 'minimal'
       run: |
-        python -c "req = open('requirements.txt').read().replace('>=', '==') ; open('requirements.txt', 'w').write(req)"
+        sed -E -i '/dependencies = \[/,/]/ s/>=([^,<]+)/==\1/g' pyproject.toml
 
     # - name: Cache pip
     #   uses: actions/cache@v2
@@ -52,13 +52,11 @@ jobs:
       # if: steps.cache.outputs.cache-hit != 'true'
       run: |
         python -m pip install --upgrade --user pip setuptools coverage
-        pip install -r requirements.txt
+        pip install -e .[test]
         python --version
         pip --version
         pip list
 
     - name: Run tests
       run: |
-        # tox --sitepackages
-        python setup.py build_ext --inplace
         nosetests -v

.gitignore

@@ -14,3 +14,6 @@ htmlcov
 .idea
 build
 cover
+
+# Version file
+tract_querier/_version.py

pyproject.toml

@@ -0,0 +1,69 @@
+[build-system]
+requires = [
+    "setuptools",
+    "setuptools_scm",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tract_querier"
+description = "WMQL: Query language for automatic tract extraction from full-brain tractographies with a registered template on top of them"
+readme = "README.md"
+license = {file = "license.rst"}
+authors = [
+  {name = "Demian Wassermann"}, {email = "[email protected]"}
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS"
+]
+dependencies = [
+    "numpy>=1.19.5,<2.0.0",
+    "nibabel>=2.0,<3.0",
+    "six>=1.10",
+    "vtk"
+]
+dynamic = ["version"]
+requires-python = ">=3.9"
+
+[project.optional-dependencies]
+doc = [
+    "numpydoc",
+]
+test = [
+    "coverage",
+    "nose",
+]
+
+[project.urls]
+documentation = "http://demianw.github.io/tract_querier"
+homepage = "http://demianw.github.io/tract_querier"
+repository = "https://github.com/demianw/tract_querier"
+
+[project.scripts]
+tract_math = "scripts.tract_math:main"
+tract_querier = "scripts.tract_querier:main"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+tract_querier = [
+    "data/FreeSurfer.qry",
+    "data/JHU_MNI_SS_WMPM_Type_I.qry",
+    "data/JHU_MNI_SS_WMPM_Type_II.qry",
+    "data/freesurfer_queries.qry",
+    "data/mori_queries.qry",
+]
+
+[tool.setuptools.packages]
+find = {}  # Scanning implicit namespaces is active by default
+
+[tool.setuptools_scm]
+write_to = "tract_querier/_version.py"