Update Python packaging

MANIFEST.in

@@ -0,0 +1,5 @@
+include CHANGELOG.* CONTRIBUTORS.* LICENSE tox.ini
+graft nidm
+graft docs
+graft test
+global-exclude *.py[cod]

README.rst

@@ -16,11 +16,6 @@ Dependencies
 * `Graphviz <http://graphviz.org>`_ (native package):
 * Fedora: `dnf install graphviz`
 * OS-X: `brew install graphviz`
-* Datalad (optional): `pip install datalad`
-* Sklearn: `pip install scikit-learn`
-* Statsmodels: `pip install statsmodels`
-* Statistics: `pip install statistics`
-* Patsy: `pip install patsy`
 
 Installation
 ============

nidm/__init__.py

@@ -1,7 +1,8 @@
 from __future__ import absolute_import, division, print_function
-from .version import __version__
 import __main__
 
+__version__ = "3.9.7"
+
 try:
     import etelemetry
     etelemetry.check_available_version("incf-nidash/pynidm", __version__)

nidm/experiment/tools/bidsmri2nidm.py

@@ -79,7 +79,7 @@ def getsha512(filename):
     return sha512_hash.hexdigest()
 
 
-def main(argv):
+def main():
     parser = ArgumentParser(description=
 """This program will represent a BIDS MRI dataset as a NIDM RDF document and provide user with opportunity to annotate
 the dataset (i.e. create sidecar files) and associate selected variables with broader concepts to make datasets more
@@ -896,4 +896,4 @@ def bidsmri2project(directory, args):
 
 
 if __name__ == "__main__":
-    main(sys.argv[1:])
+    main()

nidm/experiment/tools/csv2nidm.py

@@ -73,7 +73,7 @@
 
 
 
-def main(argv):
+def main():
     parser = ArgumentParser(description='This program will load in a CSV file and iterate over the header \
      variable names performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim \
      tagged terms that fuzzy match the variable names.  The user will then interactively pick \
@@ -387,4 +387,4 @@ def main(argv):
 
 
 if __name__ == "__main__":
-   main(sys.argv[1:])
+   main()

nidm/experiment/tools/nidm_utils.py

@@ -41,7 +41,7 @@
 from graphviz import Source
 import tempfile
 
-def main(argv):
+def main():
 
     parser = ArgumentParser(description='This program contains various NIDM-Experiment utilities')
     sub = parser.add_subparsers(dest='command')
@@ -120,4 +120,4 @@ def main(argv):
 
 
 if __name__ == "__main__":
-   main(sys.argv[1:])
+   main()

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 46.4.0"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,71 @@
+[metadata]
+name = pynidm
+version = attr:nidm.__version__
+description = PYNIDM: a Python NIDM library and tools
+long_description = file:README.rst
+long_description_content_type = text/x-rst
+author = INCF-NIDASH developers
+author_email = [email protected]
+maintainer = INCF-NIDASH developers
+maintainer_email = [email protected]
+license = Apache-2.0
+license_files = LICENSE
+url = https://github.com/incf-nidash/PyNIDM
+
+classifiers =
+    Development Status :: 3 - Alpha
+    Environment :: Console
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: Apache Software License
+    Operating System :: MacOS :: MacOS X
+    Operating System :: POSIX :: Linux
+    Programming Language :: Python :: 3
+    Topic :: Scientific/Engineering
+
+[options]
+packages = find_namespace:
+include_package_data = True
+python_requires = >=3.8
+install_requires =
+    click
+    click-option-group
+    cognitiveatlas
+    datalad
+    duecredit
+    etelemetry
+    graphviz
+    joblib
+    numpy >= 1.16.5
+    ontquery ~= 0.2.3
+    orthauth >= 0.0.12
+    pandas
+    patsy
+    prov
+    pybids >= 0.12.4
+    pydot
+    pydotplus
+    pygithub
+    pyld >= 1.0.5, <2.0
+    pytest
+    rapidfuzz
+    rdflib
+    rdflib-jsonld
+    requests
+    scikit-learn
+    simplejson
+    statsmodels
+    tabulate
+    validators
+
+[options.packages.find]
+include =
+    nidm
+    nidm.*
+
+[options.entry_points]
+console_scripts =
+    bidsmri2nidm = nidm.experiment.tools.bidsmri2nidm:main
+    csv2nidm = nidm.experiment.tools.csv2nidm:main
+    nidm_query = nidm.experiment.tools.nidm_query:query
+    nidm_utils = nidm.experiment.tools.nidm_utils:main
+    pynidm = nidm.experiment.tools.click_main:cli