[MAINT] update packaging (#65)

* update packaging(

* move cli

* un example during tests

* typo

* lint and format

* run test by default with tox

* drop python 3.7 and test on 3.12

* rely on hacthling vcs for versioning

* use pyproject for codespell config

* add load to init

* bump action version

* add other packages for testing

.github/workflows/codespell.yml

@@ -17,6 +17,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/test.yml

@@ -13,31 +13,21 @@ concurrency:
 
 jobs:
     test:
-
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
                 os: [ubuntu-latest, macOS-latest, windows-latest] 
-                python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+                python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
             fail-fast: false
-
         steps:
-
         -   name: Clone repo
             uses: actions/checkout@v4
-
         -   name: Set up Python ${{ matrix.python-version }}
             uses: actions/setup-python@v4
             with:
                 python-version: ${{ matrix.python-version }}
-
         -   name: Install dependencies
-            run: |
-                pip install --upgrade setuptools
-                pip install -r requirements.txt
-                python setup.py install # install nidmresults from sources
-                pip install ddt
-
+            run: pip install tox
         -   name: Run tests
-            run: python test/test_reader.py
+            run: tox run -e tests
 

.github/workflows/update_precommit_hooks.yml

@@ -0,0 +1,53 @@
+---
+name: update precommit hooks
+
+
+on:
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#            ┌───────────── minute (0 - 59)
+#            │ ┌───────────── hour (0 - 23)
+#            │ │ ┌───────────── day of the month (1 - 31)
+#            │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+#            │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            * * * * *
+    schedule:
+    -   cron: 0 0 1 1,4,7,10 * # every 3 months
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    update_precommit_hooks:
+
+    # only run on upstream repo
+        if: github.repository_owner == 'neuropower'
+
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install pre-commit
+            run: pip install pre-commit
+        -   name: Update pre-commit hooks
+            run: pre-commit autoupdate
+        -   name: Create Pull Request
+            uses: peter-evans/create-pull-request@v6
+            with:
+                commit-message: pre-commit hooks auto-update
+                base: main
+                token: ${{ secrets.GITHUB_TOKEN }}
+                delete-branch: true
+                title: '[BOT] update pre-commit hooks'
+                body: done via this [GitHub Action](https://github.com/${{ github.repository_owner }}/neurodesign/blob/master/.github/workflows/update_precommit_hooks.yml)

.gitignore

@@ -1,11 +1,24 @@
 *.bak
 
-build/*
-*egg*/*
-dist/*
 .DS_Store
+
+.vscode
+
+*egg*/*
 *.pyc
+build/
+dist/
+
+env/
+venv/
+
+# handled by hatch
+nidmresults/_version.py
 
 *.nidm.zip
 
-test/data
+debug.log
+
+test/data
+
+.tox

.pre-commit-config.yaml

@@ -0,0 +1,73 @@
+---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+# -   repo: https://github.com/pre-commit/pre-commit-hooks
+#     rev: v4.5.0
+#     hooks:
+#     -   id: check-ast
+#     -   id: check-case-conflict
+#     -   id: check-json
+#     -   id: check-merge-conflict
+#     -   id: check-toml
+#     -   id: check-yaml
+#     -   id: end-of-file-fixer
+#     -   id: mixed-line-ending
+#     -   id: trailing-whitespace
+
+# -   repo: https://github.com/pycqa/isort
+#     rev: 5.13.2
+#     hooks:
+#     -   id: isort
+#         args: [--profile, black, --settings-path, pyproject.toml]
+
+# -   repo: https://github.com/asottile/pyupgrade
+#     rev: v3.15.0
+#     hooks:
+#     -   id: pyupgrade
+#         args: [--py38-plus]
+
+# -   repo: https://github.com/psf/black-pre-commit-mirror
+#     rev: 24.1.1
+#     hooks:
+#     -   id: black
+#         args: [--config, pyproject.toml]
+
+# -   repo: https://github.com/adamchainz/blacken-docs
+#     rev: 1.16.0
+#     hooks:
+#     -   id: blacken-docs
+#         additional_dependencies:
+#         -   black==23.9.1
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell
+        args: [--toml, pyproject.toml]
+        additional_dependencies: [tomli]
+
+# -   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+#     rev: 0.2.3
+#     hooks:
+#     -   id: yamlfmt
+#         args: [--mapping, '4', --sequence, '4', --offset, '0']
+
+-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.12.0
+    hooks:
+    -   id: pretty-format-toml
+        args: [--autofix, --indent, '4']
+
+# -   repo: https://github.com/pre-commit/pygrep-hooks
+#     rev: v1.10.0
+#     hooks:
+#     -   id: rst-backticks
+
+# -   repo: https://github.com/pyCQA/flake8
+#     rev: 7.0.0
+#     hooks:
+#     -   id: flake8
+#         args: [--config, .flake8, --verbose, nilearn, examples, maint_tools]
+#         additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions]

README.md

@@ -1,6 +1,9 @@
 # nidmresults
 A Python library to read and write [NIDM-Results](http://nidm.nidash.org/specs/nidm-results.html) packs.
 
+specification: http://nidm.nidash.org/specs/nidm-results.html
+manuscript: https://dx.doi.org/10.1038/sdata.2016.102
+
 You are free to copy, modify, and distribute nidmresults with attribution under the terms of the MIT license. See the [LICENSE file](LICENSE.md) for details.
 
 ## Install

examples/ex_read_nidm.py

@@ -1,8 +1,6 @@
 # Example: reading a NIDM pack available on NeuroVault
 import os
 import json
-import shutil
-import tempfile
 import nidmresults as nidm
 import urllib.request
 
@@ -11,7 +9,7 @@
 nidmpack = "2210_fsl_default_130.nidm.zip"
 
 if not os.path.isfile(nidmpack):
-    print('Downloading ' + nidmpack)
+    print(f'Downloading {nidmpack}')
     urllib.request.urlretrieve(nidm_url, nidmpack)
 
 # Known issues with NIDM packs in collection 2210

nidmresults/__init__.py

@@ -1,10 +1,11 @@
 import os
-from pkg_resources import get_distribution
 
-from .load import load
+from nidmresults.load import load
+
+from nidmresults._version import __version__
 
 latest_owlfile = os.path.join(
     os.path.dirname(os.path.dirname(__file__)), 'nidmresults', 'owl',
     "nidm-results_130.owl")
 
-__version__ = get_distribution('nidmresults').version
+__all__ = ["load"]

bin/nidm_mkda_convert → nidmresults/cli/nidm_mkda_convert.py

@@ -1,33 +1,38 @@
 #!/usr/bin/python
-"""
-Create a database suitable for use with MKDA toolbox
+"""Create a database suitable for use with MKDA toolbox.
 
 @author: Camille Maumet <c.m.j.maumet@warwick.ac.uk>
 @copyright: University of Warwick 2013-2014
 """
 
-from __future__ import division, print_function, absolute_import
-import os
+from __future__ import absolute_import, division, print_function
+
 import argparse
-from nidmresults.graph import Graph
+import os
+import sys
+
 from nidmresults import __version__
+from nidmresults.graph import Graph
 
-if __name__ == "__main__":
+
+def main(argv=sys.argv):
     parser = argparse.ArgumentParser(
-        description='Convert a set of NIDM-Results packs to an MKDA-compliant \
-        csv file.')
+        description="Convert a set of NIDM-Results packs to an MKDA-compliant \
+        csv file."
+    )
     parser.add_argument(
-        '-o', '--outfile',
-        help='Name of the csv file.', default="mkda.csv")
+        "-o", "--outfile", help="Name of the csv file.", default="mkda.csv"
+    )
     parser.add_argument(
-        'nidmpacks',
-        help='Path to NIDM-Results packs (.nidm.zip) separated by spaces.',
-        nargs="+")
+        "nidmpacks",
+        help="Path to NIDM-Results packs (.nidm.zip) separated by spaces.",
+        nargs="+",
+    )
     parser.add_argument(
-        '--version', action='version',
-        version='{version}'.format(version=__version__))
+        "--version", action="version", version="{version}".format(version=__version__)
+    )
 
-    args = parser.parse_args()
+    args = parser.parse_args(argv[1:])
 
     nidmpacks = args.nidmpacks
 
@@ -47,8 +52,13 @@
             first = False
 
         if not os.path.isfile(nidmpack):
-            raise Exception("Unknown file: "+str(nidmpack))
+            raise Exception("Unknown file: " + str(nidmpack))
 
         nidmgraph = Graph(nidm_zip=nidmpack)
-        con_ids = nidmgraph.serialize(outfile, "mkda", overwrite=overwrite,
-                                      last_used_con_id=max(con_ids.values()))
+        con_ids = nidmgraph.serialize(
+            outfile, "mkda", overwrite=overwrite, last_used_con_id=max(con_ids.values())
+        )
+
+
+if __name__ == "__main__":
+    main()