Packaging the visualizer

.gitignore

@@ -13,3 +13,5 @@ venv*
 venv3.11/
 .idea/*
 .pytest_cache/*
+build/*
+*.egg-info

bids_prov/visualize.py

@@ -111,12 +111,15 @@ def main(filename: str, output_file=None, omit_details=True) -> None:
     viz_jsonld11(jsonld11, output_file)
 
 
-if __name__ == "__main__":
-
+def entry_point():
+    """ A command line tool for the visualize module """
     parser = argparse.ArgumentParser()
     parser.add_argument("--input_file", type=str, default="res.jsonld", help="data jsonld file ")
     parser.add_argument("--output_file", type=str, default="res.png", help="output dir where results are written")
     opt = parser.parse_args()
 
     main(opt.input_file, output_file=opt.output_file, omit_details=True)
     # >> python -m   bids_prov.visualize --input_file ./res_temp.jsonld  --output_file res.png
+
+if __name__ == "__main__":
+    entry_point()

examples/from_parsers/context_2024_05_23_08h10m05s.txt → examples/from_parsers/context_2024_06_10_14h38m10s.txt

@@ -1,4 +1,4 @@
-Date : 2024_05_23_08h10m05s
+Date : 2024_06_10_14h38m10s
 Processing files...
     file= nidmresults-examples/afni_alt_onesided_proc.sub_001
     file= nidmresults-examples/afni_alt_onesided_proc.sub_001
@@ -69,4 +69,4 @@ Processing files...
     file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
     file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
     file= nidmresults-examples/spm_thr_voxelunct4_batch.m
-End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:01.882820
+End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:01.877882

pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "bids_prov"
+authors = [
+    "Camille Maumet",
+    "Satrajit Ghosh",
+    "Stefan Appelhoff",
+    "Chris Markiewicz",
+    "Yaroslav Halchenko",
+    "Jean-Baptiste Poline",
+    "Rémi Adon",
+    "Hermann Courteille",
+    "Thomas Betton",
+    "Cyril Regan",
+    "Boris Clénet"
+]
+description = "BIDS extension proposal 28 : BIDS Provenance"
+version = "0.1.0"
+readme = "README.md"
+requires-python = ">=3.10, <3.11"
+license = "CC-BY-4.0"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Medical Science Apps."
+]
+include = ["bids_prov/visualize.py"]
+exclude = ["bids_prov*"]
+
+[tool.poetry.dependencies]
+python = "^3.10.0"
+beautifulsoup4 = "^4.12.3"
+boutiques = "^0.5.26"
+click = "^8.1.7"
+deepdiff = "^7.0.1"
+graphviz = "^0.20.3"
+rdflib = "^7.0.0"
+rdflib-jsonld = "^0.6.2"
+prov = "^2.0.0"
+pydot = "^2.0.0"
+pyld = "^2.0.4"
+pyyaml = "^6.0.1"
+requests = "^2.32.3"
+
+[tool.poetry.group.dev.dependencies]
+black = "^24.4.2"
+markdownify = "^0.12.1"
+pre-commit = "^3.7.1"
+pytest-cov = "^5.0.0"
+
+[tool.poetry.scripts]
+bids_prov_visualizer = "bids_prov.visualize:entry_point"