ENH: make everything pip installable through pyproject.toml

Add commandline entries to all python scripts

nih2mne/calc_mnetrans.py

@@ -471,8 +471,7 @@ def view_coreg(dsname=None, trans_file=None, subjects_dir=None):
                        surfaces=['head', 'white'], coord_frame='meg')
     _ = input('Press enter to close')
 
-
-if __name__=='__main__':
+def main():    
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument('-subjects_dir', help='''Set SUBJECTS_DIR different
@@ -526,7 +525,8 @@ def view_coreg(dsname=None, trans_file=None, subjects_dir=None):
     if args.view_coreg:
         view_coreg(args.dsname, mne_trans_name, subjects_dir)
 
-
+if __name__=='__main__':
+    main()        
 
 
 

nih2mne/make_meg_bids.py

@@ -635,7 +635,8 @@ def _get_conversion_dict(input_path=None, subject_in=None, bids_id=None,
 # =============================================================================
 # Commandline Options
 # =============================================================================
-if __name__ == '__main__':
+
+def main():
     import argparse
     parser = argparse.ArgumentParser('''
         Convert MEG dataset to default Bids format using the MEG hash ID or 
@@ -969,4 +970,6 @@ def _get_conversion_dict(input_path=None, subject_in=None, bids_id=None,
         #            deriv_path=deriv_path, 
         #            surf=surf)
 
-
+if __name__ == '__main__':
+    main()
+

nih2mne/megcore_prep_mri_bids.py

@@ -288,7 +288,7 @@ def preproc(bids_path=None,
 
 
 #%% Commandline Options parsing
-if __name__=='__main__':
+def main():
     import argparse
     parser = argparse.ArgumentParser(description=desc)
     single_parser = parser.add_argument_group('Single File only')
@@ -367,6 +367,8 @@ def preproc(bids_path=None,
         mripreproc(bids_path, t1_bids_path, deriv_path, surf=proc_surf)
 
 
+if __name__=='__main__':
+    main()
 
 #%% Some minimal tests
 #$(pwd)/nih2mne/megcore_prep_mri_bids.py -gen_swarmfile -swarm_fname TEST.sh -bids_root /fast/BIDS_HV_V1/bids/

nih2mne/utilities/fix_dsname.py

@@ -38,8 +38,10 @@ def fixDsName(input_name):
             # print(out_name)
             shutil.move(in_name, out_name)
 
-if __name__=='__main__':
+def main():
     input_name = sys.argv[1]
     fixDsName(input_name)
-
+
+if __name__=='__main__':
+    main()
 

nih2mne/utilities/make_meg_bids_fromcsv.py

@@ -133,7 +133,7 @@ def make_serial_proc(csvfile, run=False, return_cmd=False):
         import subprocess
         subprocess.run(cmd_chain)
 
-if __name__ == '__main__':
+def main():
     import argparse
     template = op.join(op.dirname(__file__),'..', 'templates', 'bids_entry_template.csv')
     template = op.abspath(template)
@@ -161,3 +161,5 @@ def make_serial_proc(csvfile, run=False, return_cmd=False):
     elif args.write_swarmf:
         make_swarm_file(csvfile, write=True)
 
+if __name__ == '__main__':
+    main()

nih2mne/utilities/print_bids_table.py

@@ -41,8 +41,7 @@ def get_bids_table(bids_dir, ses='1'):
     return dframe
 
 
-
-if __name__ == '__main__':
+def main():    
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument('-bids_dir', 
@@ -78,6 +77,7 @@ def get_bids_table(bids_dir, ses='1'):
         pivot.to_csv(out_fname)
         print(f'Table saved to {out_fname}')
 
-
+if __name__ == '__main__':
+    main()    
 
 

nih2mne/utilities/qa_fids.py

@@ -72,8 +72,7 @@ def plot_fids_qa(subjid=None, bids_root=None, outfile=None):
         )
     plt.show()
 
-
-if __name__ == '__main__':
+def main():
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument('-subject',
@@ -113,5 +112,6 @@ def plot_fids_qa(subjid=None, bids_root=None, outfile=None):
             except:
                 print(f'Failed to create QA image for {subject}')
 
-
+if __name__ == '__main__':
+    main()    
 

pyproject.toml

@@ -0,0 +1,52 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nih2mne"
+description = "General integration functions for mne and mne-bids for NIH users"
+readme = "README.md"
+requires-python = "<3.12"
+#keywords = ["one", "two"]
+
+authors = [
+  { name="Jeff Stout", email="[email protected]" },
+]
+
+license = {text = "UNLICENSE"}
+classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: UNLICENSE",
+        "Operating System :: Linux/Unix",
+    ]
+dependencies = [
+'mne<1.7', 'numpy', 'pytest', 'joblib', 'nibabel','mne_bids','pandas', 'wget',
+'pyctf-lite @ git+https://github.com/nih-megcore/[email protected]#egg=pyctf-lite' 
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+testing = ['datalad','pytest','pygit2']
+
+[project.scripts]
+"bstags.py"='nih2mne.bstags:main'
+"calc_mnetrans.py"='nih2mne.calc_mnetrans:main'
+"make_meg_bids.py"='nih2mne.make_meg_bids:main'
+"make_meg_bids_fromcsv.py" = 'nih2mne.utilities.make_meg_bids_fromcsv:main'
+"print_bids_table.py"='nih2mne.utilities.print_bids_table:main'
+"fix_dsname.py"='nih2mne.utilities.fix_dsname:main'
+"megcore_prep_mri_bids.py"='nih2mne.megcore_prep_mri_bids:main'
+"qa_fids.py"='nih2mne.utilities.qa_fids:main'
+#'nih2mne/eyetracking_preprocessing.py',
+#'cmdline/make_bids_fs_swarm.sh',
+
+
+"process_meg.py" = "enigmeg.process_meg:main"
+"enigma_prep_QA.py" = 'enigmeg.QA.enigma_prep_QA:main'
+"Run_enigma_QA_GUI.py" = 'enigmeg.QA.Run_enigma_QA_GUI:main'
+"parse_bids.py" =  'enigmeg.parse_bids:main'
+
+
+[tool.setuptools.packages.find]
+include = ["nih2mne*"]
+#exclude = ["extras*", "conda*"]