From 32312f7c1e01f4a5c068e6775372afa3219d69cf Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Thu, 31 Jul 2025 10:59:21 -0700
Subject: [PATCH 01/16] initial working cli

---
 basicrta/cli.py     |  89 +++++++++++++++++++++++++++++
 basicrta/combine.py | 132 ++++++++++++++++++++++++++++++++++++++++++--
 pyproject.toml      |   3 +
 3 files changed, 219 insertions(+), 5 deletions(-)
 create mode 100644 basicrta/cli.py

diff --git a/basicrta/cli.py b/basicrta/cli.py
new file mode 100644
index 0000000..1731678
--- /dev/null
+++ b/basicrta/cli.py
@@ -0,0 +1,89 @@
+"""
+basicrta
+A package to extract binding kinetics from molecular dynamics simulations
+"""
+
+# Add imports here
+from importlib.metadata import version
+from basicrta import *
+import argparse
+import subprocess
+
+__version__ = version("basicrta")
+
+commands = ['contacts', 'cluster', 'combine', 'kinetics', 'gibbs']
+
+def main():
+    parser = argparse.ArgumentParser(prog='basicrta')
+    #parser.add_argument('command', help='Step in workflow to execute', nargs='+')
+    subparsers = parser.add_subparsers(dest='command')
+
+    
+    parserA = subparsers.add_parser('contacts', help='Ahelp')
+    parserA.add_argument('--top', type=str, help='Topology')
+    parserA.add_argument('--traj', type=str, help='Trajectory')
+    parserA.add_argument('--sel1', type=str, help='First selection (group for'
+                         'which tau is to be calculated)')
+    parserA.add_argument('--sel2', type=str, help='Second selection (group of'
+                         'interest in interactions with first selection)')
+    parserA.add_argument('--cutoff', type=float, help='Value to use (in A) for'
+                         'the maximum separation distance that constitutes a'
+                         'contact.')
+    parserA.add_argument('--nproc', type=int, default=1, help='Number of'
+                         'processes to use')
+    parserA.add_argument('--nslices', type=int, default=100, help='Number of'
+                         'trajectory segments to use (if encountering a'
+                         'memoryerror, try using a greater value)')
+
+    parserB = subparsers.add_parser('combine', add_help=True, help='Bhelp')
+    parserB.add_argument('--contacts', nargs='+', required=True,
+                         help="List of contact pickle files to combine (e.g.," 
+                         "contacts_7.0.pkl from different runs)")
+    parserB.add_argument( '--output', type=str, default='combined_contacts.pkl',
+                         help="Output filename for combined contacts (default:"
+                         "combined_contacts.pkl)")
+    parserB.add_argument( '--no-validate', action='store_true', help="Skip"
+                         "compatibility validation (use with caution)")
+
+    parserC = subparsers.add_parser('cluster', help='Chelp')
+    parserC.add_argument('--nproc', type=int, default=1)
+    parserC.add_argument('--cutoff', type=float)
+    parserC.add_argument('--niter', type=int, default=110000)
+    parserC.add_argument('--prot', type=str, default=None, nargs='?')
+    parserC.add_argument('--label-cutoff', type=float, default=3,
+                         dest='label_cutoff',
+                         help='Only label residues with tau > '
+                         'LABEL-CUTOFF * <tau>. ')
+    parserC.add_argument('--structure', type=str, nargs='?')
+    # use  for default values
+    parserC.add_argument('--gskip', type=int, default=1000, 
+                         help='Gibbs skip parameter for decorrelated samples;'
+                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
+    parserC.add_argument('--burnin', type=int, default=10000, 
+                         help='Burn-in parameter, drop first N samples as equilibration;'
+                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
+
+    parserD = subparsers.add_parser('gibbs', help='Dhelp')
+    parserD.add_argument('--contacts')
+    parserD.add_argument('--resid', type=int, default=None)
+    parserD.add_argument('--nproc', type=int, default=1)
+    parserD.add_argument('--niter', type=int, default=110000)
+    parserD.add_argument('--ncomp', type=int, default=15)
+
+    parserE = subparsers.add_parser('kinetics', help='Ehelp')
+    parserE.add_argument("--gibbs", type=str)
+    parserE.add_argument("--contacts", type=str)
+    parserE.add_argument("--top_n", type=int, nargs='?', default=None)
+    parserE.add_argument("--step", type=int, nargs='?', default=1)
+    parserE.add_argument("--wdensity", action='store_true')
+    
+    args = parser.parse_args()
+    keys, values = vars(args).keys(), vars(args).values()
+    inarr = [[f"--{key}", f"{value}"] for key, value in zip(keys, values) if key!='command']
+    inlist = [aset for alist in inarr for aset in alist]
+    subprocess.run(['python',
+                    f'/home/r2/opt/basicrta/basicrta/{args.command}.py'] + 
+                   inlist)
+
+if __name__ == "__main__":
+    main()
diff --git a/basicrta/combine.py b/basicrta/combine.py
index 826b159..52f691d 100644
--- a/basicrta/combine.py
+++ b/basicrta/combine.py
@@ -9,10 +9,135 @@
 
 import os
 import argparse
-from basicrta.contacts import CombineContacts
 
+class CombineContacts(object):
+    """Class to combine contact timeseries from multiple repeat runs.
+    
+    This class enables pooling data from multiple trajectory repeats and
+    calculating posteriors from all data together, rather than analyzing
+    each run separately.
+    
+    :param contact_files: List of contact pickle files to combine
+    :type contact_files: list of str
+    :param output_name: Name for the combined output file (default: 'combined_contacts.pkl')
+    :type output_name: str, optional
+    :param validate_compatibility: Whether to validate that files are compatible (default: True)
+    :type validate_compatibility: bool, optional
+    """
+    
+    def __init__(self, contact_files, output_name='combined_contacts.pkl', 
+                 validate_compatibility=True):
+        self.contact_files = contact_files
+        self.output_name = output_name
+        self.validate_compatibility = validate_compatibility
+        
+        if len(contact_files) < 2:
+            raise ValueError("At least 2 contact files are required for combining")
+            
+    def _load_contact_file(self, filename):
+        """Load a contact pickle file and return data and metadata."""
+        if not os.path.exists(filename):
+            raise FileNotFoundError(f"Contact file not found: {filename}")
+            
+        with open(filename, 'rb') as f:
+            contacts = pickle.load(f)
+            
+        metadata = contacts.dtype.metadata
+        return contacts, metadata
+        
+    def _validate_compatibility(self, metadatas):
+        """Validate that contact files are compatible for combining."""
+        reference = metadatas[0]
+        
+        # Check that all files have the same atom groups
+        for i, meta in enumerate(metadatas[1:], 1):
+            # Compare cutoff
+            if meta['cutoff'] != reference['cutoff']:
+                raise ValueError(f"Incompatible cutoffs: file 0 has {reference['cutoff']}, "
+                               f"file {i} has {meta['cutoff']}")
+                               
+            # Compare atom group selections by checking if resids match
+            ref_ag1_resids = set(reference['ag1'].residues.resids)
+            ref_ag2_resids = set(reference['ag2'].residues.resids)
+            meta_ag1_resids = set(meta['ag1'].residues.resids)
+            meta_ag2_resids = set(meta['ag2'].residues.resids)
+            
+            if ref_ag1_resids != meta_ag1_resids:
+                raise ValueError(f"Incompatible ag1 residues between file 0 and file {i}")
+            if ref_ag2_resids != meta_ag2_resids:
+                raise ValueError(f"Incompatible ag2 residues between file 0 and file {i}")
+                
+        # Check timesteps and warn if different
+        timesteps = [meta['ts'] for meta in metadatas]
+        if not all(abs(ts - timesteps[0]) < 1e-6 for ts in timesteps):
+            print("WARNING: Different timesteps detected across runs:")
+            for i, (filename, ts) in enumerate(zip(self.contact_files, timesteps)):
+                print(f"  File {i} ({filename}): dt = {ts} ns")
+            print("This may affect residence time estimates, especially for fast events.")
+            
+    def run(self):
+        """Combine contact files and save the result."""
+        print(f"Combining {len(self.contact_files)} contact files...")
+        
+        all_contacts = []
+        all_metadatas = []
+        
+        # Load all contact files
+        for i, filename in enumerate(self.contact_files):
+            print(f"Loading file {i+1}/{len(self.contact_files)}: {filename}")
+            contacts, metadata = self._load_contact_file(filename)
+            all_contacts.append(contacts)
+            all_metadatas.append(metadata)
+            
+        # Validate compatibility if requested
+        if self.validate_compatibility:
+            print("Validating file compatibility...")
+            self._validate_compatibility(all_metadatas)
+            
+        # Combine contact data
+        print("Combining contact data...")
+        
+        # Calculate total size and create combined array
+        total_size = sum(len(contacts) for contacts in all_contacts)
+        reference_metadata = all_metadatas[0].copy()
+        
+        # Extend metadata to include trajectory source information
+        reference_metadata['source_files'] = self.contact_files
+        reference_metadata['n_trajectories'] = len(self.contact_files)
+        
+        # Determine number of columns (5 for raw contacts, 4 for processed)
+        n_cols = all_contacts[0].shape[1]
+        
+        # Create dtype with extended metadata
+        combined_dtype = np.dtype(np.float64, metadata=reference_metadata)
+        
+        # Add trajectory source column (will be last column)
+        combined_contacts = np.zeros((total_size, n_cols + 1), dtype=np.float64)
+        
+        # Combine data and add trajectory source information
+        offset = 0
+        for traj_idx, contacts in enumerate(all_contacts):
+            n_contacts = len(contacts)
+            # Copy original contact data
+            combined_contacts[offset:offset+n_contacts, :n_cols] = contacts[:]
+            # Add trajectory source index
+            combined_contacts[offset:offset+n_contacts, n_cols] = traj_idx
+            offset += n_contacts
+            
+        # Create final memmap with proper dtype
+        final_contacts = combined_contacts.view(combined_dtype)
+        
+        # Save combined contacts
+        print(f"Saving combined contacts to {self.output_name}...")
+        final_contacts.dump(self.output_name, protocol=5)
+        
+        print(f"Successfully combined {len(self.contact_files)} files into {self.output_name}")
+        print(f"Total contacts: {total_size}")
+        print(f"Added trajectory source column (index {n_cols}) for kinetic clustering support")
+        
+        return self.output_name
 
-def main():
+if __name__ == "__main__":
     """Main function for combining contact files."""
     parser = argparse.ArgumentParser(
         description="Combine contact timeseries from multiple repeat runs. "
@@ -82,6 +207,3 @@ def main():
         print(f"ERROR: {e}")
         return 1
 
-
-if __name__ == '__main__':
-    exit(main())
diff --git a/pyproject.toml b/pyproject.toml
index 33b8c1c..f3991e6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,6 +49,9 @@ doc = [
 source = "https://github.com/becksteinlab/basicrta"
 documentation = "https://basicrta.readthedocs.io"
 
+[project.scripts]
+basicrta = "basicrta.cli:main"
+
 [tool.setuptools]
 py-modules = []
 

From 0f0fedec75f3720f5847207a705e6f4202df45bb Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Sat, 2 Aug 2025 18:34:53 -0700
Subject: [PATCH 02/16] taking parser from submodules

---
 basicrta/cli.py      | 114 +++++++++++++++++++++----------------------
 basicrta/contacts.py |  40 +++++++++------
 2 files changed, 81 insertions(+), 73 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index 1731678..e4bacff 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -19,63 +19,63 @@ def main():
     subparsers = parser.add_subparsers(dest='command')
 
     
-    parserA = subparsers.add_parser('contacts', help='Ahelp')
-    parserA.add_argument('--top', type=str, help='Topology')
-    parserA.add_argument('--traj', type=str, help='Trajectory')
-    parserA.add_argument('--sel1', type=str, help='First selection (group for'
-                         'which tau is to be calculated)')
-    parserA.add_argument('--sel2', type=str, help='Second selection (group of'
-                         'interest in interactions with first selection)')
-    parserA.add_argument('--cutoff', type=float, help='Value to use (in A) for'
-                         'the maximum separation distance that constitutes a'
-                         'contact.')
-    parserA.add_argument('--nproc', type=int, default=1, help='Number of'
-                         'processes to use')
-    parserA.add_argument('--nslices', type=int, default=100, help='Number of'
-                         'trajectory segments to use (if encountering a'
-                         'memoryerror, try using a greater value)')
-
-    parserB = subparsers.add_parser('combine', add_help=True, help='Bhelp')
-    parserB.add_argument('--contacts', nargs='+', required=True,
-                         help="List of contact pickle files to combine (e.g.," 
-                         "contacts_7.0.pkl from different runs)")
-    parserB.add_argument( '--output', type=str, default='combined_contacts.pkl',
-                         help="Output filename for combined contacts (default:"
-                         "combined_contacts.pkl)")
-    parserB.add_argument( '--no-validate', action='store_true', help="Skip"
-                         "compatibility validation (use with caution)")
-
-    parserC = subparsers.add_parser('cluster', help='Chelp')
-    parserC.add_argument('--nproc', type=int, default=1)
-    parserC.add_argument('--cutoff', type=float)
-    parserC.add_argument('--niter', type=int, default=110000)
-    parserC.add_argument('--prot', type=str, default=None, nargs='?')
-    parserC.add_argument('--label-cutoff', type=float, default=3,
-                         dest='label_cutoff',
-                         help='Only label residues with tau > '
-                         'LABEL-CUTOFF * <tau>. ')
-    parserC.add_argument('--structure', type=str, nargs='?')
-    # use  for default values
-    parserC.add_argument('--gskip', type=int, default=1000, 
-                         help='Gibbs skip parameter for decorrelated samples;'
-                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
-    parserC.add_argument('--burnin', type=int, default=10000, 
-                         help='Burn-in parameter, drop first N samples as equilibration;'
-                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
-
-    parserD = subparsers.add_parser('gibbs', help='Dhelp')
-    parserD.add_argument('--contacts')
-    parserD.add_argument('--resid', type=int, default=None)
-    parserD.add_argument('--nproc', type=int, default=1)
-    parserD.add_argument('--niter', type=int, default=110000)
-    parserD.add_argument('--ncomp', type=int, default=15)
-
-    parserE = subparsers.add_parser('kinetics', help='Ehelp')
-    parserE.add_argument("--gibbs", type=str)
-    parserE.add_argument("--contacts", type=str)
-    parserE.add_argument("--top_n", type=int, nargs='?', default=None)
-    parserE.add_argument("--step", type=int, nargs='?', default=1)
-    parserE.add_argument("--wdensity", action='store_true')
+#    parserA = subparsers.add_parser('contacts', help='Ahelp')
+#    parserA.add_argument('--top', type=str, help='Topology')
+#    parserA.add_argument('--traj', type=str, help='Trajectory')
+#    parserA.add_argument('--sel1', type=str, help='First selection (group for'
+#                         'which tau is to be calculated)')
+#    parserA.add_argument('--sel2', type=str, help='Second selection (group of'
+#                         'interest in interactions with first selection)')
+#    parserA.add_argument('--cutoff', type=float, help='Value to use (in A) for'
+#                         'the maximum separation distance that constitutes a'
+#                         'contact.')
+#    parserA.add_argument('--nproc', type=int, default=1, help='Number of'
+#                         'processes to use')
+#    parserA.add_argument('--nslices', type=int, default=100, help='Number of'
+#                         'trajectory segments to use (if encountering a'
+#                         'memoryerror, try using a greater value)')
+#
+#    parserB = subparsers.add_parser('combine', add_help=True, help='Bhelp')
+#    parserB.add_argument('--contacts', nargs='+', required=True,
+#                         help="List of contact pickle files to combine (e.g.," 
+#                         "contacts_7.0.pkl from different runs)")
+#    parserB.add_argument( '--output', type=str, default='combined_contacts.pkl',
+#                         help="Output filename for combined contacts (default:"
+#                         "combined_contacts.pkl)")
+#    parserB.add_argument( '--no-validate', action='store_true', help="Skip"
+#                         "compatibility validation (use with caution)")
+#
+#    parserC = subparsers.add_parser('cluster', help='Chelp')
+#    parserC.add_argument('--nproc', type=int, default=1)
+#    parserC.add_argument('--cutoff', type=float)
+#    parserC.add_argument('--niter', type=int, default=110000)
+#    parserC.add_argument('--prot', type=str, default=None, nargs='?')
+#    parserC.add_argument('--label-cutoff', type=float, default=3,
+#                         dest='label_cutoff',
+#                         help='Only label residues with tau > '
+#                         'LABEL-CUTOFF * <tau>. ')
+#    parserC.add_argument('--structure', type=str, nargs='?')
+#    # use  for default values
+#    parserC.add_argument('--gskip', type=int, default=1000, 
+#                         help='Gibbs skip parameter for decorrelated samples;'
+#                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
+#    parserC.add_argument('--burnin', type=int, default=10000, 
+#                         help='Burn-in parameter, drop first N samples as equilibration;'
+#                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
+#
+#    parserD = subparsers.add_parser('gibbs', help='Dhelp')
+#    parserD.add_argument('--contacts')
+#    parserD.add_argument('--resid', type=int, default=None)
+#    parserD.add_argument('--nproc', type=int, default=1)
+#    parserD.add_argument('--niter', type=int, default=110000)
+#    parserD.add_argument('--ncomp', type=int, default=15)
+#
+#    parserE = subparsers.add_parser('kinetics', help='Ehelp')
+#    parserE.add_argument("--gibbs", type=str)
+#    parserE.add_argument("--contacts", type=str)
+#    parserE.add_argument("--top_n", type=int, nargs='?', default=None)
+#    parserE.add_argument("--step", type=int, nargs='?', default=1)
+#    parserE.add_argument("--wdensity", action='store_true')
     
     args = parser.parse_args()
     keys, values = vars(args).keys(), vars(args).values()
diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index 2117c31..4a61dde 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -364,23 +364,9 @@ def run(self):
         
         return self.output_name
 
-
-if __name__ == '__main__':
-    """DOCSSS
-    """
-    import argparse
-    parser = argparse.ArgumentParser(description="Create the primary contact \
-                                     map and collect contacts based on the \
-                                     desired cutoff distance")
-    parser.add_argument('--top', type=str, help="Topology")
-    parser.add_argument('--traj', type=str)
-    parser.add_argument('--sel1', type=str)
-    parser.add_argument('--sel2', type=str)
-    parser.add_argument('--cutoff', type=float)
-    parser.add_argument('--nproc', type=int, default=1)
-    parser.add_argument('--nslices', type=int, default=100)
+def main():
+    parser = get_parser()
     args = parser.parse_args()
-
     u = mda.Universe(args.top, args.traj)
     cutoff, nproc, nslices = args.cutoff, args.nproc, args.nslices
     ag1 = u.select_atoms(args.sel1)
@@ -396,3 +382,25 @@ def run(self):
 
     ProcessContacts(cutoff, mapname, nproc=nproc).run()
 
+
+def get_parser():
+    import argparse
+    parser = argparse.ArgumentParser(description="Create the primary contact \
+                                     map and collect contacts based on the \
+                                     desired cutoff distance")
+    parser.add_argument('--top', type=str, help="Topology")
+    parser.add_argument('--traj', type=str)
+    parser.add_argument('--sel1', type=str)
+    parser.add_argument('--sel2', type=str)
+    parser.add_argument('--cutoff', type=float)
+    parser.add_argument('--nproc', type=int, default=1)
+    parser.add_argument('--nslices', type=int, default=100)
+    return parser
+
+
+if __name__ == '__main__':
+    exit(main())
+    """DOCSSS
+    """
+
+

From 2bf2b216c94b63577f8f08fa190ed01d2fd144bc Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Fri, 14 Nov 2025 16:26:26 -0600
Subject: [PATCH 03/16] in-progress cli

---
 basicrta/cli.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index e4bacff..6289abc 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -14,10 +14,11 @@
 commands = ['contacts', 'cluster', 'combine', 'kinetics', 'gibbs']
 
 def main():
+    from basicrta.contacts import get_parser
     parser = argparse.ArgumentParser(prog='basicrta')
     #parser.add_argument('command', help='Step in workflow to execute', nargs='+')
     subparsers = parser.add_subparsers(dest='command')
-
+    subparsers.add_parser(get_parser)
     
 #    parserA = subparsers.add_parser('contacts', help='Ahelp')
 #    parserA.add_argument('--top', type=str, help='Topology')

From 66e947242e9c374d2058b39ad7f8bdb1accbc745 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Wed, 19 Nov 2025 15:28:47 -0600
Subject: [PATCH 04/16] working cli that takes parser from each script

---
 basicrta/cli.py      | 83 +++++++-------------------------------------
 basicrta/cluster.py  | 15 +++++---
 basicrta/combine.py  |  9 +++--
 basicrta/gibbs.py    | 12 +++++--
 basicrta/kinetics.py | 12 +++++--
 5 files changed, 48 insertions(+), 83 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index 6289abc..cb4bce3 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -3,88 +3,29 @@
 A package to extract binding kinetics from molecular dynamics simulations
 """
 
-# Add imports here
 from importlib.metadata import version
 from basicrta import *
 import argparse
 import subprocess
+import importlib
+import sys
 
 __version__ = version("basicrta")
 
 commands = ['contacts', 'cluster', 'combine', 'kinetics', 'gibbs']
 
 def main():
-    from basicrta.contacts import get_parser
-    parser = argparse.ArgumentParser(prog='basicrta')
-    #parser.add_argument('command', help='Step in workflow to execute', nargs='+')
-    subparsers = parser.add_subparsers(dest='command')
-    subparsers.add_parser(get_parser)
+    parser = argparse.ArgumentParser(prog='basicrta', add_help=True)
+    subparsers = parser.add_subparsers()
     
-#    parserA = subparsers.add_parser('contacts', help='Ahelp')
-#    parserA.add_argument('--top', type=str, help='Topology')
-#    parserA.add_argument('--traj', type=str, help='Trajectory')
-#    parserA.add_argument('--sel1', type=str, help='First selection (group for'
-#                         'which tau is to be calculated)')
-#    parserA.add_argument('--sel2', type=str, help='Second selection (group of'
-#                         'interest in interactions with first selection)')
-#    parserA.add_argument('--cutoff', type=float, help='Value to use (in A) for'
-#                         'the maximum separation distance that constitutes a'
-#                         'contact.')
-#    parserA.add_argument('--nproc', type=int, default=1, help='Number of'
-#                         'processes to use')
-#    parserA.add_argument('--nslices', type=int, default=100, help='Number of'
-#                         'trajectory segments to use (if encountering a'
-#                         'memoryerror, try using a greater value)')
-#
-#    parserB = subparsers.add_parser('combine', add_help=True, help='Bhelp')
-#    parserB.add_argument('--contacts', nargs='+', required=True,
-#                         help="List of contact pickle files to combine (e.g.," 
-#                         "contacts_7.0.pkl from different runs)")
-#    parserB.add_argument( '--output', type=str, default='combined_contacts.pkl',
-#                         help="Output filename for combined contacts (default:"
-#                         "combined_contacts.pkl)")
-#    parserB.add_argument( '--no-validate', action='store_true', help="Skip"
-#                         "compatibility validation (use with caution)")
-#
-#    parserC = subparsers.add_parser('cluster', help='Chelp')
-#    parserC.add_argument('--nproc', type=int, default=1)
-#    parserC.add_argument('--cutoff', type=float)
-#    parserC.add_argument('--niter', type=int, default=110000)
-#    parserC.add_argument('--prot', type=str, default=None, nargs='?')
-#    parserC.add_argument('--label-cutoff', type=float, default=3,
-#                         dest='label_cutoff',
-#                         help='Only label residues with tau > '
-#                         'LABEL-CUTOFF * <tau>. ')
-#    parserC.add_argument('--structure', type=str, nargs='?')
-#    # use  for default values
-#    parserC.add_argument('--gskip', type=int, default=1000, 
-#                         help='Gibbs skip parameter for decorrelated samples;'
-#                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
-#    parserC.add_argument('--burnin', type=int, default=10000, 
-#                         help='Burn-in parameter, drop first N samples as equilibration;'
-#                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
-#
-#    parserD = subparsers.add_parser('gibbs', help='Dhelp')
-#    parserD.add_argument('--contacts')
-#    parserD.add_argument('--resid', type=int, default=None)
-#    parserD.add_argument('--nproc', type=int, default=1)
-#    parserD.add_argument('--niter', type=int, default=110000)
-#    parserD.add_argument('--ncomp', type=int, default=15)
-#
-#    parserE = subparsers.add_parser('kinetics', help='Ehelp')
-#    parserE.add_argument("--gibbs", type=str)
-#    parserE.add_argument("--contacts", type=str)
-#    parserE.add_argument("--top_n", type=int, nargs='?', default=None)
-#    parserE.add_argument("--step", type=int, nargs='?', default=1)
-#    parserE.add_argument("--wdensity", action='store_true')
-    
-    args = parser.parse_args()
-    keys, values = vars(args).keys(), vars(args).values()
-    inarr = [[f"--{key}", f"{value}"] for key, value in zip(keys, values) if key!='command']
-    inlist = [aset for alist in inarr for aset in alist]
-    subprocess.run(['python',
-                    f'/home/r2/opt/basicrta/basicrta/{args.command}.py'] + 
-                   inlist)
+    for command in commands:
+        subparser = importlib.import_module(f"basicrta.{command}").get_parser()
+        subparsers.add_parser(f'{command}', parents=[subparser], add_help=False)
+
+    args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
+
+    if len(sys.argv) == 2:
+        subparsers.choices[f'{sys.argv[1]}'].print_help()
 
 if __name__ == "__main__":
     main()
diff --git a/basicrta/cluster.py b/basicrta/cluster.py
index 3c48999..8acbb47 100644
--- a/basicrta/cluster.py
+++ b/basicrta/cluster.py
@@ -212,10 +212,7 @@ def b_color_structure(self, structure):
 
         u.select_atoms('protein').write('tau_bcolored.pdb')
 
-
-if __name__ == "__main__":  #pragma: no cover
-    # the script is tested in the test_cluster.py but cannot be accounted for
-    # in the coverage report
+def get_parser():
     import argparse
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument('--nproc', type=int, default=1)
@@ -234,7 +231,10 @@ def b_color_structure(self, structure):
     parser.add_argument('--burnin', type=int, default=10000, 
                         help='Burn-in parameter, drop first N samples as equilibration;'
                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
+    return parser
 
+def main():
+    parser = get_parser()
     args = parser.parse_args()
 
     pp = ProcessProtein(args.niter, args.prot, args.cutoff, 
@@ -243,3 +243,10 @@ def b_color_structure(self, structure):
     pp.get_taus()
     pp.write_data()
     pp.plot_protein(label_cutoff=args.label_cutoff)
+
+
+if __name__ == "__main__":  #pragma: no cover
+    # the script is tested in the test_cluster.py but cannot be accounted for
+    # in the coverage report
+    exit(main())
+
diff --git a/basicrta/combine.py b/basicrta/combine.py
index 52f691d..40dd350 100644
--- a/basicrta/combine.py
+++ b/basicrta/combine.py
@@ -137,7 +137,7 @@ def run(self):
         
         return self.output_name
 
-if __name__ == "__main__":
+def get_parser():
     """Main function for combining contact files."""
     parser = argparse.ArgumentParser(
         description="Combine contact timeseries from multiple repeat runs. "
@@ -164,7 +164,10 @@ def run(self):
         action='store_true',
         help="Skip compatibility validation (use with caution)"
     )
-    
+    return parser
+
+def main():
+    parser = get_parser()
     args = parser.parse_args()
     
     # Validate input files exist
@@ -207,3 +210,5 @@ def run(self):
         print(f"ERROR: {e}")
         return 1
 
+if __name__ == "__main__":
+    exit(main())    
diff --git a/basicrta/gibbs.py b/basicrta/gibbs.py
index bbdc4d8..3fdc483 100644
--- a/basicrta/gibbs.py
+++ b/basicrta/gibbs.py
@@ -287,7 +287,7 @@ def cluster(self, method="GaussianMixture", **kwargs):
         setattr(self.processed_results, 'indicator', pindicator)
         setattr(self.processed_results, 'labels', all_labels)
 
-    def process_gibbs(self, show=True):
+    def process_gibbs(self, show=False):
         r"""
         Process the samples collected from the Gibbs sampler.
         :meth:`process_gibbs` can be called multiple times to check the
@@ -804,8 +804,7 @@ def plot_surv(self, scale=1, remove_noise=False, save=False, xlim=None,
                         's_vs_t.pdf', bbox_inches='tight')
         plt.show()
 
-
-if __name__ == '__main__':
+def get_parser():
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument('--contacts')
@@ -813,6 +812,10 @@ def plot_surv(self, scale=1, remove_noise=False, save=False, xlim=None,
     parser.add_argument('--nproc', type=int, default=1)
     parser.add_argument('--niter', type=int, default=110000)
     parser.add_argument('--ncomp', type=int, default=15)
+    return parser
+
+def main():
+    parser = get_parser()
     args = parser.parse_args()
 
     contact_path = os.path.abspath(args.contacts)
@@ -820,3 +823,6 @@ def plot_surv(self, scale=1, remove_noise=False, save=False, xlim=None,
 
     ParallelGibbs(contact_path, nproc=args.nproc, ncomp=args.ncomp,
                   niter=args.niter).run(run_resids=args.resid)
+
+if __name__ == '__main__':
+    exit(main())
diff --git a/basicrta/kinetics.py b/basicrta/kinetics.py
index 8613092..d2a651e 100644
--- a/basicrta/kinetics.py
+++ b/basicrta/kinetics.py
@@ -203,9 +203,7 @@ def weighted_densities(self, step=1, top_n=None, filterP=0):
 
                 d.results.density.export(outname)
 
-
-if __name__ == "__main__":
-    from basicrta.gibbs import Gibbs
+def get_parser():
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument("--gibbs", type=str)
@@ -213,6 +211,11 @@ def weighted_densities(self, step=1, top_n=None, filterP=0):
     parser.add_argument("--top_n", type=int, nargs='?', default=None)
     parser.add_argument("--step", type=int, nargs='?', default=1)
     parser.add_argument("--wdensity", action='store_true')
+    return parser
+
+def main():
+    from basicrta.gibbs import Gibbs
+    parser = get_parser()
     args = parser.parse_args()
 
     g = Gibbs().load(args.gibbs)
@@ -220,3 +223,6 @@ def weighted_densities(self, step=1, top_n=None, filterP=0):
     mk.create_traj(top_n=args.top_n)
     if args.wdensity:
         mk.weighted_densities(step=args.step, top_n=args.top_n)
+
+if __name__ == "__main__":
+    exit(main())

From 7c18872785cd7c5e5a8bd12c054f9e77b0e82ff3 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Wed, 19 Nov 2025 17:12:13 -0600
Subject: [PATCH 05/16] forgot to add script execution, should be working now

---
 basicrta/cli.py     | 13 +++++++++++++
 basicrta/cluster.py |  8 ++++----
 basicrta/gibbs.py   |  2 +-
 3 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index cb4bce3..d2ea640 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -26,6 +26,19 @@ def main():
 
     if len(sys.argv) == 2:
         subparsers.choices[f'{sys.argv[1]}'].print_help()
+        sys.exit()
+
+    print(sys.argv[2:])
+    #keys, values = vars(args).keys(), vars(args).values()
+    #inarr = [[f"--{key}", f"{value}"] for key, value in zip(keys, values) if
+    #         value is not None]
+    #inlist = [aset for alist in inarr for aset in alist]
+    #subprocess.run(['python',
+    #                f'/home/r2/opt/basicrta/basicrta/{sys.argv[1]}.py'] + 
+    #                inlist) 
+    subprocess.run(['python',
+                    f'/home/r2/opt/basicrta/basicrta/{sys.argv[1]}.py'] +
+                    sys.argv[2:]) 
 
 if __name__ == "__main__":
     main()
diff --git a/basicrta/cluster.py b/basicrta/cluster.py
index 8acbb47..595b1b7 100644
--- a/basicrta/cluster.py
+++ b/basicrta/cluster.py
@@ -219,10 +219,10 @@ def get_parser():
     parser.add_argument('--cutoff', type=float)
     parser.add_argument('--niter', type=int, default=110000)
     parser.add_argument('--prot', type=str, default=None, nargs='?')
-    parser.add_argument('--label-cutoff', type=float, default=3,
-            dest='label_cutoff',
-            help='Only label residues with tau > '
-            'LABEL-CUTOFF * <tau>. ')
+    parser.add_argument('--label_cutoff', type=float, default=3,
+                        dest='label_cutoff',
+                        help='Only label residues with tau > '
+                        'LABEL-CUTOFF * <tau>. ')
     parser.add_argument('--structure', type=str, nargs='?')
     # use  for default values
     parser.add_argument('--gskip', type=int, default=1000, 
diff --git a/basicrta/gibbs.py b/basicrta/gibbs.py
index 3fdc483..9fa6939 100644
--- a/basicrta/gibbs.py
+++ b/basicrta/gibbs.py
@@ -808,7 +808,7 @@ def get_parser():
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument('--contacts')
-    parser.add_argument('--resid', type=int, default=None)
+    parser.add_argument('--resid', type=int)
     parser.add_argument('--nproc', type=int, default=1)
     parser.add_argument('--niter', type=int, default=110000)
     parser.add_argument('--ncomp', type=int, default=15)

From 807266aed83cca3a4be568dd64e63099b28cb245 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Thu, 20 Nov 2025 07:14:20 -0600
Subject: [PATCH 06/16] removed subprocess call

---
 basicrta/cli.py      | 14 ++------------
 basicrta/cluster.py  |  2 ++
 basicrta/combine.py  |  2 ++
 basicrta/contacts.py |  3 +++
 basicrta/gibbs.py    |  2 ++
 basicrta/kinetics.py |  2 ++
 6 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index d2ea640..d351e44 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -27,18 +27,8 @@ def main():
     if len(sys.argv) == 2:
         subparsers.choices[f'{sys.argv[1]}'].print_help()
         sys.exit()
-
-    print(sys.argv[2:])
-    #keys, values = vars(args).keys(), vars(args).values()
-    #inarr = [[f"--{key}", f"{value}"] for key, value in zip(keys, values) if
-    #         value is not None]
-    #inlist = [aset for alist in inarr for aset in alist]
-    #subprocess.run(['python',
-    #                f'/home/r2/opt/basicrta/basicrta/{sys.argv[1]}.py'] + 
-    #                inlist) 
-    subprocess.run(['python',
-                    f'/home/r2/opt/basicrta/basicrta/{sys.argv[1]}.py'] +
-                    sys.argv[2:]) 
+               
+    importlib.import_module(f"basicrta.{sys.argv[1]}").main()
 
 if __name__ == "__main__":
     main()
diff --git a/basicrta/cluster.py b/basicrta/cluster.py
index e4942e0..aa093f4 100644
--- a/basicrta/cluster.py
+++ b/basicrta/cluster.py
@@ -256,6 +256,8 @@ def get_parser():
     parser.add_argument('--burnin', type=int, default=10000, 
                         help='Burn-in parameter, drop first N samples as equilibration;'
                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
+    # this is to make the cli work, should be just a temporary solution
+    parser.add_argument('cluster', nargs='?')
     return parser
 
 def main():
diff --git a/basicrta/combine.py b/basicrta/combine.py
index 40dd350..7bf3851 100644
--- a/basicrta/combine.py
+++ b/basicrta/combine.py
@@ -164,6 +164,8 @@ def get_parser():
         action='store_true',
         help="Skip compatibility validation (use with caution)"
     )
+    # this is to make the cli work, should be just a temporary solution
+    parser.add_argument('combine', nargs='?')
     return parser
 
 def main():
diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index 4a61dde..cac62c0 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -367,6 +367,7 @@ def run(self):
 def main():
     parser = get_parser()
     args = parser.parse_args()
+    print(args)
     u = mda.Universe(args.top, args.traj)
     cutoff, nproc, nslices = args.cutoff, args.nproc, args.nslices
     ag1 = u.select_atoms(args.sel1)
@@ -395,6 +396,8 @@ def get_parser():
     parser.add_argument('--cutoff', type=float)
     parser.add_argument('--nproc', type=int, default=1)
     parser.add_argument('--nslices', type=int, default=100)
+    # this is to make the cli work, should be just a temporary solution
+    parser.add_argument('contacts', nargs='?')
     return parser
 
 
diff --git a/basicrta/gibbs.py b/basicrta/gibbs.py
index 41b8b53..c73a2bd 100644
--- a/basicrta/gibbs.py
+++ b/basicrta/gibbs.py
@@ -859,6 +859,8 @@ def get_parser():
     parser.add_argument('--nproc', type=int, default=1)
     parser.add_argument('--niter', type=int, default=110000)
     parser.add_argument('--ncomp', type=int, default=15)
+    # this is to make the cli work, should be just a temporary solution
+    parser.add_argument('gibbs', nargs='?')
     return parser
 
 def main():
diff --git a/basicrta/kinetics.py b/basicrta/kinetics.py
index d2a651e..b0d6e69 100644
--- a/basicrta/kinetics.py
+++ b/basicrta/kinetics.py
@@ -211,6 +211,8 @@ def get_parser():
     parser.add_argument("--top_n", type=int, nargs='?', default=None)
     parser.add_argument("--step", type=int, nargs='?', default=1)
     parser.add_argument("--wdensity", action='store_true')
+    # this is to make the cli work, should be just a temporary solution
+    parser.add_argument('kinetics', nargs='?')
     return parser
 
 def main():

From 5fc67850fe9116c6c12006b076732f876a6d1d2b Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Thu, 20 Nov 2025 11:50:40 -0600
Subject: [PATCH 07/16] removed unnecessary print statement

---
 basicrta/contacts.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index cac62c0..c922c9d 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -367,7 +367,6 @@ def run(self):
 def main():
     parser = get_parser()
     args = parser.parse_args()
-    print(args)
     u = mda.Universe(args.top, args.traj)
     cutoff, nproc, nslices = args.cutoff, args.nproc, args.nslices
     ag1 = u.select_atoms(args.sel1)

From 688a3ef48ebe0e8102ebee6d4e6d66864ece176b Mon Sep 17 00:00:00 2001
From: Ricky Sexton <risexto878@gmail.com>
Date: Mon, 24 Nov 2025 10:37:13 -0600
Subject: [PATCH 08/16] added help strings/subcommand description to cli

---
 basicrta/cli.py      |  7 ++++---
 basicrta/contacts.py | 23 +++++++++++++++++------
 2 files changed, 21 insertions(+), 9 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index d351e44..5a3404b 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -15,12 +15,13 @@
 commands = ['contacts', 'cluster', 'combine', 'kinetics', 'gibbs']
 
 def main():
-    parser = argparse.ArgumentParser(prog='basicrta', add_help=True)
-    subparsers = parser.add_subparsers()
+    parser = argparse.ArgumentParser(prog='basicrta', add_help=False)
+    subparsers = parser.add_subparsers(help='Step in the basicrta workflow to execute.')
     
     for command in commands:
         subparser = importlib.import_module(f"basicrta.{command}").get_parser()
-        subparsers.add_parser(f'{command}', parents=[subparser], add_help=False)
+        subparsers.add_parser(f'{command}', parents=[subparser, parser], add_help=True,
+                              description=subparser.description, conflict_handler='resolve')
 
     args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
 
diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index c922c9d..4725da6 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -389,12 +389,23 @@ def get_parser():
                                      map and collect contacts based on the \
                                      desired cutoff distance")
     parser.add_argument('--top', type=str, help="Topology")
-    parser.add_argument('--traj', type=str)
-    parser.add_argument('--sel1', type=str)
-    parser.add_argument('--sel2', type=str)
-    parser.add_argument('--cutoff', type=float)
-    parser.add_argument('--nproc', type=int, default=1)
-    parser.add_argument('--nslices', type=int, default=100)
+    parser.add_argument('--traj', type=str, help="Trajectory")
+    parser.add_argument('--sel1', type=str, help="Primary atom selection, based \
+                        on MDAnalysis atom selection. basicrta will produce \
+                        tau for each residue in this atom group.")
+    parser.add_argument('--sel2', type=str, help="Secondary atom selection, \
+                        based on MDAnalysis atom selection. basicrta will \
+                        collect contacts between each residue of this group \
+                        with each residue of `sel1`.")
+    parser.add_argument('--cutoff', type=float, help="""Value to use for defining 
+                        a contact (in Angstrom). Any atom of `sel2` that is at
+                        a distance less than or equal to `cutoff` of any atom
+                        in `sel1` will be considered in contact.""")
+    parser.add_argument('--nproc', type=int, default=1, help="""Number of 
+                        processes to use in multiprocessing""")
+    parser.add_argument('--nslices', type=int, default=100, help="""Number of 
+                        slices to break the trajectory into. Increase this to
+                        reduce the amount of memory needed for each process.""")
     # this is to make the cli work, should be just a temporary solution
     parser.add_argument('contacts', nargs='?')
     return parser

From 7ad82028489032c12804445787ad62fb81f20edd Mon Sep 17 00:00:00 2001
From: Ricky Sexton <risexto878@gmail.com>
Date: Mon, 24 Nov 2025 11:17:26 -0600
Subject: [PATCH 09/16] added argument requirements

---
 basicrta/contacts.py |  2 +-
 basicrta/gibbs.py    | 12 +++++++-----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index 4725da6..bd75759 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -400,7 +400,7 @@ def get_parser():
     parser.add_argument('--cutoff', type=float, help="""Value to use for defining 
                         a contact (in Angstrom). Any atom of `sel2` that is at
                         a distance less than or equal to `cutoff` of any atom
-                        in `sel1` will be considered in contact.""")
+                        in `sel1` will be considered in contact.""", required=True)
     parser.add_argument('--nproc', type=int, default=1, help="""Number of 
                         processes to use in multiprocessing""")
     parser.add_argument('--nslices', type=int, default=100, help="""Number of 
diff --git a/basicrta/gibbs.py b/basicrta/gibbs.py
index c73a2bd..b5b2e56 100644
--- a/basicrta/gibbs.py
+++ b/basicrta/gibbs.py
@@ -854,11 +854,13 @@ def plot_surv(self, scale=1, remove_noise=False, save=False, xlim=None,
 def get_parser():
     import argparse
     parser = argparse.ArgumentParser()
-    parser.add_argument('--contacts')
-    parser.add_argument('--resid', type=int)
-    parser.add_argument('--nproc', type=int, default=1)
-    parser.add_argument('--niter', type=int, default=110000)
-    parser.add_argument('--ncomp', type=int, default=15)
+    required = parser.add_argument_group('required arguments')
+    optional = parser.add_argument_group('optional arguments')
+    required.add_argument('--contacts', required=True)
+    optional.add_argument('--resid', type=int)
+    optional.add_argument('--nproc', type=int, default=1)
+    optional.add_argument('--niter', type=int, default=110000)
+    optional.add_argument('--ncomp', type=int, default=15)
     # this is to make the cli work, should be just a temporary solution
     parser.add_argument('gibbs', nargs='?')
     return parser

From 873a5017592eb108cd3031ddd19ad159e22468a0 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Mon, 24 Nov 2025 15:00:32 -0600
Subject: [PATCH 10/16] added help

---
 basicrta/cli.py      | 25 +++++++++++++++----------
 basicrta/cluster.py  | 30 +++++++++++++++++++++---------
 basicrta/combine.py  |  8 +++++---
 basicrta/contacts.py | 20 +++++++++++---------
 basicrta/gibbs.py    | 27 +++++++++++++++++++--------
 basicrta/kinetics.py | 23 ++++++++++++++++-------
 6 files changed, 87 insertions(+), 46 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index 5a3404b..d9ad3c4 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -12,23 +12,28 @@
 
 __version__ = version("basicrta")
 
-commands = ['contacts', 'cluster', 'combine', 'kinetics', 'gibbs']
+commands = ['contacts', 'gibbs', 'cluster', 'combine', 'kinetics']
+parser_help = '''
+Step in the basicrta workflow to execute. 
+'''
 
 def main():
-    parser = argparse.ArgumentParser(prog='basicrta', add_help=False)
-    subparsers = parser.add_subparsers(help='Step in the basicrta workflow to execute.')
+    parser = argparse.ArgumentParser(prog='basicrta', add_help=True)
+    subparsers = parser.add_subparsers(help=parser_help)
     
     for command in commands:
         subparser = importlib.import_module(f"basicrta.{command}").get_parser()
-        subparsers.add_parser(f'{command}', parents=[subparser, parser], add_help=True,
-                              description=subparser.description, conflict_handler='resolve')
-
-    args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
-
-    if len(sys.argv) == 2:
+        subparsers.add_parser(f'{command}', parents=[subparser], add_help=True,
+                              description=subparser.description, 
+                              conflict_handler='resolve',
+                              formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+                              help=subparser.description) 
+    
+    if len(sys.argv) == 2 and sys.argv[1] in commands:
         subparsers.choices[f'{sys.argv[1]}'].print_help()
         sys.exit()
-               
+    
+    parser.parse_args(args=None if sys.argv[1:] else ['--help'])
     importlib.import_module(f"basicrta.{sys.argv[1]}").main()
 
 if __name__ == "__main__":
diff --git a/basicrta/cluster.py b/basicrta/cluster.py
index aa093f4..fde7f9f 100644
--- a/basicrta/cluster.py
+++ b/basicrta/cluster.py
@@ -239,16 +239,28 @@ def b_color_structure(self, structure):
 
 def get_parser():
     import argparse
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('--nproc', type=int, default=1)
-    parser.add_argument('--cutoff', type=float)
-    parser.add_argument('--niter', type=int, default=110000)
-    parser.add_argument('--prot', type=str, default=None, nargs='?')
+    parser = argparse.ArgumentParser(description="""perform clustering for each
+                                     residue located in basicrta-{cutoff}/""",
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    required = parser.add_argument_group('required arguments')
+    
+    required.add_argument('--cutoff', required=True, type=float, help="""cutoff
+                          used in contact analysis, will cluster results in
+                          basicrta-{cutoff}/""")
+    parser.add_argument('--nproc', type=int, default=1, help="""number of
+                        processes to use in multiprocessing""")
+    parser.add_argument('--niter', type=int, default=110000, help="""number of
+                        iterations used in the gibbs sampler, used to load 
+                        gibbs_{niter}.pkl""")
+    parser.add_argument('--prot', type=str, nargs='?', help="""name of protein
+                        in tm_dict.txt, used to draw TM bars in tau vs resid 
+                        plot""")
     parser.add_argument('--label_cutoff', type=float, default=3,
                         dest='label_cutoff',
-                        help='Only label residues with tau > '
-                        'LABEL-CUTOFF * <tau>. ')
-    parser.add_argument('--structure', type=str, nargs='?')
+                        help="""Only label residues with tau > 
+                        LABEL-CUTOFF * <tau>.""")
+    parser.add_argument('--structure', type=str, nargs='?', help="""will add tau
+                        as bfactors to the structure if provided""")
     # use  for default values
     parser.add_argument('--gskip', type=int, default=100, 
                         help='Gibbs skip parameter for decorrelated samples;'
@@ -257,7 +269,7 @@ def get_parser():
                         help='Burn-in parameter, drop first N samples as equilibration;'
                         'default from https://pubs.acs.org/doi/10.1021/acs.jctc.4c01522')
     # this is to make the cli work, should be just a temporary solution
-    parser.add_argument('cluster', nargs='?')
+    parser.add_argument('cluster', nargs='?', help=argparse.SUPPRESS)
     return parser
 
 def main():
diff --git a/basicrta/combine.py b/basicrta/combine.py
index 7bf3851..6d86799 100644
--- a/basicrta/combine.py
+++ b/basicrta/combine.py
@@ -145,11 +145,13 @@ def get_parser():
                    "and calculating posteriors from all data together."
     )
     
-    parser.add_argument(
+    required = parser.add_argument_group('required arguments')
+    required.add_argument(
         '--contacts', 
         nargs='+', 
         required=True,
-        help="List of contact pickle files to combine (e.g., contacts_7.0.pkl from different runs)"
+        help="""List of contact pickle files to combine (e.g., contacts_7.0.pkl
+        from different runs)""",
     )
     
     parser.add_argument(
@@ -165,7 +167,7 @@ def get_parser():
         help="Skip compatibility validation (use with caution)"
     )
     # this is to make the cli work, should be just a temporary solution
-    parser.add_argument('combine', nargs='?')
+    parser.add_argument('combine', nargs='?', help=argparse.SUPPRESS)
     return parser
 
 def main():
diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index bd75759..807bef6 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -385,19 +385,21 @@ def main():
 
 def get_parser():
     import argparse
-    parser = argparse.ArgumentParser(description="Create the primary contact \
-                                     map and collect contacts based on the \
-                                     desired cutoff distance")
-    parser.add_argument('--top', type=str, help="Topology")
-    parser.add_argument('--traj', type=str, help="Trajectory")
-    parser.add_argument('--sel1', type=str, help="Primary atom selection, based \
+    parser = argparse.ArgumentParser(description="""Create the initial contact
+                                                 map and process it using a
+                                                 prescribed cutoff""")
+    required = parser.add_argument_group('required arguments')
+
+    required.add_argument('--top', type=str, help="Topology")
+    required.add_argument('--traj', type=str, help="Trajectory")
+    required.add_argument('--sel1', type=str, help="Primary atom selection, based \
                         on MDAnalysis atom selection. basicrta will produce \
                         tau for each residue in this atom group.")
-    parser.add_argument('--sel2', type=str, help="Secondary atom selection, \
+    required.add_argument('--sel2', type=str, help="Secondary atom selection, \
                         based on MDAnalysis atom selection. basicrta will \
                         collect contacts between each residue of this group \
                         with each residue of `sel1`.")
-    parser.add_argument('--cutoff', type=float, help="""Value to use for defining 
+    required.add_argument('--cutoff', type=float, help="""Value to use for defining 
                         a contact (in Angstrom). Any atom of `sel2` that is at
                         a distance less than or equal to `cutoff` of any atom
                         in `sel1` will be considered in contact.""", required=True)
@@ -407,7 +409,7 @@ def get_parser():
                         slices to break the trajectory into. Increase this to
                         reduce the amount of memory needed for each process.""")
     # this is to make the cli work, should be just a temporary solution
-    parser.add_argument('contacts', nargs='?')
+    parser.add_argument('contacts', nargs='?', help=argparse.SUPPRESS)
     return parser
 
 
diff --git a/basicrta/gibbs.py b/basicrta/gibbs.py
index b5b2e56..860ae44 100644
--- a/basicrta/gibbs.py
+++ b/basicrta/gibbs.py
@@ -853,16 +853,27 @@ def plot_surv(self, scale=1, remove_noise=False, save=False, xlim=None,
 
 def get_parser():
     import argparse
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(description="""run gibbs samplers for all
+                                     or a specified residue present in the
+                                     contact map""",
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     required = parser.add_argument_group('required arguments')
-    optional = parser.add_argument_group('optional arguments')
-    required.add_argument('--contacts', required=True)
-    optional.add_argument('--resid', type=int)
-    optional.add_argument('--nproc', type=int, default=1)
-    optional.add_argument('--niter', type=int, default=110000)
-    optional.add_argument('--ncomp', type=int, default=15)
+
+    required.add_argument('--contacts', required=True, help="""Contact file
+                          produced from `basicrta contacts`, default is
+                          contacts_{cutoff}.pkl""")
+    parser.add_argument('--resid', type=int, help="""run gibbs sampler for
+                          this residue. Will collect cutoff from contact file
+                          name.""")
+    parser.add_argument('--nproc', type=int, default=1, help="""number of
+                          processes to use in multiprocessing""")
+    parser.add_argument('--niter', type=int, default=110000, help="""number of
+                          iterations to use for the gibbs sampler""")
+    parser.add_argument('--ncomp', type=int, default=15, help="""number of
+                          components to use for the exponential mixture 
+                          model""")
     # this is to make the cli work, should be just a temporary solution
-    parser.add_argument('gibbs', nargs='?')
+    parser.add_argument('gibbs', nargs='?', help=argparse.SUPPRESS)
     return parser
 
 def main():
diff --git a/basicrta/kinetics.py b/basicrta/kinetics.py
index b0d6e69..06c0975 100644
--- a/basicrta/kinetics.py
+++ b/basicrta/kinetics.py
@@ -205,14 +205,23 @@ def weighted_densities(self, step=1, top_n=None, filterP=0):
 
 def get_parser():
     import argparse
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--gibbs", type=str)
-    parser.add_argument("--contacts", type=str)
-    parser.add_argument("--top_n", type=int, nargs='?', default=None)
-    parser.add_argument("--step", type=int, nargs='?', default=1)
-    parser.add_argument("--wdensity", action='store_true')
+    parser = argparse.ArgumentParser(description="""map kinetics from clustered
+                                     results onto trajectory, create weighted
+                                     densities if flag is used""")
+    required = parser.add_argument_group('required arguments')
+    required.add_argument("--gibbs", type=str, required=True, help="""gibbs pickle
+                        file to use for creating kinetic trajectories and
+                        densities""")
+    required.add_argument("--contacts", type=str, required=True, help="""contacts
+                        file used in creation of the gibbs sampler data""")
+    parser.add_argument("--top_n", type=int, nargs='?', help="""use the `top_n`
+                        most likely frames to create trajectory or densities""")
+    parser.add_argument("--step", type=int, nargs='?', default=1, help="""write
+                        out frame if frame%%step=0""")
+    parser.add_argument("--wdensity", action='store_true', help="""create
+                        weighted densities""")
     # this is to make the cli work, should be just a temporary solution
-    parser.add_argument('kinetics', nargs='?')
+    parser.add_argument('kinetics', nargs='?', help=argparse.SUPPRESS)
     return parser
 
 def main():

From 53695fe19c44c99b75c1993c7e9b54bfec795e8e Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Mon, 24 Nov 2025 15:57:18 -0600
Subject: [PATCH 11/16] added cli addition to CHANGELOG

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c2d7d6f..159b868 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ The rules for this file:
 
 ### Authors
 * @orbeckst
+* @rsexton2
 
 ### Fixed
 * Have cluster.ProcessProtein.reprocess() record "no result" if
@@ -26,6 +27,9 @@ The rules for this file:
   number of samples. Otherwise `python -m cluster` fails to process
   whole proteins.
 
+### Added
+* Added command-line interface for basicrta workflow
+
 ## [1.1.3] - 2025-09-11
 
 ### Authors

From dbf1977ed7e5f5c514461c1e637ed6381bd3461d Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Mon, 24 Nov 2025 15:57:46 -0600
Subject: [PATCH 12/16] added documentation

---
 basicrta/cli.py                     | 37 ++++++++++++++++++++++++-----
 basicrta/cluster.py                 |  7 +++---
 basicrta/combine.py                 | 11 +++++++--
 basicrta/contacts.py                | 10 ++++++++
 basicrta/gibbs.py                   |  8 +++++++
 basicrta/kinetics.py                |  7 ++++++
 docs/source/api.rst                 |  3 ++-
 docs/source/autosummary/cli.rst     |  6 +++++
 docs/source/autosummary/combine.rst |  6 +++++
 9 files changed, 83 insertions(+), 12 deletions(-)
 create mode 100644 docs/source/autosummary/cli.rst
 create mode 100644 docs/source/autosummary/combine.rst

diff --git a/basicrta/cli.py b/basicrta/cli.py
index d9ad3c4..a045694 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -1,6 +1,13 @@
 """
-basicrta
-A package to extract binding kinetics from molecular dynamics simulations
+Command line functionality of basicrta.
+
+The `main()` function of this module gets the argument parser from each of the
+scripts below and executes the `main()` function of the module called. The
+function also collects help from the subparsers and provides it at the command 
+line.
+
+Modules callable from the cli: contacts.py, gibbs.py, cluster.py, kinetics.py,
+combine.py.
 """
 
 from importlib.metadata import version
@@ -12,15 +19,29 @@
 
 __version__ = version("basicrta")
 
+# define which scripts can be ran from cli
+# can easily add functionality to cli as modules are added
 commands = ['contacts', 'gibbs', 'cluster', 'combine', 'kinetics']
-parser_help = '''
-Step in the basicrta workflow to execute. 
-'''
 
 def main():
+    """ This module provides the functionality for a command line interface for
+    basicrta scripts. The scripts available to the cli are:
+    
+    * contacts.py
+    * gibbs.py
+    * cluster.py
+    * combine.py
+    * kinetics.py
+
+    Each script is called and ran using the `main()` function of each module and 
+    the parser is passed to the cli using the `get_parser()` function. Any
+    module added to the cli needs to have both functions.
+    """
     parser = argparse.ArgumentParser(prog='basicrta', add_help=True)
-    subparsers = parser.add_subparsers(help=parser_help)
+    subparsers = parser.add_subparsers(help="""step in the basicrta workflow to
+                                       execute""")
     
+    # collect parser from each script in `commands`
     for command in commands:
         subparser = importlib.import_module(f"basicrta.{command}").get_parser()
         subparsers.add_parser(f'{command}', parents=[subparser], add_help=True,
@@ -29,11 +50,15 @@ def main():
                               formatter_class=argparse.ArgumentDefaultsHelpFormatter,
                               help=subparser.description) 
     
+    # print subparser help if no arguments given
     if len(sys.argv) == 2 and sys.argv[1] in commands:
         subparsers.choices[f'{sys.argv[1]}'].print_help()
         sys.exit()
     
+    # print basicrta help if no subcommand given
     parser.parse_args(args=None if sys.argv[1:] else ['--help'])
+
+    # execute basicrta script
     importlib.import_module(f"basicrta.{sys.argv[1]}").main()
 
 if __name__ == "__main__":
diff --git a/basicrta/cluster.py b/basicrta/cluster.py
index fde7f9f..83d4ed3 100644
--- a/basicrta/cluster.py
+++ b/basicrta/cluster.py
@@ -1,3 +1,7 @@
+"""This module provides the ProcessProtein class, which collects and processes
+Gibbs sampler data.
+"""
+
 import os
 import gc
 import warnings
@@ -11,9 +15,6 @@
 from basicrta.gibbs import Gibbs
 gc.enable()
 
-"""This module provides the ProcessProtein class, which collects and processes
-Gibbs sampler data.
-"""
 
 class ProcessProtein(object):
     r"""ProcessProtein is the class that collects and processes Gibbs sampler
diff --git a/basicrta/combine.py b/basicrta/combine.py
index 6d86799..8d27924 100644
--- a/basicrta/combine.py
+++ b/basicrta/combine.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 """
-Command-line interface for combining contact timeseries from multiple repeat runs.
+Combine contact timeseries from multiple repeat runs.
 
 This module provides functionality to combine contact files from multiple 
 trajectory repeats, enabling pooled analysis of binding kinetics.
@@ -138,7 +138,12 @@ def run(self):
         return self.output_name
 
 def get_parser():
-    """Main function for combining contact files."""
+    """Create parser, parse command line arguments, and return ArgumentParser
+    object.
+
+    :return: An ArgumentParser instance with command line arguments stored.
+    :rtype: `ArgumentParser` object
+    """
     parser = argparse.ArgumentParser(
         description="Combine contact timeseries from multiple repeat runs. "
                    "This enables pooling data from multiple trajectory repeats "
@@ -171,6 +176,8 @@ def get_parser():
     return parser
 
 def main():
+    """Execute this function when this script is called from the command line.
+    """
     parser = get_parser()
     args = parser.parse_args()
     
diff --git a/basicrta/contacts.py b/basicrta/contacts.py
index 807bef6..f17503b 100644
--- a/basicrta/contacts.py
+++ b/basicrta/contacts.py
@@ -1,3 +1,13 @@
+"""
+Create contact maps between two atom groups.
+
+This module provides the `MapContacts` class, which creates the initial contact
+map between the two atom groups using a maximum cutoff (`max_cutoff`), which
+provides for quicker processing if creating results for multiple cutoffs. The 
+`ProcessContacts` class takes the initial contact map and creates the processed
+contact map based on the prescribed cutoff.
+"""
+
 from tqdm import tqdm
 from MDAnalysis.lib import distances
 from multiprocessing import Pool, Lock
diff --git a/basicrta/gibbs.py b/basicrta/gibbs.py
index 860ae44..0c49382 100644
--- a/basicrta/gibbs.py
+++ b/basicrta/gibbs.py
@@ -1,3 +1,11 @@
+""" 
+Perform Gibbs samplers and process data.
+
+This module provides the `ParallelGibbs` class, which parallelizes the creation
+of Gibbs samplers for each residue in the contact map. This module also provides
+the `Gibbs` class, which allows for the loading and processing of the gibbs
+sampler data, as well as plotting and saving processed results.
+"""
 import os
 import gc
 import pickle
diff --git a/basicrta/kinetics.py b/basicrta/kinetics.py
index 06c0975..818c390 100644
--- a/basicrta/kinetics.py
+++ b/basicrta/kinetics.py
@@ -1,3 +1,10 @@
+"""
+Map kinetics from gibbs data to md trajectory.
+
+This module provides the `MapKinetics` class, which creates trajectories and
+weighted densities based on the clustered gibbs data and original trajectory.
+"""
+
 from tqdm import tqdm
 from basicrta.util import get_start_stop_frames
 import numpy as np
diff --git a/docs/source/api.rst b/docs/source/api.rst
index ea1acdb..2580a39 100644
--- a/docs/source/api.rst
+++ b/docs/source/api.rst
@@ -9,5 +9,6 @@ API Documentation
    contacts
    cluster
    kinetics
+   combine
    util
-
+   cli
diff --git a/docs/source/autosummary/cli.rst b/docs/source/autosummary/cli.rst
new file mode 100644
index 0000000..4a04c36
--- /dev/null
+++ b/docs/source/autosummary/cli.rst
@@ -0,0 +1,6 @@
+cli
+===
+
+.. automodule:: cli
+   :members:
+   :undoc-members:
\ No newline at end of file
diff --git a/docs/source/autosummary/combine.rst b/docs/source/autosummary/combine.rst
new file mode 100644
index 0000000..21eb381
--- /dev/null
+++ b/docs/source/autosummary/combine.rst
@@ -0,0 +1,6 @@
+combine
+=======
+
+.. automodule:: combine
+   :members:
+   :undoc-members:
\ No newline at end of file

From dea8eb5ee36ab960bf68d8014efe733bb3d60819 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Wed, 26 Nov 2025 14:20:37 -0600
Subject: [PATCH 13/16] added a few tests

---
 basicrta/tests/test_cli.py | 61 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 basicrta/tests/test_cli.py

diff --git a/basicrta/tests/test_cli.py b/basicrta/tests/test_cli.py
new file mode 100644
index 0000000..c7623f8
--- /dev/null
+++ b/basicrta/tests/test_cli.py
@@ -0,0 +1,61 @@
+"""
+Tests for combining contact timeseries from multiple repeat runs.
+"""
+import basicrta
+import os
+import pytest
+import numpy as np
+import pickle
+import subprocess
+import basicrta.cli
+import importlib
+from basicrta.contacts import CombineContacts
+
+
+class TestCLI:
+    """Test class for cli.py functionality."""
+    modules = basicrta.cli.commands
+        
+    def test_cli_modules(self):
+        """Test cli as module"""
+        for module in self.modules:
+            #help successfully printed
+            help_ret = subprocess.run(['python', '-m', f'basicrta.{module}', 
+                                     '--help'])
+            assert help_ret.returncode == 0
+            
+            # error if required arguments not given
+            nohelp = subprocess.run(['python', '-m', f'basicrta.{module}'])
+            assert nohelp.returncode == 2
+
+    def test_cli_entrypoint(self):
+        # print general help if no command given
+        assert subprocess.run('basicrta').returncode == 0
+
+        for module in self.modules:
+            #help successfully printed
+            help_ret = subprocess.run(['basicrta', f'{module}', '--help'])
+            assert help_ret.returncode == 0
+
+            # help is printed if no arguments given
+            nohelp = subprocess.run(['basicrta', f'{module}'])
+            assert nohelp.returncode == 0
+
+    def test_get_parser(self):
+        import importlib
+        import argparse
+        for module in self.modules:
+            parser = importlib.import_module(f"basicrta.{module}").get_parser()
+            assert type(parser) == argparse.ArgumentParser
+
+    def test_call_main_empty(self):
+        for module in self.modules:
+            with pytest.raises(SystemExit):
+                importlib.import_module(f"basicrta.{module}").main()
+
+#    def test_call_main(self):
+#        
+#        for module in self.modules:
+#            with pytest.raises(SystemExit):
+#                importlib.import_module(f"basicrta.{module}").main()
+

From d50d4a1c00add1c26816fa64c18b7be85bc2140c Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Wed, 26 Nov 2025 14:56:24 -0600
Subject: [PATCH 14/16] added test

---
 basicrta/cli.py            |  2 +-
 basicrta/tests/test_cli.py | 25 +++++++++++++++++--------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/basicrta/cli.py b/basicrta/cli.py
index a045694..b9e6822 100644
--- a/basicrta/cli.py
+++ b/basicrta/cli.py
@@ -11,7 +11,7 @@
 """
 
 from importlib.metadata import version
-from basicrta import *
+import basicrta
 import argparse
 import subprocess
 import importlib
diff --git a/basicrta/tests/test_cli.py b/basicrta/tests/test_cli.py
index c7623f8..e6e09b2 100644
--- a/basicrta/tests/test_cli.py
+++ b/basicrta/tests/test_cli.py
@@ -9,6 +9,7 @@
 import subprocess
 import basicrta.cli
 import importlib
+import argparse
 from basicrta.contacts import CombineContacts
 
 
@@ -41,9 +42,7 @@ def test_cli_entrypoint(self):
             nohelp = subprocess.run(['basicrta', f'{module}'])
             assert nohelp.returncode == 0
 
-    def test_get_parser(self):
-        import importlib
-        import argparse
+    def test_get_module_parsers(self):
         for module in self.modules:
             parser = importlib.import_module(f"basicrta.{module}").get_parser()
             assert type(parser) == argparse.ArgumentParser
@@ -53,9 +52,19 @@ def test_call_main_empty(self):
             with pytest.raises(SystemExit):
                 importlib.import_module(f"basicrta.{module}").main()
 
-#    def test_call_main(self):
-#        
-#        for module in self.modules:
-#            with pytest.raises(SystemExit):
-#                importlib.import_module(f"basicrta.{module}").main()
+    def test_cli_script_call(self):
+            #help successfully printed
+            help_ret = subprocess.run(['python', '-m', 'basicrta.cli', 
+                                       '--help'])
+            assert help_ret.returncode == 0
+            
+            # error if required arguments not given
+            nohelp = subprocess.run(['python', '-m', 'basicrta.cli'])
+            assert nohelp.returncode == 2
+
+
+#    def test_call_main_args(self):
+#        with mock.patch('sys.argv', ['cluster', '--cutoff', '6.9']):
+#            importlib.import_module(f"basicrta.cluster").main()
+
 

From 3c5b372c1b3b08dfe1516aca032b2679eed9bc98 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Wed, 26 Nov 2025 15:04:51 -0600
Subject: [PATCH 15/16] fixed test

---
 basicrta/tests/test_cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/basicrta/tests/test_cli.py b/basicrta/tests/test_cli.py
index e6e09b2..e466240 100644
--- a/basicrta/tests/test_cli.py
+++ b/basicrta/tests/test_cli.py
@@ -58,9 +58,9 @@ def test_cli_script_call(self):
                                        '--help'])
             assert help_ret.returncode == 0
             
-            # error if required arguments not given
+            # print help if arguments not given
             nohelp = subprocess.run(['python', '-m', 'basicrta.cli'])
-            assert nohelp.returncode == 2
+            assert nohelp.returncode == 0
 
 
 #    def test_call_main_args(self):

From 143c0e05d216260d0b98f649a2f5b6b2f34edb74 Mon Sep 17 00:00:00 2001
From: Ricky Sexton <rsexton2@asu.edu>
Date: Wed, 26 Nov 2025 15:13:26 -0600
Subject: [PATCH 16/16] referenced issue in CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 159b868..fb2dcb1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,7 +28,7 @@ The rules for this file:
   whole proteins.
 
 ### Added
-* Added command-line interface for basicrta workflow
+* Added command-line interface for basicrta workflow (Issue #20)
 
 ## [1.1.3] - 2025-09-11