Paper published.

README.md

@@ -104,25 +104,15 @@ The following functions can also be imported from mergem:
 Citation
 ======
 Please cite mergem using: <br>
-<br> [mergem: merging and comparing genome-scale metabolic models using universal identifiers](https://doi.org/10.1101/2022.07.14.499633)
-<br> A. Hari, D. Lobo.
-<br> <b>bioRxiv</b>, doi:10.1101/2022.07.14.499633, 2022
-
-------
+<br> [mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers](https://doi.org/10.1093/nargab/lqae010)
+<br> A. Hari, A. Zarrabi, D. Lobo
+<br> <b>NAR Genomics and Bioinformatics</b>, 6(1), lqae010, 2024
 
 ------
 Acknowledgements 
 ======
 
-This package was developed at [The Lobo Lab](https://lobolab.umbc.edu), University of Maryland Baltimore County.
-
-------
-
-References
-======
-The following publications have contributed towards the development of this package:
-* [Fluxer: a web application to compute and visualize genome-scale metabolic flux networks](https://doi.org/10.1093/nar/gkaa409).
-* [COBRApy: COnstraints-Based Reconstruction and Analysis for Python](http://dx.doi.org/doi:10.1186/1752-0509-7-74).
+This package was developed at [The Lobo Lab](https://lobolab.umbc.edu), University of Maryland, Baltimore County.
 
 ------
 

docs/source/citation.rst

@@ -3,9 +3,9 @@ Citing mergem
 *******************************
 Please cite mergem using:
 
- | `mergem: merging and comparing genome-scale metabolic models using universal identifiers <https://doi.org/10.1101/2022.07.14.499633>`_
- | A. Hari, D. Lobo.
- | **bioRxiv** , doi:10.1101/2022.07.14.499633 , 2022
+ | `mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers <https://doi.org/10.1093/nargab/lqae010>`_
+ | A. Hari, A. Zarrabi, D. Lobo
+ | **NAR Genomics and Bioinformatics**, 6(1), lqae010, 2024
 
 Contributors:
 

mergem/__version.py

@@ -1 +1 @@
-_version = '0.27.0'
+_version = '1.0.0'

mergem/cli.py

@@ -35,6 +35,11 @@ def main(input_filenames, obj, o=None, v=False, up=False, s=False, e=False, p=Fa
     and saves the merged model as .xml. Users can optionally select the objective, provide
     an output filename for the merged model, and translate the models to a different namespace.
 
+    Citation:
+    mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers
+    A. Hari, A. Zarrabi, D. Lobo
+    NAR Genomics and Bioinformatics 6(1), lqae010, 2024
+
     Lobo Lab (https://lobolab.umbc.edu)
     """
     model_filenames = input_filenames