Zstone19 · pre-commit-ci · Aug 31, 2026 · Aug 31, 2026
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
     -   id: check-yaml
     -   id: no-commit-to-branch
@@ -22,7 +22,7 @@ repos:
 
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.1
     hooks:
     -   id: isort
         name: isort (python)
@@ -34,6 +34,6 @@ repos:
 
 
 -   repo: https://github.com/alan-turing-institute/CleverCSV-pre-commit
-    rev: v0.8.2
+    rev: v0.8.5
     hooks:
       - id: clevercsv-standardize
diff --git a/README.md b/README.md
@@ -111,4 +111,4 @@ To cite the pyPetal code itself, use the [ASCL reference](https://ascl.net/2401.
     Stone Z., 2024, version xxxx, Astrophysics Source Code Library, record ascl:2401.004
 ```
 
-Cite the paper pyPetal was used in: [Shen et al. (2023)](https://ui.adsabs.harvard.edu/abs/2023arXiv230501014S/abstract) 
+Cite the paper pyPetal was used in: [Shen et al. (2023)](https://ui.adsabs.harvard.edu/abs/2023arXiv230501014S/abstract)
diff --git a/docs/mica2_toc.rst b/docs/mica2_toc.rst
@@ -2,13 +2,13 @@
 MICA2
 =======
 
-MICA2 is a more complex tool used to correlate two light curves in a non-parametric fashion to find the transfer function between the two, 
+MICA2 is a more complex tool used to correlate two light curves in a non-parametric fashion to find the transfer function between the two,
 as a sum of either Gaussians or tophat functions. MICA2 is much more flexible in its functionality, though this comes with much more complex
 customization from the user in terms of parameters chosen and types of analysis possible. These tutorials provide instructions
 on in-depth usage of MICA2 and understanding of its arguments and outputs.
 
 While these tutorials do a sufficient job of introducing the user to the basic functionality of MICA2, the user is encouraged to read the
-MICA2 `documentation <https://mica2.readthedocs.io/en/latest/index.html>`_ and/or `repository <https://github.com/LiyrAstroph/MICA2>`_ for 
+MICA2 `documentation <https://mica2.readthedocs.io/en/latest/index.html>`_ and/or `repository <https://github.com/LiyrAstroph/MICA2>`_ for
 more in-depth information on the software. In addition, the user can read the associated `paper <https://ui.adsabs.harvard.edu/abs/2016ApJ...831..206L/abstract>`_
 for any additional details.
 
@@ -20,7 +20,7 @@ for any additional details.
 
     pyPetal extends this functionality, so that the MICA2 module can utilize ``mpiexec``. However, if this is done, all other module will
     only be run on one core (as they are optimized for python multi-threading instead of MPI). If the user wishes to only use the MICA2 module,
-    it may be best to run using ``mpiexec``. If the user wishes to use the other modules, it may be best to run the MICA2 module separately 
+    it may be best to run using ``mpiexec``. If the user wishes to use the other modules, it may be best to run the MICA2 module separately
     from the other modules.
 
 

diff --git a/docs/pl_args.rst b/docs/pl_args.rst
@@ -370,7 +370,7 @@ MICA2 arguments:
       - Whether or not the order of the time lags makes a difference (i.e., whether or not the time lags are allowed to be equal). If order doesn't matter, MICA2 will be able to fit all light curves in one run. If set to :python:`True`, a separate MICA2 run will be performed for each line.
       - :python:`bool`
       - :python:`True`
-    
+
 
 
 

diff --git a/examples/mica2_output1/yelm/mica2/data/data_input.txt b/examples/mica2_output1/yelm/mica2/data/data_input.txt
@@ -277,4 +277,3 @@
 1960.980490 4.184530 0.041990
 1968.984490 4.680230 0.046580
 1976.988490 4.417370 0.044310
-
diff --git a/examples/mica2_output1/yelm/mica2/data/limits.txt b/examples/mica2_output1/yelm/mica2/data/limits.txt
@@ -1,29 +1,29 @@
-0  0.000000e+00  0.000000e+00  -9.205811e+00  2.291202e+00  2.746387e-03  9.427186e+00  
-1  0.000000e+00  0.000000e+00  -5.598647e+00  8.234217e-01  2.746387e-03  9.427186e+00  
-2  0.000000e+00  0.000000e+00  -5.168633e+00  -1.940815e+00  1.014567e+00  9.427186e+00  
-3  0.000000e+00  0.000000e+00  -4.717707e+00  -3.525592e+00  3.355616e+00  9.427186e+00  
-4  0.000000e+00  0.000000e+00  -4.398488e+00  -4.014441e+00  4.450590e+00  9.427186e+00  
-5  0.000000e+00  0.000000e+00  -4.320638e+00  -4.108975e+00  4.831877e+00  9.427186e+00  
-6  0.000000e+00  0.000000e+00  -4.288085e+00  -4.144914e+00  5.016759e+00  6.918264e+00  
-7  0.000000e+00  0.000000e+00  -4.267850e+00  -4.166484e+00  5.158052e+00  6.292329e+00  
-8  0.000000e+00  0.000000e+00  -4.247806e+00  -4.187138e+00  5.306227e+00  5.941505e+00  
-9  0.000000e+00  0.000000e+00  -4.240002e+00  -4.195745e+00  5.369966e+00  5.827415e+00  
-10  0.000000e+00  0.000000e+00  -4.228552e+00  -4.207074e+00  5.470446e+00  5.688082e+00  
-11  0.000000e+00  0.000000e+00  -4.223890e+00  -4.211670e+00  5.514173e+00  5.637154e+00  
-12  0.000000e+00  0.000000e+00  -4.221818e+00  -4.213796e+00  5.533368e+00  5.614478e+00  
-13  0.000000e+00  0.000000e+00  -4.220504e+00  -4.215076e+00  5.546187e+00  5.601168e+00  
-14  0.000000e+00  0.000000e+00  -4.219261e+00  -4.216346e+00  5.558872e+00  5.588131e+00  
-15  0.000000e+00  0.000000e+00  -4.218688e+00  -4.216889e+00  5.564184e+00  5.582463e+00  
-16  0.000000e+00  0.000000e+00  -4.218451e+00  -4.217143e+00  5.566797e+00  5.579898e+00  
-17  0.000000e+00  0.000000e+00  -4.218144e+00  -4.217444e+00  5.569784e+00  5.576941e+00  
-18  0.000000e+00  0.000000e+00  -4.218034e+00  -4.217559e+00  5.570933e+00  5.575747e+00  
-19  0.000000e+00  0.000000e+00  -4.217954e+00  -4.217638e+00  5.571734e+00  5.574930e+00  
-20  0.000000e+00  0.000000e+00  -4.217879e+00  -4.217715e+00  5.572517e+00  5.574164e+00  
-21  0.000000e+00  0.000000e+00  -4.217847e+00  -4.217747e+00  5.572830e+00  5.573840e+00  
-22  0.000000e+00  0.000000e+00  -4.217823e+00  -4.217770e+00  5.573065e+00  5.573604e+00  
-23  0.000000e+00  0.000000e+00  -4.217811e+00  -4.217783e+00  5.573194e+00  5.573476e+00  
-24  0.000000e+00  0.000000e+00  -4.217805e+00  -4.217788e+00  5.573248e+00  5.573421e+00  
-25  0.000000e+00  0.000000e+00  -4.217802e+00  -4.217792e+00  5.573284e+00  5.573386e+00  
-26  0.000000e+00  0.000000e+00  -4.217800e+00  -4.217794e+00  5.573305e+00  5.573364e+00  
-27  0.000000e+00  0.000000e+00  -4.217799e+00  -4.217795e+00  5.573317e+00  5.573353e+00  
-28  0.000000e+00  0.000000e+00  -4.217798e+00  -4.217796e+00  5.573323e+00  5.573347e+00  
+0  0.000000e+00  0.000000e+00  -9.205811e+00  2.291202e+00  2.746387e-03  9.427186e+00
+1  0.000000e+00  0.000000e+00  -5.598647e+00  8.234217e-01  2.746387e-03  9.427186e+00
+2  0.000000e+00  0.000000e+00  -5.168633e+00  -1.940815e+00  1.014567e+00  9.427186e+00
+3  0.000000e+00  0.000000e+00  -4.717707e+00  -3.525592e+00  3.355616e+00  9.427186e+00
+4  0.000000e+00  0.000000e+00  -4.398488e+00  -4.014441e+00  4.450590e+00  9.427186e+00
+5  0.000000e+00  0.000000e+00  -4.320638e+00  -4.108975e+00  4.831877e+00  9.427186e+00
+6  0.000000e+00  0.000000e+00  -4.288085e+00  -4.144914e+00  5.016759e+00  6.918264e+00
+7  0.000000e+00  0.000000e+00  -4.267850e+00  -4.166484e+00  5.158052e+00  6.292329e+00
+8  0.000000e+00  0.000000e+00  -4.247806e+00  -4.187138e+00  5.306227e+00  5.941505e+00
+9  0.000000e+00  0.000000e+00  -4.240002e+00  -4.195745e+00  5.369966e+00  5.827415e+00
+10  0.000000e+00  0.000000e+00  -4.228552e+00  -4.207074e+00  5.470446e+00  5.688082e+00
+11  0.000000e+00  0.000000e+00  -4.223890e+00  -4.211670e+00  5.514173e+00  5.637154e+00
+12  0.000000e+00  0.000000e+00  -4.221818e+00  -4.213796e+00  5.533368e+00  5.614478e+00
+13  0.000000e+00  0.000000e+00  -4.220504e+00  -4.215076e+00  5.546187e+00  5.601168e+00
+14  0.000000e+00  0.000000e+00  -4.219261e+00  -4.216346e+00  5.558872e+00  5.588131e+00
+15  0.000000e+00  0.000000e+00  -4.218688e+00  -4.216889e+00  5.564184e+00  5.582463e+00
+16  0.000000e+00  0.000000e+00  -4.218451e+00  -4.217143e+00  5.566797e+00  5.579898e+00
+17  0.000000e+00  0.000000e+00  -4.218144e+00  -4.217444e+00  5.569784e+00  5.576941e+00
+18  0.000000e+00  0.000000e+00  -4.218034e+00  -4.217559e+00  5.570933e+00  5.575747e+00
+19  0.000000e+00  0.000000e+00  -4.217954e+00  -4.217638e+00  5.571734e+00  5.574930e+00
+20  0.000000e+00  0.000000e+00  -4.217879e+00  -4.217715e+00  5.572517e+00  5.574164e+00
+21  0.000000e+00  0.000000e+00  -4.217847e+00  -4.217747e+00  5.572830e+00  5.573840e+00
+22  0.000000e+00  0.000000e+00  -4.217823e+00  -4.217770e+00  5.573065e+00  5.573604e+00
+23  0.000000e+00  0.000000e+00  -4.217811e+00  -4.217783e+00  5.573194e+00  5.573476e+00
+24  0.000000e+00  0.000000e+00  -4.217805e+00  -4.217788e+00  5.573248e+00  5.573421e+00
+25  0.000000e+00  0.000000e+00  -4.217802e+00  -4.217792e+00  5.573284e+00  5.573386e+00
+26  0.000000e+00  0.000000e+00  -4.217800e+00  -4.217794e+00  5.573305e+00  5.573364e+00
+27  0.000000e+00  0.000000e+00  -4.217799e+00  -4.217795e+00  5.573317e+00  5.573353e+00
+28  0.000000e+00  0.000000e+00  -4.217798e+00  -4.217796e+00  5.573323e+00  5.573347e+00
Original file line number	Diff line number	Diff line change
Expand Up		@@ -370,7 +370,7 @@ MICA2 arguments:
		- Whether or not the order of the time lags makes a difference (i.e., whether or not the time lags are allowed to be equal). If order doesn't matter, MICA2 will be able to fit all light curves in one run. If set to :python:`True`, a separate MICA2 run will be performed for each line.
		- :python:`bool`
		- :python:`True`





Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -277,4 +277,3 @@
		1960.980490 4.184530 0.041990
		1968.984490 4.680230 0.046580
		1976.988490 4.417370 0.044310