Fixed issue with master flat not being included since UTIL_MASTER_FLA…

…T is no longer suppported, added the create_sof parameter to the Pipeline methods that call an EsoRex routine

README.rst

@@ -40,7 +40,7 @@ Documentation can be found at `http://pycrires.readthedocs.io <http://pycrires.r
 Attribution
 -----------
 
-Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and `Landman et al. (2023) <https://arxiv.org/abs/2311.13527>`_  specifically when using the dedicated routines for spatially-resolved sources.
+Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and `Landman et al. (2023) <https://ui.adsabs.harvard.edu/abs/2024A%26A...682A..48L/abstract>`_ specifically when using the dedicated routines for spatially-resolved sources.
 
 Contributing
 ------------

docs/about.rst

@@ -11,7 +11,7 @@ Contact
 Attribution
 -----------
 
-Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and `Landman et al. (2023) <https://arxiv.org/abs/2311.13527>`_ specifically when using the dedicated routines for spatially-resolved sources.
+Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and `Landman et al. (2023) <https://ui.adsabs.harvard.edu/abs/2024A%26A...682A..48L/abstract>`_ specifically when using the dedicated routines for spatially-resolved sources.
 
 Contributing
 ------------

docs/running.rst

@@ -33,6 +33,9 @@ Below, there is an full example for reducing and calibrating the `CRIRES+ <https
 .. tip::
   The pipeline will automatically download any missing calibration files (e.g. dark frames with specific DIT). After downloading and uncompressing, it is important to rerun the pipeline such that the calibration files are included with the data reduction.
 
+.. tip::
+  Set ``verbose=True`` to print the output from ``EsoRex`` to check for potential issues with the reduction.
+
 .. code-block:: python
 
   import pycrires
@@ -55,7 +58,7 @@ Below, there is an full example for reducing and calibrating the `CRIRES+ <https
   pipeline.util_calib(calib_type='fpet', verbose=False)
   pipeline.util_extract(calib_type='fpet', verbose=False)
   pipeline.util_wave(calib_type='fpet', poly_deg=4, wl_err=0.01, verbose=False)
-  pipeline.obs_nodding(verbose=False, correct_bad_pixels=True, extraction_required=True)
+  pipeline.obs_nodding(verbose=False, correct_bad_pixels=True, extraction_required=True, check_existing=False)
   pipeline.run_skycalc(pwv=1.)
   pipeline.plot_spectra(nod_ab='A', telluric=True, corrected=False, file_id=0)