pypeit · kbwestfall · Mar 31, 2026 · Feb 18, 2026 · Feb 18, 2026 · Feb 18, 2026
diff --git a/.gitignore b/.gitignore
@@ -69,6 +69,7 @@ Thumbs.db
 ######################################
 */version.py
 */cython_version.py
+*/pkg/version.py
 
 # ADDED by KBW
 .eggs

diff --git a/doc/api/pypeit.cache.rst b/doc/api/pypeit.cache.rst
diff --git a/doc/api/pypeit.logger.rst b/doc/api/pypeit.logger.rst
diff --git a/doc/api/pypeit.pkg.cache.rst b/doc/api/pypeit.pkg.cache.rst
@@ -0,0 +1,8 @@
+pypeit.pkg.cache module
+=======================
+
+.. automodule:: pypeit.pkg.cache
+   :members:
+   :private-members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/doc/api/pypeit.pkg.exceptions.rst b/doc/api/pypeit.pkg.exceptions.rst
@@ -0,0 +1,8 @@
+pypeit.pkg.exceptions module
+============================
+
+.. automodule:: pypeit.pkg.exceptions
+   :members:
+   :private-members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/doc/api/pypeit.exceptions.rst → doc/api/pypeit.pkg.logger.rst b/doc/api/pypeit.exceptions.rst → doc/api/pypeit.pkg.logger.rst
@@ -1,7 +1,7 @@
-pypeit.exceptions module
+pypeit.pkg.logger module
 ========================
 
-.. automodule:: pypeit.exceptions
+.. automodule:: pypeit.pkg.logger
    :members:
    :private-members:
    :show-inheritance:

diff --git a/doc/api/pypeit.pkg.pypeitdata.rst b/doc/api/pypeit.pkg.pypeitdata.rst
@@ -0,0 +1,8 @@
+pypeit.pkg.pypeitdata module
+============================
+
+.. automodule:: pypeit.pkg.pypeitdata
+   :members:
+   :private-members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/doc/api/pypeit.pkg.rst b/doc/api/pypeit.pkg.rst
@@ -0,0 +1,23 @@
+pypeit.pkg package
+==================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pypeit.pkg.cache
+   pypeit.pkg.exceptions
+   pypeit.pkg.logger
+   pypeit.pkg.pypeitdata
+   pypeit.pkg.version
+
+Module contents
+---------------
+
+.. automodule:: pypeit.pkg
+   :members:
+   :private-members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/doc/api/pypeit.pkg.version.rst b/doc/api/pypeit.pkg.version.rst
@@ -0,0 +1,8 @@
+pypeit.pkg.version module
+=========================
+
+.. automodule:: pypeit.pkg.version
+   :members:
+   :private-members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/doc/api/pypeit.pypeitdata.rst b/doc/api/pypeit.pypeitdata.rst
diff --git a/doc/api/pypeit.rst b/doc/api/pypeit.rst
@@ -13,6 +13,7 @@ Subpackages
    pypeit.images
    pypeit.move_median
    pypeit.par
+   pypeit.pkg
    pypeit.scripts
    pypeit.setup_gui
    pypeit.spectrographs
@@ -27,15 +28,13 @@ Submodules
    pypeit.alignframe
    pypeit.archive
    pypeit.bitmask
-   pypeit.cache
    pypeit.calibframe
    pypeit.calibrations
    pypeit.coadd1d
    pypeit.coadd2d
    pypeit.coadd3d
    pypeit.datamodel
    pypeit.edgetrace
-   pypeit.exceptions
    pypeit.exposure
    pypeit.extraction
    pypeit.find_objects
@@ -44,7 +43,6 @@ Submodules
    pypeit.history
    pypeit.inputfiles
    pypeit.io
-   pypeit.logger
    pypeit.manual_extract
    pypeit.metadata
    pypeit.multislit_flexure
@@ -53,7 +51,6 @@ Submodules
    pypeit.outputfiles
    pypeit.pypeit
    pypeit.pypeit_steps
-   pypeit.pypeitdata
    pypeit.pypeitsetup
    pypeit.sampling
    pypeit.scattlight

diff --git a/doc/api/pypeit.scripts.rst b/doc/api/pypeit.scripts.rst
@@ -60,6 +60,7 @@ Submodules
    pypeit.scripts.skysub_regions
    pypeit.scripts.tellfit
    pypeit.scripts.trace_edges
+   pypeit.scripts.util
    pypeit.scripts.version
    pypeit.scripts.view_fits
 

diff --git a/doc/api/pypeit.scripts.util.rst b/doc/api/pypeit.scripts.util.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.util module
+==========================
+
+.. automodule:: pypeit.scripts.util
+   :members:
+   :private-members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/doc/dev/new_script.rst b/doc/dev/new_script.rst
@@ -31,8 +31,8 @@ The important components of the scripts are:
    :class:`~pypeit.scripts.scriptbase.ScriptBase` as their base class.  Note
    that the class has no instantiation method.
 
- * The :func:`~pypeit.scripts.scriptbase.ScriptBase.get_parser` function is used
-   to return an instance of `argparse.ArgumentParser`_ used to parse the
+ * The :func:`~pypeit.scripts.scriptbase.ScriptBase.get_parser` function 
+   returns an instance of :class:`argparse.ArgumentParser` used to parse the
    command-line arguments.
 
  * The :func:`~pypeit.scripts.scriptbase.ScriptBase.main` function performs the
@@ -52,26 +52,35 @@ The base class, :class:`~pypeit.scripts.scriptbase.ScriptBase`, provides the
 common entry point function
 (:func:`~pypeit.scripts.scriptbase.ScriptBase.entry_point`) used during
 installation.  To ensure that the script is properly installed by `pip`_, you
-need to add this entry point to the ``setup.cfg`` file.  All of the PypeIt
-scripts are listed in the ``[options.entry_points]`` group.  To add your script,
-you enter a new line with the following format:
+need to add this entry point to the ``pypeit/pyproject.toml`` file.  All of the
+PypeIt scripts are listed in the ``[options.entry_points]`` group.  To add your
+script, you enter a new line with the following format:
 
 .. code-block:: ini
 
     pypeit_new_script = pypeit.scripts.new_script:NewScript.entry_point
 
-Lastly, you should add the import of the script module to the
-``pypeit/scripts/__init__.py`` file; i.e., add:
+Lastly, you should add the script module name to the ``__all__`` list in
+the ``pypeit/scripts/__init__.py`` file; i.e., add:
 
 .. code-block:: python
 
-    from pypeit.scripts import new_script
+    __all__ = [
+        ...
+        'new_script',
+        ...
+    ]
+
+Preferably add the new script name in a way that maintains the alphabetical
+ordering of the scripts in the list.
 
 Note that the script files in the ``pypeit/scripts`` directory:
 
- * Should not be executable (i.e., no xs in their permissions)
- * Should not start with an env statement; i.e., ``#!/usr/bin/env python``
- * Should not end with the ``if __name__ == '__main__':`` block
+- Should not be executable (i.e., no ``x`` in their permissions)
+
+- Should not start with an env statement; i.e., ``#!/usr/bin/env python``
+
+- Should not end with the ``if __name__ == '__main__':`` block
 
 Creating the executables from the raw script files is all handled by `pip`_
 installing PypeIt.  To ensure the script is installed, from the top-level

diff --git a/doc/dev/new_spectrograph.rst b/doc/dev/new_spectrograph.rst
@@ -11,8 +11,8 @@ Here are notes on how to add a new spectrograph from scratch or to add a new
 mode. To do so, you should install PypeIt following the development path;
 see :doc:`../installing` and :doc:`development`.
 
-Entirely New
-============
+Adding an entirely new spectrograph
+===================================
 
 PypeIt defines instrument-specific behavior/parameters using a python
 class hierarchy; see :class:`~pypeit.spectrographs.spectrograph.Spectrograph`
@@ -33,8 +33,8 @@ The class-hierarchy is used by PypeIt to specify certain instrument
 modes, like spectrograph arm, that inherit from a common base class. For
 example, :class:`~pypeit.spectrographs.keck_lris.KeckLRISSpectrograph`
 implements many of the methods that are common to both arms (red and blue) of
-the spectrograph. These include methods used to read raw files, used to
-define header cards with required :doc:`metadata`, and used to determine the type of
+the spectrograph. These include methods used to read raw files, to
+define header cards with required :doc:`metadata`, and to determine the type of
 frame (arc, dome, bias, etc) based on that :doc:`metadata`. The
 :class:`~pypeit.spectrographs.spectrograph.Spectrograph` instance for each
 LRIS arm inherits these methods common to them both by subclassing from
@@ -52,20 +52,29 @@ spectrograph has a similar set of modes, see
 Having said all of that, the basic steps one needs to follow to introduce a
 new spectrograph are as follows:
 
-#. Build a new file called ``telescope_spectrograph.py`` file and put it in the
-   ``pypeit/spectrographs/`` directory.
+#. Build a new file called ``{telescope}_{spectrograph}.py`` file and put it in
+   the ``pypeit/spectrographs/`` directory.
 
-#. Add the new module to the list imported by
-   ``pypeit/spectrographs/__init__.py``.
+#. Add the name of the new module to the ``__all__`` list defined in
+   ``pypeit/spectrographs/__init__.py``.  E.g.
 
-#. Generate a new Telescope object in (if new)
-   ``pypeit/telescopes.py``.
+   .. code-block:: python
 
-#. Add telescope name to valid_telescopes in
+        __all__ = [
+            ...
+            'keck_lris',
+            ...
+        ]
+
+   Please maintain the alphabetical ordering of the modules listed.
+
+#. Generate a new Telescope object in ``pypeit/telescopes.py``, as needed.
+
+#. Add the telescope name to the list of ``valid_telescopes`` in
    ``pypeit/par/pypeitpar.py``.
 
 #. Set the algorithmic path: the class attribute, ``pypeline``, must be
-   ``'MultiSlit'``, ``'Echelle'``, or ``'IFU'``.
+   ``'MultiSlit'``, ``'Echelle'``, or ``'SlicerIFU'``.
 
 #. Set the default parameters PypeIt uses during the reduction; see
    :ref:`parameters`, and, e.g.,
@@ -95,20 +104,18 @@ new spectrograph are as follows:
    compare to, e.g.,
    :func:`~pypeit.spectrographs.keck_deimos.KeckDEIMOSSpectrograph.get_rawimage`.
 
-#. For echelle spectrographs, there are numerous methods required that provide
-   details for the (currently fixed) format of the orders.  See, e.g.,
+#. For fixed-format echelle spectrographs, there are numerous methods that
+   provide details for the expected format of the orders.  See, e.g.,
    :class:`~pypeit.spectrographs.vlt_xshooter.VLTXShooterNIRSpectrograph`.
 
-#. You may need to generate wavelength solutions for your setups. You can use the
-   :ref:`pypeit_identify` utility, and add this to the PypeIt archive by
+#. You may need to generate wavelength solutions for your setups. You can use
+   the :ref:`pypeit_identify` utility, and add this to the PypeIt archive by
    following the steps outlined in the :doc:`../calibrations/construct_template`
    documentation.  See :ref:`wave_calib`.
 
-
 See this `example PR <https://github.com/pypeit/PypeIt/pull/1179>`_ for the
 SOAR/Goodman spectrograph.
 
-
 Near-IR
 +++++++
 
@@ -119,14 +126,14 @@ an example.
 Tests
 +++++
 
-For a spectrograph to be supported going forth, we require a minimum set
-of tests.  These are:
+For a spectrograph to be designated as being "supported" by PypeIt, we require a
+minimum set of tests.  These are:
 
     - A full run of the pipeline for each grating/mode of the spectrograph in
       the `PypeIt Development Suite`_.
 
-    - A simple unit test that check an image can be loaded.  This needs to be
-      added to the `PypeIt Development Suite`_; see `here
+    - A simple unit test that checks that an image can be loaded.  This needs to
+      be added to the `PypeIt Development Suite`_; see `here
       <https://github.com/pypeit/PypeIt-development-suite/blob/main/unit_tests/test_load_images.py>`__.
 
 Docs
@@ -135,9 +142,18 @@ Docs
 We request that the following docs be updated to advertise the new
 spectrograph:
 
-- Update the top-level ``CHANGES.rst``
+- Include a comment noting the addition of the relevant spectrograph module in
+  the most recent release doc in ``doc/releases``.  There is typically a section
+  for "Instrument-specific" changes.
 
 - If specific advice is important/useful, add an instrument specific doc to the
   ``doc/spectrographs`` directory and link the doc in the
   ``doc/specrographs/spectrographs.rst`` doc.
 
+- It will be helpful to users to have a tutorial to follow when using PypeIt to
+  reduce data from the newly supported spectrograph.  Please either add a new
+  tutorial (see, e.g., ``doc/tutorials/lris_howto.rst``) or add a comment in
+  ``doc/tutorials/tutorials.rst`` pointing users to a spectrograph tutorial that
+  is very similar (or identical) to the procedures that should be used for the
+  new spectrograph.
+
diff --git a/doc/help/pypeit_show_1dspec.rst b/doc/help/pypeit_show_1dspec.rst
@@ -2,14 +2,15 @@
 
     $ pypeit_show_1dspec -h
     usage: pypeit_show_1dspec [-h] [-v VERBOSITY] [--log_file LOG_FILE]
-                              [--log_level LOG_LEVEL] [--list] [--exten EXTEN]
-                              [--obj OBJ] [--extract EXTRACT] [--flux] [-m]
+                              [--log_level LOG_LEVEL] [--list] [--exten EXTEN |
+                              --obj OBJ] [--extract {BOX,OPT}] [--flux] [-m]
                               file
 
     Show a 1D spectrum
 
     positional arguments:
-      file                  Spectral file
+      file                  PypeIt spec1d file (this script does not work with
+                            coadd_1dspec output spectra).
 
     options:
       -h, --help            show this help message and exit
@@ -25,12 +26,13 @@
                             Verbosity level for the log file. If a log file is
                             produce and this is None, the file log will match the
                             console stream log. (default: None)
-      --list                List the extensions only? (default: False)
-      --exten EXTEN         FITS extension (default: 1)
-      --obj OBJ             Object name in lieu of extension, e.g.
+      --list                Instead of plotting any spectra, simply list the
+                            extensions with spectra (default: False)
+      --exten EXTEN         Number of the extension to plot (default: 1)
+      --obj OBJ             Extension (object) name to plot, e.g.
                             SPAT0424-SLIT0000-DET01 (default: None)
-      --extract EXTRACT     Extraction method. Default is OPT. ['BOX', 'OPT']
-                            (default: OPT)
-      --flux                Show fluxed spectrum? (default: False)
-      -m, --unmasked        Only show unmasked data. (default: True)
+      --extract {BOX,OPT}   Method used to extract the spectrum (default: OPT)
+      --flux                Show the flux-calibrated spectrum (if available)
+                            (default: False)
+      -m, --unmasked        Only show the unmasked data. (default: True)
 
diff --git a/doc/help/run_pypeit.rst b/doc/help/run_pypeit.rst
@@ -6,7 +6,7 @@
                       pypeit_file
 
     PypeIt: The Python Spectroscopic Data Reduction Pipeline
-    Version 2.0.1.dev45+g1d735d64c
+    Version 2.0.1.dev23+g72bf91080.d20260323
 
     Available spectrographs include:
         aat_uhrf, apf_levy, bok_bc, gemini_flamingos1, gemini_flamingos2,

diff --git a/doc/include/links.rst b/doc/include/links.rst
@@ -126,6 +126,7 @@
 .. _pdb: https://docs.python.org/3/library/pdb.html
 .. _IPython.embed: https://ipython.readthedocs.io/en/stable/api/generated/IPython.terminal.embed.html#function
 .. _pytest: https://docs.pytest.org/en/latest/
+.. _shapely: https://shapely.readthedocs.io/en/stable/manual.html
 .. _scikit-image: https://scikit-image.org/
 .. _bottleneck: https://bottleneck.readthedocs.io/en/latest/
 .. _specutils: https://specutils.readthedocs.io/en/stable/