Merge pull request #1745 from pypeit/staged

Merges develop into release (1.15.0 tag prep)
pypeit · Dec 15, 2023 · 49bf329 · 49bf329
2 parents ff02b9d + 4a570ee
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,10 @@
+
+****************************************************************************
+USE OF THIS FILE IS NOW DEPRECATED.  CHANGES SHOULD BE ADDED TO THE RELEVANT
+RELEASE FILE IN doc/releases
+****************************************************************************
+
+
 1.14.0 (18 Sep 2023)
 --------------------
 
@@ -51,7 +58,7 @@
       files that have frametype None (this prevent ``run_pypeit`` to crash)
     - Added a function ``check_spectrograph()`` (currently only defined for LRIS),
       that checks (during ``pypeit_setup``) if the selected spectrograph is the
-      corrected one for the data used. 
+      corrected one for the data used.
 
 
 1.13.0 (2 June 2023)

diff --git a/README.rst b/README.rst
@@ -1,12 +1,9 @@
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/pypeit?label=PyPI&logo=pypi&logoColor=white
-    :target: https://pypi.org/project/pypeit/
+    :target: https://pypi.org/project/pypeit/#history
 
-.. |Conda| image:: https://img.shields.io/conda/vn/conda-forge/pypeit?label=conda%20version
-    :target: https://anaconda.org/conda-forge/pypeit
-
-.. |CondaDownloads| image:: https://img.shields.io/conda/dn/conda-forge/pypeit?label=conda%20downloads
-    :target: https://anaconda.org/conda-forge/pypeit
+.. |pypi_downloads| image:: https://img.shields.io/pypi/dm/pypeit
+    :target: https://pypi.org/project/pypeit/#files
 
 .. |License| image:: https://img.shields.io/github/license/pypeit/PypeIt
    :target: https://github.com/pypeit/PypeIt/blob/release/LICENSE.rst
@@ -50,7 +47,7 @@
 PypeIt |forks| |stars|
 ======================
 
-|github| |pypi| |conda| |CondaDownloads| |License|
+|github| |pypi| |pypi_downloads| |License|
 
 |docs| |CITests| |Coverage| 
 
@@ -67,7 +64,7 @@ PypeIt is designed to be used by both advanced spectroscopists with prior data
 reduction expertise and astronomers with no prior experience of data reduction.
 It is highly configurable and designed to be applied to any standard
 slit-imaging spectrograph, including long-slit, multi-slit, as well as
-cross-dispersed echelle spectra.  **The spectrogaphs that PypeIt can be used
+cross-dispersed echelle spectra.  **The spectrographs that PypeIt can be used
 with are listed** `here
 <https://pypeit.readthedocs.io/en/release/spectrographs/spectrographs.html>`__.
 

diff --git a/doc/api/pypeit.coadd3d.rst b/doc/api/pypeit.coadd3d.rst
@@ -0,0 +1,8 @@
+pypeit.coadd3d module
+=====================
+
+.. automodule:: pypeit.coadd3d
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.core.gui.edge_inspector.rst b/doc/api/pypeit.core.gui.edge_inspector.rst
@@ -0,0 +1,8 @@
+pypeit.core.gui.edge\_inspector module
+======================================
+
+.. automodule:: pypeit.core.gui.edge_inspector
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.core.gui.gui_util.rst b/doc/api/pypeit.core.gui.gui_util.rst
@@ -0,0 +1,8 @@
+pypeit.core.gui.gui\_util module
+================================
+
+.. automodule:: pypeit.core.gui.gui_util
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.core.gui.rst b/doc/api/pypeit.core.gui.rst
@@ -7,6 +7,8 @@ Submodules
 .. toctree::
    :maxdepth: 4
 
+   pypeit.core.gui.edge_inspector
+   pypeit.core.gui.gui_util
    pypeit.core.gui.identify
    pypeit.core.gui.object_find
    pypeit.core.gui.skysub_regions

diff --git a/doc/api/pypeit.core.rst b/doc/api/pypeit.core.rst
@@ -40,6 +40,7 @@ Submodules
    pypeit.core.procimg
    pypeit.core.pydl
    pypeit.core.qa
+   pypeit.core.scattlight
    pypeit.core.skysub
    pypeit.core.slitdesign_matching
    pypeit.core.telluric

diff --git a/doc/api/pypeit.core.scattlight.rst b/doc/api/pypeit.core.scattlight.rst
@@ -0,0 +1,8 @@
+pypeit.core.scattlight module
+=============================
+
+.. automodule:: pypeit.core.scattlight
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.rst b/doc/api/pypeit.rst
@@ -15,6 +15,7 @@ Subpackages
    pypeit.move_median
    pypeit.par
    pypeit.scripts
+   pypeit.setup_gui
    pypeit.spectrographs
    pypeit.specutils
 
@@ -31,6 +32,7 @@ Submodules
    pypeit.calibrations
    pypeit.coadd1d
    pypeit.coadd2d
+   pypeit.coadd3d
    pypeit.datamodel
    pypeit.edgetrace
    pypeit.extraction
@@ -47,6 +49,7 @@ Submodules
    pypeit.pypeitsetup
    pypeit.pypmsgs
    pypeit.sampling
+   pypeit.scattlight
    pypeit.sensfilearchive
    pypeit.sensfunc
    pypeit.setup_package

diff --git a/doc/api/pypeit.scattlight.rst b/doc/api/pypeit.scattlight.rst
@@ -0,0 +1,8 @@
+pypeit.scattlight module
+========================
+
+.. automodule:: pypeit.scattlight
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.scripts.chk_scattlight.rst b/doc/api/pypeit.scripts.chk_scattlight.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.chk\_scattlight module
+=====================================
+
+.. automodule:: pypeit.scripts.chk_scattlight
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.scripts.edge_inspector.rst b/doc/api/pypeit.scripts.edge_inspector.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.edge\_inspector module
+=====================================
+
+.. automodule:: pypeit.scripts.edge_inspector
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.scripts.rst b/doc/api/pypeit.scripts.rst
@@ -15,13 +15,15 @@ Submodules
    pypeit.scripts.chk_for_calibs
    pypeit.scripts.chk_noise_1dspec
    pypeit.scripts.chk_noise_2dspec
+   pypeit.scripts.chk_scattlight
    pypeit.scripts.chk_tilts
    pypeit.scripts.chk_wavecalib
    pypeit.scripts.coadd_1dspec
    pypeit.scripts.coadd_2dspec
    pypeit.scripts.coadd_datacube
    pypeit.scripts.collate_1d
    pypeit.scripts.compare_sky
+   pypeit.scripts.edge_inspector
    pypeit.scripts.flux_calib
    pypeit.scripts.flux_setup
    pypeit.scripts.identify
@@ -40,6 +42,7 @@ Submodules
    pypeit.scripts.sensfunc
    pypeit.scripts.setup
    pypeit.scripts.setup_coadd2d
+   pypeit.scripts.setup_gui
    pypeit.scripts.show_1dspec
    pypeit.scripts.show_2dspec
    pypeit.scripts.show_arxiv

diff --git a/doc/api/pypeit.scripts.setup_gui.rst b/doc/api/pypeit.scripts.setup_gui.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.setup\_gui module
+================================
+
+.. automodule:: pypeit.scripts.setup_gui
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.setup_gui.controller.rst b/doc/api/pypeit.setup_gui.controller.rst
@@ -0,0 +1,8 @@
+pypeit.setup\_gui.controller module
+===================================
+
+.. automodule:: pypeit.setup_gui.controller
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.setup_gui.dialog_helpers.rst b/doc/api/pypeit.setup_gui.dialog_helpers.rst
@@ -0,0 +1,8 @@
+pypeit.setup\_gui.dialog\_helpers module
+========================================
+
+.. automodule:: pypeit.setup_gui.dialog_helpers
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.setup_gui.model.rst b/doc/api/pypeit.setup_gui.model.rst
@@ -0,0 +1,8 @@
+pypeit.setup\_gui.model module
+==============================
+
+.. automodule:: pypeit.setup_gui.model
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.setup_gui.rst b/doc/api/pypeit.setup_gui.rst
@@ -0,0 +1,23 @@
+pypeit.setup\_gui package
+=========================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pypeit.setup_gui.controller
+   pypeit.setup_gui.dialog_helpers
+   pypeit.setup_gui.model
+   pypeit.setup_gui.text_viewer
+   pypeit.setup_gui.view
+
+Module contents
+---------------
+
+.. automodule:: pypeit.setup_gui
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.setup_gui.text_viewer.rst b/doc/api/pypeit.setup_gui.text_viewer.rst
@@ -0,0 +1,8 @@
+pypeit.setup\_gui.text\_viewer module
+=====================================
+
+.. automodule:: pypeit.setup_gui.text_viewer
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.setup_gui.view.rst b/doc/api/pypeit.setup_gui.view.rst
@@ -0,0 +1,8 @@
+pypeit.setup\_gui.view module
+=============================
+
+.. automodule:: pypeit.setup_gui.view
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/calibrations/align.rst b/doc/calibrations/align.rst
@@ -47,14 +47,14 @@ the spatial alignment.
 Trouble Shooting
 ================
 
-If your image appears to be in err, here are the things to consider:
+If your image appears to be in error, here are the things to consider:
 
  - Is one or more of your input alignment frames junk?
 
  - Check each of your input alignment frames. Some might be mislabeled.
 
  - If some alignments are apparently missing, you might want to check
-   that the slits are currently traced.
+   that the slits are correctly traced.
 
 Current Alignments Data Model
 =============================

diff --git a/doc/calibrations/calibrations.rst b/doc/calibrations/calibrations.rst
@@ -128,6 +128,7 @@ The primary calibration procedures are, in the order they're performed:
    wave_calib
    Slit Alignment (IFU only) <alignment>
    flat_fielding
+   scattlight
 
 Follow the above links for a detailed description of each step, and how the
 default calibration procedures may be **modified** to suit your needs.

diff --git a/doc/calibrations/image_proc.rst b/doc/calibrations/image_proc.rst
@@ -140,7 +140,7 @@ Read and Digitization Noise
 
 Readnoise variance, :math:`V_{\rm rn}`, is calculated by
 :func:`~pypeit.core.procimg.rn2_frame`.  The calculation requires the detector
-readnoise (RN in elections, e-) and, possibly, gain (:math:`g` in e-/ADU)
+readnoise (RN in electrons, e-) and, possibly, gain (:math:`g` in e-/ADU)
 for each amplifier, which are provided for each amplifier by the
 :class:`~pypeit.images.detector_container.DetectorContainer` object defined for
 each detector in each :class:`~pypeit.spectrographs.spectrograph.Spectrograph`
@@ -166,7 +166,7 @@ parameter.  If you need to add digitization noise for your instrument, please
 Overscan Subtraction
 --------------------
 
-If available, the raw-image reader for each spectrograph returns the overscan
+If available, the raw image reader for each spectrograph returns the overscan
 region of the detector; see
 :func:`~pypeit.spectrographs.spectrograph.Spectrograph.get_rawimage`.  Overscan
 subtraction uses this region of the image to subtract a per-frame bias level;
@@ -180,7 +180,7 @@ is propagated to the image-processing error budget.
 Trimming & Re-orientation
 -------------------------
 
-The raw-image reader for each spectrograph returns the primary data region of
+The raw image reader for each spectrograph returns the primary data region of
 the detector; see
 :func:`~pypeit.spectrographs.spectrograph.Spectrograph.get_rawimage`.  Trimming
 crops the image to only include the primary data region; see
@@ -220,16 +220,16 @@ pixel-to-pixel bias-level correction in the science region of the detector.  To
 perform bias subtraction, include bias frames in your :ref:`pypeit_file` and set
 ``use_biasimage`` to true.  The bias correction (see
 :func:`~pypeit.images.rawimage.RawImage.subtract_bias`) is applied *after*
-trimming and orientation.  Uncertainty in the bias subtraction is propagated to
-the image-processing error budget. 
+trimming, orientation, and overscan subtraction.
+Uncertainty in the bias subtraction is propagated to the image-processing error budget.
 
 Dark Subtraction
 ----------------
 
 In addition to readnoise and gain, our instrument-specific
 :class:`~pypeit.images.detector_container.DetectorContainer` objects also
 provide the expected dark current; see :ref:`detectors`.  The tabulated dark
-current must be in elections per pixel per *hour*.  Note that:
+current must be in electrons per pixel per *hour*.  Note that:
 
     - "per pixel" means per *unbinned* pixel; dark current in a binned pixel is
       :math:`N_{\rm bin}` higher than in an unbinned pixel