Changes to EDR LSS documentation after fixing variables for EDR.

Author: aureliocarnero

doc/DESI_ROOT/vac/RELEASE/index.rst

@@ -3,7 +3,9 @@ RELEASE
 =======
 
 ``${DESI_ROOT}/vac/RELEASE`` contains the Value Added Catalogs (VAC) associated with a
-particular data release. The value of ``RELEASE`` will typically be ``edr``, ``dr1``, and so on.
+particular data release. The value of ``RELEASE`` will typically be ``edr``, ``dr1``, and so on. 
+
+In the case of the LSS catalogs, only the EDR release is host under the vac directory. For Data Releases (DR), the LSS catalos sits under ``${DESI_ROOT}/survey/catalogs`` 
 
 Within this directory, each VAC will have a unique name.
 

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/altmtl/UnivUNUM/index.rst

@@ -2,18 +2,18 @@
 lss
 ===
 
-``$DESI_ROOT/vac/RELEASE/lss`` contains LSS catalogs reading from most other DESI products, ready for archiving with
+``$DESI_ROOT/vac/edr/lss`` contains LSS catalogs for EDR, reading from most other DESI products, ready for archiving with
 the early data release. Intermediate files are saved, until we build the clustering-ready catalogs
 (including weights).
 
-``VERSION`` contains different possible versions of the LSS catalogs, given a production run and a tile selection. As of the EDR release date, there is one single version named ``v2.0`` (we use v2.0 in order to distinguish these catalogs from an internal DESI earlier v1.0 version).
+``v2.0`` represents the final EDR LSS version (we use v2.0 in order to distinguish these catalogs from an internal DESI earlier v1.0 version).
 
 The final clustering-ready catalogs can be found under :ref:`LSScats/clustering<clustering>`, together with the random samples for the same target types.
-Information about the different target types and the use of the different weights can be found in `EDR. DESI Collaboration (in prep.)`_ and in the explanation of :ref:`LSScats<lsscats>` subdirectory.
+Information about the different target types and the use of the different weights can be found in `EDR. DESI Collaboration (2024)`_ and in the explanation of :ref:`LSScats<lsscats>` subdirectory.
 
 The catalogs are generated using tools from github_lss_repository_. For EDR we use the `github release tag v2.0.0-EDR`_
 
-.. _EDR. DESI Collaboration (in prep.): https://arxiv.org/abs/2306.06308
+.. _EDR. DESI Collaboration (2024): https://iopscience.iop.org/article/10.3847/1538-3881/ad3217
 
 .. _github_lss_repository: https://github.com/desihub/LSS
 
@@ -23,4 +23,4 @@ The catalogs are generated using tools from github_lss_repository_. For EDR we u
 .. toctree::
    :maxdepth: 1
 
-   VERSION/index
+   v2.0/index

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/altmtl/index.rst

@@ -6,14 +6,14 @@ clustering
 
 ``clustering`` contains LSS catalogs, separated by target types (:ref:`see here for references<lsscats>`), that have been prepared to be used directly to obtain clustering statistics. It includes both data for randoms (separated into 18 files given ``{RANN}``).
 
-Descriptions on how to use these to obtain clustering measurements are fully given in `EDR. DESI Collaboration (in prep.)`_ and in `Lasker et al (in prep.)`_. Any cuts applied to the data catalogs should be equally applied to the random catalogs.
+Descriptions on how to use these to obtain clustering measurements are fully given in `EDR. DESI Collaboration (2024)`_ and in `Lasker et al (2024)`_. Any cuts applied to the data catalogs should be equally applied to the random catalogs.
 
 Any number of the random catalogs, ``{RANN}`` can be used (with the impact only on statistical precision). Large-scale clustering measurements can be accurately obtained via the columns :py:attr:`RA`, :py:attr:`DEC`, :py:attr:`Z`, :py:attr:`WEIGHT`.
 
 For small-scales, pairwise inverse-probability (PIP) weights can be obtained via the BITWEIGHTS column and we further recommend angular up-weighting (as in `Mohammad et al. (2020)`_). If using PIP weights, the :py:attr:`WEIGHT` column should still be used for the random counts (but not used for the data counts).
 
-.. _EDR. DESI Collaboration (in prep.): https://arxiv.org/abs/2306.06308
-.. _Lasker et al (in prep.): https://ui.adsabs.harvard.edu/public-libraries/XCj7bW-vSMaNZVV0C0QyGA
+.. _EDR. DESI Collaboration (2024): https://iopscience.iop.org/article/10.3847/1538-3881/ad3217
+.. _Lasker et al (2024): https://arxiv.org/abs/2404.03006
 .. _Mohammad et al. (2020): https://academic.oup.com/mnras/article/498/1/128/5891251
 
 .. toctree::

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/index.rst

@@ -5,7 +5,7 @@
 LSScats
 =======
 
-``$DESI_ROOT/vac/RELEASE/lss/SPECPROD/SURVEY/VERSION/LSScats`` contains the directories for ``full`` (including information on all targets) and ``clustering`` (only information needed for clustering measurements and weights/cuts to optimize those clustering measurements). Files detailing the estimated n(z) in units of (h/Mpc)^3 are also here.
+``$DESI_ROOT/vac/edr/lss/v2.0/LSScats`` contains the directories for ``full`` (including information on all targets) and ``clustering`` (only information needed for clustering measurements and weights/cuts to optimize those clustering measurements). Files detailing the estimated n(z) in units of (h/Mpc)^3 are also here.
 
 Catalogs were created for the four extra-galactic DESI target types: LRG, ELG, QSO, and BGS. For all except QSO, catalogs are produced for additional sub-type definitions. In the cases where the sub-type corresponds to a bitname from `SV3 targeting`_, we use that name:
 

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/inputs_wspec/index.rst

@@ -0,0 +1,12 @@
+========
+UnivUNUM
+========
+
+``$DESI_ROOT/vac/edr/lss/v2.0/altmtl/UnivUNUM`` refers to 128 Univ ``{UNUM}`` directories. Each contains a ``dark`` and a ``bright`` directory. Each of these contains the alternative MTL history for the particular seeding of subpriorities.
+
+.. toctree::
+   :maxdepth: 1
+
+   dark/index
+   bright/index
+

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/potential_assignments/index.rst

@@ -0,0 +1,12 @@
+======
+altmtl
+======
+
+``$DESI_ROOT/vac/edr/lss/v2.0/altmtl`` contains the Merged Target List (MTL) ledgers ( :ref:`see, e.g., <mtl_ledger>`) with subpriorities re-seeded, but following the fiber-specific observational information on whether the target assigned to a particular positioner was successful. There are 128 realizations, each in a separate ``Univ{UNUM}`` directory, each of which is split into ``dark`` and ``bright`` programs.
+
+.. toctree::
+   :maxdepth: 1
+
+   UnivUNUM/index
+
+

doc/DESI_ROOT/vac/RELEASE/lss/index.rst

@@ -0,0 +1,13 @@
+=======
+v2.0
+=======
+
+``$DESI_ROOT/vac/edr/lss/v2.0`` contains directories for the end-products LSS catalogs (``LSScats``), inputs based on processing of the spectroscopic reductions (``inputs_wspec``) and from processing of fiberassign information (``potential_assignments``), as well as the Alternative Merged Target List (MTL) ledgers (``altmtl``).  
+
+.. toctree::
+   :maxdepth: 1
+
+   altmtl/index
+   LSScats/index
+   inputs_wspec/index
+   potential_assignments/index

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/LSScats/clustering/clustering_dat.rst doc/DESI_ROOT/vac/RELEASE/lss/v2.0/LSScats/clustering/clustering_dat.rst

@@ -0,0 +1,14 @@
+.. _inputs_wspec:
+
+============
+inputs_wspec
+============
+
+``$DESI_ROOT/vac/edr/lss/v2.0/inputs_wspec`` contains directories for data and randoms including the precursor files of the LSScats. It includes files with information about the observed location+tile, merged files between mtl files, spectroscopic information and potential assigments, as well as other suplementary output files, for example, a list of bad fibers in the LRG and BGS samples and the ELG dark time emission line outputs. 
+
+
+.. toctree::
+   :maxdepth: 1
+
+   data/index
+   random/index

doc/DESI_ROOT/vac/RELEASE/lss/VERSION/LSScats/clustering/clustering_ran.rst doc/DESI_ROOT/vac/RELEASE/lss/v2.0/LSScats/clustering/clustering_ran.rst

@@ -0,0 +1,12 @@
+=====================
+potential_assignments
+=====================
+
+``$DESI_ROOT/vac/edr/lss/v2.0/potential_assignments`` contains directories for the potential assigment outputs from fiber assigment, reading from :ref:`$DESI_TARGET/fiberassign<fiberassign>` and concatenated into single files, for data and randoms separately. In the case of randoms, it also contains the complete fiber assigment files run with the same configuration as with the data. 
+
+
+.. toctree::
+   :maxdepth: 1
+
+   data/index
+   random/index