.

docs/Utils/Deprecating-programs-and-protocols/index.rst

@@ -5,18 +5,15 @@ Deprecating programs
 
 We have a "legacy" folder with programs and code that is outdated. Some of the reasons we did this are uninteresting code, programs that do not have a protocol and are not used, and programs that are not used and are difficult to maintain. You can `visit the issue <https://github.com/I2PC/xmipp/issues/681>`_ with more information and the list of deprecated programs and protocols can be found `here <https://github.com/I2PC/xmipp/wiki/List-of-deprecated-programs-and-protocols>`_.
 
-We managed to speed up the installation time by 25%, and we were also able to reduce the lines of code to maintain and the number of code smells that were reported by `SonarCloud <https://sonarcloud.io/project/issues?id=Xmipp&languages=cpp&resolved=false&rules=cpp%3AS1172&types=CODE_SMELL>`_.
+We managed to speed up the installation time by 25%, and we were also able to reduce the lines of code to maintain and the number of code smells that were reported by `SonarCloud <https://sonarcloud.io/projects>`_.
 
-However, it is possible to recover a program if anyone needs it. Here's how to do it:
-
-If you are an external user, please contact us (opening an issue is a good way, `see here <https://github.com/I2PC/xmipp/issues/new>`_).
-
-If you are part of the Xmipp team:
-
-Each deprecated program has an associated `commit <https://github.com/I2PC/xmipp/pull/685>`_. Visit it and review all the changes the program needs to be recovered. Here are some clues:
+However, it is possible to recover a program if anyone needs it. If you are an external user,
+ please contact us (opening an issue is a good way, `see here <https://github.com/I2PC/xmipp/issues/new>`_). 
+ If you are part of the Xmipp team: Each deprecated program has an associated `commit <https://github.com/I2PC/xmipp/pull/685>`_. 
+ Visit it and review all the changes the program needs to be recovered. Here are some clues:
 
 - Go to the legacy folder and
-- Search in the _applications/programs_ folder for the folder of your program.
-- Search in the _libraries_ folder for the script of your program.
-- Most of the deprecated programs had a test; go to the commit and search in _tests_programs_xmipp.py_ for the test of your program.
+- Search in the applications/programs folder for the folder of your program.
+- Search in the libraries folder for the script of your program.
+- Most of the deprecated programs had a test; go to the commit and search in tests_programs_xmipp.py for the test of your program.
 - The last step is to remove the program that has been recovered from this list (see listDeprecatedFiles() in utils.py).

docs/XmippField/ListOfPublications/index.rst

@@ -107,6 +107,7 @@ Jin2014
 
 Jonic2005
 ^^^^^^^^^
+::
 
 -  title = Spline-based image-to-volume registration for
    three-dimensional electron microscopy
@@ -205,6 +206,7 @@ PascualMontano2002
 
 Rosenthal2003
 ^^^^^^^^^^^^^
+::
 
 -  Author=Rosenthal P. B. and Henderson R.
 -  Title=Optimal determination of particle orientation absolute hand and
@@ -238,6 +240,8 @@ Scheres2005a
 Scheres2005b
 ^^^^^^^^^^
 
+::
+   
 -  author = Scheres Sjors H.W. and Valle Mikel and Carazo José-María
 -  title = Fast maximum-likelihood refinement of electron microscopy
    images.

docs/XmippField/Releases-scipion-em-xmippTomo/index.rst

@@ -0,0 +1,20 @@
+
+Releases scipion-em-xmippTomo
+=========================
+
+V3.23.07 - Morpheus
+--------------------------
+   - New protocols
+      - project_subtomograms (for obtaining sobtomogram projections)
+      - extract_particlestacks (extract from tilt series and SetOfTiltSeriesParticle)
+      - denoising_confidence
+      - extract_particlestacks
+      - deep_misalignment_detection (misalignment detection in tomographic reconstructions from high-contrast regions)
+      - peak_high_contrast (for detecting high contrast regions in tomographic reconstruction)
+   - Protocols updated 
+      - project_top: Subtomo projector compatible with hdf stacks. Test fixed. Projections keep orientation, Ignore alignments in projection
+      - subtomo_map_back, score_coordinates: Mapback scales any reference to match the tomogram sampling
+      - subtomo_map_back: Mapback waits now when scheduled and not the reference is needed,  works with 3d classes, works with "other tomograms"
+      - project_subtomograms: Parallelized protocol 
+- Update requirements.txt
+- Fix tests: protocol_extract_subtomos, monotomo, crop, resize, xmipptomo

docs/index.rst

@@ -21,8 +21,9 @@ The recommended way for users (not developers) to install and use Xmipp is via t
     :hidden:
     :caption: Xmipp-Field
 
-    XmippField/Releases-scipion-em-xmipp/index
     XmippField/Releases-xmipp-program/index
+    XmippField/Releases-scipion-em-xmipp/index
+    XmippField/Releases-scipion-em-xmippTomo/index
     XmippField/ListOfPublications/index