Merge pull request #888 from I2PC/release-3.24.06

Release 3.24.06

.clang-format

@@ -0,0 +1,82 @@
+Language: Cpp
+BasedOnStyle: Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: None
+AlignOperands: Align
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: Empty
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortIfStatementsOnASingleLine: Never  # To avoid conflict, set this "Never" and each "if statement" should include brace when coding
+AllowShortLambdasOnASingleLine: Inline
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterCaseLabel: false
+  AfterClass: false
+  AfterStruct: false
+  AfterControlStatement: Never
+  AfterEnum: false
+  AfterFunction: true
+  AfterNamespace: false
+  AfterUnion: false
+  AfterExternBlock: false
+  BeforeCatch: false
+  BeforeElse: false
+  BeforeLambdaBody: false
+  IndentBraces: false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakInheritanceList: BeforeColon
+ColumnLimit: 120
+CompactNamespaces: false
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: true  # Make sure the * or & align on the left
+ReferenceAlignment: Right
+EmptyLineBeforeAccessModifier: LogicalBlock
+FixNamespaceComments: true
+IncludeBlocks: Preserve
+IndentCaseLabels: true
+IndentPPDirectives: None
+IndentWidth: 4
+KeepEmptyLinesAtTheStartOfBlocks: true
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: Inner
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PointerAlignment: Left
+ReflowComments: false
+SeparateDefinitionBlocks: Always   # Only support for clang-format 14
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceBeforeSquareBrackets: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: Latest
+TabWidth: 4
+UseTab: Always
+

.github/workflows/build.yml

@@ -12,6 +12,8 @@ jobs:
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-22.04
+    env:
+      SEND_INSTALLATION_STATISTICS: "False"
     steps:
       # Installing apt dependencies
       - name: Install dependencies
@@ -20,7 +22,7 @@ jobs:
           sudo apt-get install -y libfftw3-dev libopenmpi-dev libhdf5-dev libtiff5-dev python3-numpy python3-dev libsqlite3-dev default-jdk git cmake libopencv-dev openmpi-bin
       
       # Setting up Python
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@main
         with:
           python-version: '3.9.15' # Version range or exact version of a Python version to use, using SemVer's version range syntax
 
@@ -32,18 +34,18 @@ jobs:
            pip install scons numpy
 
        # Installing CUDA                
-      - uses: Jimver/cuda-toolkit@v0.2.11
+      - uses: Jimver/cuda-toolkit@master
         id: cuda-toolkit
         with:
           cuda: '11.8.0'
           method: network
           sub-packages: '["nvcc", "toolkit"]'
 
       # Using CCache to speed C/C++ compilation
-      - uses: hendrikmuhs/ccache-action@v1.2
+      - uses: hendrikmuhs/ccache-action@main
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@main
         with:
             fetch-depth: 0
 

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v14.0.6
+  hooks:
+  - id: clang-format
+    types_or: [c++, c, cuda]

CHANGELOG.md

@@ -1,4 +1,43 @@
-   ## Release 3.23.11 - Nereus
+   ## Release 3.24.06 - O...
+   ### Xmipp Programs 
+   - New programs
+      - xtomo tigre reconstruction: This program provides a variety of algorithms to reconstruct tomogram from a set of tilt series
+      - graph_max_cut: split volume program
+      - tomo_simulate_tilt_series: simualtion of ts, tomograms and coordinates
+   - Programs updated
+      - Deep_center: interface simplified, calculate shift for particles
+      - deep_misalignment_detection: update model
+      - pdb_label_from_volume:Added CIF format support
+      - resolution_monotomo: Fast subtomo extraction
+      - resolution_monotomo: accelarating monotomo with float
+      - tomogram_reconstruction: tigre reconstruction added
+      - tomo_extract_subtomograms: solving some bugs and enhancing performance
+      - tomo_extract_particlestacks: solving some bugs and enhancing performance
+   - Programs fixed
+      - movie_estimate_gain: Initialize sigma values
+      - resolution_localfilter: double not integer
+      - movie_estimate_gain: Initialize sigma values
+      - project_tomography: internal loop
+      - pdb: Fixed PDB write function when no categories are present
+      - fourier_filter:Fix WEDGE option in FourierFilter
+      - resolution_pdb_bfactor:fix unaccounted column in res bfac pdb
+      - fourier_filter: Fixing missing cone
+   ### Installation and user guide
+   - Fixed PyXmipp installation
+   - Update pythorch version on DLTK pyTorch enviroment
+   - Fix DLTK installation
+   - Removed force flag on conda installations (new conda version)
+   ### More Xmipp 
+   - API for collecting xmipp installation statistics
+   - Local average added: Now the micrograph scissor annotates the local intensity value around the particles in the original micrographs.
+   - Added support for half precision float micrographs
+   - Wipe out memory ouptut in cuFFT
+   - Deprecated deep_denoising
+   - Fix for rare axis orderings in MRC/MAP files
+   - Adding fixed extension to tomo
+
+
+ ## Release 3.23.11 - Nereus
    ### Xmipp Programs 
 
    - New programs

README.md

@@ -12,7 +12,7 @@ This is the main repository, which contains the majority of the source code for
 
 
 ## Getting started
-The recommended way for users (not developers) to install and use Xmipp is via the [Scipion](http://scipion.i2pc.es/) framework, where you can use Xmipp with other Cryo-EM-related software. Xmipp  will be installed during Scipion installation (pay attemption on the -noXmipp flag). The Scipion installer should take care of all dependencies for you, however, you can make its life easier if you have your compiler, CUDA and HDF5 library ready and available in the standard paths. Read below for more details about these softwares requirements. Follow the official [installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html#installation) of Scipion for more details.
+To have a complete overview about Xmipp please visit the [documentation web](https://i2pc.github.io/docs/). The recommended way for users (not developers) to install and use Xmipp is via the [Scipion](http://scipion.i2pc.es/) framework, where you can use Xmipp with other Cryo-EM-related software. Xmipp  will be installed during Scipion installation (pay attemption on the -noXmipp flag). The Scipion installer should take care of all dependencies for you, however, you can make its life easier if you have your compiler, CUDA and HDF5 library ready and available in the standard paths. Read below for more details about these softwares requirements. Follow the official [installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html#installation) of Scipion for more details.
 
 ## Installation requirements
 ### Supported OS