Release 3.24.12

.github/workflows/build.yml

@@ -6,59 +6,30 @@ on:
   pull_request:
     branches: [ devel, master ]
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   build:
-    # The type of runner that the job will run on
     runs-on: ubuntu-22.04
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    # Disabling shallow clone is recommended for improving relevancy of reporting
     steps:
-#      - name: Extract branch name
-#        shell: bash
-#        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
-#        id: extract_branch
-
-
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y scons libfftw3-dev libopenmpi-dev openmpi-bin libhdf5-dev python3-numpy python3-dev libtiff5-dev unzip libopencv-dev
+          sudo apt-get install -y libfftw3-dev libopenmpi-dev openmpi-bin libhdf5-dev python3-numpy python3-dev libtiff5-dev unzip
 
       - name: Export CI variables
         run: echo "BUILD_DIR=CIBuild" >> $GITHUB_ENV
 
       # Using CCache to speed C/C++ compilation
-      - uses: hendrikmuhs/[email protected]
-
-      # Installing CUDA
-#      - uses: Jimver/[email protected]
-#        id: cuda-toolkit
-#        with:
-#          cuda: '11.8.0'
-#          method: network
-#          sub-packages: '["nvcc", "toolkit"]'
+      - 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
 
-      - name: Fetching Xmipp
-        run: ./scripts/ci_build
-
-      - name: Getting xmipp.conf
-        run: ./xmipp config #all br=${{ steps.extract_branch.outputs.branch }} noAsk
-        working-directory: ${{ env.BUILD_DIR }}
-        env:
-          CIBuild: 1
-          BUILD_TESTS: True
-
       # If we got here, Xmipp can be build with this xmippCore
       # Build only the core to be able to run the static code analysis
       - name: Compile XmippCore
         run: |
-          cp ${BUILD_DIR}/xmipp.conf ./
-          python3 $(which scons) . -j4
+          cmake -S . -B build/ -DXMIPP_VERSIONS_FILE=build/versions.txt
+          cmake --build build/ -j 4
+

.github/workflows/release.yml

@@ -0,0 +1,33 @@
+name: Release new version
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  generate-new-release:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout repository
+      uses: actions/checkout@main
+
+    - name: Retrieve tag name, release name & changelog
+      run: |
+        echo "TAG_NAME=$(python ./scripts/version.py)" >> $GITHUB_OUTPUT
+        awk '/## Release/{if (p) exit; p=1} p' CHANGELOG.md | tail -n +2 > latest_changelog.md
+        echo "RELEASE_NAME=$(python ./scripts/version.py --keep-format)" >> $GITHUB_OUTPUT
+      id: variables
+
+    - name: Generate tag
+      id: tag_version
+      uses: mathieudutour/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        custom_tag: ${{ steps.variables.outputs.TAG_NAME }}
+
+    - name: Create a GitHub release
+      uses: ncipollo/release-action@main
+      with:
+        tag: ${{ steps.tag_version.outputs.new_tag }}
+        name: ${{ steps.variables.outputs.RELEASE_NAME }}
+        bodyFile: latest_changelog.md

.gitignore

@@ -26,6 +26,7 @@
 
 #### Python
 *.pyc
+__pycache__
 
 #### Eclipse and so on
 .project
@@ -34,9 +35,6 @@
 .classpath
 .idea
 
-# Scons auxiliary files
-.sconsign.dblite
-
 # Other
 gmon.out
 *~
@@ -55,4 +53,6 @@ gmon.out
 /Debug/
 
 # VS Code
-.vscode
+.vscode
+
+build/

CHANGELOG.md

@@ -1,10 +1,8 @@
-## devel
+## Release 3.24.12 - Poseidon
+   - Details about the changes on [Xmipp repository](https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md)
 
-## ms_fix_pixelsize
-11/August/2023: Fixed pixel size not being properly stored
+## Release 3.24.06 - Oceanus
+   - Details about the changes on [Xmipp repository](https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md)
 
-## ms_transpose_MRC
-11/August/2023: MRC files with axis order other than default is now supported
-
-## co_MRCFileFormat
-22/July/2021: .ali, .preali, .rec added to the set of MRC file
+## Release 3.23.11 - Nereus
+   - Details about the changes on [Xmipp repository](https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md)

CMakeLists.txt

@@ -0,0 +1,117 @@
+#***************************************************************************
+# Authors:     Oier Lauzirika Zarrabeitia ([email protected])
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# 02111-1307  USA
+#
+#  All comments concerning this program package may be sent to the
+#  e-mail address '[email protected]'
+# ***************************************************************************
+
+cmake_minimum_required(VERSION 3.16)
+
+# Define the project
+project(
+  XmippCore
+	VERSION 3.24.06
+	LANGUAGES C CXX
+)
+
+include(GNUInstallDirs)
+
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules)
+
+# Find dependencies
+find_package(HDF5 1.8 COMPONENTS C CXX REQUIRED)
+if(XMIPP_VERSIONS_FILE)
+	file(APPEND ${XMIPP_VERSIONS_FILE} "HDF5=${HDF5_VERSION}\n")
+endif()
+
+find_package(TIFF REQUIRED)
+
+find_package(JPEG REQUIRED)
+if(XMIPP_VERSIONS_FILE)
+	file(APPEND ${XMIPP_VERSIONS_FILE} "JPEG=${JPEG_VERSION}\n")
+endif()
+
+find_package(SQLite3 REQUIRED)
+if(XMIPP_VERSIONS_FILE)
+	file(APPEND ${XMIPP_VERSIONS_FILE} "SQLite3=${SQLite3_VERSION}\n")
+endif()
+
+find_package(Threads REQUIRED)
+
+find_package(FFTW REQUIRED)
+
+find_library(LIBSTDCXX_LIBRARY stdc++)
+
+# Register all source and header files
+file(GLOB_RECURSE 
+	SOURCES 
+		${CMAKE_CURRENT_SOURCE_DIR}/core/*.cpp 
+		${CMAKE_CURRENT_SOURCE_DIR}/core/*.cc
+		${CMAKE_CURRENT_SOURCE_DIR}/core/*.c
+)
+file(GLOB_RECURSE 
+	HEADERS 
+		${PROJECT_SOURCE_DIR}/include/*.h 
+		${PROJECT_SOURCE_DIR}/include/*.hpp
+)
+
+# Create the shared library
+add_library(${PROJECT_NAME} SHARED ${SOURCES})
+set_target_properties(
+	${PROJECT_NAME} PROPERTIES 
+	CXX_STANDARD 17
+)
+target_include_directories(
+	${PROJECT_NAME} 
+	PUBLIC 
+		${CMAKE_CURRENT_SOURCE_DIR}
+		${HDF5_INCLUDE_DIRS}
+)
+target_precompile_headers(
+	${PROJECT_NAME} 
+	PUBLIC ${HEADERS}
+)
+target_link_libraries(
+	${PROJECT_NAME}
+	PUBLIC
+		TIFF::TIFF
+		SQLite::SQLite3
+		JPEG::JPEG
+		Threads::Threads
+		FFTW::Double
+		FFTW::Float
+		FFTW::DoubleThreads
+		FFTW::FloatThreads
+		${HDF5_LIBRARIES}
+)
+
+if(LIBSTDCXX_LIBRARY)
+	message("Linking to libstdc++ at ${LIBSTDCXX_LIBRARY}")
+	target_link_libraries(
+        	${PROJECT_NAME}
+        	PUBLIC
+			${LIBSTDCXX_LIBRARY}
+	)
+
+endif()
+
+# Install library's binary files and headers
+install(
+	TARGETS ${PROJECT_NAME}
+ 	LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+)