merge develop

Author: marcschefer

.github/workflows/dependencies.txt

@@ -2,6 +2,8 @@ $PYTHON-devel
 $PYTHON-numpy
 $PYTHON-pytest
 $PYTHON-sphinx
+$PYTHON-setuptools
+$PYTHON-dnf
 CCfits-devel
 blas-devel
 $BOOST-$PYTHON-devel

.github/workflows/main.yml

@@ -47,9 +47,6 @@ jobs:
       matrix:
         os-type: [fedora]
         os-version: ${{ fromJson(needs.get_fedora_releases.outputs.stable) }}
-        include:
-          - os-type: centos
-            os-version: 7
     container: ${{ matrix.os-type }}:${{ matrix.os-version }}
     steps:
       - name: Checkout
@@ -58,14 +55,14 @@ jobs:
         id: package-version
         uses: astrorama/actions/[email protected]
       - name: Install dependencies
-        uses: astrorama/actions/setup-dependencies@v3.4
+        uses: astrorama/actions/setup-dependencies@v3.7
         with:
           dependency-list: .github/workflows/dependencies.txt
       - name: Build
         id: build
         uses: astrorama/actions/[email protected]
       - name: Upload RPM to GitHub
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.os-type }}${{ matrix.os-version }}
           path: ${{ steps.build.outputs.rpm-dir }}/*.rpm
@@ -85,6 +82,7 @@ jobs:
 # Run tests #
 #############
   litmus-test:
+    if: ${{ always() }}
     needs: [ build, get_fedora_releases ]
     runs-on: ubuntu-latest
     strategy:
@@ -95,21 +93,21 @@ jobs:
     container: ${{ matrix.os-type }}:${{ matrix.os-version }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install dependencies
-        uses: astrorama/actions/setup-dependencies@v3
+        uses: astrorama/actions/setup-dependencies@v3.7
         with:
           dependency-list: .github/workflows/test-dependencies.txt
       - name: Download RPM
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: ${{ matrix.os-type }}${{ matrix.os-version }}
       - name: Install SourceXtractor++
         run: yum install -y SourceXtractorPlusPlus*.x86_64.rpm
       - name: Run tests
         run: ./.github/workflows/run-litmus.sh
       - name: Upload reports and logs
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.os-type }}${{ matrix.os-version }}-test-results
           path: /tmp/sourcex/

.github/workflows/run-litmus.sh

@@ -6,6 +6,8 @@ TARGET_BRANCH=${GITHUB_BASE_REF:-$GITHUB_REF}
 # In the case of pull requests, this is the origin branch
 ORIGIN_BRANCH=${GITHUB_HEAD_REF:-$GITHUB_REF}
 
+export GIT_CLONE_PROTECTION_ACTIVE=false
+
 # Platform-specific configuration
 source /etc/os-release
 

.jenkinsFile

@@ -0,0 +1,3 @@
+#!groovy
+@Library('integration-library@release-9') _
+pipelineElements(artifactId:"SourceXtractorPlusPlus", groupId:"EL", component:'eden.3.0')

CMakeLists.txt

@@ -6,4 +6,4 @@ find_package(ElementsProject)
 #---------------------------------------------------------------
 
 # Declare project name and version
-elements_project(SourceXtractorPlusPlus 0.20 USE Alexandria 2.28 DESCRIPTION "SourceXtractor++, the next generation SExtractor")
+elements_project(SourceXtractorPlusPlus 1.1.0 USE Alexandria 2.32.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")

README.md

@@ -17,13 +17,13 @@ Documentation: https://astrorama.github.io/SourceXtractorPlusPlus/
 SourceXtractor++ is available on [Anaconda Cloud for Linux and MacOSX](https://anaconda.org/astrorama/sourcextractor)
 
 ```bash
-conda install -c conda-forge -c astrorama sourcextractor==0.19
+conda install -c conda-forge -c astrorama sourcextractor==1.0.3
  ```
 
 We would recommend, however, to install it into its own environment.
 
 ```bash
-conda create -n sourcex -c astrorama -c conda-forge sourcextractor==0.19
+conda create -n sourcex -c astrorama -c conda-forge sourcextractor==1.0.3
 conda activate sourcex
  ```
 
@@ -36,15 +36,15 @@ conda activate sourcex-dev
 
 We recommend always using an explicit version number as there is no guarantee that `conda` will install the latest version otherwise.
 
-## Fedora / CentOS
+## Fedora
 
-SourceXtractor++ is shipped directly in Fedora and CentOS. It can be installed simply as follows:
+SourceXtractor++ is shipped directly in Fedora. It can be installed simply as follows:
 
 ```bash
 sudo dnf install sourcextractor++
 ```
 
-[We also build our own RPMs as part of our CI setup](http://repository.astro.unige.ch/euclid/devel/)
+[We also build our own RPMs as part of our CI setup](http://repository.astro.unige.ch/euclid/)
 They can be installed adding a `.repo` file under `/etc/yum.repos.d` with the following content:
 
 ```ini
@@ -81,7 +81,8 @@ dnf install SourceXtractorPlusPlus
 ## Test Data Set
 
 A test data set covering various data reduction scenarios is available [here](https://cloud.physik.lmu.de/index.php/s/3K4KemBsw5y9yqd).
-I contains the input data, all relevant configuration files, the SourceXtractor++ commands and the expected output results for a reference.
+It contains the input data, all relevant configuration files, the SourceXtractor++ commands and the expected output results for a reference.
+The test data set is described as a [pre-print](http://arxiv.org/abs/2212.02428) for the corresponding conference proceedings.
 
 ## Discussion group for SourceXtractor++ users
 
@@ -96,7 +97,7 @@ join the group (if a google account is at hand) or to ask us to add you as a mem
 While we are working on several refereed papers describing SourceXtractor++ and its software architecture, the software package can be referenced with two ADASS conference proceedings:
 
 - [Bertin, E.; Schefer, M. ; Apostolakos, N. ; Álvarez-Ayllón, A.; Dubath, P. ; Kümmel, M.: 2020ASPC..527..461B](https://ui.adsabs.harvard.edu/abs/2020ASPC..527..461B/abstract)
-- [Kümmel, M. ; Bertin, E.; Schefer, M. ; Apostolakos, N. ; Álvarez-Ayllón, A.; Dubath, P.: 2020ASPC..527...29K](https://ui.adsabs.harvard.edu/abs/2020ASPC..527...29K/abstract) 
+- [Kümmel, M.; Álvarez-Ayllón, A.; Bertin, E.; Dubath, P.; Gavazzi, R.; Hartley, W.; Schefer, M.: 2022arXiv221202428K](https://ui.adsabs.harvard.edu/abs/2022arXiv221202428K/abstract) 
 
 Resources for the SourceXtractor++ development are in most part provided by funding from the [Euclid satellite project](https://www.euclid-ec.org/) via the various national agencies.
 For Euclid Consortium papers it is sufficient to point to the [SourceXtractor++ webpage](https://github.com/astrorama/SourceXtractorPlusPlus) and add

SEBenchmarks/src/program/BenchBackgroundModel.cpp

@@ -80,7 +80,7 @@ class BenchBackgroundModel : public Elements::Program {
     if (i != args.end())
       return i->second.as<std::string>();
     auto input = boost::filesystem::path(m_detection_config.getDetectionImagePath());
-    auto basename = input.leaf();
+    auto basename = input.filename();
     while (!basename.extension().empty())
       basename = basename.stem();
     auto algo = args.at("algorithm").as<std::string>();

SEFramework/SEFramework/Aperture/TransformedAperture.h

@@ -25,6 +25,7 @@
 #define _SEFRAMEWORK_SEFRAMEWORK_APERTURE_TRANSFORMEDAPERTURE_H
 
 #include "Aperture.h"
+#include <array>
 
 namespace SourceXtractor {
 

SEFramework/SEFramework/Image/Image.h

@@ -23,6 +23,7 @@
 #ifndef _SEFRAMEWORK_IMAGE_IMAGE_H
 #define _SEFRAMEWORK_IMAGE_IMAGE_H
 
+#include <cstdint>
 #include <memory>
 
 #include "SEUtils/Types.h"

SEFramework/SEFramework/Image/ImageChunk.h

@@ -24,9 +24,11 @@
 #ifndef _SEFRAMEWORK_IMAGE_IMAGECHUNK_H_
 #define _SEFRAMEWORK_IMAGE_IMAGECHUNK_H_
 
+#include "SEFramework/Image/Image.h"
+
 #include <cassert>
+#include <vector>
 
-#include "SEFramework/Image/Image.h"
 
 namespace SourceXtractor {