Merge pull request #494 from astrorama/develop

Release 0.18

Author: mkuemmel

.github/workflows/doc.yml

@@ -0,0 +1,48 @@
+name: doc
+
+on:
+  push:
+    paths:
+      - 'doc/**'
+      - 'SEImplementation/python/**'
+  pull_request:
+    paths:
+      - 'doc/**'
+      - 'SEImplementation/python/**'
+
+jobs:
+
+#############
+# Build doc #
+#############
+  build:
+    name: Make HTML doc
+    continue-on-error: false
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Install dependencies
+        run: pip3 install -r doc/requirements.txt
+
+      - name: Build
+        run: |
+          cd doc
+          make html
+
+      - name: Set destination dir
+        if: github.ref_name != 'master'
+        run: |
+          echo "DOC_DEST=${{ github.ref_name }}" >> $GITHUB_ENV
+
+      - name: Deploy
+        if: success()
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: doc-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: doc/build/html/
+          destination_dir: ${{ env.DOC_DEST }}
+

.gitignore

@@ -9,3 +9,5 @@ __pycache__
 /.settings/
 .pydevproject
 /packages
+/doc/build/
+/build/

CMakeLists.txt

@@ -6,4 +6,4 @@ find_package(ElementsProject)
 #---------------------------------------------------------------
 
 # Declare project name and version
-elements_project(SourceXtractorPlusPlus 0.17 USE Alexandria 2.25.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")
+elements_project(SourceXtractorPlusPlus 0.18 USE Alexandria 2.25.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")

ModelFitting/src/lib/Engine/GSLEngine.cpp

@@ -23,6 +23,7 @@
 #include "ModelFitting/Engine/GSLEngine.h"
 #include "ModelFitting/Engine/LeastSquareEngineManager.h"
 #include <ElementsKernel/Exception.h>
+#include <array>
 #include <chrono>
 #include <gsl/gsl_blas.h>
 #include <gsl/gsl_multifit_nlinear.h>

ModelFitting/src/lib/Engine/LevmarEngine.cpp

@@ -14,12 +14,13 @@
  * along with this library; if not, write to the Free Software Foundation, Inc.,
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
  */
-/** 
+/**
  * @file LevmarEngine.cpp
  * @date August 17, 2015
  * @author Nikolaos Apostolakos
  */
 
+#include <array>
 #include <cmath>
 #include <mutex>
 

README.md

@@ -59,3 +59,19 @@ And install with
 dnf install SourceXtractorPlusPlus
 ```
 
+## References and Acknowledgment
+
+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) 
+
+The ressources for the SourceXtractor++ development are mostly provided by funding from the Euclid satellite project 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
+the standard EC acknowledgement text.
+
+For scientific publication which are non EC papers we would be greatful if the following acknowledgment could be added:
+```
+This research made use of {\tt SourceXtractor++}\footnote{https://github.com/astrorama/SourceXtractorPlusPlus},
+an open source software package developed for the Euclid satellite project.
+```

SEFramework/SEFramework/Output/Output.h

@@ -1,4 +1,4 @@
-/** Copyright © 2019 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
+/** Copyright © 2019-2022 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
  *
  * This library is free software; you can redistribute it and/or modify it under
  * the terms of the GNU Lesser General Public License as published by the Free
@@ -24,30 +24,27 @@
 #ifndef _SEFRAMEWORK_PIPELINE_OUTPUT_H_
 #define _SEFRAMEWORK_PIPELINE_OUTPUT_H_
 
-#include "SEUtils/Observable.h"
-#include "SEFramework/Source/SourceInterface.h"
+#include "SEFramework/Pipeline/PipelineStage.h"
 #include "SEFramework/Source/SourceGroupInterface.h"
+#include "SEFramework/Source/SourceInterface.h"
 
 namespace SourceXtractor {
 
-class Output :
-    public Observer<std::shared_ptr<SourceInterface>>,
-    public Observer<std::shared_ptr<SourceGroupInterface>> {
+class Output : public PipelineReceiver<SourceGroupInterface> {
 
 public:
-
   virtual ~Output() = default;
 
-  void handleMessage(const std::shared_ptr<SourceInterface>& source) override {
-    outputSource(*source);
-  }
-
-  void handleMessage(const std::shared_ptr<SourceGroupInterface>& source_group) override {
+  void receiveSource(std::unique_ptr<SourceGroupInterface> source_group) override {
     for (auto& source : *source_group) {
       outputSource(source);
     }
   }
 
+  void receiveProcessSignal(const ProcessSourcesEvent&) override {
+    // pass
+  }
+
   virtual void outputSource(const SourceInterface& source) = 0;
 
   /// @return Number of elements written

SEFramework/SEFramework/Pipeline/Deblending.h

@@ -1,4 +1,4 @@
-/** Copyright © 2019 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
+/** Copyright © 2019-2022 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
  *
  * This library is free software; you can redistribute it and/or modify it under
  * the terms of the GNU Lesser General Public License as published by the Free
@@ -23,7 +23,7 @@
 #ifndef _SEFRAMEWORK_PIPELINE_DEBLENDING_H
 #define _SEFRAMEWORK_PIPELINE_DEBLENDING_H
 
-#include "SEUtils/Observable.h"
+#include "SEFramework/Pipeline/PipelineStage.h"
 #include "SEFramework/Source/SourceGroupInterface.h"
 #include "SEFramework/Task/TaskProvider.h"
 
@@ -53,8 +53,7 @@ class DeblendStep {
  * for deblending the group.
  *
  */
-class Deblending : public Observer<std::shared_ptr<SourceGroupInterface>>,
-  public Observable<std::shared_ptr<SourceGroupInterface>> {
+class Deblending : public PipelineReceiver<SourceGroupInterface>, public PipelineEmitter<SourceGroupInterface> {
 
 public:
 
@@ -65,7 +64,9 @@ class Deblending : public Observer<std::shared_ptr<SourceGroupInterface>>,
   explicit Deblending(std::vector<std::shared_ptr<DeblendStep>> deblend_steps);
 
   /// Handles a new SourceGroup, applies the DeblendSteps and then notifies the observers with the result
-  void handleMessage(const std::shared_ptr<SourceGroupInterface>& group) override;
+  void receiveSource(std::unique_ptr<SourceGroupInterface> group) override;
+
+  void receiveProcessSignal(const ProcessSourcesEvent& event) override;
 
   /// Returns the set of required properties to compute the deblending
   std::set<PropertyId> requiredProperties() const;

SEFramework/SEFramework/Pipeline/Measurement.h

@@ -1,4 +1,4 @@
-/** Copyright © 2019 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
+/** Copyright © 2019-2022 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
  *
  * This library is free software; you can redistribute it and/or modify it under
  * the terms of the GNU Lesser General Public License as published by the Free
@@ -25,18 +25,16 @@
 #define _SEFRAMEWORK_PIPELINE_MEASUREMENT_H_
 
 
-#include "SEUtils/Observable.h"
+#include "SEFramework/Pipeline/PipelineStage.h"
 #include "SEFramework/Source/SourceGroupInterface.h"
 #include "SEFramework/Task/TaskProvider.h"
 
 namespace SourceXtractor {
 
-class Measurement :
-    public Observer<std::shared_ptr<SourceGroupInterface>>,
-    public Observable<std::shared_ptr<SourceGroupInterface>> {
+class Measurement : public PipelineReceiver<SourceGroupInterface>, public PipelineEmitter<SourceGroupInterface> {
 public:
 
-  virtual ~Measurement() = default;
+  ~Measurement() override = default;
 
   virtual void startThreads() = 0;
   virtual void stopThreads() = 0;

SEFramework/SEFramework/Pipeline/Partition.h

@@ -23,7 +23,7 @@
 #ifndef _SEFRAMEWORK_PIPELINE_PARTITION_H
 #define _SEFRAMEWORK_PIPELINE_PARTITION_H
 
-#include "SEUtils/Observable.h"
+#include "SEFramework/Pipeline/PipelineStage.h"
 #include "SEFramework/Source/SourceInterface.h"
 
 namespace SourceXtractor {
@@ -36,13 +36,12 @@ namespace SourceXtractor {
  */
 class PartitionStep {
 public:
-
   /**
    * @brief Destructor
    */
   virtual ~PartitionStep() = default;
 
-  virtual std::vector<std::shared_ptr<SourceInterface>> partition(std::shared_ptr<SourceInterface> source) const = 0;
+  virtual std::vector<std::unique_ptr<SourceInterface>> partition(std::unique_ptr<SourceInterface> source) const = 0;
 };
 
 /**
@@ -54,10 +53,9 @@ class PartitionStep {
  * notified to the Observers one by one.
  *
  */
-class Partition : public Observer<std::shared_ptr<SourceInterface>>, public Observable<std::shared_ptr<SourceInterface>> {
+class Partition : public PipelineReceiver<SourceInterface>, public PipelineEmitter<SourceInterface> {
 
 public:
-
   /**
    * @brief Destructor
    */
@@ -66,8 +64,8 @@ class Partition : public Observer<std::shared_ptr<SourceInterface>>, public Obse
   /// Constructor - takes a vector of PartitionSteps to be applied in order
   explicit Partition(std::vector<std::shared_ptr<PartitionStep>> steps);
 
-  /// Handles a Source (applies PartitionSteps) and notifies the Observers for every Source in the final result
-  void handleMessage(const std::shared_ptr<SourceInterface>& source) override;
+  void receiveSource(std::unique_ptr<SourceInterface> source) override;
+  void receiveProcessSignal(const ProcessSourcesEvent& event) override;
 
 private:
   std::vector<std::shared_ptr<PartitionStep>> m_steps;
@@ -76,5 +74,4 @@ class Partition : public Observer<std::shared_ptr<SourceInterface>>, public Obse
 
 } /* namespace SourceXtractor */
 
-
 #endif