Remove link to user documentation

the documentation is not ready:
remove link

.github/workflows/release.yml

@@ -43,45 +43,41 @@ jobs:
         if: startsWith(matrix.os, 'macos')
         run: tools/install_macos_sdk.sh
 
-      - name: Build Conda Package
+      - name: Build and Upload Conda Package
         shell: bash -el {0}
         run: |
           mamba install conda-build boa anaconda-client
           cd conda-recipe
-          
           # Use older conda_build_config -> boost-cpp 1.78
           curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
           # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
-          conda mambabuild . --output-folder ../conda-bld
-
-      - name: Upload Conda Package
-        shell: bash -el {0}
-        run: |
+          conda mambabuild . --output-folder conda-bld
           anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u tpeulen --force conda-bld/**/*.tar.bz2
+          
 
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
-
-    steps:
-      - uses: actions/checkout@v4
-
-      # Used to host cibuildwheel
-      - uses: actions/setup-python@v3
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.16.5
-
-      - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
-        # to supply options, put them in 'env', like:
-        # env:
-        #   CIBW_SOME_OPTION: value
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: ./wheelhouse/*.whl
+#  build_wheels:
+#    name: Build wheels on ${{ matrix.os }}
+#    runs-on: ${{ matrix.os }}
+#    strategy:
+#      matrix:
+#        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#
+#      # Used to host cibuildwheel
+#      - uses: actions/setup-python@v3
+#
+#      - name: Install cibuildwheel
+#        run: python -m pip install cibuildwheel==2.16.5
+#
+#      - name: Build wheels
+#        run: python -m cibuildwheel --output-dir wheelhouse
+#        # to supply options, put them in 'env', like:
+#        # env:
+#        #   CIBW_SOME_OPTION: value
+#
+#      - uses: actions/upload-artifact@v4
+#        with:
+#          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+#          path: ./wheelhouse/*.whl

.gitlab-ci.yml

@@ -61,9 +61,12 @@ conda:build:windows:
   <<: *build
   tags:
     - win
-  script:
-    - conda activate base
-    - .\tools\build.bat
+  script: |
+    conda activate base
+    copy /Y tools\.condarc %userprofile%
+    copy /Y tools\conda_build_config.yaml conda_build_config.yaml
+    mamba install -y boa doxygen cmake
+    conda mambabuild conda-recipe --output-folder bld-dir
 
 conda:test:linux:
   stage: test

README.md

@@ -177,4 +177,4 @@ are not supported.
 Copyright 2007-2024 tttrlib developers.
 Licensed under the BSD-3-Clause
 
-[3]: https://github.com/fluorescence-tools/tttrlib/doc/logos/mashup.png "tttrlib FLIM"
+[3]: https://github.com/Fluorescence-Tools/tttrlib/blob/master/doc/logos/mashup.png?raw=true "tttrlib FLIM"

conda-recipe/meta.yaml

@@ -36,7 +36,7 @@ requirements:
     - numpy
   run:
     - python
-    - {{ pin_compatible('numpy') }}
+    - {{ pin_compatible('numpy', max_pin='x.x') }}
     - boost-cpp
     - hdf5
     - tqdm

examples/correlation/plot_confocor3_two_ch_correlation.py

@@ -25,7 +25,7 @@
 # ------------
 # The photon data registered by different detectors are saved in separate files.
 # Read the data of all channels that should be correlated into separate containers.
-fns = [str(p) for p in pathlib.Path('../../tttr-data/cz/fcs').glob('5a6ce6a348a08e3da9f7c0ab4ee0ce94_R1_P1_K1_Ch*.raw')]
+fns = [str(p) for p in pathlib.Path('../../tttr-data/cz/fcs').glob('b02f1b794ef4110bcde513983548ee4b_R1_P12_K1_Ch*.raw')]
 tttr_data = [tttrlib.TTTR(fn, 'CZ-RAW') for fn in fns]
 
 #%%

include/CLSMFrame.h

@@ -20,120 +20,67 @@ class CLSMFrame: public TTTRSelection{
 
 public:
 
-    /*!
-     * \brief Get a vector containing pointers to the CLSMLines in the CLSMFrame.
-     *
-     * This function returns a vector containing pointers to the CLSMLines stored
-     * in the CLSMFrame.
-     *
-     * @return A vector of CLSMLine pointers.
-     */
-    std::vector<CLSMLine*> get_lines() {
+    std::vector<CLSMLine*> get_lines(){
         return lines;
     }
 
-
-    /*!
-     * \brief Get the number of lines in the CLSMFrame.
-     *
-     * @return The number of lines in the CLSMFrame.
-     */
+    /// Get the number of lines in the CLSMFrame
     size_t size() final{
         return lines.size();
     }
 
-    /*!
-     * \brief Default constructor for CLSMFrame.
-     *
-     * This constructor creates an empty CLSMFrame object.
-     */
     CLSMFrame();
 
     /*!
-     * \brief Copy constructor for CLSMFrame.
+     * Copy constructor
      *
-     * @param old_frame [in] Reference to the existing CLSMFrame object to be copied.
-     * @param fill [in] If set to false, the content of the pixels is not copied.
+     * @param fill if set to false the content of the pixels is not copied
      */
-    CLSMFrame(const CLSMFrame& old_frame, bool fill = true) : TTTRSelection(old_frame) {
-        for (auto& l : old_frame.lines) {
+    CLSMFrame(const CLSMFrame& old_frame, bool fill = true) : TTTRSelection(old_frame){
+        for(auto l: old_frame.lines){
             lines.emplace_back(new CLSMLine(*l, fill));
         }
     }
 
-    /*!
-     * \brief Destructor for CLSMFrame.
-     *
-     * Deletes dynamically allocated CLSMLine objects in the lines vector.
-     */
-    virtual ~CLSMFrame() {
-        for (auto& l : lines) {
-            delete l;
+    virtual ~CLSMFrame(){
+        for(auto l: lines){
+            delete(l);
         }
     }
 
-    /*!
-     * \brief Constructor for CLSMFrame with specified frame indices and a TTTR object.
-     *
-     * This constructor initializes a CLSMFrame object with the specified frame indices
-     * (frame_start to frame_stop) using a TTTR (Time-Tagged Time-Resolved) data object.
-     *
-     * @param frame_start [in] The starting frame index for the CLSMFrame.
-     * @param frame_stop [in] The stopping frame index for the CLSMFrame.
-     * @param tttr [in] Pointer to a TTTR object containing time-resolved data.
-     */
     explicit CLSMFrame(size_t frame_start, size_t frame_stop, TTTR* tttr);
 
     /*!
-     * \brief Append a CLSMLine to the current CLSMFrame.
-     *
-     * @param line [in] Pointer to the CLSMLine to be appended.
+     * Append a line to the current frame
+     * @param line
      */
-    void append(CLSMLine* line);
+    void append(CLSMLine * line);
 
     /*!
-     * \brief Retrieve a pointer to the CLSMLine with the specified line number.
      *
-     * @param i_line [in] The line number.
-     * @return A pointer to the CLSMLine with the requested number.
+     * @param i_line the line number
+     * @return a pointer to the line with requested number
      */
-    CLSMLine* operator[](unsigned int i_line) {
+    CLSMLine* operator[](unsigned int i_line){
         return lines[i_line];
     }
 
-    /*!
-     * \brief Add the corresponding CLSMLines of another CLSMFrame to the current frame.
-     *
-     * This operator performs element-wise addition, adding each CLSMLine of the
-     * right-hand side (rhs) CLSMFrame to the corresponding CLSMLine of the current frame.
-     *
-     * @param rhs [in] The right-hand side CLSMFrame to be added.
-     * @return A reference to the modified current CLSMFrame.
-     */
-    CLSMFrame& operator+=(const CLSMFrame& rhs) {
-        for (std::size_t i = 0; i < lines.size(); ++i) {
-            *lines[i] += *rhs.lines[i];
+    CLSMFrame& operator+=(const CLSMFrame& rhs){
+        int i = 0;
+        for(auto l: lines){
+            *l += *rhs.lines[i];
         }
         return *this;
     }
 
     /*!
-     * \brief Crop the CLSMFrame by selecting a region of lines and pixels.
-     *
-     * This function crops the CLSMFrame by selecting a specific range of lines
-     * (from line_start to line_stop) and pixels (from pixel_start to pixel_stop).
-     *
-     * @param line_start [in] The starting line index for cropping.
-     * @param line_stop [in] The stopping line index for cropping.
-     * @param pixel_start [in] The starting pixel index for cropping.
-     * @param pixel_stop [in] The stopping pixel index for cropping.
+     * Crops a frame
      */
     void crop(
-        int line_start, int line_stop,
-        int pixel_start, int pixel_stop
+            int line_start, int line_stop,
+            int pixel_start, int pixel_stop
     );
 
-
 };