Merge pull request #40 from Fluorescence-Tools/development

Development

.github/workflows/conda-build.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.10"]
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v2

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10"]
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v2
@@ -49,35 +49,8 @@ jobs:
           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
+          # 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
           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

README.md

@@ -172,6 +172,13 @@ is recommended.
 Legacy 32-bit platforms and versions of programming languages, e.g., Python 2.7
 are not supported.
 
+## Citation
+If you use this software please also check the pre-print:
+>tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling;
+Thomas-Otavio Peulen, Katherina Hemmen, Annemarie Greife, Benjamin M. Webb, Suren Felekyan, Andrej Sali, 
+Claus A. M. Seidel, Hugo Sanabria, Katrin G. Heinze; [https://arxiv.org/abs/2402.17252](arXiv:2402.17252)
+>
+
 ## License
 
 Copyright 2007-2024 tttrlib developers.

conda-recipe/meta.yaml

@@ -6,8 +6,7 @@ package:
   version: {{ data.get('version') }}
 
 source:
-  path: ../
-#  git_url: ..
+  path: ..
 
 build:
   number: 1

ext/python/CLSMImage.py

@@ -102,7 +102,10 @@ def __init__(
         if tttr_data is not None:
             header = tttr_data.header
             self.header = header
-            settings_kwargs.update(self.read_clsm_settings(tttr_data))
+            try:
+                settings_kwargs.update(self.read_clsm_settings(tttr_data))
+            except:
+                print("Error reading TTTR CLSM header")
         # Overwrite if user defined inputs make sense
         if isinstance(marker_frame_start, int):
             settings_kwargs['marker_frame_start'] = [marker_frame_start]