Update for Numpy 2.0

.github/workflows/tests.yml

@@ -1,80 +1,75 @@
 name: Tests
 
 on: [push, pull_request]
+
 jobs:
+  Download:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: conda-incubator/setup-miniconda@v4
+        with:
+          auto-update-conda: true
+          channels: conda-forge
+          python-version: "3.12"
+          activate-environment: test
+      - name: Install Pooch
+        shell: bash -l {0}
+        run: conda install -c conda-forge pooch
+      - name: Download Files
+        shell: bash -l {0}
+        run: |
+          cd tests
+          python fetch_files.py
+      - uses: actions/cache@v6
+        id: filecache
+        with:
+          path: ./tests/data
+          enableCrossOsArchive: true
+          key: testfiles
   build:
-    runs-on: ${{matrix.os}}
+    needs: Download
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, windows-latest, macos-latest]
-        python-version: ["3.8", "3.10", "3.12"]
-        exclude:
-          - os: macOS-latest
-            python-version: "3.7"
-          - os: windows-latest
-            python-version: "3.7"           
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.12", "3.14"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
           fetch-depth: 0
-      # - name: Setup Python ${{matrix.python-version}}
-      #   uses: actions/setup-python@v4
-      #   with:
-      #     python-version: ${{matrix.python-version}}
-      - uses: conda-incubator/setup-miniconda@v3
+      - name: Restore Cached Files
+        id: cache-action
+        uses: actions/cache/restore@v6
+        with:
+          path: ./tests/data
+          key: testfiles
+          enableCrossOsArchive: true
+      - name: Install Conda
+        uses: conda-incubator/setup-miniconda@v4
         with:
           auto-update-conda: true
-          activate-environment: test
           channels: conda-forge
           python-version: ${{ matrix.python-version }}
-      - name: Upgrade pip
+          activate_environment: test
+      - name: Apple Silicon Oddities
+        if: matrix.os == 'macos-latest'
         shell: bash -l {0}
-        run: python -m pip install --upgrade pip
-      - name: MacOS install hdf5 dependencies
-        if: runner.os == 'macOS'
         run: |
-          brew install hdf5
-          export HDF5_DIR=/usr/local/
-          export BLOSC_DIR=/usr/local/
+          brew install c-blosc hdf5
+          export HDF5_DIF=/opt/homebrew/opt/hdf5
+          export BLOSC_DIR=/opt/homebrew/opt/c-blosc
       - name: Install Dependencies
         shell: bash -l {0}
         run: |
-          conda install -c conda-forge cython numpy numba nbconvert pytest jupyter scipy pandas matplotlib pytables phconvert lmfit pybroom seaborn setuptools pyqt
-      - name: Install project
-        shell: bash -l {0}
-        run: |
-          python -m pip install . 
-      - name: Download files Unix
-        if: runner.os != 'Windows'
-        shell: bash -l {0} 
-        run: |
-          cd notebooks
-          mkdir data
-          cd data
-          wget -N http://files.figshare.com/2182604/12d_New_30p_320mW_steer_3.hdf5
-          wget -N http://files.figshare.com/2182601/0023uLRpitc_NTP_20dT_0.5GndCl.hdf5
-          wget -N https://zenodo.org/record/5902313/files/HP3_TE150_SPC630.hdf5
-          wget -N https://zenodo.org/record/5902313/files/HP3_TE200_SPC630.hdf5
-          wget -N https://zenodo.org/record/5902313/files/HP3_TE250_SPC630.hdf5
-          wget -N https://zenodo.org/record/5902313/files/HP3_TE300_SPC630.hdf5
-          cd ../..
-      - name: Downlaod files Windows
-        if: runner.os == 'Windows'
+          conda install -c conda-forge pip
+          python -m pip install setuptools build
+          conda install -c conda-forge cython numpy numba nbconvert pytest jupyter scipy pandas matplotlib pytables phconvert lmfit pybroom seaborn pyqt pooch
+      - name: Install Project
         shell: bash -l {0}
-        run: |
-          cd notebooks
-          mkdir data
-          cd data
-          curl.exe -L --output 12d_New_30p_320mW_steer_3.hdf5 --url http://files.figshare.com/2182604/12d_New_30p_320mW_steer_3.hdf5
-          curl.exe -L --output 0023uLRpitc_NTP_20dT_0.5GndCl.hdf5 --url http://files.figshare.com/2182601/0023uLRpitc_NTP_20dT_0.5GndCl.hdf5
-          curl.exe -L --output HP3_TE150_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE150_SPC630.hdf5
-          curl.exe -L --output HP3_TE200_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE200_SPC630.hdf5
-          curl.exe -L --output HP3_TE250_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE250_SPC630.hdf5
-          curl.exe -L --output HP3_TE300_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE300_SPC630.hdf5
-          cd ..
-          cd ..
-
+        run:
+          pip install .
       - name: Test project
         shell: bash -l {0}
         run: |
@@ -83,3 +78,35 @@ jobs:
           cd ..
           cd tests
           python -m pytest
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: build
+    strategy:
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-14]
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Restore Cached Files
+        id: cache-action
+        uses: actions/cache/restore@v6
+        with:
+          path: ./tests/data
+          key: testfiles
+          enableCrossOsArchive: true
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v4.2.0
+        env:
+          CIBW_SKIP: "cp310-win_arm64"
+          CIBW_TEST_REQUIRES: pytest numpy matplotlib scipy pandas tables seaborn lmfit phconvert pooch
+          CIBW_BEFORE_TEST: python -m pip install pytest
+          CIBW_CACHE_PATH: $GITHUB_WORKSPACE/tests/data
+          CIBW_TEST_COMMAND: python -m pytest {package}/tests/ 
+          CIBW_TEST_SKIP: "*win* cp315-macosx_arm64 cp315t-macosx_* cp315t-manylinux_aarch64 *musllinux* cp315t-manylinux_x86_64 cp313-manylinux_aarch64"
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl

docs/source/absolute_beginner.rst

@@ -32,7 +32,7 @@ The installation should take a few seconds.
 If you notice any error please report it by opening a new issue on the
 `FRETBursts GitHub Issues <https://github.com/OpenSMFS/FRETBursts/issues>`_.
 
-Alternatively create an environment from one of our yaml files where we have verified compatibility of all versions of the software: :downlaod:`frbmin.yml <downloads/frbmin.yml>`
+Alternatively create an environment from one of our yaml files where we have verified compatibility of all versions of the software: :download:`frbmin.yml <downloads/frbmin.yml>`
 
 First download `frbmin.yml`
 

docs/source/downloads/frbcmplt.yml

@@ -5,6 +5,8 @@ channels:
 dependencies:
   - python=3.10
   - importlib_metadata
+  - setuptools
+  - build
   - pytest=7.4.0
   - cython=3.0.10
   - ipython=8.24.0

docs/source/index.rst

@@ -64,6 +64,11 @@ Single-molecule FRET burst analysis
     <br>
 
 
+**Attention** FRETBursts will only be minimally supported from now on.
+
+The package `smfBursts <https://smfbursts.readthedocs.io>`__ is replacing the functionality of FRETBursts.
+Users are recomended to start migrating their piplines.
+
 **FRETBursts** is an open-source
 python package for burst analysis of freely-diffusing
 `single-molecule FRET <https://en.wikipedia.org/wiki/Single-molecule_FRET>`__

fretbursts/burst_plot.py

@@ -63,7 +63,8 @@
 from .scroll_gui import ScrollingToolQT
 from . import gui_selection as gs
 
-
+# so compatible with old and new version of numpy
+trapz = np.trapezoid if hasattr(np, 'trapezoid') else np.trapz
 ##
 # Globals
 #
@@ -295,8 +296,8 @@ def _burst_info(d, ich, burst_index):
     burst = d.mburst[ich][burst_index]
     params = dict(
         b_index=burst_index,
-        start_ms=float(burst.start) * d.clk_p * 1e3,
-        width_ms=float(burst.width) * d.clk_p * 1e3,
+        start_ms=float(burst.start[0]) * d.clk_p * 1e3,
+        width_ms=float(burst.width[0]) * d.clk_p * 1e3,
         nt=d.nt[ich][burst_index],
         nd=d.nd[ich][burst_index],
         na=d.na[ich][burst_index],
@@ -1098,7 +1099,7 @@ def _fitted_E_plot(d, i=0, F=1, no_E=False, ax=None, show_model=True,
             ax2.fill_between(x, scale*y, lw=lw, alpha=alpha, edgecolor=color,
                              facecolor=fillcolor, zorder=10)
         if verbose:
-            print('Fit Integral:', np.trapz(scale*y, x))
+            print('Fit Integral:', trapz(scale*y, x))
 
     ax2.axvline(d.E_fit[i], lw=3, color=red, ls='--', alpha=0.6)
     xtext = 0.6 if d.E_fit[i] < 0.6 else 0.2
@@ -1779,17 +1780,17 @@ def hist_ph_delays(
 
     efun = lambda t, r: np.exp(-r*t)*r
     try:
-        re = bg.exp_fit(ph, tail_min_us=efit_tail_min_us)[0]
+        re = bg.exp_fit(ph, tail_min_us=efit_tail_min_us)[0][0]
         re_do = True
     except:
         re_do = False
     try:
-        rg = bg.exp_hist_fit(ph, tail_min_us=efit_tail_min_us, binw=hfit_bin_ms*1e-3)[0]
+        rg = bg.exp_hist_fit(ph, tail_min_us=efit_tail_min_us, binw=hfit_bin_ms*1e-3)[0][0]
         rg_do = True
     except:
         rg_do = False
     try:
-        rc = bg.exp_cdf_fit(ph, tail_min_us=efit_tail_min_us)[0]
+        rc = bg.exp_cdf_fit(ph, tail_min_us=efit_tail_min_us)[0][0]
         rc_do = True
     except:
         rc_do = False
@@ -1851,7 +1852,7 @@ def hist_mdelays(d, i=0, m=10, bins_s=(0, 10, 0.02), period=0,
     max_delay_th_F = m/rate_ch_kcps/d.F
 
     burst_domain = bin_x < max_delay_th_F
-    burst_integral = np.trapz(x=bin_x[burst_domain],
+    burst_integral = trapz(x=bin_x[burst_domain],
                               y=mdelays_hist_y[burst_domain])
 
     ax.set_title("I = %.1f %%" % (burst_integral*100), fontsize='small')