Update to 0.8.0 (#48)

* Fixed nsalex group data replicating first stream issue * Fixed issues with burstlib_ext * Full plotting updates and general bug fixex * Fix notebook kdeplot call * Fixed latest seaborn compatibility issues * Update readthedocs configurations * Minor plotting updates * Revert "Minor plotting updates" This reverts commit f1e7de5. * Update all np.flot to np.float64 * Fixed np.float -> float data type change * Update tests.yml * Update tests.yml * Update tests.yml * Shrink test environments * Update setup.cfg * Update tests.yml * Update tests.yml * Update setup.cfg * Update tests.yml * Update tests.yml * Added pyproject.toml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Fix np.hstack of iterable * Update tests.yml * Remove Python 3.6 tests * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update versioneer.py * Upaded versioneer.py to v 0.19 * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Make pyproject.toml primary config file * Updated to setuptools_scm * Hopefully working build * Add more pyproject.toml specs * Debugged and restructured scm management * Added kde scatter * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Fixed setuptools_scm version requirement in pyproject.toml * Fixed missing try import * Fixed import typo * Fixed plotting version requirements * Fixed pyproject.toml * Moved nbrun to notebooks directory * Fixed notebooks * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Update tests.yml * Test without conda * Update tests.yml * Run nbrun.py from notebooks folder * Update tests.yml * tests bypass indirect import path * Revert to non fb named c modules * Fixed setup.py typos * Revert to fretbursts._c for cython packages * Moved assumed location of pytest call * Update build_wheel.yml * Update build_wheel.yml * Deprecated python 3.6 support * Skip pure python cibw builds * Require matplotlib tests * Install pyqt in tests * Updated documentation with env yaml files * Use importlib for docs version * Update release notes for version release * Update release notes * Update build_wheels.yml * Update build_wheels.yml * Update build_wheels.yml
OpenSMFS · May 31, 2024 · 16a50fa · 16a50fa
1 parent c51b088
commit 16a50fa
Show file tree

Hide file tree

Showing 51 changed files with 1,162 additions and 2,862 deletions.
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
@@ -0,0 +1,32 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, windows-2022, macos-13, macos-14]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_SKIP: "pp*"
+          # CIBW_TEST_REQUIRES: pytest, numpy == 1.20.1, matplotlib, scipy, pandas, tables, numba, seaborn, lmfit, phconvert
+          # CIBW_BEFORE_TEST: python -m pip install pytest
+          # CIBW_TEST_COMMAND: python -m pytest {package}/tests
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,59 +1,85 @@
 name: Tests
 
-on: 
-  push:
-    branch:
-      - gitactions
-  pull_request:
-    branch:
-      - gitactions
+on: [push, pull_request]
 jobs:
   build:
-
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
-
+        os: [ubuntu-22.04, windows-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.12"]
+        exclude:
+          - os: macOS-latest
+            python-version: "3.7"
+          - os: windows-latest
+            python-version: "3.7"           
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Python ${{matrix.python-version}}
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+        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
         with:
-          python-version: ${{matrix.python-version}}
+          auto-update-conda: true
+          activate-environment: test
+          channels: conda-forge
+          python-version: ${{ matrix.python-version }}
+      - name: Upgrade pip
+        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/
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: |
+          conda install cython numpy numba nbconvert pytest jupyter scipy pandas matplotlib pytables phconvert lmfit pybroom seaborn setuptools build 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'
+        shell: bash -l {0}
         run: |
-          curl.exe --output 2182604/12d_New_30p_320mW_steer_3.hdf5 --url http://files.figshare.com/2182604/12d_New_30p_320mW_steer_3.hdf5
-          curl.exe --output 0023uLRpitc_NTP_20dT_0.5GndCl.hdf5 --url http://files.figshare.com/2182601/0023uLRpitc_NTP_20dT_0.5GndCl.hdf5
-          curl.exe --output HP3_TE150_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE150_SPC630.hdf5
-          curl.exe --output HP3_TE200_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE200_SPC630.hdf5
-          curl.exe --output HP3_TE250_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE250_SPC630.hdf5
-          curl.exe --output HP3_TE300_SPC630.hdf5 --url https://zenodo.org/record/5902313/files/HP3_TE300_SPC630.hdf5
-      - name: Upgrade pip
-        run: python -m pip install --upgrade pip
-      - name: Windows 3.6 Oddities
-        if: matrix.python-version == 3.6 && runner.os == 'Windows'
-        run: python -m pip install pywinpty==1.1.6
-      - name: Install Dependencies
-        run: |
-          python -m pip install pytest cython numpy scipy pandas matplotlib seaborn
-          python -m pip install jupyter nbconvert lmfit phconvert pybroom
-      - name: Install project
-        run: |
-          python setup.py sdist
-          python -m pip install .
+          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 ..
+
       - name: Test project
+        shell: bash -l {0}
         run: |
-          python fretbursts/tests/nbrun.py notebooks
+          cd notebooks
+          python nbrun.py .
+          cd ..
+          cd tests
           python -m pytest
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 burstsearch/build/
 docs/source/_themes/
 *ipynb_checkpoints*
+fretbursts/_version.py
 
 *build/
 *egg-info/
@@ -30,5 +31,6 @@ notebooks/out
 notebooks/wip
 .cache
 *.csv
+*.mat
 _*
 docs/source/modules/generated
diff --git a/.travis.yml b/.travis.yml
diff --git a/LongDescription.md b/LongDescription.md
@@ -0,0 +1,20 @@
+FRETBursts
+==========
+
+**FRETBursts** is a software toolkit for burst analysis of confocal
+single-molecule FRET (smFRET) measurements. It can analyze both single-spot
+and multi-spot smFRET data with or without alternating laser excitation (ALEX).
+
+For more info please refer to:
+
+- **FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET**
+  *Ingargiola et. al.* (2016). PLoS ONE doi: `10.1371/journal.pone.0160716 <10.1371/journal.pone.0160716>`__.
+
+
+Quick links:
+
+- `FRETBursts Homepage <http://opensmfs.github.io/FRETBursts/>`_
+- `FRETBursts Reference Documentation <http://fretbursts.readthedocs.org>`_
+- `FRETBursts Tutorials <https://github.com/OpenSMFS/FRETBursts_notebooks>`_
+
+See also `Release Notes <http://fretbursts.readthedocs.io/en/latest/releasenotes.html>`__.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,2 @@
-include versioneer.py
-include fretbursts/_version.py
 include LICENSE.txt
 include README.md
diff --git a/appveyor.yml b/appveyor.yml
diff --git a/docs/source/absolute_beginner.rst b/docs/source/absolute_beginner.rst
@@ -6,8 +6,9 @@ Getting started for the absolute python beginner
 Before running FRETBursts you need to install a python distribution that
 includes the Jupyter/IPython Notebook application.
 
-You can find a quick guide for installing the software and running your first
-notebook here:
+We recomend using Anaconda, which you can find instructions for downloading and installing here: `Anaconda installation instructions <https://docs.anaconda.com/free/anaconda/install/index.html>`_.
+
+You can find a guide for jupyter notebooks here:
 
 - |jupyter_quick_guide|
 
@@ -31,6 +32,19 @@ 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>`
+
+First download `frbmin.yml`
+
+Then run the following in your terminal::
+
+    conda env create -f frbmin.yml
+    conda activate frbmin
+
+.. note::
+    You may need to replace frbmin.yml with the path to the file you downloaded.
+    :ref:`instalation` provides other yaml files for more complete environments.
+
 Running FRETBursts tutorial notebook
 ------------------------------------
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -54,8 +54,9 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('../..'))
 import fretbursts
-version = fretbursts._version.get_versions()['version'][:13]
-release = version
+from importlib.metadata import version as get_version
+release: str = get_version("fretbursts")
+version: str = ".".join(release).split('.')[:2])
 
 import sphinx_bootstrap_theme
 html_theme = 'bootstrap'

diff --git a/docs/source/downloads/frbcmplt.yml b/docs/source/downloads/frbcmplt.yml
@@ -0,0 +1,23 @@
+name: frbcmplt
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - importlib_metadata
+  - pytest=7.4.0
+  - cython=3.0.10
+  - ipython=8.24.0
+  - jupyter=1.0.0
+  - numpy=1.26.4
+  - numba=0.59.1
+  - pytables=3.9.2
+  - matplotlib=3.8.4
+  - pandas=2.2.2
+  - scipy=1.13.1
+  - seaborn=0.13.1
+  - pyqt=5.15.9
+  - lmfit=1.2.2
+  - phconvert=0.9.1
+  - pybroom=0.2
+
diff --git a/docs/source/downloads/frbmin.yml b/docs/source/downloads/frbmin.yml
@@ -0,0 +1,19 @@
+name: frbmin
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - importlib_metadata
+  - ipython=8.24.0
+  - jupyter=1.0.0
+  - numpy=1.26.4
+  - pytables=3.9.2
+  - matplotlib=3.8.4
+  - pandas=2.2.2
+  - scipy=1.13.1
+  - seaborn=0.13.1
+  - pyqt=5.15.9
+  - lmfit=1.2.2
+  - phconvert=0.9.1
+