Merge pull request #57 from harripd/master

Combined updates

.github/workflows/tests.yml

@@ -41,6 +41,7 @@ jobs:
            activate-environment: test
       - name: Apple Silicon oddities
         if: matrix.os == 'macos-14'
+        shell: bash -l {0}
         run: |
           brew install c-blosc hdf5
           export HDF5_DIR=/opt/homebrew/opt/hdf5
@@ -56,17 +57,17 @@ jobs:
       # #     conda init --all
       # #     conda create -n test python=${{matrix.python-version}}
       # #     conda activate test
-      - name: Test conda instalation
-        shell: bash -l {0}
-        run: conda info
       - name: Install Dependencies
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools build
-          # python -m pip install numpy tables matplotlib pandas
-          conda install numpy cython pytest
+          conda install numpy cython pytest pyyaml jupyter
           conda install pytables matplotlib pandas numba
+      - name: Old Python dependencies
+        if: matrix.python-version <= 3.9
+        shell: bash -l {0}
+        run: pip install importlib_resources
       - name: build phconvert
         shell: bash -l {0}
         run: |
@@ -80,26 +81,24 @@ jobs:
           wget https://ndownloader.figshare.com/files/3350669 -O dsdna_d7d17_50_50_1.spc
           wget https://ndownloader.figshare.com/files/3350672 -O Pre.ht3
           wget https://ndownloader.figshare.com/files/3350663 -O 0023uLRpitc_NTP_20dT_0.5GndCl.sm
-          wget https://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip
-          unzip Cy3.Cy5_diff_PIE-FRET.ptu.zip
           wget https://ndownloader.figshare.com/files/6955091 -O 161128_DM1_50pM_pH74.ptu
           wget https://ndownloader.figshare.com/files/14828594 -O 20161027_DM1_1nM_pH7_20MHz1.ptu
           wget https://ndownloader.figshare.com/files/13675271 -O TestFile_2.ptu
           wget https://ndownloader.figshare.com/files/14850533 -O trace_T2_300s_1_coincidence.ptu
           wget https://ndownloader.figshare.com/files/14890535 -O nanodiamant_histo.phu
           wget https://github.com/dwaithe/FCS_point_correlator/raw/master/focuspoint/topfluorPE_2_1_1_1.pt3
+          wget https://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip
+          unzip Cy3.Cy5_diff_PIE-FRET.ptu.zip
           wget https://github.com/Photon-HDF5/phconvert/files/1380341/DNA_FRET_0.5nM.pt3.zip
           unzip DNA_FRET_0.5nM.pt3.zip
           wget https://github.com/Photon-HDF5/phconvert/files/1336330/data.zip
           unzip data.zip
           cd ../..
-      - name: Downlid files Windows
+      - name: Download files Windows
         shell: bash -l {0}
         if: runner.os == 'Windows'
         run: |
           cd notebooks/data
-          curl.exe -L --output Cy3.Cy5_diff_PIE-FRET.ptu.zip --url https://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip
-          7z e Cy3.Cy5_diff_PIE-FRET.ptu.zip
           curl.exe -L --output dsdna_d7d17_50_50_1.set --url https://ndownloader.figshare.com/files/3350666
           curl.exe -L --output dsdna_d7d17_50_50_1.spc --url https://ndownloader.figshare.com/files/3350669
           curl.exe -L --output Pre.ht3 --url https://ndownloader.figshare.com/files/3350672
@@ -110,14 +109,18 @@ jobs:
           curl.exe -L --output trace_T2_300s_1_coincidence.ptu --url https://ndownloader.figshare.com/files/14850533
           curl.exe -L --output nanodiamant_histo.phu --url https://ndownloader.figshare.com/files/14890535
           curl.exe -L --output topfluorPE_2_1_1_1.pt3 --url https://github.com/dwaithe/FCS_point_correlator/raw/master/focuspoint/topfluorPE_2_1_1_1.pt3
+          curl.exe -L --output Cy3.Cy5_diff_PIE-FRET.ptu.zip --url https://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip
+          7z e Cy3.Cy5_diff_PIE-FRET.ptu.zip
           curl.exe -L --output DNA_FRET_0.5nM.pt3.zip --url https://github.com/Photon-HDF5/phconvert/files/1380341/DNA_FRET_0.5nM.pt3.zip
           7z e DNA_FRET_0.5nM.pt3.zip
+          curl.exe -L --output data.zip --url https://github.com/Photon-HDF5/phconvert/files/1336330/data.zip
+          7z e data.zip
           cd ..
           cd ..
       - name: Test project
         shell: bash -l {0}
         run: |
           pytest
-          # pip install pyyaml
-          # python -m tests/nbrun.py /notebooks/*
+          cd notebooks
+          python ../tests/nbrun.py
         

.gitignore

@@ -19,3 +19,4 @@ notebooks/*-out.ipynb
 *.ht3
 *.ptu
 *.set
+phconvert/_version.py

MANIFEST.in

@@ -1,4 +1,4 @@
-include versioneer.py
-include phconvert/_version.py
 include LICENSE.txt
 include README.md
+include phconvert/specs/*.json
+include phconvert/v04/specs/*.json

docs/conf.py

@@ -37,7 +37,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('..'))
 import phconvert
-version = phconvert._version.get_versions()['version']
+version = phconvert.__version__
 if on_rtd:
     # RTD modifies conf.py so the git repo becomes dirty
     # We strip the '-dirty' that would generate a wrong verion string

notebooks/Convert us-ALEX SM files to Photon-HDF5 - YAML.ipynb

@@ -175,7 +175,7 @@
    "outputs": [],
    "source": [
     "with open(str(meta_filename)) as f:\n",
-    "    metadata = yaml.load(f)\n",
+    "    metadata = yaml.load(f, Loader=yaml.Loader)\n",
     "metadata"
    ]
   },
@@ -262,7 +262,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "# Create Photon-HDF5"
@@ -291,9 +294,9 @@
   "anaconda-cloud": {},
   "hide_input": false,
   "kernelspec": {
-   "display_name": "py36",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "py36"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -305,7 +308,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.0"
+   "version": "3.12.3"
   },
   "nav_menu": {},
   "toc": {
@@ -341,5 +344,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

packaging.md

@@ -17,7 +17,7 @@ python setup.py sdist
 Build universal wheel:
 
 ```
-python setup.py bdist_wheel --universal
+python -m build
 ```
 
 Upload distributions:
@@ -31,7 +31,6 @@ twine upload dist/*
 Form phconvert source folder:
 
 ```
-conda build conda.recipe --python=2.7
-conda build conda.recipe --python=3.4
+conda build conda.recipe --python=3.9
 ```
 

phconvert/__init__.py

@@ -3,40 +3,6 @@
 #
 # Copyright (C) 2015 Antonino Ingargiola <[email protected]>
 #
-from phconvert._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
-
-import sys
-
-if sys.version_info < (3,):
-    raise ImportError(
-    """You are running phconvert %s on Python 2
-
-phconvert 0.9 and above are no longer compatible with Python 2, and you still
-ended up with this version installed. That's unfortunate; sorry about that.
-It should not have happened. Make sure you have pip >= 9.0 to avoid this kind
-of issue, as well as setuptools >= 24.2:
-
- $ pip install pip setuptools --upgrade
-
-Your choices:
-
-- Upgrade to Python 3.
-
-- Install an older version of phconvert:
-
- $ pip install 'phconvert<0.9'
-
-It would be great if you can figure out how this version ended up being
-installed, and try to check how to prevent that for future users.
-
-Feel free to report the issue to:
-
-https://github.com/Photon-HDF5/phconvert/issues
-
-""" % __version__)
-
 import phconvert.loader
 import phconvert.hdf5
 import phconvert.v04
@@ -49,3 +15,6 @@
 if has_matplotlib:
     import phconvert.plotter
     del matplotlib
+
+
+from phconvert._version import version as __version__