Merge branch 'main' into 112-userwarning-error-while-time-integrating…

…-monitors

.github/workflows/main.yml

@@ -12,24 +12,23 @@ jobs:
     runs-on: ${{ matrix.os}}
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10','3.11']
+        python-version: ['3.10','3.11']
         os: [ubuntu-latest, macOS-latest, windows-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
-        # This path is specific to Ubuntu
-        path: ~/.cache/pip
+        path: ${{ env.pythonLocation }}
         # Look to see if there is a cache hit for the corresponding requirements file
-        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('requirements.txt') }}
         restore-keys: |
-         ${{ runner.os }}-pip-
+         ${{ runner.os }}-py${{ matrix.python-version }}-pip-
           ${{ runner.os }}-
     - name: Install dependencies
       run: |
@@ -58,6 +57,8 @@ jobs:
         unzip PSS300nm_C_ccd100.zip
         wget https://github.com/usnistgov/PyHyperScattering/releases/download/0.0.0-example-data/smi_example.zip
         unzip smi_example.zip
+        wget https://github.com/usnistgov/PyHyperScattering/releases/download/0.0.0-example-data/CMS_giwaxs_series.zip
+        unzip CMS_giwaxs_series.zip
     - name: Fetch and unzip example data (Windows)
       if: ${{ matrix.os == 'windows-latest' }}
       run: |
@@ -71,7 +72,11 @@ jobs:
         unzip PSS300nm_C_ccd100.zip
         C:\msys64\usr\bin\wget.exe https://github.com/usnistgov/PyHyperScattering/releases/download/0.0.0-example-data/smi_example.zip
         unzip smi_example.zip
+        C:\msys64\usr\bin\wget.exe https://github.com/usnistgov/PyHyperScattering/releases/download/0.0.0-example-data/CMS_giwaxs_series.zip
+        unzip CMS_giwaxs_series.zip
     - name: Test with pytest
+      env: 
+         TILED_API_KEY: ${{ secrets.TILED_API_KEY }}
       run: |
         #pytest -v
         #temporarily disabling coverage for memory usage
@@ -81,7 +86,7 @@ jobs:
         coverage report
         coverage html
     - name: Upload coverage report
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: coverage-${{ matrix.os}}-${{ matrix.python-version }}.html
         path: htmlcov/index.html

.github/workflows/python-publish.yml

@@ -19,11 +19,11 @@ jobs:
 
     steps:    
     - name: Fetch repo  
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -33,7 +33,7 @@ jobs:
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@v1.8.14
       with:
         user: __token__
         password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/python-test-publish-all.yml

@@ -22,11 +22,11 @@ jobs:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     steps:
     - name: Fetch repo  
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -39,7 +39,7 @@ jobs:
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@v1.8.14
       with:
         user: __token__
         password: ${{ secrets.TEST_PYPI_TOKEN }}

.gitignore

@@ -12,18 +12,18 @@ venv/*
 OrientationRunDec2019/**
 **/*.p
 **/.*
-**/*.ipynb
 *.png
 *.h5
 *.nxs
+.ipynb_checkpoints
 Example/**
 example-data/**
 src/__pycache__
 *.egg-info
 src/PyHyperScattering/__pycache__
 src/PyHyperScattering/.ipynb_checkpoints/*
 dist
-docs/_build/*
+dcs/_build/*
 docs/_build/html/*
 *.pyc
 example_data/11012/Dark_56367-AI.txt

pyproject.toml

@@ -1,6 +1,100 @@
 [build-system]
-requires = [
-    "setuptools>=42",
-    "wheel"
-]
+requires = ["setuptools", "wheel", "versioneer[toml]"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "PyHyperScattering"
+dynamic = ["version"]
+authors = [
+    {name = "Peter Beaucage", email = "peter.beaucage@nist.gov"},
+]
+description = "Utilities for loading, reducing, fitting, and plotting hyperspectral x-ray and neutron scattering data."
+readme = "README.md"
+requires-python = ">=3.6"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: Freely Distributable",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "h5py",
+    "numpy<2",
+    "pandas",
+    "pyfai",
+    "pyopencl",
+    "scikit-image",
+    "scipy",
+    "pillow",
+    "xarray",
+    "tqdm",
+    "astropy",
+    "fabio",
+    "nodejs",
+    "silx==2.0.0",
+    "pygix",
+    "pydata_sphinx_theme",
+    "numexpr<2.8.5",
+]
+
+[project.optional-dependencies]
+bluesky = [
+    "tiled[all]>=0.1.0a74",
+    "databroker[all]>=2.0.0b10",
+    "bottleneck"
+]
+performance = [
+    "pyopencl",
+    "dask",
+    "cupy"
+]
+ui = [
+    "holoviews==1.16.2",
+    "hvplot"
+]
+doc = [
+        "sphinx",
+        "pydata_sphinx_theme"
+        ]
+test =  [
+        "pytest",
+         "black",
+         "codecov",
+         "pylint"
+         ]
+all = [
+    "tiled[all]>=0.1.0a74",
+    "databroker[all]>=2.0.0b10",
+    "bottleneck",
+    "pyopencl",
+    "dask",
+    "cupy",
+    "holoviews==1.16.2",
+    "hvplot",
+    "sphinx",
+    "pydata_sphinx_theme",
+    "pytest",
+    "black",
+    "codecov",
+    "pylint"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/usnistgov/pyhyperscattering"
+"Bug Tracker" = "https://github.com/usnistgov/pyhyperscattering/issues"
+"Project Site" = "https://www.nist.gov/laboratories/tools-instruments/polarized-resonant-soft-x-ray-scattering-p-rsoxs"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "src/PyHyperScattering/_version.py"
+versionfile_build = "PyHyperScattering/_version.py"
+tag_prefix = ""
+parentdir_prefix = "pyhyperscattering-"

requirements-bluesky.txt

@@ -1,2 +1,3 @@
-tiled[client]>=0.1.0a74
+tiled[all]>=0.1.0a74
 databroker[all]>=2.0.0b10
+bottleneck

requirements.txt

@@ -3,9 +3,12 @@ astropy
 fabio
 h5py
 nodejs
-numpy
+numpy<2
 pandas
+# pygix fails to improt if silx > 2.0.0 
+silx==2.0.0
 pyfai
+pygix
 scikit-image
 scipy
 pillow