Merge pull request #21 from woutdenolf/support_py3_12

Support py3 12

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+extend-ignore = E203,E501,E701
+max-line-length = 88
+exclude = [".eggs"]

.flake8_nb

@@ -0,0 +1,3 @@
+[flake8_nb]
+extend-ignore = E203,E501,E701
+max-line-length = 88

.github/workflows/ci.yml

@@ -1,83 +1,66 @@
-name: CI
+name: Unit Tests, Linting, and Formatting Checks
 
 on:
-  # Triggers the workflow on push only for the master branch or pull request events
   push:
-    branches: [ master ]
+    branches:
+      - master
   pull_request:
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-defaults:
-  run:
-    shell: bash
+    branches:
+      - master
 
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }} ${{ matrix.name-suffix }}"
+  test:
     runs-on: ${{ matrix.os }}
+
     strategy:
       matrix:
-        include:
-          - name-suffix: "Linux"
-            os: ubuntu-20.04
-            python-version: 3.6
-            BUILD_COMMAND: sdist
-          #- name-suffix: "Mac"
-          #  os: macos-latest
-          #  python-version: 3.8
-          #  BUILD_COMMAND: sdist
-          #- name-suffix: "Windows"
-          #  os: windows-latest
-          #  python-version: 3.9
-          #  BUILD_COMMAND: sdist
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-      # Runs a single command using the runners shell
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
+      - name: Upgrade pip
+        run: |
+          python -m pip install --upgrade pip
+
+      - name: Run linting with Flake8
+        if: ${{ matrix.python-version == '3.12' }}
+        run: |
+          pip install "flake8 >=4" "flake8_nb >= 0.3.1"
+          flake8 .
+
+      - name: Check code formatting with Black
+        if: ${{ matrix.python-version == '3.12' }}
+        run: |
+          pip install "black[jupyter] >=25"
+          black --check .
+
+      - name: Build source distribution
+        run: |
+          pip install build
+          python -m build -s
+
+      - name: Install source distribution
+        run: |
+          pip install --pre "$(ls dist/*.tar.gz)[test]"
+
+      - name: Install non-pypi dependencies
+        if: false
         run: |
           if [ ${{ runner.os }} == 'Windows' ]; then
             call tools\\windows-install-deps.bat -y -t -s -u
           else
             set +e  # subprocesses that return >0 should not stop the script
             source tools/linux-install-deps.sh -y -t -s -u
-              cprint "AAAAAAAAAAAAAAAA"
-              pip_bin
-              pip_bin list
-              python -m pip list
-              cprint "AAAAAAAAAAAAAAAA"
           fi
 
-      - name: Print python info
+      - name: Run tests
         run: |
-          cprint "AAAAAAAAAAAAAAAA"
-          pip_bin
-          pip_bin list
-          python -m pip list
-          cprint "AAAAAAAAAAAAAAAA"
-          python -m pip list
-          python ci/info_platform.py
-
-      - name: Generate source package or wheel
-        run: |
-          python setup.py ${{ matrix.BUILD_COMMAND }}
-          ls dist
-
-      - name: Install package
-        run: python -m pip install --pre --find-links dist/ spectrocrunch
-
-      - name: Run the tests
-        run: python -m unittest -v spectrocrunch.tests.test_all.test_suite
+          pytest --pyargs spectrocrunch

.gitignore

@@ -1,24 +1,17 @@
-*.py[cod]
-
-# Generated
-build
-dist
-*.egg*
-doc/source/apidocs
+# Hidden files
+.*
+!.gitignore
+!.flake8
+!.flake8_nb
 
-# Temporary files
-*~
-*.h5
-*.nx5
-*.hdf5
-log.*
-*.png
-*.log
-*.*.txt
-*.cprof
-.[^.]*
-test.*
+# Byte / compiled / optimized
+*.py[cod]
+__pycache__/
+*.so
 
-# Generated data
-testresults
-testdata
+# Distribution / packaging
+/build/
+/dist/
+*.egg-info/
+.eggs/
+/doc/_generated

CHANGELOG.md

@@ -0,0 +1,25 @@
+# Change Log
+
+## develop (unreleased)
+
+- Noise propagation for fullfield XANES and micro-XANES (fluo and transmission)
+- Alignment of XRF maps on raw spectrum (integrated with dead time correction, flux normalization, and detector summing)
+- HDF5 based job pipelines
+- File system proxies
+
+## 0.0.1-alpha2 (unreleased)
+
+- Cross-section calculations combining xraylib (tables) with fdmnes (calculation)
+- Parse ESRF ID21 specific fullfield data
+- Fullfield XANES normalization
+- Parse ESRF ID16b specific fluoXAS data
+- ESRF ID21 specific data visualization
+- 1D spectrum alignment (only phase correlation and simple properties)
+
+## genesis (unreleased)
+
+- Initial version for Python 2.7
+- Image alignment based on phase correlation, SIFT, Elastix, and simple image properties (max, min, centroid, and gaussfit)
+- XRF fitting and deadtime correction of fluoXAS stacks using pyMca
+- fluoXAS normalization
+- Parse ESRF ID21 specific fluoXAS data

LICENSE.md

@@ -0,0 +1,20 @@
+# MIT License
+
+**Copyright (c) 2021 European Synchrotron Radiation Facility**
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+# SpectroCrunch: spectroscopic imaging library (XRF/XAS)
+
+> **Warning:**  
+> This library is deprecated and no longer maintained.  
+> It is replaced by [ewoksfluo](https://ewoksfluo.readthedocs.io) and [ewoksndreg](https://ewoksndreg.readthedocs.io).
+
+## Getting started
+
+### Install from PyPi
+
+```bash
+pip install [--user] spectrocrunch
+```
+
+### Install from source
+
+```bash
+git clone https://github.com/woutdenolf/spectrocrunch
+cd spectrocrunch
+pip install [--user] .
+```
+
+### Install non-pypi dependencies
+
+```bash
+git clone https://github.com/woutdenolf/spectrocrunch
+. spectrocrunch/tools/linux-install-deps.sh [-u]
+```
+
+### Test
+
+```bash
+pip install -e .[test]
+pytest .
+```