Merge branch 'main' of https://github.com/jochenstahn/amor

.github/workflows/release.yml

@@ -0,0 +1,68 @@
+name: Release
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    tags:
+      - "*"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      build-items:
+        description: 'Items to be build'
+        required: true
+        default: 'all'
+        type: choice
+        options:
+          - all
+          - windows
+          - linux
+          - mac
+
+jobs:
+  build-ubuntu-latest:
+    runs-on: ubuntu-latest
+    if: ${{ (github.event_name != 'workflow_dispatch') || (contains(fromJson('["all", "linux"]'), github.event.inputs.build-items)) }}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+        pip install -r requirements.txt
+    - name: Build PyPI package
+      run: |
+        python3 -m build
+    - name: Upload to PyPI
+      if: github.event_name != 'workflow_dispatch'
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}
+        skip-existing: true
+    - name: Archive distribution
+      uses: actions/upload-artifact@v4
+      with:
+        name: linux-dist
+        path: |
+          dist/*.tar.gz
+
+  release:
+    if: github.event_name != 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    needs: [build-ubuntu-latest]
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        name: linux-dist
+    - uses: ncipollo/release-action@v1
+      with:
+        artifacts: "amor*.tar.gz"
+        token: ${{ secrets.GITHUB_TOKEN }}
+        allowUpdates: true

.github/workflows/unit_tests.yml

@@ -0,0 +1,37 @@
+name: Unit Testing
+
+on:
+  push:
+      branches:
+        - main
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install -r requirements.txt
+
+      - name: Test with pytest
+        run: |
+          cd tests
+          python -m pytest --pyargs .

.gitignore

@@ -5,6 +5,6 @@
 __pycache__
 raw
 .idea
-test_data
+test_results
 build
 dist

README.md

@@ -1,12 +0,0 @@
-Software repository for the neutron reflectometer Amor at the Paul Scherrer Institut, Switzerland
-
-reduction of the raw files (.hdf) to reflectivity files in one of the representations of the **ORSO reflectivity file format**:
-
-> `eos.py`  
-> `neos.py` : version for playing and testing
-
-visualisation of the content of a raw file (.hdf):
-
-> `events2histogram.py`
-
-#TODO: real readme for final system needed.

README.rst

@@ -0,0 +1,27 @@
+EOS - The AMOR focusing reflectometry data reduction software
+-------------------------------------------------------------
+
+.. image:: https://img.shields.io/pypi/v/amor-eos.svg
+        :target: https://pypi.python.org/pypi/amor-eos/
+
+
+Software repository for the neutron reflectometer Amor at the Paul Scherrer Institut, Switzerland
+
+Reduction of the raw files (.hdf) to reflectivity files in one of the representations of the **ORSO reflectivity file format**:
+
+  eos.py --help
+
+visualisation of the content of a raw file (.hdf):
+
+  events2histogram.py
+
+:TODO: real readme for final system needed.
+
+Installation
+------------
+Create a virtual python environment (>3.8) and install the PyPI package:
+
+  pip install amor-eos
+
+On Windows you can also use the binary eos.exe that you find in the 
+[GitHub Releases]([https://github.com/jochenstahn/amor/releases/latest) section

libeos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by eos.py script.
 """
 
-__version__ = '2.1.1'
-__date__    = '2024-10-22'
+__version__ = '2.1.2'
+__date__    = '2024-10-30'

pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,32 @@
+[bdist_wheel]
+universal = 1
+
+[metadata]
+name = amor_eos
+version = attr: libeos.__version__
+author = Jochen Stahn - Paul Scherrer Institut
+author_email = jochen.stahn@psi.ch
+description = EOS reflectometry reduction for AMOR instrument
+long_description = Reduces data obtained by focusing time of flight neutron reflectivity to full reflectivity curve.
+license = MIT
+classifiers =
+    Programming Language :: Python :: 3
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Topic :: Scientific/Engineering
+    Development Status :: 5 - Production/Stable
+
+[options]
+python_requires = >=3.8
+packages =
+    libeos
+scripts =
+    eos.py
+install_requires =
+    numpy
+    h5py
+    orsopy
+    numba
+
+[project.urls]
+Homepage = "https://github.com/jochenstahn/amor"

tests/test_full_analysis.py

@@ -21,15 +21,14 @@ class FullAmorTest(TestCase):
         self.pr.enable()
         self.reader_config = options.ReaderConfig(
                 year=2023,
-                dataPath=os.path.join('..', "test_data"),
-                raw=(os.path.join('..', "test_data"),)
+                rawPath=(os.path.join('..', "test_data"),),
                 )
 
     def tearDown(self):
         self.pr.disable()
         for fi in ['test.Rqz.ort', '614.norm']:
             try:
-                os.unlink(os.path.join(self.reader_config.dataPath, fi))
+                os.unlink(os.path.join(self.reader_config.rawPath[0], fi))
             except FileNotFoundError:
                 pass
 
@@ -38,6 +37,8 @@ class FullAmorTest(TestCase):
         experiment_config = options.ExperimentConfig(
                 chopperPhase=-13.5,
                 chopperPhaseOffset=-5,
+                monitorType=options.Defaults.monitorType,
+                lowCurrentThreshold=options.Defaults.lowCurrentThreshold,
                 yRange=(11., 41.),
                 lambdaRange=(2., 15.),
                 qzRange=(0.005, 0.30),
@@ -60,7 +61,8 @@ class FullAmorTest(TestCase):
                 )
         output_config = options.OutputConfig(
                 outputFormats=["Rqz.ort"],
-                outputName='test'
+                outputName='test',
+                outputPath=os.path.join('..', 'test_results'),
                 )
         config=options.EOSConfig(self.reader_config, experiment_config, reduction_config, output_config)
         # run three times to get similar timing to noslicing runs
@@ -75,6 +77,8 @@ class FullAmorTest(TestCase):
         experiment_config = options.ExperimentConfig(
                 chopperPhase=-13.5,
                 chopperPhaseOffset=-5,
+                monitorType=options.Defaults.monitorType,
+                lowCurrentThreshold=options.Defaults.lowCurrentThreshold,
                 yRange=(11., 41.),
                 lambdaRange=(2., 15.),
                 qzRange=(0.005, 0.30),
@@ -91,12 +95,13 @@ class FullAmorTest(TestCase):
                 thetaRangeR=(-12., 12.),
                 fileIdentifier=["610", "611", "608,612-613", "609"],
                 scale=[1],
-                normalisationFileIdentifier=["614"],
+                normalisationFileIdentifier=["608"],
                 autoscale=(True, True)
                 )
         output_config = options.OutputConfig(
                 outputFormats=["Rqz.ort"],
-                outputName='test'
+                outputName='test',
+                outputPath=os.path.join('..', 'test_results'),
                 )
         config=options.EOSConfig(self.reader_config, experiment_config, reduction_config, output_config)
         reducer = reduction.AmorReduction(config)