New parameter and Numpy2 (#209)

* update np.Inf to match Numpy2

* update to new parameter

* Update imports from Refl1d

* Update imports

* make ruff happy

* make ruff happy

* Removed Python 3.9

* Update ci

* change dependency

* Update dependency on EasyScience

* Pin dependencies

Author: henrikjacobsenfys

.github/workflows/documentation-build.yml

@@ -34,7 +34,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install Pandoc, repo and dependencies
       run: |
         sudo apt install pandoc

.github/workflows/python-ci.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     runs-on: ${{ matrix.os }}
@@ -74,7 +74,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
 
     - name: Install dependencies and build
       run: |

.github/workflows/python-package.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11','3.12']
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:

.github/workflows/python-publish.yml

@@ -27,7 +27,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.10
 
     - name: Install dependencies and build
       run: |

CONTRIBUTING.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python 3.9, 3.10, and 3.11, and for PyPy. Check
+3. The pull request should work for Python, 3.10, 3.11 and 3.12, and for PyPy. Check
    https://travis-ci.com/easyScience/EasyReflectometryLib/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

pyproject.toml

@@ -21,48 +21,49 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Development Status :: 3 - Alpha"
 ]
-requires-python = ">=3.9,<3.13"
+
+requires-python = ">=3.10,<3.13"
+
 dependencies = [
-    "easyscience>=1.2.0",
-    "scipp>=23.12.0",
-    "refnx>=0.1.15",
-    "refl1d",
-    "orsopy>=0.0.4",
-    "pint==0.23", # Only to ensure that unit is reported as dimensionless rather than empty string
-    "xhtml2pdf>=0.2.16"
+    "easyscience==1.3.0",
+    "scipp==25.2.0",
+    "refnx==0.1.52",
+    "refl1d[webview]==1.0.0a12",
+    "orsopy==1.2.1",
+    "xhtml2pdf==0.2.17",
 ]
 
 [project.optional-dependencies]
 dev = [
-    "build",
-    "codecov>=2.1.11",
-    "coverage",
-    "coveralls",
-    "flake8>=6.0.0",
-    "ipykernel",
-    "jupyter>=1.0.0",
-    "jupyterlab",
-    "plopp",
-    "pooch",
-    "pytest>=5.2",
-    "pytest-cov>=3.0.0",
-    "ruff",
-    "toml>=0.10",
-    "yapf>=0.31.0",
+    "build==1.2.2.post1",
+    "codecov==2.1.13",
+    "coverage==7.7.0",
+    "coveralls==4.0.1",
+    "flake8==7.1.2",
+    "ipykernel==6.29.5",
+    "jupyter==1.1.1",
+    "jupyterlab==4.3.6",
+    "plopp==25.3.0",
+    "pooch==1.8.2",
+    "pytest==8.3.5",
+    "pytest-cov==6.0.0",
+    "ruff==0.11.0",
+    "toml==0.10.2",
+    "yapf==0.43.0",
 ]
+
 docs = [
-    "myst_parser",
-    "nbsphinx",
-    "sphinx_autodoc_typehints",
-    "sphinx_book_theme",
-    "sphinx-copybutton",
-    "toml"
+    "myst_parser==4.0.1",
+    "nbsphinx==0.9.7",
+    "sphinx_autodoc_typehints==3.0.1",
+    "sphinx_book_theme==1.1.4",
+    "sphinx-copybutton==0.5.2",
+    "toml==0.10.2",
 ]
 
 [project.urls]
@@ -131,10 +132,9 @@ force-single-line = true
 legacy_tox_ini = """
 [tox]
 isolated_build = True
-envlist = py{3.9,3.10,3.11,3.12}
+envlist = py{3.10,3.11,3.12}
 [gh-actions]
 python =
-        3.9: py39
         3.10: py310
         3.11: py311
         3.12: py312

src/easyreflectometry/calculators/refl1d/wrapper.py

@@ -3,8 +3,8 @@
 from typing import Tuple
 
 import numpy as np
-from refl1d import model
 from refl1d import names
+from refl1d.sample.layers import Repeat
 
 from easyreflectometry.model import PercentageFwhm
 
@@ -34,16 +34,16 @@ def create_layer(self, name: str):
             magnetism = names.Magnetism(rhoM=0.0, thetaM=0.0)
         else:
             magnetism = None
-        self.storage['layer'][name] = model.Slab(name=str(name), magnetism=magnetism)
+        self.storage['layer'][name] = names.Slab(name=str(name), magnetism=magnetism)
 
     def create_item(self, name: str):
         """
         Create an item using Repeat.
 
         :param name: The name of the item
         """
-        self.storage['item'][name] = model.Repeat(
-            model.Stack(model.Slab(names.SLD(), thickness=0, interface=0)), name=str(name)
+        self.storage['item'][name] = Repeat(
+            names.Stack(names.Slab(names.SLD(), thickness=0, interface=0)), name=str(name)
         )
         del self.storage['item'][name].stack[0]
 
@@ -66,7 +66,7 @@ def get_layer_value(self, name: str, key: str) -> float:
         :param key: The given value keys
         """
         if key in ['magnetism_rhoM', 'magnetism_thetaM']:
-            return getattr(self.storage['layer'][name].magnetism, key.split('_')[-1])
+            return getattr(self.storage['layer'][name].magnetism, key.split('_')[-1]).value #TODO: check if we want to return the raw value or the full Parameter  # noqa: E501
         return super().get_layer_value(name, key)
 
     def create_model(self, name: str):
@@ -267,18 +267,18 @@ def _get_polarized_probe(
     return names.PolarizedQProbe(xs=four_probes, name='polarized')
 
 
-def _build_sample(storage: dict, model_name: str) -> model.Stack:
-    sample = model.Stack()
+def _build_sample(storage: dict, model_name: str) -> names.Stack:
+    sample = names.Stack()
     # -1 to reverse the order
     for i in storage['model'][model_name]['items'][::-1]:
         if i.repeat.value == 1:
             # -1 to reverse the order
             for j in range(len(i.stack))[::-1]:
                 sample |= i.stack[j]
         else:
-            stack = model.Stack()
+            stack = names.Stack()
             # -1 to reverse the order
             for j in range(len(i.stack))[::-1]:
                 stack |= i.stack[j]
-            sample |= model.Repeat(stack, repeat=i.repeat.value)
+            sample |= Repeat(stack, repeat=i.repeat.value)
     return sample

src/easyreflectometry/model/model.py

@@ -9,8 +9,8 @@
 
 import numpy as np
 from easyscience import global_object
-from easyscience.Objects.new_variable import Parameter
 from easyscience.Objects.ObjectClasses import BaseObj
+from easyscience.Objects.variable import Parameter
 
 from easyreflectometry.sample import BaseAssembly
 from easyreflectometry.sample import Sample
@@ -26,15 +26,15 @@
         'url': 'https://github.com/reflectivity/edu_outreach/blob/master/refl_maths/paper.tex',
         'value': 1.0,
         'min': 0,
-        'max': np.Inf,
+        'max': np.inf,
         'fixed': True,
     },
     'background': {
         'description': 'Linear background to include in reflectometry data',
         'url': 'https://github.com/reflectivity/edu_outreach/blob/master/refl_maths/paper.tex',
         'value': 1e-8,
         'min': 0.0,
-        'max': np.Inf,
+        'max': np.inf,
         'fixed': True,
     },
     'resolution': {

src/easyreflectometry/project.py

@@ -11,7 +11,7 @@
 from easyscience import global_object
 from easyscience.fitting import AvailableMinimizers
 from easyscience.fitting.fitter import DEFAULT_MINIMIZER
-from easyscience.Objects.new_variable import Parameter
+from easyscience.Objects.variable import Parameter
 from scipp import DataGroup
 
 from easyreflectometry.calculators import CalculatorFactory

src/easyreflectometry/sample/assemblies/repeating_multilayer.py

@@ -2,7 +2,7 @@
 from typing import Union
 
 from easyscience import global_object
-from easyscience.Objects.new_variable import Parameter
+from easyscience.Objects.variable import Parameter
 
 from easyreflectometry.utils import get_as_parameter