Promoting develop to master version 0.0.3

.github/workflows/codeql-analysis.yml

@@ -2,10 +2,10 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [master, pre-release, develop]
+    branches: [ main, pre-release, develop ]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [master]
+    branches: [ main ]
   schedule:
     - cron: '0 16 * * 5'
 

.github/workflows/documentation_build.yml → .github/workflows/documentation-deploy.yml

@@ -1,10 +1,12 @@
-# This is a basic workflow to help you get started with Actions
+# This pipeline 
+# - build html documentation 
+# - deploy html documentation to gh-pages branch of the same repository
 
-name: Build Documentation
+name: Build and Deploy Documentation
 
 # Controls when the workflow will run
 on:
-  # Triggers the workflow on push or pull request events but only for the master branch
+  # Triggers the workflow on push or pull request events but only for the main branch
   push:
     branches: [ main ]
 
@@ -24,15 +26,14 @@ jobs:
     - name: Upgrade pip
       run: |
         python -m pip install --upgrade pip
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install EasyReflectometry and dependencies
+    - name: Install Pandoc, EasyReflectometry and dependencies
       run: |
         sudo apt install pandoc
-        pip install -r requirements-dev.txt
-        pip install .
+        pip install . '.[dev]'
     - name: Build and Commit
       uses: sphinx-notes/pages@master
       with:

.github/workflows/ci_pip.yml → .github/workflows/python-ci.yml

@@ -1,3 +1,15 @@
+# This workflow will for a variety of Python versions 
+# - install the code base
+# - lint the code base
+# - test the code base
+# - upload the test coverage to codecov
+#
+# It will also
+# - build the package
+# - check the package
+#
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
 name: CI using pip
 
 on: [push, pull_request]
@@ -8,62 +20,61 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ['3.9', '3.10', '3.11']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     runs-on: ${{ matrix.os }}
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Setup Poetry
-      uses: Gr1N/setup-poetry@v7
-
     - name: Install dependencies
-      run: |
-        poetry update
+      run: pip install -e '.[dev]'
+
     - name: Lint with flake8
       run: |
-        poetry add flake8
         # stop the build if there are Python syntax errors or undefined names
-        poetry run flake8 ./EasyReflectometry --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 ./EasyReflectometry --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        poetry run flake8 ./EasyReflectometry --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 ./EasyReflectometry --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with tox
       run: |
-        poetry add -D tox tox-gh-actions coverage
-        poetry run tox
+        pip install tox tox-gh-actions coverage
+        tox
+
     - name: Upload coverage
-      uses: codecov/codecov-action@v1.0.7
+      uses: codecov/codecov-action@v3
       with:
         name: Pytest coverage
         env_vars: OS,PYTHON,GITHUB_ACTIONS,GITHUB_ACTION,GITHUB_REF,GITHUB_REPOSITORY,GITHUB_HEAD_REF,GITHUB_RUN_ID,GITHUB_SHA,COVERAGE_FILE
       env:
         OS: ${{ matrix.os }}
         PYTHON: ${{ matrix.python-version }}
 
-  test_Packaging:
+  Package_Testing:
 
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
-    - name: Setup Poetry
-      uses: Gr1N/setup-poetry@v7
+    - name: Install dependencies and build
+      run: |
+        pip install -e '.[dev]'
+        python -m build
 
     - name: Check Build
       run: |
-        pip install twine
-        poetry build
-        python -m twine check dist/*
+        cd ./dist
+        pytest ../

.github/workflows/python-package.yml

@@ -1,20 +1,24 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will for a variety of Python versions
+# - build a python package
+# - run tests on the produced package
+# - upload the package as an artifact
+#
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package testing
+name: Create Python Package
 
 on:
   push:
-    branches: [master, pre-release]
+    branches: [ main, pre-release ]
   pull_request:
-    branches: [master, pre-release]
+    branches: [ main, pre-release ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.9', '3.10', '3.11']
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:
@@ -23,15 +27,14 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: Gr1N/setup-poetry@v7
-    - name: Install dependencies
+    - name: Install dependencies and build
       run: |
-        poetry update
-        poetry build
+        pip install -e '.[dev]'
+        python -m build
     - name: Test with pytest
       run: |
         cd ./dist
-        poetry run pytest ../
+        pytest ../
     - uses: actions/upload-artifact@v2
       with:
         name: EasyReflectometrys - Python ${{ matrix.python-version }}

.github/workflows/python-publish.yml

@@ -1,12 +1,14 @@
-# This workflows will upload a Python Package using Twine when a release is created
+# This workflows will
+# - deploy already produced artifacts to PyIP
+#
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
-name: Upload Python Package
+name: Deploy Python Package
 
 on:
   workflow_dispatch:
   push:
-    branches: [ master ]
+    branches: [ main ]
     tags:
       - 'v*'
 
@@ -20,16 +22,16 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - uses: Gr1N/setup-poetry@v7
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        poetry update
+        pip install -e '.[dev]'
     - name: Build
       run: |
-        poetry build
+        pip install build
     - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -38,9 +38,13 @@ build
 # Docs
 docs/_build 
 
+# VSCode
+.vscode
+
 # Misc
 ..*
 *.log
 *.zip
 .ci/
 .idea/
+

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.rst.
-3. The pull request should work for Python 3.8, 3.9, and 3.10, and for PyPy. Check
+3. The pull request should work for Python 3.9, 3.10, and 3.11, and for PyPy. Check
    https://travis-ci.com/easyScience/EasyReflectometryLib/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

EasyReflectometry/__init__.py

@@ -1,4 +1,4 @@
 MAJOR = 0
 MINOR = 0
-MICRO = 2
-__version__ = f'{MAJOR:d}.{MINOR:d}.{MICRO:d}'
+MICRO = 3
+__version__ = f'{MAJOR:d}.{MINOR:d}.{MICRO:d}'

EasyReflectometry/calculators/bornagain.py

@@ -22,7 +22,7 @@ def __init__(self):
 
     def create_material(self, name):
         """
-        Create a material using SLD. 
+        Create a material using SLD.
 
         :param name: The name of the material
         :type name: str
@@ -60,7 +60,8 @@ def update_material(self, name, **kwargs):
         if 'imag' in kwargs.keys():
             if kwargs['imag'] < 0:
                 raise ValueError(
-                    'The BornAgain interface does not support negative imaginary scattering length densities'
+                    'The BornAgain interface does not support negative '
+                    'imaginary scattering length densities'
                 )
             imag = kwargs['imag'] * 1e-6
         self.storage['material'][name] = ba.MaterialBySLD(str(name), real, imag)

EasyReflectometry/calculators/refl1d.py

@@ -3,7 +3,7 @@
 from typing import Tuple
 
 from easyCore import np
-from refl1d import names, model, experiment
+from refl1d import names, model
 
 
 class Refl1d:
@@ -169,7 +169,8 @@ def add_item(self, item_name: str, model_name: str):
         :param item_name: items to add to model
         :param model_name: name for the model
         """
-        self.storage['model'][model_name]['items'].append(self.storage['item'][item_name])
+        self.storage['model'][model_name]['items'].append(
+            self.storage['item'][item_name])
 
     def remove_layer_from_item(self, layer_name: str, item_name: str):
         """
@@ -189,7 +190,8 @@ def remove_item(self, item_name: str, model_name: str):
         :param item_name: The item name
         :param model_name: The model name
         """
-        item_idx = self.storage['model'][model_name]['items'].index(self.storage['item'][item_name])
+        item_idx = self.storage['model'][model_name]['items'].index(
+            self.storage['item'][item_name])
         del self.storage['model'][model_name]['items'][item_idx]
         del self.storage['item'][item_name]
 

EasyReflectometry/calculators/refnx.py

@@ -13,7 +13,7 @@ def __init__(self):
             'material': {},
             'layer': {},
             'item': {},
-            'model': {}  #reflect.ReflectModel(reflect.Structure())
+            'model': {}
         }
 
     def reset_storage(self):
@@ -24,7 +24,7 @@ def reset_storage(self):
             'material': {},
             'layer': {},
             'item': {},
-            'model': {}  # reflect.ReflectModel(reflect.Structure())
+            'model': {}
         }
 
     def create_material(self, name: str):
@@ -211,11 +211,13 @@ def calculate(self, x_array: np.ndarray, model_name: str) -> np.ndarray:
         :param model_name: Name for the model
         :return: points calculated at `x`
         """
-        structure = _remove_unecessary_stacks(self.storage['model'][model_name].structure)
-        model = reflect.ReflectModel(structure,
-                                     scale=self.storage['model'][model_name].scale.value,
-                                     bkg=self.storage['model'][model_name].bkg.value,
-                                     dq=self.storage['model'][model_name].dq.value)
+        structure = _remove_unecessary_stacks(
+            self.storage['model'][model_name].structure)
+        model = reflect.ReflectModel(
+            structure,
+            scale=self.storage['model'][model_name].scale.value,
+            bkg=self.storage['model'][model_name].bkg.value,
+            dq=self.storage['model'][model_name].dq.value)
         return model(x_array)
 
     def sld_profile(self, model_name: str) -> Tuple[np.ndarray, np.ndarray]:
@@ -225,10 +227,12 @@ def sld_profile(self, model_name: str) -> Tuple[np.ndarray, np.ndarray]:
         :param model_name: Name for the model
         :return: z and sld(z)
         """
-        return _remove_unecessary_stacks(self.storage['model'][model_name].structure).sld_profile()
+        return _remove_unecessary_stacks(
+            self.storage['model'][model_name].structure).sld_profile()
 
 
-def _remove_unecessary_stacks(current_structure: reflect.Structure) -> reflect.Structure:
+def _remove_unecessary_stacks(
+        current_structure: reflect.Structure) -> reflect.Structure:
     """
     Removed unnecessary reflect.Stack objects from the structure.