Use Trusted publishing for pypi and update dependencies

* Update __version__.py

* update build python version

* update sphinx version for docs

* Fix settings to create docs

* Update requirements

* force compatible sphinx version

* change sphinx version

* fix typo

* Try trusted publishing for PyPi uploads

* Properly use trusted publishing

---------

Co-authored-by: Christian Dam Vedel <158568093+damskii9992@users.noreply.github.com>

Author: henrikjacobsenfys

.github/workflows/python-publish.yml

@@ -21,13 +21,15 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
+    
     steps:
     - uses: actions/checkout@v4
 
     - uses: actions/setup-python@v5
       with:
-        python-version: 3.10
+        python-version: 3.12
 
     - name: Install dependencies and build
       run: |
@@ -36,5 +38,5 @@ jobs:
 
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_PASSWORD }}
+      #with:
+      #  password: ${{ secrets.PYPI_PASSWORD }}

docs/src/api/model.rst

@@ -1,4 +1,4 @@
-.. automodule:: easyreflectometry.experiment.model
+.. automodule:: easyreflectometry.model
     :members:
     :undoc-members:
     :show-inheritance:

docs/src/api/sample.rst

@@ -1,5 +1,5 @@
 
-.. automodule:: easyreflectometry.sample.sample
+.. automodule:: easyreflectometry.sample
     :members:
     :undoc-members:
     :show-inheritance:

docs/src/conf.py

@@ -25,7 +25,8 @@
 
 import easyreflectometry
 
-sys.path.insert(0, os.path.abspath('../src'))
+# sys.path.insert(0, os.path.abspath('../src'))
+sys.path.insert(0, str(Path(__file__).resolve().parents[2] / "src"))
 
 main_root = Path(__file__).parents[2]
 sys.path.append(str(main_root))

pyproject.toml

@@ -60,8 +60,9 @@ dev = [
 docs = [
     "myst_parser==4.0.1",
     "nbsphinx==0.9.7",
-    "sphinx_autodoc_typehints==3.0.1",
-    "sphinx_book_theme==1.1.4",
+    "sphinx",
+    "sphinx_autodoc_typehints",
+    "sphinx-book-theme==1.1.4",
     "sphinx-copybutton==0.5.2",
     "toml==0.10.2",
 ]

src/easyreflectometry/__version__.py

@@ -1 +1 @@
-__version__ = '1.3.0'
+__version__ = '1.3.1'

src/easyreflectometry/data/__init__.py

@@ -4,8 +4,8 @@
 from .measurement import load_as_dataset
 
 __all__ = [
-    load,
-    load_as_dataset,
-    ProjectData,
-    DataSet1D,
+    "load",
+    "load_as_dataset",
+    "ProjectData",
+    "DataSet1D",
 ]

src/easyreflectometry/model/__init__.py

@@ -5,9 +5,9 @@
 from .resolution_functions import ResolutionFunction
 
 __all__ = (
-    LinearSpline,
-    PercentageFwhm,
-    ResolutionFunction,
-    Model,
-    ModelCollection,
+    "LinearSpline",
+    "PercentageFwhm",
+    "ResolutionFunction",
+    "Model",
+    "ModelCollection",
 )

src/easyreflectometry/sample/__init__.py

@@ -14,18 +14,18 @@
 from .elements.materials.material_solvated import MaterialSolvated
 
 __all__ = (
-    BaseAssembly,
-    GradientLayer,
-    Layer,
-    LayerAreaPerMolecule,
-    LayerCollection,
-    Material,
-    MaterialCollection,
-    MaterialDensity,
-    MaterialMixture,
-    MaterialSolvated,
-    Multilayer,
-    RepeatingMultilayer,
-    Sample,
-    SurfactantLayer,
+    "BaseAssembly",
+    "GradientLayer",
+    "Layer",
+    "LayerAreaPerMolecule",
+    "LayerCollection",
+    "Material",
+    "MaterialCollection",
+    "MaterialDensity",
+    "MaterialMixture",
+    "MaterialSolvated",
+    "Multilayer",
+    "RepeatingMultilayer",
+    "Sample",
+    "SurfactantLayer",
 )