Merge branch 'main' into diporderstructurefactor

Author: kjfisch

.github/ISSUE_TEMPLATE/Bug.md

@@ -20,14 +20,14 @@ What happened instead. Add as much detail as you can. Include (copy and paste) s
 **Code to reproduce the behavior**
 
 <!--
-Show us how to reproduce the failiure. If you can, use trajectory files from the test data folder in `tests/data` or `https://github.com/maicos-devel/maicos/tree/main/tests/data`
+Show us how to reproduce the failiure. If you can, use trajectory files from the test data folder in `tests/data` or `https://github.com/maicos-devel/scatterkit/tree/main/tests/data`
 
 You can also attach (small) files to the section below or add URLs where to download an archive with all necessary files.
 
 Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible.
 
 ``` python
-import maicos
+import scatterkit
 
 ....
 
@@ -39,7 +39,7 @@ import maicos
 <!--
 Please complete the following information to help us understand the issue better.
 
-- Which version are you using? (run `python -c "import maicos as mda; print(maicos.__version__)"`)
+- Which version are you using? (run `python -c "import scatterkit; print(scatterkit.__version__)"`)
 - Which version of Python (`python -V`)?
 - Which operating system?
 ---

.github/workflows/build.yml

@@ -70,7 +70,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/project/maicos
+      url: https://pypi.org/project/scatterkit
     permissions:
       id-token: write
       contents: write

CHANGELOG.rst

@@ -9,6 +9,12 @@ CHANGELOG file
   - keep the format consistent (79 char width, Y/M/D date format) and do not
     use tabs but use spaces for formatting
 
+Unreleased
+----------
+Henrik Stooß
+
+- Update the documentation (#8)
+
 v0.0.1 (2025/08/05)
 -------------------
 Kira Fischer, Philip Loche

docs/src/conf.py

@@ -204,7 +204,7 @@
 # -- Extension configuration -------------------------------------------------
 
 # Configuration for intersphinx: refer to the Python standard library
-# and other packages used by MAICoS
+# and other packages used by scatterkit
 intersphinx_mapping = {
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),

docs/src/contributors.rst

@@ -1,27 +1,6 @@
 Contributors
 ############
 
-Thank you to all of the developers, programmers, and researchers who
-contributed to the creation of MAICoS.
-
-We also thank the `Institute for Computational Physics`_ (University of
-Stuttgart), group members of `Roland Netz`_ at Freie Universität Berlin,
-and the Stuttgart Center for Simulation Science and the German Research
-Council (DFG) for funding through the Cluster of Excellence `EXC 2075`_
-"Data-integrated Simulation Science".
-
-History
--------
-
-MAICoS was first developed in `Roland Netz`_'s group at the Freie University of
-Berlin by `Alexander Schlaich`_ and `Philip Loche`_, and is now mostly developed
-and maintained at the `Institute for Physics of functional Materials`_ (Hamburg University of Technology).
-
-.. _Roland Netz: https://www.physik.fu-berlin.de/en/einrichtungen/ag/ag-netz/index.html
-.. _Philip Loche: https://people.epfl.ch/philip.loche
-.. _Alexander Schlaich:  https://tuhh.de/ipfm/people/schlaich
-.. _Institute for Computational Physics: https://www.icp.uni-stuttgart.de/
-.. _EXC 2075: https://www.simtech.uni-stuttgart.de/exc/
-.. _Institute for Physics of functional Materials: https://www.tuhh.de/ipfm/
+This project exists thanks to all the people who contribute.
 
 .. include:: ../../AUTHORS.rst

examples/README.rst

@@ -4,12 +4,12 @@ How-to guides
 =============
 
 Like a cooking recipe, How-to guides help you solve key problems and use cases. If you
-are a total MAICoS beginner, you should start with the :ref:`userdoc-get-started`
+are a total scatterkit beginner, you should start with the :ref:`userdoc-get-started`
 section. Otherwise this section consists of introductory examples and examples
-demonstrating specific features of MAICoS' using its Python API.
+demonstrating specific features of scatterkit using its Python API.
 
-For running the examples install maicos with the ``examples`` optional dependencies.
+For running the examples install scatterkit with the ``examples`` optional dependencies.
 
 .. code-block:: bash
 
-    pip install maicos[examples]
+    pip install scatterkit[examples]

setup.py

@@ -5,7 +5,7 @@
 #
 # Released under the GNU Public Licence, v3 or any higher version
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Setup file for MAICoS package.
+"""Setup file for scatterkit package.
 
 Credit to MDAnalysis setup.py.
 """

src/scatterkit/__init__.py

@@ -1,4 +1,4 @@
-"""scatterkit: SAXS analysis of MD trajectories."""
+"""scatterkit: scattering analysis of MD trajectories."""
 
 __authors__ = "MAICoS Developer Team"
 

src/scatterkit/lib/_cmath.pyx

@@ -29,7 +29,7 @@ cpdef tuple compute_structure_factor(
     ):
     r"""Calculates scattering vectors and corresponding structure factors.
 
-    Use via ``from maicos.lib.math import structure_factor``
+    Use via ``from scatterkit.lib.math import structure_factor``
 
     The structure factors are calculated according to
 

tests/requirements.txt

@@ -5,4 +5,3 @@ pytest-cov
 pytest-mock
 pytest-xdist
 setuptools
-sympy