Move and remove modules (#524)

Author: PicoCentauri

.codecov.yml

@@ -3,7 +3,6 @@ coverage:
     - "examples/.*"
     - "src/maicos/_version.py"
     - "tests/.*"
-    - "versioneer.py"
   status:
     project:
       default:

.github/workflows/build.yml

@@ -6,7 +6,6 @@ on:
       # build wheels in PR if this file changed
       - ".github/workflows/build.yml"
       # build wheels in PR if any of the build system files changed
-      - "**/setup.py"
       - "**/pyproject.toml"
       - "**/MANIFEST.in"
   schedule:
@@ -16,29 +15,8 @@ on:
     # allow manual triggering of the workflow
 
 jobs:
-  build-wheels:
-    name: wheels / ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # macos-13 is an intel runner, macos-15 is apple silicon
-        os: [ubuntu-24.04, ubuntu-24.04-arm, windows-2025, macos-13, macos-15]
-
-    steps:
-      - uses: actions/checkout@v5
-        with:
-          fetch-depth: 0
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v3.2.1
-
-      - uses: actions/upload-artifact@v5
-        with:
-          name: wheel-${{ matrix.os }}
-          path: ./wheelhouse/*.whl
-
-  build-sdist:
-    name: sdist
+  build:
+    name: build
     runs-on: ubuntu-latest
 
     steps:
@@ -55,18 +33,20 @@ jobs:
       - name: Install dependencies
         run: python -m pip install tox
 
-      - name: Test build integrity and create sdist
+      - name: Test build integrity and build sdist
         run: tox -e build
 
       - uses: actions/upload-artifact@v5
         with:
-          name: sdist
-          path: dist/*.tar.gz
+          name: files
+          path: |
+            dist/*.tar.gz
+            dist/*.whl
 
   release:
     name: Release package
     if: startsWith(github.ref, 'refs/tags/v') && github.event_name == 'workflow_dispatch'
-    needs: [build-wheels, build-sdist]
+    needs: [build]
     runs-on: ubuntu-latest
     environment:
       name: pypi

.gitignore

@@ -20,6 +20,7 @@ __pycache__/
 build/
 dist/
 sg_execution_times.rst
+_version.py
 
 # Allow maicos share text files
 !maicos/share/*.dat

CHANGELOG.rst

@@ -13,6 +13,11 @@ Unreleased
 ----------
 Philip Loche, Kira Fischer, Francis Jose, Philipp Staerk, Henrik Stooß
 
+- Move ``DielectricSpectrum``, ``lib.math.FT``, ``lib.math.iFT`` to spectrakit package.
+  (#524)
+- Move ``Saxs``, ``DiporderStructureFactor``, ``RDFDiporder``, ``lib.math.atomic_form_factor``,
+  ``lib.math.rdf_structure_factor``,  to scatterkit package. (#524)
+- Remove ``KineticEnergy`` and ``DipoleAngle`` module. (#524)
 - Implement error calculation for observables with multiple samples (#494)
 - Bump minimal Python version to 3.11 and MDAnalysis to 2.10.0 (#529)
 - Added support for Python 3.14 in CI workflows (#529)

MANIFEST.in

@@ -1,15 +1,11 @@
-graft docs
 graft src
 
-# If you are encounter problems with .c file use
-# git update-index --assume-unchanged src/maicos/lib/*.c
-
 include *.rst
 include LICENSE
-include versioneer.py
 
 prune .tox
 prune developer
+prune docs
 prune examples
 prune tests
 prune benchmarks
@@ -21,5 +17,3 @@ exclude .readthedocs.yml
 exclude .codecov.yml
 exclude tox.ini
 exclude asv.conf.json
-
-global-exclude *.py[cod] __pycache__/* *.so *.dylib

README.rst

@@ -13,10 +13,10 @@ MAICoS
 **MAICoS** stands for **Molecular Analysis for Interfacial and Confined Systems**. It is
 an object-oriented **Python** toolkit for analyzing the structure and dynamics of
 interfacial and confined fluids from molecular simulations. Combined with `MDAnalysis`_,
-MAICoS enables the extraction of density profiles, dielectric constants, structure
-factors, and transport properties from trajectory files generated by LAMMPS, GROMACS,
-CHARMM, or NAMD simulations. MAICoS is open source and released under the **GNU General
-Public License v3.0**.
+MAICoS enables the extraction of density profiles, dielectric constants, and transport
+properties from trajectory files generated by LAMMPS, GROMACS, CHARMM, or NAMD
+simulations. MAICoS is open source and released under the **GNU General Public License
+v3.0**.
 
 MAICoS is designed both for beginners in molecular simulations with no prior Python
 experience— offering a descriptive **Command Line Interface (CLI)**—and for experienced
@@ -104,12 +104,8 @@ Currently, MAICoS supports the following analysis modules (alphabetically):
      - Cylindrical dielectric profiles
    * - DielectricPlanar
      - Planar dielectric profiles
-   * - DielectricSpectrum
-     - Linear dielectric spectrum
    * - DielectricSphere
      - Spherical dielectric profiles
-   * - DipoleAngle
-     - Time series of dipole moment angles
    * - DiporderCylinder
      - Cylindrical dipolar order parameters
    * - DiporderPlanar
@@ -118,16 +114,10 @@ Currently, MAICoS supports the following analysis modules (alphabetically):
      - Spherical radial distribution function between dipoles
    * - DiporderSphere
      - Spherical dipolar order parameters
-   * - DiporderStructureFactor
-     - Structure factor for dipoles
-   * - KineticEnergy
-     - Time series of kinetic energies
    * - PDFCylinder
      - Cylindrical shell-wise 1D pair distribution functions
    * - PDFPlanar
      - Slab-wise planar 2D pair distribution functions
-   * - Saxs
-     - Small-angle X-ray scattering (SAXS): structure factors and scattering intensities
    * - TemperaturePlanar
      - Temperature profiles in a Cartesian geometry
    * - VelocityCylinder

developer/check_changelog.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 """Check if the CHANGELOG has been modified with respect to the main branch."""
 import os
 

developer/clean_dist_check.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 """Clean dist files after tox -e build."""
 from pathlib import Path