WIP Working on review and suggestions

.github/workflows/testing.yml

@@ -1,6 +1,8 @@
+name: tests
+
 on:
   push:
-
+    branches: [main]
   pull_request:
     branches: [main]
 
@@ -26,8 +28,10 @@ jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        # OVITO does not yet ship wheels for Python 3.13, so we cap at 3.12.
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4
@@ -48,6 +52,15 @@ jobs:
       - name: Test
         run: pytest --cov=wetting_angle_kit --cov-report=xml
 
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
   docs:
     runs-on: ubuntu-latest
 

.gitignore

@@ -1,5 +1,5 @@
 # Auto-generated version file
-wetting_angle_kit/_version.py
+src/wetting_angle_kit/_version.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 default_language_version:
   python: python3
-exclude: ^(.github/|tests/test_data/abinit/)
+exclude: ^(\.github/|docs/build/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
   rev: v0.4.6
@@ -33,12 +33,9 @@ repos:
   rev: v1.10.0
   hooks:
   - id: mypy
-    files: ^src/
+    files: ^wetting_angle_kit/
     additional_dependencies:
     - tokenize-rt==4.1.0
-    - types-paramiko
-    - pydantic~=2.0
-    - types-python-dateutil
 - repo: https://github.com/codespell-project/codespell
   rev: v2.3.0
   hooks:

README.md

@@ -47,15 +47,16 @@ conda install --strict-channel-priority -c https://conda.ovito.org -c conda-forg
 
 
 ```python
-from wetting_angle_kit import (
-    XYZParser, SlicedContactAngleAnalyzer, BinningContactAngleAnalyzer,
-    detect_parser_type, contact_angle_analyzer
+from wetting_angle_kit.contact_angle_methods import (
+    BinningContactAngleAnalyzer,
+    SlicedContactAngleAnalyzer,
 )
+from wetting_angle_kit.parsers import XYZParser
 
 trajectory_file = "trajectory.xyz"
 parser = XYZParser(trajectory_file)
 
-sliced = SlicedContactAngleAnalyzer(parser, output_repo="out_sliced", atom_indices=oxygen_ids, droplet_geometry="spherical", delta_gamma=5)
+sliced = SlicedContactAngleAnalyzer(parser, output_dir="out_sliced", atom_indices=oxygen_ids, droplet_geometry="spherical", delta_gamma=5)
 results = sliced.analyze(frame_range=range(0, 50))
 print(results["mean_angle"], results["std_angle"])
 

docs/examples/binning_ca.py

@@ -1,13 +1,13 @@
 # Import necessary modules
-from wetting_angle_kit.contact_angle_method import contact_angle_analyzer
-from wetting_angle_kit.parser import DumpParser, DumpWaterMoleculeFinder
+from wetting_angle_kit.contact_angle_methods import contact_angle_analyzer
+from wetting_angle_kit.parsers import LammpsDumpParser, LammpsDumpWaterFinder
 
 # --- Step 1: Define the trajectory file ---
 filename = "../../tests/trajectories/traj_spherical_drop_4k.lammpstrj"
 
 # --- Step 2: Initialize the water molecule finder ---
 # This identifies O and H atoms in water molecules
-wat_find = DumpWaterMoleculeFinder(
+wat_find = LammpsDumpWaterFinder(
     filename,
     particle_type_wall={3},  # Wall atom types
     oxygen_type=1,  # Oxygen atom type
@@ -29,7 +29,7 @@
 }
 
 # --- Step 5: Initialize the parser ---
-parser = DumpParser(filename)
+parser = LammpsDumpParser(filename)
 
 # --- Step 6: Create the contact angle analyzer ---
 analyzer = contact_angle_analyzer(

docs/examples/parsing_trajectory_files.py

@@ -1,24 +1,24 @@
 """
-Example: Using DumpParser and     DumpWaterMoleculeFinder
+Example: Using LammpsDumpParser and LammpsDumpWaterFinder
 
 This example shows how to:
 1. Identify water molecules in a LAMMPS dump file.
 2. Extract only their oxygen atom coordinates.
 """
 
-from wetting_angle_kit.parser import (
-    ASE_Parser,
-    ASE_WaterMoleculeFinder,
-    DumpParser,
-    DumpWaterMoleculeFinder,
+from wetting_angle_kit.parsers import (
+    AseParser,
+    AseWaterFinder,
+    LammpsDumpParser,
+    LammpsDumpWaterFinder,
     XYZParser,
 )
 
 # --- Define input file ---
 filename = "../../tests/trajectories/traj_10_3_330w_nve_4k_reajust.lammpstrj"
 
 # --- Initialize water molecule finder ---
-wat_find = DumpWaterMoleculeFinder(
+wat_find = LammpsDumpWaterFinder(
     filename,
     particle_type_wall={3},  # atom type for wall
     oxygen_type=1,  # atom type for oxygen
@@ -30,9 +30,12 @@
 print(f"Number of water molecules: {len(oxygen_indices)}")
 
 # --- Initialize parser ---
-parser = DumpParser(filename)
+parser = LammpsDumpParser(filename)
 
 # --- Extract only oxygen coordinates for frame 0 ---
+# For LammpsDumpParser, `indices` are LAMMPS particle IDs (because LAMMPS may
+# reorder atoms between frames). For XYZParser/AseParser, `indices` are
+# 0-based positional indices.
 oxygen_positions = parser.parse(frame_index=0, indices=oxygen_indices)
 print("Extracted oxygen coordinates shape:", oxygen_positions.shape)
 
@@ -41,7 +44,7 @@
 # print("All atom positions shape:", all_positions.shape)
 
 """
-Example: Using ASE_Parser and ASE_WaterMoleculeFinder
+Example: Using AseParser and AseWaterFinder
 
 This example demonstrates how to:
 1. Identify water oxygens in an ASE trajectory.
@@ -52,18 +55,19 @@
 filename = "../../tests/trajectories/slice_10_mace_mlips_cylindrical_2_5.traj"
 
 # --- Initialize water molecule finder ---
-wat_find = ASE_WaterMoleculeFinder(
+wat_find = AseWaterFinder(
     filename,
     particle_type_wall=["C"],  # element name for wall
-    oh_cutoff=0.4,  # O–H cutoff distance (Å)
+    oh_cutoff=1.2,  # O–H bond cutoff (Å); ASE NeighborList handles the
+    # per-atom splitting internally now.
 )
 
 # --- Get oxygen indices for frame 0 ---
 oxygen_indices = wat_find.get_water_oxygen_indices(frame_index=0)
 print(f"Number of water molecules: {len(oxygen_indices)}")
 
 # --- Initialize parser ---
-parser = ASE_Parser(filename)
+parser = AseParser(filename)
 
 # --- Extract oxygen coordinates only ---
 oxygen_positions = parser.parse(frame_index=0, indices=oxygen_indices)

docs/examples/sliced_ca.py

@@ -0,0 +1,39 @@
+"""Sliced contact-angle example.
+
+Runs the per-frame sliced (circle-fitting) analyzer on a LAMMPS dump
+file and prints the resulting mean contact angle.
+"""
+
+from wetting_angle_kit.contact_angle_methods import contact_angle_analyzer
+from wetting_angle_kit.parsers import LammpsDumpParser, LammpsDumpWaterFinder
+
+# --- Step 1: Define the trajectory file ---
+filename = "../../tests/trajectories/traj_spherical_drop_4k.lammpstrj"
+
+# --- Step 2: Identify the water molecules (oxygen-bonded-to-two-H) ---
+wat_find = LammpsDumpWaterFinder(
+    filename,
+    particle_type_wall={3},  # Wall atom types
+    oxygen_type=1,
+    hydrogen_type=2,
+)
+
+# `oxygen_indices` are LAMMPS particle IDs for the dump format.
+oxygen_indices = wat_find.get_water_oxygen_ids(frame_index=0)
+print("Number of water molecules:", len(oxygen_indices))
+
+# --- Step 3: Build the sliced analyzer ---
+parser = LammpsDumpParser(filename)
+analyzer = contact_angle_analyzer(
+    method="sliced",
+    parser=parser,
+    output_dir="results_sliced_example",
+    atom_indices=oxygen_indices,
+    droplet_geometry="spherical",
+    delta_gamma=20,  # Azimuthal step for spherical slicing (degrees)
+)
+
+# --- Step 4: Run analysis for a frame range ---
+results = analyzer.analyze([1])
+print("Mean contact angle (°):", results["mean_angle"])
+print("Frames analyzed:", results["frames_analyzed"])

docs/examples/visualisation_sliced_traj.py

@@ -1,38 +1,41 @@
+"""End-to-end example: sliced contact-angle pipeline plus visualization.
+
+Run a single-frame sliced analysis on a LAMMPS dump file and save a PNG of
+the droplet with the fitted circle, surface contour, and tangent at the
+contact point.
+"""
+
 import numpy as np
 
-from wetting_angle_kit.contact_angle_method.sliced_method import ContactAngleSliced
-from wetting_angle_kit.parser import (
-    DumpParser,
-    DumpWallParser,
-    DumpWaterMoleculeFinder,
+from wetting_angle_kit.contact_angle_methods.sliced import ContactAngleSliced
+from wetting_angle_kit.parsers import (
+    LammpsDumpParser,
+    LammpsDumpWallParser,
+    LammpsDumpWaterFinder,
 )
-from wetting_angle_kit.visualization_statistics_angles import Droplet_sliced_Plotter
+from wetting_angle_kit.visualization import DropletSlicePlotter
 
 # --- 1. Define the Input Trajectory ---
-# Note: Ensure this path points to your actual .lammpstrj file location
-filename = (
-    "../wetting_angle_kit/tests/trajectories/traj_10_3_330w_nve_4k_reajust.lammpstrj"
-)
+# Adjust this to point to your local .lammpstrj file.
+filename = "../../tests/trajectories/traj_10_3_330w_nve_4k_reajust.lammpstrj"
 
 # --- 2. Identify Water Molecules ---
-wat_find = DumpWaterMoleculeFinder(
+wat_find = LammpsDumpWaterFinder(
     filename, particle_type_wall={3}, oxygen_type=1, hydrogen_type=2
 )
 
 oxygen_indices = wat_find.get_water_oxygen_ids(frame_index=0)
 print("Number of water molecules detected:", len(oxygen_indices))
 
 # --- 3. Parse Atomic Coordinates ---
-parser = DumpParser(filepath=filename)
+parser = LammpsDumpParser(filepath=filename)
 oxygen_position = parser.parse(frame_index=10, indices=oxygen_indices)
 
-coord_wall = DumpWallParser(filename, particule_liquid_type={1, 2})
-wall_coords = coord_wall.parse(frame_index=1)
+# Wall particles are everything not in the liquid types.
+coord_wall = LammpsDumpWallParser(filename, liquid_particle_types=[1, 2])
+wall_coords = coord_wall.parse(frame_index=10)
 
 # --- 4. Compute Contact Angles ---
-#
-
-
 processor = ContactAngleSliced(
     liquid_coordinates=oxygen_position,
     liquid_geom_center=np.mean(oxygen_position, axis=0),
@@ -43,10 +46,10 @@
 )
 
 list_alfas, array_surfaces, array_popt = processor.predict_contact_angle()
-print("Mean contact angles (°):", list_alfas)
+print("Per-slice contact angles (°):", list_alfas)
 
 # --- 5. Visualize the Droplet ---
-plotter = Droplet_sliced_Plotter(center=True, show_wall=True, molecule_view=True)
+plotter = DropletSlicePlotter(center=True, show_wall=True, molecule_view=True)
 
 plotter.plot_surface_points(
     oxygen_position=oxygen_position,
@@ -57,4 +60,4 @@
     alpha=list_alfas[0],
 )
 
-print(" Plot saved as 'droplet_plot.png'")
+print("Plot saved as 'droplet_plot.png'")

docs/source/API/index.rst

@@ -6,7 +6,7 @@ Complete reference for all modules, classes, and functions in wetting_angle_kit.
 Parser Module
 -------------
 
-.. automodule:: wetting_angle_kit.parser
+.. automodule:: wetting_angle_kit.parsers
    :members:
    :undoc-members:
    :show-inheritance:
@@ -17,14 +17,14 @@ Contact Angle Methods
 Base Analyzer
 ^^^^^^^^^^^^^
 
-.. automodule:: wetting_angle_kit.contact_angle_method.contact_angle_analyzer
+.. automodule:: wetting_angle_kit.contact_angle_methods.analyzer
    :members:
    :show-inheritance:
 
 Sliced Method
 ^^^^^^^^^^^^^
 
-.. automodule:: wetting_angle_kit.contact_angle_method.sliced_method
+.. automodule:: wetting_angle_kit.contact_angle_methods.sliced
    :members:
    :undoc-members:
    :show-inheritance:
@@ -33,7 +33,7 @@ Sliced Method
 Binning Method
 ^^^^^^^^^^^^^
 
-.. automodule:: wetting_angle_kit.contact_angle_method.binning_method
+.. automodule:: wetting_angle_kit.contact_angle_methods.binning
    :members:
    :undoc-members:
    :show-inheritance:
@@ -42,7 +42,7 @@ Binning Method
 Visualization and Statistics
 -----------------------------
 
-.. automodule:: wetting_angle_kit.visualization_angles
+.. automodule:: wetting_angle_kit.visualization
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/conf.py

@@ -7,7 +7,7 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("../../"))
+sys.path.insert(0, os.path.abspath("../../src"))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

docs/source/introduction/Installation.rst

@@ -9,7 +9,9 @@ Before installing wetting_angle_kit, ensure you have the following prerequisites
 1. **Python 3.9 or higher**: Make sure you have Python 3.9 or higher installed on your system.
 2. **Conda**: Ensure you have Conda installed. If not, you can install it from `here <https://docs.conda.io/en/latest/miniconda.html>`_.
 
-## Optional Dependencies Strategy
+Optional Dependencies Strategy
+------------------------------
+
 OVITO and ASE are only imported inside the respective parser classes. Installing the package
 without extras keeps dependencies minimal. Calling an OVITO/ASE parser without installing
 raises a clear ImportError with installation instructions.
@@ -18,7 +20,7 @@ Installation Options
 --------------------
 
 Core (only for xyz file analysis)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash