int fixed

.github/workflows/ci.yml

@@ -0,0 +1,58 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      # 🔧 NEW: ensure modern packaging tools before installing anything
+      - name: Upgrade pip, setuptools, and wheel
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install pytest pytest-cov flake8
+
+      - name: Install package
+        run: pip install -e .
+
+      - name: Lint with flake8
+        run: |
+          # Fail on syntax errors or undefined names; treat everything else as a warning
+          flake8 pylipid --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 pylipid --count --exit-zero --max-line-length=120 --statistics
+
+      - name: Run tests
+        run: |
+          pytest tests/ -v --cov=pylipid --cov-report=term-missing
+
+      - name: Upload coverage report
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: .coverage

README.rst

@@ -1,65 +1,135 @@
+PyLipID - Analysis of Protein–Lipid Interactions from Molecular Dynamics
+============================================================
 
-==========================================================
-PyLipID - A Python Package For Lipid Interactions Analysis
-==========================================================
-
-.. image:: https://travis-ci.com/wlsong/PyLipID.svg?branch=master
-   :target: https://travis-ci.com/github/wlsong/PyLipID
+.. image:: https://github.com/pstansfeld/PyLipID/actions/workflows/ci.yml/badge.svg
+   :target: https://github.com/pstansfeld/PyLipID/actions/workflows/ci.yml
 .. image:: https://img.shields.io/pypi/v/PyLipID
    :target: https://pypi.org/project/pylipid/
+.. image:: https://img.shields.io/pypi/pyversions/PyLipID
+   :target: https://pypi.org/project/pylipid/
 
 .. image:: docs/static/pylipid_logo_smallsize.png
-    :align: center
+   :align: center
 
+PyLipID is a Python package for analysing lipid–protein interactions from
+Molecular Dynamics (MD) simulations. It supports coarse-grained and all-atom
+simulations, handles formats supported by MDTraj, and works in scripts or
+Jupyter notebooks.
 
-PyLipID is a python package for analyzing lipid interactions with membrane proteins from
-Molecular Dynamics Simulations. PyLipID has the following main features, please check out
-the tutorials for examples and the documentations for the API functionalities:
+Documentation: https://pylipid.readthedocs.io
 
-    * Detection of binding sites via calculating community structures in the interactions networks.
-    * Calculation of lipid koff and residence time for interaction with binding sites and residues.
-    * Analysis of lipid interactions with binding sites and residues using a couple of metrics.
-    * Generation of representative bound poses for binding sites.
-    * Analysis of bound poses for binding sites via automated clustering scheme.
-    * Adoption of a dual-cutoff scheme to overcome the 'rattling in cage' effect of coarse-grained simulations.
-    * Generation of manuscript-ready figures for analysis.
+Features
+========
 
-PyLipID can be used from Jupyter (former IPython, recommended), or by writing Python scripts.
-The documentaion and tutorials can be found at `pylipid.readthedocs.io <https://pylipid.readthedocs.io>`_.
+- Dual-cutoff contact detection to improve coarse-grained accuracy.
+- Binding site detection using NetworkX Louvain community analysis.
+- Kinetic parameters: koff and residence times per residue and site.
+- Interaction metrics including occupancy, count, duration.
+- Representative bound pose extraction and clustering.
+- SASA calculations per residue and site.
+- Publication-ready plots and PyMOL scripts.
 
 Installation
 ============
 
-We recommend installing PyLipID using the package installer `pip`:
+From PyPI::
+
+    pip install pylipid
+
+From source::
+
+    git clone https://github.com/pstansfeld/PyLipID
+    cd PyLipID
+    pip install .
+
+Editable/development install::
+
+    pip install -e .
+
+Requires Python >= 3.9.
 
-``pip install pylipid``
+Quick Start
+===========
 
-Alternatively, PyLipID can be installed from the source code. The package is available for
-download on Github via:
+.. code-block:: python
 
-``git clone https://github.com/wlsong/PyLipID``
+    from pylipid.api import LipidInteraction
 
-Once the source code is downloaded, enter the source code directory and install the package as follow:
+    trajfile_list = ["run1/protein_lipids.xtc", "run2/protein_lipids.xtc"]
+    topfile_list  = ["run1/protein_lipids.gro", "run2/protein_lipids.gro"]
 
-``python setup.py install``
+    li = LipidInteraction(
+        trajfile_list,
+        topfile_list=topfile_list,
+        cutoffs=[0.55, 0.8],
+        lipid="CHOL",
+        nprot=1,
+    )
 
+    li.collect_residue_contacts()
+    li.compute_residue_duration()
+    li.compute_residue_koff()
+    li.compute_binding_nodes(threshold=4)
+    li.compute_site_koff()
 
-Citation |DOI for Citing PyEMMA|
-================================
+    li.plot("Residence Time")
+    li.save_data("Dataset")
+    li.save_pymol_script(pdb_file="receptor.pdb")
 
-If you use PyLipID in scientific research, please cite the following paper: ::
+What's New in v1.6.0
+====================
 
-	@article{song_pylipid_2022,
-		author = {Song, Wanling. and Corey, Robin A. and Ansell, T. Bertie. and
-		            Cassidy, C. Keith. and Horrell, Michael R. and Duncan, Anna L.
-		            and Stansfeld, Phillip J. and Sansom, Mark S.P.},
-		title = {PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations},
-		journal = {J. Chem. Theory Comput},
-		year = {2022},
-		url = {https://doi.org/10.1021/acs.jctc.1c00708},
-		doi = {10.1021/acs.jctc.1c00708},
-		urldate = {2022-02-18},
-	}
+Bug Fixes
+---------
+- Corrected binding-site detection off-by-one error.
+- Fixed calculate_scores returning None.
+- Fixed sparse_corrcoef matrix type issues.
+- Fixed DataFrame column/index mismatches in analyze_bound_poses.
+- Fixed missing return in compute_residue_lipidcount.
+- Fixed write_PDB errors for .gro files lacking chain IDs.
+- Fixed figure overwriting in plot_koff.
+- Updated deprecated Matplotlib calls.
+- Fixed LogNorm crash on zero-containing matrices.
+- Replaced np.float128 with np.longdouble.
+- Corrected output directory typo.
 
-.. |DOI for Citing PyEMMA| image:: https://img.shields.io/badge/DOI-10.1021/acs.jctc.1c00708-blue
+Performance
+-----------
+- collect_residue_contacts now calls md.compute_distances once per residue.
+- Nested progress bars implemented.
+
+Dependencies
+------------
+- Removed python-louvain; using NetworkX built-in Louvain.
+- Minimum versions added.
+- Dropped Python < 3.9.
+
+Packaging & CI
+--------------
+- Migrated to pyproject.toml.
+- CI moved from Travis CI to GitHub Actions.
+
+Citation
+========
+
+.. image:: https://img.shields.io/badge/DOI-10.1021/acs.jctc.1c00708-blue
    :target: https://doi.org/10.1021/acs.jctc.1c00708
+
+::
+
+    @article{song_pylipid_2022,
+        author  = {Song, Wanling and Corey, Robin A. and Ansell, T. Bertie and
+                   Cassidy, C. Keith and Horrell, Michael R. and Duncan, Anna L.
+                   and Stansfeld, Phillip J. and Sansom, Mark S.P.},
+        title   = {PyLipID: A Python package for analysis of protein-lipid
+                   interactions from MD simulations},
+        journal = {J. Chem. Theory Comput.},
+        year    = {2022},
+        doi     = {10.1021/acs.jctc.1c00708},
+        url     = {https://doi.org/10.1021/acs.jctc.1c00708},
+    }
+
+License
+=======
+
+MIT License. See LICENSE.txt.

pylipid/__init__.py

@@ -14,4 +14,26 @@
 # copies or substantial portions of the Software.
 ##############################################################################
 
+# --- BEGIN: macOS-safe bootstrap -------------------------------------------
+# Ensures PyLipID runs safely on macOS by:
+#   1) forcing multiprocessing to use 'spawn'
+#   2) preventing GUI backends from loading in worker processes
+import multiprocessing as _mp
+
+try:
+    # Safe on macOS — harmless on Linux/Windows
+    _mp.set_start_method("spawn", force=True)
+except RuntimeError:
+    # Already set or protected — ignore
+    pass
+
+# Use a non-interactive backend so importing PyLipID never loads macOS AppKit
+try:
+    import matplotlib
+    matplotlib.use("Agg", force=True)
+except Exception:
+    pass
+# --- END: macOS-safe bootstrap ---------------------------------------------
+
 from ._version import __version__
+from .api import LipidInteraction

pylipid/_version.py

@@ -14,4 +14,4 @@
 # copies or substantial portions of the Software.
 ##############################################################################
 
-__version__ = '1.5.14'
+__version__ = '1.6.0'