Updating CG-HADDOCK branch from main version

.github/workflows/ci.yml

@@ -18,14 +18,15 @@ on:
 
 jobs:
   ci:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     permissions:
       contents: read
       actions: read
       checks: write
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
       fail-fast: false
 
     steps:
@@ -35,35 +36,36 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: install system dependencies
+      - name: install system dependencies (Linux)
+        if: runner.os == 'Linux'
         run: |
           sudo apt-get update
           sudo apt-get install -y openmpi-bin libopenmpi3 libopenmpi-dev
 
+      - name: install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install open-mpi
+
       - name: install haddock3 with extra dependencies
-        run: pip install '.[mpi,dev,docs,notebooks]'
+        run: pip install -e '.[mpi,dev,docs,notebooks]'
 
       - name: run unit tests
         run: >-
-          pytest --random-order tests/
-          --cov --cov-report=term-missing --cov-append
-          --hypothesis-show-statistics
+          pytest -v --random-order tests/
+          --cov --cov-report=
 
       - name: run integration tests
         run: >-
-          pytest --random-order integration_tests/
-          --cov --cov-report=term-missing --cov-append
-          --hypothesis-show-statistics
+          pytest -v --random-order integration_tests/
 
       - name: generate coverage report
         run: |
           coverage report
           coverage xml
 
       - uses: codacy/codacy-coverage-reporter-action@v1
-        if: >-
-          ${{ github.event_name != 'pull_request' ||
-          github.event.pull_request.head.repo.full_name == github.repository }}
+        if: matrix.python-version == '3.14'
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: ./coverage.xml
@@ -73,35 +75,3 @@ jobs:
         run: |
           sphinx-apidoc -f -e -o docs/ src/haddock -d 1
           sphinx-build docs haddock3-docs
-
-  dev:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      actions: read
-      checks: write
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.13"
-
-      - name: install system dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y openmpi-bin libopenmpi3 libopenmpi-dev
-
-      - name: install haddock3 in editable mode
-        run: pip install -e '.[mpi,dev,docs,notebooks]'
-
-      - name: check installed binaries
-        run: |
-          required_bins="contact_fcc cns haddock-restraints fast-rmsdmatrix"
-          for bin in $required_bins; do
-            if [ ! -x "src/haddock/bin/$bin" ]; then
-              echo "src/haddock/bin/$bin is missing or not executable"; exit 1;
-            fi
-          done
-          ls -l src/haddock/bin

.github/workflows/stale.yml

@@ -23,11 +23,12 @@ jobs:
         with:
           stale-pr-message: "This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days."
           stale-issue-message: "This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days."
-          close-pr-message: 'This PR was closed because it has been stalled for 5 days with no activity.'
-          close-issue-message: 'This issue was closed because it has been stalled for 5 days with no activity.'
+          close-pr-message: "This PR was closed because it has been stalled for 5 days with no activity."
+          close-issue-message: "This issue was closed because it has been stalled for 5 days with no activity."
           days-before-stale: 30
           days-before-close: 5
-          exempt-issue-labels: "bug"
+          exempt-issue-labels: "bug, planned-long-term"
           exempt-pr-labels: "bug"
+          exempt-draft-pr: true
           remove-stale-when-updated: true
           operations-per-run: 100

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+- 2025-12-15: Added missing NGA glycan parameters - Issue #1462
+- 2025-11-25: Simplify the use of multiple ambig archives
+- 2025-11-19: Corrected CNS verbosity settings - Issue #1446
+- 2025-11-19: Added zinc-finger docking example, related to Issue #1445
+- 2025-11-19: Corrected flexref module for Issue #1445 
+- 2025-11-17: Added possibility to use alascan with ligands - Issue #1411
+- 2025-10-22: Allow the definition of chain combinations to be used for scoring - Issue #1414
 - 2025-09-11: Added `grid` mode
 - 2025-09-11: Corrected antibody-antigen notebook - Issue #1383
 - 2025-09-09: Removes undesired directory created when running the uni-tests - Issue #1380

MANIFEST.in

@@ -27,4 +27,5 @@ recursive-include varia *.inc
 recursive-include varia *.lua
 recursive-include varia *.md
 include src/haddock/bin/*
+include src/haddock/cns/bin/*
 include src/haddock/libs/assets/*

README.md

@@ -2,14 +2,15 @@
 
 ![haddock3-logo](https://raw.githubusercontent.com/haddocking/haddock3/refs/heads/main/docs/figs/HADDOCK3-logo.png)
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10527751.svg)](https://doi.org/10.5281/zenodo.10527751)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16914680.svg)](https://doi.org/10.5281/zenodo.16914680)
 [![Research Software Directory](https://img.shields.io/badge/rsd-haddock3-00a3e3.svg)](https://research-software-directory.org/software/haddock3)
 [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
 [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8844/badge)](https://www.bestpractices.dev/projects/8844)
 
 [![Downloads](https://static.pepy.tech/badge/haddock3)](https://pepy.tech/project/haddock3)
 ![PyPI - Version](https://img.shields.io/pypi/v/haddock3)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/haddock3)
+[![SBGrid Badge](https://img.shields.io/badge/haddock3-blue?label=SBGrid&labelColor=%3D)](https://sbgrid.org/software/titles/haddock3)
 
 [![ci](https://github.com/haddocking/haddock3/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/haddock3/actions/workflows/ci.yml)
 [![pages](https://github.com/haddocking/haddock3/actions/workflows/pages.yml/badge.svg)](https://github.com/haddocking/haddock3/actions/workflows/pages.yml)

docs/INSTALL.md

@@ -81,32 +81,6 @@ the instructions on the project's website. Remember to install it under
 the same Python environment you created for HADDOCK3. If you have any
 doubts, please let us know.
 
-### `gdock` (outdated)
-
-1. Clone the latest version:
-
-```
-cd some-folder
-git clone https://github.com/rvhonorato/gdock.git
-```
-
-2. Install Python3+ dependencies
-
-```
-pip install deap scipy mgzip biopython
-```
-
-3. Set `GDOCK_PATH`
-
-```
-export GDOCK_PATH=some-folder
-```
-
-**Important**: These are not the full `gdock` installation
-instructions as only the model generation is used here. Please check the
-[repository page](https://github.com/rvhonorato/gdock) for more
-information.
-
 ## `openmm`
 
 The use of the openmm module requires the installation of both OpenMM and pdbfixer.