prody · vbadwaj · Jul 18, 2025 · Jul 18, 2025 · Jul 22, 2025
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,43 +1,40 @@
-# This is a basic workflow to help you get started with Actions
-
 name: CI
-
-# Controls when the action will run.
 on: [push, pull_request, workflow_dispatch]
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   build:
-    runs-on: ubuntu-latest
+    # run once for each OS / Python combo
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, macos-latest]
         python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: MatteoH2O1999/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda create --yes -n test python=${{ matrix.python-version }}
-        source activate test
-        conda config --add channels conda-forge
-        conda install --yes numpy scipy nose requests
-        conda install --yes pdbfixer mdtraj openmm
-        conda install -c bioconda clustalw
-        pip install mmtf-python scikit-learn
-        pip install .
-        python setup.py build_ext --inplace --force
-    - name: Test with pytest
-      run: |
-        source activate test
-        conda install --yes pytest
-        pytest
-
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: MatteoH2O1999/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Add conda to PATH
+        run: echo $CONDA/bin >> $GITHUB_PATH
+
+      - name: Install dependencies & build
+        run: |
+          conda create -n test python=${{ matrix.python-version }} --yes
+          source activate test
+          conda config --add channels conda-forge
+          conda install --yes numpy scipy nose requests pdbfixer mdtraj openmm
+          conda install -c bioconda --yes clustalw
+          pip install mmtf-python scikit-learn
+          pip install .
+          python setup.py build_ext --inplace --force
+
+      - name: Test with pytest
+        run: |
+          source activate test
+          conda install --yes pytest
+          pytest
diff --git a/INSTALL.rst b/INSTALL.rst
@@ -6,7 +6,7 @@ Installation
 Required Software
 -----------------
 
-* `Python`_ 2.7, 3.6 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages. 
+* `Python`_ 3.10 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages. 
 
 .. _Anaconda: https://www.anaconda.com/products/individual
 
@@ -32,24 +32,14 @@ this package.
 Quick Install
 -------------
 
-If you have pip_ installed, type the following::
 
-  pip install -U ProDy
+We officially recommend installing through conda::
 
-If you don't have pip_, please download an installation file and
-follow the instructions.
+  conda install -c conda-forge prody
 
-If you have conda installed, you can also type the following instead::
 
-  conda install ProDy
-
-
-Download & Install
-------------------
-
-After installing the required packages, you will need to download a suitable
-ProDy source or installation file from http://python.org/pypi/ProDy.
-For changes and list of new features see :ref:`changes`.
+Installing From Source (not recommended)
+----------------------------------------
 
 **Linux**
 
@@ -72,23 +62,9 @@ schemes in `Installing Python Modules`_.
 
 For installing ProDy, please follow the Linux installation instructions.
 
-**Windows**
-
-Remove previously installed ProDy release from :program:`Uninstall a program`
-in :guilabel:`Control Panel`.
-
-Download :file:`ProDy-1.{x}.{y}.win32-py2.{z}.exe` and run to install ProDy.
-
-To be able use :ref:`prody-apps` and :ref:`evol-apps` in command prompt
-(:program:`cmd.exe`), append Python and scripts folders (e.g.
-:file:`C:\\Python27` and :file:`C:\\Python27\\Scripts`) to :envvar:`PATH`
-environment variable.
-
 Recommended Software
 --------------------
 
-* `Scipy`_, when installed, replaces linear algebra module of Numpy.
-  Scipy linear algebra module is more flexible and can be faster.
 * `IPython`_ is a must have for interactive ProDy sessions.
 * `PyReadline`_ for colorful IPython sessions on Windows.
 * `MDAnalysis`_ or `MDTraj`_ for reading molecular dynamics trajectories.
@@ -109,6 +85,9 @@ Following software is included in the ProDy installation packages:
 * `argparse`_ is used to implement applications and provided for
   compatibility with Python 2.6.
 
+* `Scipy`_, when installed, replaces linear algebra module of Numpy.
+  Scipy linear algebra module is more flexible and can be faster.
+
 .. _argparse: http://code.google.com/p/argparse/
 
 

diff --git a/PKG-INFO b/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.5.0
+Version: 2.6.0
 Summary: A Python Package for Protein Dynamics Analysis
 Home-page: http://www.csb.pitt.edu/ProDy
 Author: James Krieger, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others
@@ -84,10 +84,8 @@ Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: MacOS
-Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry

diff --git a/README.rst b/README.rst
@@ -35,10 +35,12 @@ Further details are described in the ProDy papers:
   | *Bioinformatics* **2021** 37(20):3657-3659.
 
 INSTALLING PRODY
-________
-ProDy is under active development, so we recommend installing it from source from GitHub to ensure everything works properly. 
+________________
+We recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments. ProDy can be installed with the following command.
 
-We recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments. 
+conda install -c conda-forge ProDy
+
+ProDy is under active development, install it from source from GitHub if you want the most recent fixes. 
 
 Then you should download the ProDy code either as a zipped folder to extract or using git as directed at the big green button says code. For example, if you have git installed then you can do the following.
 

diff --git a/docs/release/v2.6_series.rst b/docs/release/v2.6_series.rst
@@ -0,0 +1,36 @@
+ProDy 2.6 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+
+2.6.0 (Jul 18, 2024)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+* Support for extended PDB IDs
+* Trajectory wrapping 
+* py3Dmol visualization
+* Expanded CIF file support
+* Write long resnames
+* RTB app
+
+**Bug Fixes and Improvements**:
+
+* Python 3.12 support
+* NumPy 2 support
+* KDTree extension fix
+* Fixes for WatFinder, InSty, Scipion, ClustENM(D)
+* pfam fixes
+* Test fixes 
+
+
+
+**New Contributors**:
+
+* @vbadwaj - conda release and bug fixes
+* @AnthonyBogetti - general maintenance and bug fixes
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.5.0...v2.6.0
diff --git a/prody/__init__.py b/prody/__init__.py
@@ -1,18 +1,17 @@
 """ProDy is a package for Protein Dynamics, Sequence, and Structure Analysis"""
 
-__version__ = '2.5.0'
+__version__ = '2.6.0'
 __release__ = __version__ # + '-dev' # comment out '-dev' before a release
 
 import sys
 import warnings
 
 if sys.version_info[:2] < (2, 7):
     sys.stderr.write('Python 2.6 and older is not supported\n')
-    sys.exit()
 
 if sys.version_info[0] == 3:
-    if sys.version_info[1] < 6:
-        sys.stderr.write('Python 3.5 and older is not supported\n')
+    if sys.version_info[1] < 10:
+        sys.stderr.write('Python 3.9 and older is not supported\n')
         sys.exit()
 
 try:

diff --git a/setup.py b/setup.py
@@ -186,10 +186,8 @@
                  'Intended Audience :: Science/Research',
                  'License :: OSI Approved :: MIT License',
                  'Operating System :: MacOS',
-                 'Operating System :: Microsoft :: Windows',
                  'Operating System :: POSIX',
                  'Programming Language :: Python',
-                 'Programming Language :: Python :: 2',
                  'Programming Language :: Python :: 3',
                  'Topic :: Scientific/Engineering :: Bio-Informatics',
                  'Topic :: Scientific/Engineering :: Chemistry',