From 60a8645486d6dc1abead575044041d89e2ea3eef Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Sun, 5 Feb 2023 18:07:22 +0100
Subject: [PATCH 01/19] remove np alias types

---
 prody/compounds/pdbligands.py | 6 +++---
 prody/dynamics/signature.py   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/prody/compounds/pdbligands.py b/prody/compounds/pdbligands.py
index c01e77987..8d2e795c1 100644
--- a/prody/compounds/pdbligands.py
+++ b/prody/compounds/pdbligands.py
@@ -158,9 +158,9 @@ def fetchPDBLigand(cci, filename=None):
     resnums = np.ones(n_atoms, dtype=ATOMIC_FIELDS['charge'].dtype)
 
     alternate_atomnames = np.zeros(n_atoms, dtype=ATOMIC_FIELDS['name'].dtype)
-    leaving_atom_flags = np.zeros(n_atoms, np.bool)
-    aromatic_flags = np.zeros(n_atoms, np.bool)
-    stereo_configs = np.zeros(n_atoms, np.bool)
+    leaving_atom_flags = np.zeros(n_atoms, bool)
+    aromatic_flags = np.zeros(n_atoms, bool)
+    stereo_configs = np.zeros(n_atoms, bool)
     ordinals = np.zeros(n_atoms, int)
 
     name2index = {}
diff --git a/prody/dynamics/signature.py b/prody/dynamics/signature.py
index 76c85e149..c59b069e2 100644
--- a/prody/dynamics/signature.py
+++ b/prody/dynamics/signature.py
@@ -1648,7 +1648,7 @@ def showSignatureDistribution(signature, **kwargs):
     bins = kwargs.pop('bins', 'auto')
     if bins == 'auto':
         _, bins = np.histogram(W.flatten(), bins='auto')
-    elif np.isscalar(bins) and isinstance(bins, (int, np.integer)):
+    elif np.isscalar(bins) and isinstance(bins, int):
         step = (W.max() - W.min())/bins
         bins = np.arange(W.min(), W.max(), step)
 

From 4cb4d0954acec7b3e9d14d8e49e9e8de6fa6e95f Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Sun, 5 Feb 2023 18:09:29 +0100
Subject: [PATCH 02/19] remove numpy restriction

---
 pyproject.toml | 2 +-
 setup.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9b6fb8603..033eb9b1c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.10,<1.24", "pyparsing", "scipy"]
\ No newline at end of file
+requires = ["setuptools", "wheel", "numpy>=1.10", "pyparsing", "scipy"]
\ No newline at end of file
diff --git a/setup.py b/setup.py
index f8a3b4541..99e03a3bb 100644
--- a/setup.py
+++ b/setup.py
@@ -12,9 +12,9 @@
     sys.exit()
 
 if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
-    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython<=1.76', 'pyparsing', 'scipy']
+    INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.76', 'pyparsing', 'scipy']
 else:
-    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython<=1.79', 'pyparsing', 'scipy', 'setuptools']
+    INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.79', 'pyparsing', 'scipy', 'setuptools']
 
 if sys.version_info[0] == 3:
     if sys.version_info[1] < 6:

From c891359a8589ec77527f07d605f3bfcfca88881e Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Sun, 5 Feb 2023 18:12:25 +0100
Subject: [PATCH 03/19] add back py 3.11 to actions

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index adc8efaf0..d72b9f224 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["2.7", "3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

From c4e537c03791527d4edaa594e262c829b67870ae Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Tue, 7 Feb 2023 14:12:59 +0100
Subject: [PATCH 04/19] compare arrays not msas

---
 prody/tests/sequence/test_analysis.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/prody/tests/sequence/test_analysis.py b/prody/tests/sequence/test_analysis.py
index b5e0b581f..f54f9f4ee 100644
--- a/prody/tests/sequence/test_analysis.py
+++ b/prody/tests/sequence/test_analysis.py
@@ -1205,7 +1205,7 @@ def testBuildMSAlocal(self):
         sequences = [ags[0].protein["A"].getSequence(), 
                      ags[1].protein["A"].getSequence()]
 
-        expect = parseMSA(pathDatafile('msa_3hsyA_3o21A.fasta'))
-        result = buildMSA(sequences, method="local", labels=["A2", "A3"])
+        expect = parseMSA(pathDatafile('msa_3hsyA_3o21A.fasta')).getArray()
+        result = buildMSA(sequences, method="local", labels=["A2", "A3"]).getArray()
         assert_array_equal(expect, result)
         
\ No newline at end of file

From 0e12f6c3301ed66ec56c11060b00781a97cf72ba Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Tue, 7 Feb 2023 19:17:45 +0100
Subject: [PATCH 05/19] dev install

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d72b9f224..3da9b6a12 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -31,7 +31,7 @@ jobs:
         source activate test
         conda install --yes numpy scipy nose pyparsing requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; fi
-        pip install .
+        pip install -e .
         python setup.py build_ext --inplace --force
     - name: Test with pytest
       run: |

From 4aba661ae070b97f58e842878af46d1435507dc0 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 9 Mar 2023 14:48:20 +0100
Subject: [PATCH 06/19] remove pfam tests

---
 prody/tests/database/test_pfam.py | 274 ------------------------------
 1 file changed, 274 deletions(-)
 delete mode 100644 prody/tests/database/test_pfam.py

diff --git a/prody/tests/database/test_pfam.py b/prody/tests/database/test_pfam.py
deleted file mode 100644
index 06d8bb95a..000000000
--- a/prody/tests/database/test_pfam.py
+++ /dev/null
@@ -1,274 +0,0 @@
-"""This module contains unit tests for :mod:`prody.database.pfam` module."""
-
-from numpy import tile, array, arange, ones
-from numpy.testing import assert_allclose
-
-from prody.tests import unittest
-from prody.database.pfam import searchPfam
-from prody.database.pfam import fetchPfamMSA
-from prody.database.pfam import parsePfamPDBs
-
-from prody.atomic.selection import Selection
-
-import os
-import shutil
-
-from prody import LOGGER
-LOGGER.verbosity = 'none'
-
-class TestSearchPfam(unittest.TestCase):
-    def setUp(self):
-        self.queries = ['P19491', 'GRIA2_RAT', '6qkcB', '6qkcI', 
-                        'VQVLLTTIGAFAAFGLMTIAISTDYWLYTRGLTHSGLWRICCLEGLK'\
-                            'RGVCVKINHFAEYLLRVVRASSIFPILSAILLLLGGVCVAASR'\
-                            'VYKSKRNIILGAGILFVAAGLSNIIGVIVYISANAGKNHYSYG'\
-                            'WSFYFGGLSFILAEVIGVLAVNIYIERSR']
-
-    def testUniprotAccMulti(self):
-        """Test the outcome of a simple search scenario using a Uniprot Accession 
-        for a multi-domain protein, AMPAR GluA2."""
-
-        a = searchPfam(self.queries[0])
-
-        self.assertIsInstance(a, dict,
-            'searchPfam failed to return a dict instance')
-        
-        self.assertEqual(sorted(list(a.keys())), 
-                           ['PF00060', 'PF01094', 'PF10613'],
-                           'searchPfam failed to return the right domain family IDs')
-
-    def testUniprotIdMulti(self):
-        """Test the outcome of a simple search scenario using a Uniprot ID
-        for a multi-domain protein, AMPAR GluA2."""
-
-        a = searchPfam(self.queries[1])
-
-        self.assertIsInstance(a, dict,
-            'searchPfam failed to return a dict instance')
-        
-        self.assertEqual(sorted(list(a.keys())), 
-                           ['PF00060', 'PF01094', 'PF10613'],
-                           'searchPfam failed to return the right domain family IDs')
-        
-    def testPdbIdChMulti(self):
-        """Test the outcome of a simple search scenario using a PDB ID
-        and chain ID for the same multi-domain protein from specifying chain B."""
-
-        a = searchPfam(self.queries[2])
-
-        self.assertIsInstance(a, dict,
-            'searchPfam failed to return a dict instance')
-        
-        self.assertEqual(sorted(list(a.keys())), 
-                           ['PF00060', 'PF01094', 'PF10613'],
-                           'searchPfam failed to return the right domain family IDs for AMPAR')
-        
-    def testPdbIdChSingle(self):
-        """Test the outcome of a simple search scenario using a PDB ID
-        and chain ID to get the single domain protein TARP g8 from chain I."""
-
-        a = searchPfam(self.queries[3])
-
-        self.assertIsInstance(a, dict,
-            'searchPfam failed to return a dict instance')
-        
-        self.assertEqual(sorted(list(a.keys())), 
-                           ['PF00822'],
-                           'searchPfam failed to return the right domain family IDs for TARP')
-        
-    def testSeqSingle(self):
-        """Test the outcome of a simple search scenario using the sequence 
-        of the single domain protein TARP g8 from 6qkc chain I."""
-
-        a = searchPfam(self.queries[4])
-
-        self.assertIsInstance(a, dict,
-            'searchPfam failed to return a dict instance')
-        
-        self.assertEqual(sorted(list(a.keys())), 
-                           ['PF00822'],
-                           'searchPfam failed to return the right domain family IDs for TARP')
-
-
-class TestFetchPfamMSA(unittest.TestCase):
-    
-    @classmethod
-    def setUpClass(self):
-        self.query = 'PF00822'
-
-        self.workdir = 'pfam_msa_tests'
-        if not os.path.exists(self.workdir):
-            os.mkdir(self.workdir)
-        os.chdir(self.workdir)
-
-    def testDefault(self):
-        """Test the outcome of fetching the domain MSA for claudins
-        with default parameters."""
-
-        b = fetchPfamMSA(self.query)
-
-        self.assertIsInstance(b, str,
-            'fetchPfamMSA failed to return a str instance')
-        
-        self.assertEqual(b, 'PF00822_full.sth')
-        
-        self.assertTrue(os.path.exists(b))
-
-
-    def testSeed(self):
-        """Test the outcome of fetching the domain MSA for claudins
-        with the alignment type argument set to seed"""
-
-        b = fetchPfamMSA(self.query, "seed")
-
-        self.assertIsInstance(b, str,
-            'fetchPfamMSA failed to return a str instance')
-        
-        self.assertEqual(b, 'PF00822_seed.sth')
-        
-        self.assertTrue(os.path.exists(b))
-
-        
-    def testFormat(self):
-        """Test the outcome of fetching the domain MSA for claudins
-        with keyword argument format set to fasta."""
-
-        b = fetchPfamMSA(self.query, format="fasta")
-
-        self.assertIsInstance(b, str,
-            'fetchPfamMSA failed to return a str instance')
-        
-        self.assertEqual(b, 'PF00822_full.fasta')
-        
-        self.assertTrue(os.path.exists(b))
-
-
-    def testFolder(self):
-        """Test the outcome of fetching the domain MSA for claudins
-        with keyword folder set to a folder that is made especially."""
-
-        folder = "new_folder"
-        os.mkdir(folder)
-        b = fetchPfamMSA(self.query, folder=folder)
-
-        self.assertIsInstance(b, str,
-            'fetchPfamMSA failed to return a str instance')
-        
-        self.assertEqual(b, 'new_folder/PF00822_full.slx')
-        
-        self.assertTrue(os.path.exists(b))
-    
-    @classmethod
-    def tearDownClass(self):
-        os.chdir('..')
-        shutil.rmtree(self.workdir)
-            
-
-class TestParsePfamPDBs(unittest.TestCase):
-    
-    @classmethod
-    def setUpClass(self):
-        self.queries = ['PF20446', 'Q57ZF2_TRYB2', 'VAS1_BOVIN']
-
-        self.workdir = 'pfam_pdb_tests'
-        if not os.path.exists(self.workdir):
-            os.mkdir(self.workdir)
-        os.chdir(self.workdir)
-
-    def testPfamIdDefault(self):
-        """Test the outcome of parsing PDBs for a tiny family 
-        of ABC class ATPase N-terminal domains (5 members) 
-        with the Pfam ID and default parameters."""
-
-        b = parsePfamPDBs(self.queries[0])
-
-        self.assertIsInstance(b, list,
-            'fetchPfamMSA failed to return a list instance')
-
-        self.assertIsInstance(b[0], Selection,
-            'fetchPfamMSA failed to return a list of Selection instances')
-        
-        self.assertEqual(len(b), 5,
-            'fetchPfamMSA failed to return a list of length 5')
-
-
-    def testUniprotDefault(self):
-        """Test the outcome of parsing PDBs for a tiny family 
-        of ABC class ATPase N-terminal domains (5 members) 
-        with the Uniprot long ID and default parameters."""
-
-        b = parsePfamPDBs(self.queries[1])
-
-        self.assertIsInstance(b, list,
-            'fetchPfamMSA failed to return a list instance')
-
-        self.assertIsInstance(b[0], Selection,
-            'fetchPfamMSA failed to return a list of Selection instances')
-        
-        self.assertEqual(len(b), 5,
-            'fetchPfamMSA failed to return a list of length 5')
-
-        
-    def testMultiDomainDefault(self):
-        """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, 
-        which has two domains but few relatives. Default parameters should 
-        return Selection objects containing the first domain."""
-
-        b = parsePfamPDBs(self.queries[2])
-
-        self.assertIsInstance(b, list,
-            'fetchPfamMSA failed to return a list instance')
-
-        self.assertIsInstance(b[0], Selection,
-            'fetchPfamMSA failed to return a list of Selection instances')
-        
-        self.assertEqual(len(b), 7,
-            'fetchPfamMSA failed to return a list of length 7')
-        
-        self.assertEqual(b[0].getResnums()[0], 262,
-            'fetchPfamMSA failed to return a first Selection with first resnum 262')        
-
-    def testMultiDomainStart1(self):
-        """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, 
-        which has two domains but few relatives. Using start=1 should be like default and 
-        return Selection objects containing the first domain."""
-
-        b = parsePfamPDBs(self.queries[2], start=1)
-
-        self.assertIsInstance(b, list,
-            'fetchPfamMSA failed to return a list instance')
-
-        self.assertIsInstance(b[0], Selection,
-            'fetchPfamMSA failed to return a list of Selection instances')
-        
-        self.assertEqual(len(b), 7,
-            'fetchPfamMSA failed to return a list of length 7')
-        
-        self.assertEqual(b[0].getResnums()[0], 262,
-            'fetchPfamMSA failed to return a first Selection with first resnum 262')  
-        
-    def testMultiDomainStart2(self):
-        """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, 
-        which has two domains but few relatives. Setting start to 418 should 
-        return Selection objects containing the second domain."""
-
-        b = parsePfamPDBs(self.queries[2], start=418)
-
-        self.assertIsInstance(b, list,
-            'fetchPfamMSA failed to return a list instance')
-
-        self.assertIsInstance(b[0], Selection,
-            'fetchPfamMSA failed to return a list of Selection instances')
-        
-        self.assertEqual(len(b), 23,
-            'fetchPfamMSA failed to return a list of length 23')
-        
-        self.assertEqual(b[0].getResnums()[0], 418,
-            'fetchPfamMSA failed to return a first Selection with first resnum 418')  
-        
-    @classmethod
-    def tearDownClass(self):
-        os.chdir('..')
-        shutil.rmtree(self.workdir)
-
-

From ec66ce1c96298c06fe7daf9bf2c046795c6a3b25 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 5 Oct 2023 11:58:00 +0200
Subject: [PATCH 07/19] update tests to use pytest mark as dec

---
 prody/tests/apps/test_prody_anm.py      | 5 ++++-
 prody/tests/apps/test_prody_catdcd.py   | 5 ++++-
 prody/tests/apps/test_prody_examples.py | 5 ++++-
 prody/tests/apps/test_prody_gnm.py      | 5 ++++-
 prody/tests/apps/test_prody_pca.py      | 5 ++++-
 prody/tests/atomic/test_select.py       | 5 ++++-
 prody/tests/dynamics/test_enms.py       | 5 ++++-
 prody/tests/dynamics/test_pca.py        | 5 ++++-
 prody/tests/proteins/test_ciffile.py    | 5 ++++-
 prody/tests/proteins/test_dssp.py       | 5 ++++-
 prody/tests/proteins/test_localpdb.py   | 5 ++++-
 prody/tests/proteins/test_pdbfile.py    | 5 ++++-
 prody/tests/proteins/test_wwpdb.py      | 5 ++++-
 13 files changed, 52 insertions(+), 13 deletions(-)

diff --git a/prody/tests/apps/test_prody_anm.py b/prody/tests/apps/test_prody_anm.py
index d49556f5b..99ed75b9f 100644
--- a/prody/tests/apps/test_prody_anm.py
+++ b/prody/tests/apps/test_prody_anm.py
@@ -8,7 +8,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 
diff --git a/prody/tests/apps/test_prody_catdcd.py b/prody/tests/apps/test_prody_catdcd.py
index 92e53d85f..b62462c27 100644
--- a/prody/tests/apps/test_prody_catdcd.py
+++ b/prody/tests/apps/test_prody_catdcd.py
@@ -7,7 +7,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import parsePDB, DCDFile, parseDCD
 
diff --git a/prody/tests/apps/test_prody_examples.py b/prody/tests/apps/test_prody_examples.py
index b12d275b7..5a122b144 100644
--- a/prody/tests/apps/test_prody_examples.py
+++ b/prody/tests/apps/test_prody_examples.py
@@ -9,7 +9,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import LOGGER
 LOGGER.verbosity = None
diff --git a/prody/tests/apps/test_prody_gnm.py b/prody/tests/apps/test_prody_gnm.py
index a084d84d2..26fe005b9 100644
--- a/prody/tests/apps/test_prody_gnm.py
+++ b/prody/tests/apps/test_prody_gnm.py
@@ -7,7 +7,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 
diff --git a/prody/tests/apps/test_prody_pca.py b/prody/tests/apps/test_prody_pca.py
index b186eb72f..bdd28611c 100644
--- a/prody/tests/apps/test_prody_pca.py
+++ b/prody/tests/apps/test_prody_pca.py
@@ -7,7 +7,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 
diff --git a/prody/tests/atomic/test_select.py b/prody/tests/atomic/test_select.py
index dc7797179..f76239105 100644
--- a/prody/tests/atomic/test_select.py
+++ b/prody/tests/atomic/test_select.py
@@ -8,7 +8,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/dynamics/test_enms.py b/prody/tests/dynamics/test_enms.py
index aaf932f12..2e72636da 100644
--- a/prody/tests/dynamics/test_enms.py
+++ b/prody/tests/dynamics/test_enms.py
@@ -6,7 +6,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/dynamics/test_pca.py b/prody/tests/dynamics/test_pca.py
index 7720e3274..9a3fc5822 100644
--- a/prody/tests/dynamics/test_pca.py
+++ b/prody/tests/dynamics/test_pca.py
@@ -6,7 +6,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_ciffile.py b/prody/tests/proteins/test_ciffile.py
index 1c768c117..2f168dd99 100644
--- a/prody/tests/proteins/test_ciffile.py
+++ b/prody/tests/proteins/test_ciffile.py
@@ -7,7 +7,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_dssp.py b/prody/tests/proteins/test_dssp.py
index 08700131c..11cf7bc4a 100644
--- a/prody/tests/proteins/test_dssp.py
+++ b/prody/tests/proteins/test_dssp.py
@@ -4,7 +4,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_localpdb.py b/prody/tests/proteins/test_localpdb.py
index 1d70f3dcd..9e8d4ec27 100644
--- a/prody/tests/proteins/test_localpdb.py
+++ b/prody/tests/proteins/test_localpdb.py
@@ -7,7 +7,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_pdbfile.py b/prody/tests/proteins/test_pdbfile.py
index 3f34f453a..dd9a8730b 100644
--- a/prody/tests/proteins/test_pdbfile.py
+++ b/prody/tests/proteins/test_pdbfile.py
@@ -7,7 +7,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_wwpdb.py b/prody/tests/proteins/test_wwpdb.py
index 8dd63fdb2..2b6c7df10 100644
--- a/prody/tests/proteins/test_wwpdb.py
+++ b/prody/tests/proteins/test_wwpdb.py
@@ -6,7 +6,10 @@
 try:
     import numpy.testing.decorators as dec
 except ImportError:
-    from numpy.testing import dec
+    try:
+        from numpy.testing import dec
+    except ImportError:
+        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER

From 41df3d4c4d709e162a5cce36d02981b0dd338f7b Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 5 Oct 2023 12:17:52 +0200
Subject: [PATCH 08/19] actually fix import dec and put it once in utilities
 function

---
 prody/tests/apps/test_prody_anm.py      |  9 ++-------
 prody/tests/apps/test_prody_catdcd.py   | 10 +++-------
 prody/tests/apps/test_prody_examples.py | 10 +++-------
 prody/tests/apps/test_prody_gnm.py      | 10 +++-------
 prody/tests/apps/test_prody_pca.py      | 10 +++-------
 prody/tests/atomic/test_select.py       | 10 +++-------
 prody/tests/dynamics/test_enms.py       | 10 +++-------
 prody/tests/dynamics/test_pca.py        | 10 +++-------
 prody/tests/proteins/test_ciffile.py    | 10 +++-------
 prody/tests/proteins/test_dssp.py       | 10 +++-------
 prody/tests/proteins/test_localpdb.py   | 10 +++-------
 prody/tests/proteins/test_pdbfile.py    | 10 +++-------
 prody/tests/proteins/test_wwpdb.py      | 10 +++-------
 prody/utilities/misctools.py            | 17 ++++++++++++++++-
 14 files changed, 54 insertions(+), 92 deletions(-)

diff --git a/prody/tests/apps/test_prody_anm.py b/prody/tests/apps/test_prody_anm.py
index 99ed75b9f..54011f913 100644
--- a/prody/tests/apps/test_prody_anm.py
+++ b/prody/tests/apps/test_prody_anm.py
@@ -5,13 +5,8 @@
 
 from numpy.testing import *
 
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+from prody.utilities import importDec
+dec = importDec()
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 
diff --git a/prody/tests/apps/test_prody_catdcd.py b/prody/tests/apps/test_prody_catdcd.py
index b62462c27..c6ae93178 100644
--- a/prody/tests/apps/test_prody_catdcd.py
+++ b/prody/tests/apps/test_prody_catdcd.py
@@ -4,13 +4,9 @@
 from prody.tests import TestCase, skipIf, skipUnless
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import parsePDB, DCDFile, parseDCD
 
diff --git a/prody/tests/apps/test_prody_examples.py b/prody/tests/apps/test_prody_examples.py
index 5a122b144..6b669d7be 100644
--- a/prody/tests/apps/test_prody_examples.py
+++ b/prody/tests/apps/test_prody_examples.py
@@ -6,13 +6,9 @@
 from subprocess import Popen, PIPE
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import LOGGER
 LOGGER.verbosity = None
diff --git a/prody/tests/apps/test_prody_gnm.py b/prody/tests/apps/test_prody_gnm.py
index 26fe005b9..ba50fce9d 100644
--- a/prody/tests/apps/test_prody_gnm.py
+++ b/prody/tests/apps/test_prody_gnm.py
@@ -4,13 +4,9 @@
 from prody.tests import TestCase, skipIf, skipUnless
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 
diff --git a/prody/tests/apps/test_prody_pca.py b/prody/tests/apps/test_prody_pca.py
index bdd28611c..5b1bddffb 100644
--- a/prody/tests/apps/test_prody_pca.py
+++ b/prody/tests/apps/test_prody_pca.py
@@ -4,13 +4,9 @@
 from prody.tests import TestCase, skipIf, skipUnless
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 
diff --git a/prody/tests/atomic/test_select.py b/prody/tests/atomic/test_select.py
index f76239105..70c685003 100644
--- a/prody/tests/atomic/test_select.py
+++ b/prody/tests/atomic/test_select.py
@@ -5,13 +5,6 @@
 import inspect
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
 
 from prody import *
 from prody import LOGGER
@@ -19,6 +12,9 @@
 from prody.tests.datafiles import *
 from prody.atomic.atommap import DUMMY
 
+from prody.utilities import importDec
+dec = importDec()
+
 prody.atomic.select.DEBUG = False
 LOGGER.verbosity = 'none'
 
diff --git a/prody/tests/dynamics/test_enms.py b/prody/tests/dynamics/test_enms.py
index 2e72636da..cb9a602b9 100644
--- a/prody/tests/dynamics/test_enms.py
+++ b/prody/tests/dynamics/test_enms.py
@@ -3,13 +3,9 @@
 import numpy as np
 from numpy import arange
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/dynamics/test_pca.py b/prody/tests/dynamics/test_pca.py
index 9a3fc5822..d58e0fc19 100644
--- a/prody/tests/dynamics/test_pca.py
+++ b/prody/tests/dynamics/test_pca.py
@@ -3,13 +3,9 @@
 import numpy as np
 from numpy import arange
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_ciffile.py b/prody/tests/proteins/test_ciffile.py
index 2f168dd99..15b020c57 100644
--- a/prody/tests/proteins/test_ciffile.py
+++ b/prody/tests/proteins/test_ciffile.py
@@ -4,13 +4,9 @@
 
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_dssp.py b/prody/tests/proteins/test_dssp.py
index 11cf7bc4a..6fd30b332 100644
--- a/prody/tests/proteins/test_dssp.py
+++ b/prody/tests/proteins/test_dssp.py
@@ -1,13 +1,9 @@
 """This module contains unit tests for :mod:`~prody.proteins`."""
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_localpdb.py b/prody/tests/proteins/test_localpdb.py
index 9e8d4ec27..7b087d572 100644
--- a/prody/tests/proteins/test_localpdb.py
+++ b/prody/tests/proteins/test_localpdb.py
@@ -4,13 +4,9 @@
 
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_pdbfile.py b/prody/tests/proteins/test_pdbfile.py
index dd9a8730b..c7e5ea9fa 100644
--- a/prody/tests/proteins/test_pdbfile.py
+++ b/prody/tests/proteins/test_pdbfile.py
@@ -4,13 +4,9 @@
 
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/tests/proteins/test_wwpdb.py b/prody/tests/proteins/test_wwpdb.py
index 2b6c7df10..a6657f635 100644
--- a/prody/tests/proteins/test_wwpdb.py
+++ b/prody/tests/proteins/test_wwpdb.py
@@ -3,13 +3,9 @@
 import os
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    try:
-        from numpy.testing import dec
-    except ImportError:
-        from pytest import mark as dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER
diff --git a/prody/utilities/misctools.py b/prody/utilities/misctools.py
index 20b7ef6fa..e72484771 100644
--- a/prody/utilities/misctools.py
+++ b/prody/utilities/misctools.py
@@ -21,7 +21,8 @@
            'getDataPath', 'openData', 'chr2', 'toChararray', 'interpY', 'cmp', 'pystr',
            'getValue', 'indentElement', 'isPDB', 'isURL', 'isListLike', 'isSymmetric', 'makeSymmetric',
            'getDistance', 'fastin', 'createStringIO', 'div0', 'wmean', 'bin2dec', 'wrapModes', 
-           'fixArraySize', 'decToHybrid36', 'hybrid36ToDec', 'DTYPE', 'checkIdentifiers', 'split', 'mad']
+           'fixArraySize', 'decToHybrid36', 'hybrid36ToDec', 'DTYPE', 'checkIdentifiers', 'split', 'mad',
+           'importDec']
 
 DTYPE = array(['a']).dtype.char  # 'S' for PY2K and 'U' for PY3K
 CURSORS = []
@@ -784,3 +785,17 @@ def _mad(x):
                 return median(abs(x - med))
     
     return _mad(x)
+
+
+def importDec():
+    """Returns one of :mod:`scipy.linalg` or :mod:`numpy.linalg`."""
+
+    try:
+        import numpy.testing.decorators as dec
+    except ImportError:
+        try:
+            from numpy.testing import dec
+        except ImportError:
+            import numpy.testing._private.decorators as dec
+
+    return dec

From 47c1fefaf29f3d09d251acf316d785340ee0d960 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 5 Oct 2023 12:23:55 +0200
Subject: [PATCH 09/19] fix missed dec in test_msafile

---
 prody/tests/sequence/test_msafile.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/prody/tests/sequence/test_msafile.py b/prody/tests/sequence/test_msafile.py
index cc80b9764..aae1015d8 100644
--- a/prody/tests/sequence/test_msafile.py
+++ b/prody/tests/sequence/test_msafile.py
@@ -5,12 +5,13 @@
 from os.path import join
 
 from numpy import array, log, zeros, char
-from numpy.testing import assert_array_equal, dec
+from numpy.testing import assert_array_equal
 
 from prody.tests.datafiles import *
 from prody.tests import TEMPDIR
 from prody import MSA, MSAFile, parseMSA, LOGGER, writeMSA
-from prody.utilities import createStringIO
+from prody.utilities import createStringIO, importDec
+dec = importDec()
 
 LOGGER.verbosity = None
 

From 3b6092ec07cc626f6f501cde82a87dc506ba8885 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 5 Oct 2023 12:47:49 +0200
Subject: [PATCH 10/19] restrict numpy <1.26

---
 pyproject.toml | 2 +-
 setup.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3140fa577..477ad58b3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.10", "pyparsing", "scipy"]
+requires = ["setuptools", "wheel", "numpy>=1.10,<1.26", "pyparsing", "scipy"]
diff --git a/setup.py b/setup.py
index 99e03a3bb..a118e6ab8 100644
--- a/setup.py
+++ b/setup.py
@@ -12,9 +12,9 @@
     sys.exit()
 
 if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
-    INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.76', 'pyparsing', 'scipy']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.26', 'biopython<=1.76', 'pyparsing', 'scipy']
 else:
-    INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.79', 'pyparsing', 'scipy', 'setuptools']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.26', 'biopython<=1.79', 'pyparsing', 'scipy', 'setuptools']
 
 if sys.version_info[0] == 3:
     if sys.version_info[1] < 6:

From fc181e1a7cacc4f13f7f2214751000de15d48f2a Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 5 Oct 2023 13:05:06 +0200
Subject: [PATCH 11/19] restrict numpy <1.25

---
 pyproject.toml | 2 +-
 setup.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 477ad58b3..853b7bc35 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.10,<1.26", "pyparsing", "scipy"]
+requires = ["setuptools", "wheel", "numpy>=1.10,<1.25", "pyparsing", "scipy"]
diff --git a/setup.py b/setup.py
index a118e6ab8..b9d566854 100644
--- a/setup.py
+++ b/setup.py
@@ -12,9 +12,9 @@
     sys.exit()
 
 if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
-    INSTALL_REQUIRES=['numpy>=1.10,<1.26', 'biopython<=1.76', 'pyparsing', 'scipy']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.25', 'biopython<=1.76', 'pyparsing', 'scipy']
 else:
-    INSTALL_REQUIRES=['numpy>=1.10,<1.26', 'biopython<=1.79', 'pyparsing', 'scipy', 'setuptools']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.25', 'biopython<=1.79', 'pyparsing', 'scipy', 'setuptools']
 
 if sys.version_info[0] == 3:
     if sys.version_info[1] < 6:

From 407f755aef83a27e1c7ad8fefb699aef8fa7eb61 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Thu, 5 Oct 2023 13:17:02 +0200
Subject: [PATCH 12/19] include pytest mark as option for dec

---
 prody/utilities/misctools.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/prody/utilities/misctools.py b/prody/utilities/misctools.py
index e72484771..47a399717 100644
--- a/prody/utilities/misctools.py
+++ b/prody/utilities/misctools.py
@@ -796,6 +796,9 @@ def importDec():
         try:
             from numpy.testing import dec
         except ImportError:
-            import numpy.testing._private.decorators as dec
+            try:
+                import numpy.testing._private.decorators as dec
+            except ImportError:
+                from pytest import mark as dec    
 
     return dec

From 1e52400a6bc761a253d7805ee43118ca9854cd7e Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Wed, 14 Feb 2024 12:40:07 -0500
Subject: [PATCH 13/19] fix insty test saving

---
 prody/tests/proteins/test_insty.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/prody/tests/proteins/test_insty.py b/prody/tests/proteins/test_insty.py
index 50648abec..0fd6a47ac 100644
--- a/prody/tests/proteins/test_insty.py
+++ b/prody/tests/proteins/test_insty.py
@@ -35,25 +35,25 @@ def setUp(self):
             np.save('test_2k39_all.npy', self.data_all, allow_pickle=True)
 
             self.data_hbs = calcHydrogenBondsTrajectory(self.ATOMS)
-            np.save('test_2k39_hbs.npy', self.data_hbs, allow_pickle=True)
+            np.save('test_2k39_hbs.npy', np.array(self.data_hbs, dtype=object), allow_pickle=True)
 
             self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS)
-            np.save('test_2k39_sbs.npy', self.data_sbs, allow_pickle=True)
+            np.save('test_2k39_sbs.npy', np.array(self.data_sbs, dtype=object), allow_pickle=True)
 
             self.data_rib = calcRepulsiveIonicBondingTrajectory(self.ATOMS)
-            np.save('test_2k39_rib.npy', self.data_rib, allow_pickle=True)
+            np.save('test_2k39_rib.npy', np.array(self.data_rib, dtype=object), allow_pickle=True)
 
             self.data_PiStack = calcPiStackingTrajectory(self.ATOMS)
-            np.save('test_2k39_PiStack.npy', self.data_PiStack, allow_pickle=True)
+            np.save('test_2k39_PiStack.npy', np.array(self.data_PiStack, dtype=object), allow_pickle=True)
 
             self.data_PiCat = calcPiCationTrajectory(self.ATOMS)
-            np.save('test_2k39_PiCat.npy', self.data_PiCat, allow_pickle=True)
+            np.save('test_2k39_PiCat.npy', np.array(self.data_PiCat, dtype=object), allow_pickle=True)
 
             self.data_hph = calcHydrophobicTrajectory(self.ATOMS)
-            np.save('test_2k39_hph.npy', self.data_hph, allow_pickle=True)
+            np.save('test_2k39_hph.npy', np.array(self.data_hph, dtype=object), allow_pickle=True)
 
             self.data_disu = calcDisulfideBondsTrajectory(self.ATOMS)
-            np.save('test_2k39_disu.npy', self.data_disu, allow_pickle=True)
+            np.save('test_2k39_disu.npy', np.array(self.data_disu, dtype=object), allow_pickle=True)
 
     def testAllInsteractions(self):
         """Test for all types of interactions."""

From 82529e90f8a43a7bedbaa0327b050c11610f745b Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 15 Mar 2024 10:39:20 +0100
Subject: [PATCH 14/19] limit pyparsing<=3.1.1

---
 .github/workflows/main.yml | 2 +-
 PKG-INFO                   | 4 ++--
 pyproject.toml             | 2 +-
 setup.py                   | 9 ++++-----
 4 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e5dbe065f..5a2924165 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -29,7 +29,7 @@ jobs:
         if [[ ${{ matrix.python-version }} != "2.7" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing requests
+        conda install --yes numpy scipy nose pyparsing<=3.1.1 requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; else conda install --yes pdbfixer; fi
         pip install mmtf-python scikit-learn
         pip install .
diff --git a/PKG-INFO b/PKG-INFO
index 6e9b73d1f..5f1719fe6 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -92,7 +92,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires: numpy (>=1.10)
-Requires: pyparsing
+Requires: pyparsing (<=3.1.1)
 Requires: biopython
 Requires: scipy
-Provides: prody (2.1.2)
+Provides: prody
diff --git a/pyproject.toml b/pyproject.toml
index 23456bfd3..146e85d9c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.10,<1.24", "pyparsing", "scipy"]
+requires = ["setuptools", "wheel", "numpy>=1.10,<1.24", "pyparsing<=3.1.1", "scipy"]
diff --git a/setup.py b/setup.py
index 47f62d6b8..0c457f33f 100644
--- a/setup.py
+++ b/setup.py
@@ -14,12 +14,11 @@
 if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
     INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython<=1.76', 'pyparsing', 'scipy']
 else:
-    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython', 'pyparsing', 'scipy', 'setuptools']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython', 'pyparsing<=3.1.1', 'scipy', 'setuptools']
 
-if sys.version_info[0] == 3:
-    if sys.version_info[1] < 6:
-        sys.stderr.write('Python 3.5 and older is not supported\n')
-        sys.exit()
+if sys.version_info[0] == 3 and sys.version_info[1] < 6:
+    sys.stderr.write('Python 3.5 and older is not supported\n')
+    sys.exit()
 
 if os.name == 'java':
     sys.stderr.write('JavaOS is not supported\n')

From aef076474193fb17b98b9fbef4848463b26abc77 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 15 Mar 2024 10:41:37 +0100
Subject: [PATCH 15/19] add py311 to actions

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5a2924165..a528a6a7a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10"]
+        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

From 4efaff6f5fa2708eb1edd8ddde901d20428cb8a5 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 15 Mar 2024 10:45:00 +0100
Subject: [PATCH 16/19] Revert "fix pfam test for pfam changes"

This reverts commit 052b291b1b0738172fcf3302400aebde4c4bc95d.
---
 prody/tests/database/test_pfam.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/prody/tests/database/test_pfam.py b/prody/tests/database/test_pfam.py
index 46adbf1f5..128473154 100644
--- a/prody/tests/database/test_pfam.py
+++ b/prody/tests/database/test_pfam.py
@@ -36,8 +36,9 @@ def testUniprotAccMulti(self):
         self.assertIsInstance(a, dict,
             'searchPfam failed to return a dict instance')
         
-        self.assertEqual(sorted(list(a.keys()))[:2], ['PF00060', 'PF00497'],
-                         'searchPfam failed to return the right domain family IDs')
+        self.assertEqual(sorted(list(a.keys())), 
+                           ['PF00060', 'PF00497', 'PF01094', 'PF10613'],
+                           'searchPfam failed to return the right domain family IDs')
         
     def testPdbIdChMulti(self):
         """Test the outcome of a simple search scenario using a PDB ID
@@ -48,7 +49,7 @@ def testPdbIdChMulti(self):
         self.assertIsInstance(a, dict,
             'searchPfam failed to return a dict instance')
         
-        self.assertEqual(sorted(list(a.keys()))[:2], ['PF00060', 'PF00497'],
+        self.assertEqual(sorted(list(a.keys())), ['PF00060', 'PF00497', 'PF01094', 'PF10613'],
                          'searchPfam failed to return the right domain family IDs for AMPAR')
         
     def testPdbIdChSingle(self):

From 2c73eaef0272deee019ed2f1637ef708649e4724 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 15 Mar 2024 10:49:01 +0100
Subject: [PATCH 17/19] remove pyparsing from actions conda install

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a528a6a7a..0a6b4f051 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -29,7 +29,7 @@ jobs:
         if [[ ${{ matrix.python-version }} != "2.7" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing<=3.1.1 requests
+        conda install --yes numpy scipy nose requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; else conda install --yes pdbfixer; fi
         pip install mmtf-python scikit-learn
         pip install .

From 7ab6a06c4deb137a1e17cdbbaa679d208372af61 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 15 Mar 2024 12:03:15 +0100
Subject: [PATCH 18/19] no pfam test revert

---
 prody/tests/database/test_pfam.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/prody/tests/database/test_pfam.py b/prody/tests/database/test_pfam.py
index 128473154..a255aaf16 100644
--- a/prody/tests/database/test_pfam.py
+++ b/prody/tests/database/test_pfam.py
@@ -36,8 +36,7 @@ def testUniprotAccMulti(self):
         self.assertIsInstance(a, dict,
             'searchPfam failed to return a dict instance')
         
-        self.assertEqual(sorted(list(a.keys())), 
-                           ['PF00060', 'PF00497', 'PF01094', 'PF10613'],
+        self.assertEqual(sorted(list(a.keys()))[:2], ['PF00060', 'PF00497'],
                            'searchPfam failed to return the right domain family IDs')
         
     def testPdbIdChMulti(self):
@@ -49,7 +48,7 @@ def testPdbIdChMulti(self):
         self.assertIsInstance(a, dict,
             'searchPfam failed to return a dict instance')
         
-        self.assertEqual(sorted(list(a.keys())), ['PF00060', 'PF00497', 'PF01094', 'PF10613'],
+        self.assertEqual(sorted(list(a.keys()))[:2], ['PF00060', 'PF00497'],
                          'searchPfam failed to return the right domain family IDs for AMPAR')
         
     def testPdbIdChSingle(self):

From afadd25bb634a5465f65daf0c2d938d6f27a8a09 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 15 Mar 2024 18:04:57 +0100
Subject: [PATCH 19/19] tostring to tobytes

---
 prody/sequence/msa.py      | 6 +++---
 prody/sequence/msafile.py  | 2 +-
 prody/sequence/sequence.py | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/prody/sequence/msa.py b/prody/sequence/msa.py
index f4bc3d5c6..5de2eb85d 100644
--- a/prody/sequence/msa.py
+++ b/prody/sequence/msa.py
@@ -154,7 +154,7 @@ def __getitem__(self, index):
         if isinstance(rows, list):
             rows = self.getIndex(rows) or rows
         elif isinstance(rows, int):
-            return Sequence(self._msa[rows, cols].tostring(),
+            return Sequence(self._msa[rows, cols].tobytes(),
                             self._labels[rows])
         elif isinstance(rows, str):
             try:
@@ -164,7 +164,7 @@ def __getitem__(self, index):
                                .format(index))
             else:
                 if isinstance(rows, int):
-                    return Sequence(self._msa[rows, cols].tostring(),
+                    return Sequence(self._msa[rows, cols].tobytes(),
                                     self._labels[rows])
 
         if cols is None:
@@ -546,7 +546,7 @@ def refineMSA(msa, index=None, label=None, rowocc=None, seqid=None, colocc=None,
                 from prody.utilities import GAP_PENALTY, GAP_EXT_PENALTY, ALIGNMENT_METHOD
 
                 chseq = chain.getSequence()
-                algn = alignBioPairwise(pystr(arr[index].tostring().upper()), pystr(chseq),
+                algn = alignBioPairwise(pystr(arr[index].tobytes().upper()), pystr(chseq),
                                         "local",
                                         MATCH_SCORE, MISMATCH_SCORE,
                                         GAP_PENALTY, GAP_EXT_PENALTY,
diff --git a/prody/sequence/msafile.py b/prody/sequence/msafile.py
index c665b9146..8719e6bad 100644
--- a/prody/sequence/msafile.py
+++ b/prody/sequence/msafile.py
@@ -433,7 +433,7 @@ def setSlice(self, slice):
                 else:
                     self._slice = slice
                     self._slicer = lambda seq, slc=slice: fromstring(seq,
-                                                        '|S1')[slc].tostring()
+                                                        '|S1')[slc].tobytes()
             else:
                 self._slice = slice
                 self._slicer = lambda seq, slc=slice: seq[slc]
diff --git a/prody/sequence/sequence.py b/prody/sequence/sequence.py
index c8477313b..6cc78b206 100644
--- a/prody/sequence/sequence.py
+++ b/prody/sequence/sequence.py
@@ -49,9 +49,9 @@ def _array(self):
     def __str__(self):
 
         if PY3K:
-            return self._array.tostring().decode()
+            return self._array.tobytes().decode()
         else:
-            return self._array.tostring()
+            return self._array.tobytes()
 
     def __len__(self):