v2.4.2 - bug fixes, feature updates, unit tests, ci/cd updates

amckenna41 · Nov 16, 2023 · 8e9c0dc · 8e9c0dc
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diff --git a/.github/workflows/deploy_pypi.yml b/.github/workflows/deploy_pypi.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest         #platform: [ubuntu-latest, macos-latest, windows-latest]
     strategy:
       matrix:
-        python-version: [3.8]  #deploying using one Python version on 1 runner
+        python-version: [3.9]  #deploying using one Python version on 1 runner
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -38,7 +38,7 @@ jobs:
       run: |
         python3 setup.py sdist bdist_wheel
         twine check dist/*
-        twine upload dist/*
+        twine upload dist/* --verbose
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}

diff --git a/.github/workflows/deploy_test_pypi.yml b/.github/workflows/deploy_test_pypi.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest         #platform: [ubuntu-latest, macos-latest, windows-latest]
     strategy:
       matrix:
-        python-version: [3.8]  #deploying using one Python version on 1 runner
+        python-version: [3.9]  #deploying using one Python version on 1 runner
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -39,7 +39,7 @@ jobs:
       run: |
         python3 setup.py sdist bdist_wheel
         twine check dist/*
-        twine upload --repository testpypi dist/*
+        twine upload --repository testpypi dist/* --verbose
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}

diff --git a/CONFIG.md b/CONFIG.md
@@ -52,13 +52,13 @@ These config files offer a more straightforward way of making any changes to the
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede.json"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede.json"
         },
       "pseudo_amino_acid_composition":
         {
@@ -101,7 +101,7 @@ These config files offer a more straightforward way of making any changes to the
 ## Below is an explanation of each of the parameters within the JSON config files:
 
 **Dataset Parameters:**
-* `dataset[dataset]` - name of dataset.
+* `dataset[dataset]` - path of dataset.
 * `dataset[sequence_col]` - name of sequence column in dataset holding protein sequences, if left blank 'sequence' will be used by default.
 * `dataset[activity]` - name of protein activity column in dataset being studied.
 
@@ -121,11 +121,11 @@ These config files offer a more straightforward way of making any changes to the
 * `descriptors[ctd][all]` - if True then all 7 of the available physiochemical descriptors will be used when calculating the CTD descriptors. Each proeprty generates 21 features so using all properties will output 147 features. Only 1 property used by default. 
 
 * `descriptors[sequence_order_coupling_number][maxlag]` - maximum lag; length of the protein must be not less than maxlag.
-* `descriptors[sequence_order_coupling_number][distance_matrix]` - physiochemical distance matrix for calculating sequence order coupling number.
+* `descriptors[sequence_order_coupling_number][distance_matrix]` - physiochemical distance matrix name for calculating sequence order coupling number.
 
 * `descriptors[quasi_sequence_order][maxlag]` - maximum lag; length of the protein must be not less than maxlag.
 * `descriptors[quasi_sequence_order][weight]` - weighting factor to use when calculating descriptor.
-* `descriptors[quasi_sequence_order][distance_matrix]` - path to physiochemical distance matrix for calculating quasi sequence order.
+* `descriptors[quasi_sequence_order][distance_matrix]` -  physiochemical distance matrix name for calculating quasi sequence order.
 
 * `descriptors[pseudo_amino_acid_composition][lambda]` - lambda parameter that reflects the rank correlation and should be a non-negative integer and not larger than the length of the protein sequence.
 * `descriptors[pseudo_amino_acid_composition][weight]` - weighting factor to use when calculating descriptor.

diff --git a/README.md b/README.md
@@ -53,8 +53,8 @@ Two additional <strong>custom-built</strong> softwares were created alongside `p
 Requirements
 ============
 * [Python][python] >= 3.8
-* [aaindex][aaindex] >= 1.1.1
-* [protpy][protpy] >= 1.1.10
+* [aaindex][aaindex] >= 1.1.2
+* [protpy][protpy] >= 1.2.0
 * [numpy][numpy] >= 1.24.2
 * [pandas][pandas] >= 1.5.3
 * [scikit-learn][sklearn] >= 1.2.1
@@ -531,6 +531,7 @@ python3 -m unittest discover tests
 To run tests for specific module, from the main `pySAR` repo folder run:
 ```
 python -m unittest tests.MODULE_NAME -v
+-v: verbose output flag
 ```
 
 Contact

diff --git a/TODO.md b/TODO.md
@@ -268,4 +268,9 @@ To Do List:
 - [X] Recalculate and reupload descriptors_thermostability.csv.
 - [X] Add info about the colunns and dimensions of each descriptors in pre-calculated csv file - fix Issue.
 - [X] When calculating all descriptors (get_all_descriptors(export=True)), add some sort of print/tracking functionality.
-- [X] Double check all links in readme.
+- [X] Double check all links in readme.
+- [ ] Add dimensions of each dataset to https://github.com/amckenna41/pySAR/tree/master/example_datasets.
+- [ ] Go over references in descriptors module - refer to protpy.
+- [X] Update distance matrices in configs - test once protpy published.
+- [ ] Add link to medium article.
+- [X] Update aaindex version on readme.
diff --git a/config/absorption.json b/config/absorption.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/config/enantioselectivity.json b/config/enantioselectivity.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order": 
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/config/localization.json b/config/localization.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/config/thermostability.json b/config/thermostability.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/pySAR/__init__.py b/pySAR/__init__.py
@@ -1,14 +1,14 @@
 """ pySAR software metadata. """
 __name__ = 'pySAR'
-__version__ = "2.4.1"
+__version__ = "2.4.2"
 __description__ = 'A Python package used to analysis Sequence Activity Relationships (SARs) of protein sequences and their mutants using Machine Learning.'
-__author__ = 'AJ McKenna, https://github.com/amckenna41'
+__author__ = 'AJ McKenna: https://github.com/amckenna41'
 __authorEmail__ = '[email protected]'
 __maintainer__ = "AJ McKenna"
 __license__ = 'MIT'
 __url__ = 'https://github.com/amckenna41/pySAR'
 __download_url__ = "https://github.com/amckenna41/pySAR/archive/refs/heads/main.zip"
 __status__ = "Production"
 __keywords__ = ["bioinformatics", "protein engineering", "python", "pypi", "machine learning", \
-        "directed evolution", "drug discovery", "sequence activity relationships", "SAR", "aaindex", "protein descriptors"]
+        "directed evolution", "drug discovery", "sequence activity relationships", "SAR", "aaindex", "protpy", "protein descriptors"]
 __test_suite__ = "tests"
diff --git a/pySAR/descriptors.py b/pySAR/descriptors.py
@@ -88,15 +88,17 @@ class Descriptors():
          Pseudo-Amino Acid Composition. PROTEINS: Structure, Function, and
          Genetics, 2001, 43: 246-255.
     [10] Kuo-Chen Chou. Using amphiphilic pseudo amino acid composition to predict enzyme
-          subfamily classes. Bioinformatics, 2005,21,10-19.
+         subfamily classes. Bioinformatics, 2005,21,10-19.
     [11] J. Shen et al., “Predicting protein-protein interactions based only on sequences
          information,” Proc. Natl. Acad. Sci. U. S. A., vol. 104, no. 11, pp. 4337–4341, 2007.
     [12] Gisbert Schneider and Paul Wrede. The Rational Design of Amino Acid Sequences
          by Artifical Neural Networks and Simulated Molecular Evolution: Do Novo Design
          of an Idealized Leader Cleavge Site. Biophys Journal, 1994, 66, 335-344.
-    [13]  Grantham, R. (1974-09-06). "Amino acid difference formula to help explain protein
+    [13] Grantham, R. (1974-09-06). "Amino acid difference formula to help explain protein
          evolution". Science. 185 (4154): 862–864. Bibcode:1974Sci...185..862G.
          doi:10.1126/science.185.4154.862. ISSN 0036-8075. PMID 4843792. S2CID 35388307.   
+    [14] B. Hollas, “An analysis of the autocorrelation descriptor for molecules,” J. Math. Chem., 
+        vol. 33, no. 2, pp. 91–101, 2003.
     """
     def __init__(self, config_file="", protein_seqs=None, **kwargs):
 

diff --git a/pySAR/pyDSP.py b/pySAR/pyDSP.py
@@ -451,9 +451,6 @@ def consensus_freq(self, freqs):
         if (freqs.ndim == 2 and freqs.shape[1] != 2):
             raise ValueError("Only one protein sequence should be passed into the function: {}.".format(freqs))
 
-        print(self.max_freq(freqs)[0])
-        print(self.num_seqs)
-        print((self.max_freq(freqs)[0])/self.num_seqs)
         # CF = PP/N ( peak position/length of largest protein in dataset)
         CF = (self.max_freq(freqs)[0])/self.num_seqs
         return CF

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = PySAR
-version = 2.4.1
+version = 2.4.2
 description = Analysing Sequence Activity Relationships (SARs) of protein sequences and their mutants using Machine Learning.
 author = AJ McKenna
 author_email = [email protected]

diff --git a/tests/test_config/test_absorption.json b/tests/test_config/test_absorption.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/tests/test_config/test_enantioselectivity.json b/tests/test_config/test_enantioselectivity.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order": 
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/tests/test_config/test_localization.json b/tests/test_config/test_localization.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/tests/test_config/test_thermostability.json b/tests/test_config/test_thermostability.json
@@ -45,13 +45,13 @@
       "sequence_order_coupling_number":
         {
         "lag": 30,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "quasi_sequence_order":
         {
         "lag": 30,
         "weight": 0.1,
-        "distance_matrix": "schneider-wrede-physiochemical-distance-matrix.json"
+        "distance_matrix": "schneider-wrede"
         },
       "pseudo_amino_acid_composition":
         {

diff --git a/tests/test_pySAR.py b/tests/test_pySAR.py
@@ -60,14 +60,14 @@ def setUp(self):
         if not (os.path.isdir(self.test_output_folder)):
             os.makedirs(self.test_output_folder)
 
-    @unittest.skip("Skipping metadata tests.")
+    # @unittest.skip("Skipping metadata tests.")
     def test_pySAR_metadata(self):
         """ Testing correct pySAR version and metadata. """
-        self.assertEqual(pysar_.__version__, "2.4.1", 
+        self.assertEqual(pysar_.__version__, "2.4.2", 
             "pySAR version is not correct, got: {}.".format(pysar_.__version__))
         self.assertEqual(pysar_.__name__, "pySAR", 
             "pySAR software name is not correct, got: {}.".format(pysar_.__name__))
-        self.assertEqual(pysar_.__author__, "AJ McKenna, https://github.com/amckenna41", 
+        self.assertEqual(pysar_.__author__, "AJ McKenna: https://github.com/amckenna41", 
             "pySAR author is not correct, got: {}.".format(pysar_.__author__))
         self.assertEqual(pysar_.__authorEmail__, "[email protected]", 
             "pySAR author email is not correct, got: {}.".format(pysar_.__authorEmail__))
@@ -83,7 +83,7 @@ def test_pySAR_metadata(self):
             "pySAR maintainer is not correct, got: {}.".format(pysar_.__license__))
         self.assertEqual(pysar_.__keywords__, ["bioinformatics", "protein engineering", "python", \
             "pypi", "machine learning", "directed evolution", "drug discovery", "sequence activity relationships", \
-            "SAR", "aaindex", "protein descriptors"], "pySAR keywords is not correct, got: {}.".format(pysar_.__keywords__))
+            "SAR", "aaindex", "protpy", "protein descriptors"], "pySAR keywords is not correct, got: {}.".format(pysar_.__keywords__))
 
     def test_pySAR(self):
         """ Testing pySAR intialisation process and associated methods & attributes. """