Merge branch 'codedev' of https://github.com/mikelkou/fava into codedev

.github/workflows/build-and-publish.yaml

@@ -22,7 +22,7 @@ jobs:
           pip install build setuptools oldest-supported-numpy flake8
       - name: Check for syntax errors
         run: |
-          flake8 ./favapy --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 src/favapy --count --select=E9,F63,F7,F82 --show-source --statistics
       - name: Build sdist and wheels
         run: python -m build
       - uses: actions/upload-artifact@v2
@@ -67,4 +67,4 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

README.md

@@ -40,7 +40,9 @@ favapy <path-to-data-file> <path-to-save-output>
 
 -n The number of interactions in the output file (with both directions, proteinA-proteinB and proteinB-proteinA). Default value = 100000.
 
--c The cut-off on the Pearson Correlation scores.The scores can range from 1 (high correlation) to -1 (high anti-correlation). This option overwrites the number of interactions. Default value = None.
+-cor Type of correlation method ('pearson' or 'spearman'). Default value = 'pearson'
+
+-c The cut-off on the Correlation scores.The scores can range from 1 (high correlation) to -1 (high anti-correlation). This option overwrites the number of interactions. Default value = None.
 
 -d The dimensions of the intermediate\hidden layer. Default value depends on the input size.
 
@@ -50,6 +52,7 @@ favapy <path-to-data-file> <path-to-save-output>
 
 -b The  batch size. Default value = 32.
 
+
 ```
 
 If FAVA is useful for your research, consider citing [FAVA BiorXiv](https://doi.org/10.1101/2022.07.06.499022).