Correct type error to generate subnetwork in validation step.

koszullab · Apr 27, 2021 · e6b0dcd · e6b0dcd
1 parent a74366d
commit e6b0dcd
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Showing 6 changed files with 9 additions and 9 deletions.
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
@@ -26,8 +26,8 @@ jobs:
         
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{secrets.PYPI_USERNAME}}
-        TWINE_PASSWORD: ${{secrets.PYPI_PASSWORD}}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{secrets.PYPI_TOKEN}}
       run: |
         python setup.py sdist bdist_wheel
         twine upload dist/*
diff --git a/metator/partition.py b/metator/partition.py
@@ -262,7 +262,7 @@ def get_hamming_distance(core_bins_iterations, n_iter, threads):
     # matrix, in parallel
     step = 1000
     steps = np.arange(step, len(core_bins_iterations.index) + step, step)
-    split_core_bins = [core_bins_iterations[(k - step): k] for k in steps]
+    split_core_bins = [core_bins_iterations[(k - step) : k] for k in steps]
     pool = multiprocessing.Pool(processes=threads)
     res = pool.map(
         partial(

diff --git a/metator/validation.py b/metator/validation.py
@@ -271,11 +271,13 @@ def louvain_recursif(
 
             logger.info("Bin in progress: {0}".format(bin_id))
             subnetwork_file = join(tmpdir, "subnetwork_" + bin_id + ".txt")
-            bin_id = int(bin_id.split("_")[1])
+            bin_id = str(bin_id.split("_")[1])
 
             # Extract contigs
             list_contigs = list(
-                contigs_data["ID"][contigs_data["Overlapping_bin_ID"] == bin_id]
+                contigs_data["ID"][
+                    contigs_data.Overlapping_bin_ID.apply(str) == bin_id
+                ]
             )
 
             # Extract subnetwork

diff --git a/metator/version.py b/metator/version.py
@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = "1.0.0"
diff --git a/requirements.txt b/requirements.txt
@@ -8,5 +8,3 @@ pysam
 requests
 scipy
 sklearn
-seaborn
-setuptools
diff --git a/setup.py b/setup.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-"""A pipeline for binning metagenomic datasets from 3C data.
+"""A pipeline for binning metagenomic datasets from metaHiC data.
 """
 
 from setuptools import setup, find_packages
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,5 +8,3 @@ pysam @@
     requests
     scipy
     sklearn
-    seaborn
-    setuptools