From e6b0dcde44a4c6031ca9c8b33f49b7971371627a Mon Sep 17 00:00:00 2001
From: ABignaud <amaury.bignaud@pasteur.fr>
Date: Tue, 27 Apr 2021 16:23:36 +0200
Subject: [PATCH] Correct type error to generate subnetwork in validation step.

---
 .github/workflows/pypi-publish.yml | 4 ++--
 metator/partition.py               | 2 +-
 metator/validation.py              | 6 ++++--
 metator/version.py                 | 2 +-
 requirements.txt                   | 2 --
 setup.py                           | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
index 288a431..dd2b996 100644
--- 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/*
\ No newline at end of file
diff --git a/metator/partition.py b/metator/partition.py
index 319ba50..99a47ab 100644
--- 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
index 3c18e27..8e4c9b2 100644
--- 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
index 1f356cc..5becc17 100644
--- 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
index ccd1644..cdc9931 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,5 +8,3 @@ pysam
 requests
 scipy
 sklearn
-seaborn
-setuptools
diff --git a/setup.py b/setup.py
index f469f4f..37cc513 100644
--- 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