Merge pull request #169 from labgem/dev

Small patches on the v2.0.0

LICENSE.txt

@@ -20,7 +20,7 @@ the two main principles guiding its drafting:
 The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) 
 license are: 
 
-Commissariat � l'�nergie atomique et aux �nergies alternatives - CEA, a
+Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
 public scientific, technical and industrial research establishment,
 having its principal place of business at 25 rue Leblanc, immeuble Le
 Ponant D, 75015 Paris, France.
@@ -341,7 +341,7 @@ The Licensee expressly undertakes:
 
 The Licensee undertakes not to directly or indirectly infringe the
 intellectual property rights on the Software of the Holder and/or
-Contributors, and to take, where applicable, vis-�-vis its staff, any
+Contributors, and to take, where applicable, vis-à-vis its staff, any
 and all measures required to ensure respect of said intellectual
 property rights of the Holder and/or Contributors.
 

MANIFEST.in

@@ -1,5 +1,6 @@
-include README.rst
+include README.md
 include VERSION
 include LICENSE.txt
-recursive-include images *.png *.gif
+recursive-exclude docs *
+recursive-exclude testingDataset *
 recursive-include ppanggolin *

VERSION

@@ -1 +1 @@
-2.0.0
+2.0.1

pyproject.toml

@@ -35,7 +35,7 @@ classifiers=[
     "Programming Language :: Python :: 3",
     "Topic :: Scientific/Engineering :: Bio-Informatics"]
 requires-python = ">=3.8"
-license = {file="LICENCE.txt"}
+license = {file="LICENSE.txt"}
 
 [project.optional-dependencies]
 doc = [
@@ -67,9 +67,8 @@ python_deps = [
 [project.urls]
 Homepage = "https://labgem.genoscope.cns.fr/2023/04/27/ppanggolin/"
 Repository = "https://github.com/labgem/PPanGGOLiN/"
+Documentation = "https://ppanggolin.readthedocs.io"
 #Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
-#Documentation = "https://readthedocs.org"
-#
 #
 [project.scripts]
 ppanggolin = "ppanggolin.main:main"

setup.py

@@ -7,7 +7,7 @@
 setup(
     ext_modules=[
         Extension(
-            extra_compile_args=['-fcommon'],
+            extra_compile_args=['-fcommon', '-Wno-int-conversion'],
             name="nem_stats",
             sources=[NEM_DIR_PATH + 'nem_stats.pyx',
                      NEM_DIR_PATH + 'nem_exe.c',