Preparing project directory

LICENSE

+-  Licencied under CeCill-C
+   (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and
+   GPLv3
+
+-  Intellectual property belongs to IRD/UMR DIADE.
+
+-  Written by Clothilde Chenal and Christine Tranchant-Dubreuil
+
+-  Copyright 2021

LICENSE.md

-* Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and GPLv3
-
-* Intellectual property belongs to IRD/UMR DIADE.
-
-* Written by Clothilde Chenal and Christine Tranchant-Dubreuil
-
-* Copyright 2021
\ No newline at end of file

README.md

-<img src="docs/source/_images/frangiPANe.png" width=60% align=center>
-
-frangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assembly approach. It consists in a Jupyter Notebook application that centralizes code,documentation and interactive visualizations together
-
- ### Requirements
-
- * Docker : https://docs.docker.com/get-docker/
- * Python3 (v3.9.7) : https://www.python.org/
- * biopython : https://biopython.org/
- * panel : https://panel.holoviz.org/
-
- * abyss : https://github.com/bcgsc/abyss/blob/master/README.md
- * bwa (v. 0.7.17) : https://github.com/lh3/bwa/blob/master/README.md
- * ea-utils (fastq-stats, v 1.01) : https://expressionanalysis.github.io/ea-utils/
- * samtools (v1.10) : http://www.htslib.org/
- * assembly-stats : https://github.com/sanger-pathogens/assembly-stats
- * cd-hit : https://github.com/weizhongli/cdhit/blob/master/README
- * mnimap2
- * girafe 
-
-### How to use FrangiPANe ?
-
-##### Clone the git repository  
-
-```
-git clone ...
-```
-
-
-##### Run FrangiPANe
-
-```
- snakemake -r -c1
-```
-
-* Download a dataset to test frangiPANe 
-
-```
-wget https://itrop.ird.fr/frangiPANe/data_test.tar.gz
-tar zxvf data_test.tar.gz
-```
-
-### Licence
-
-* Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and GPLv3
-
-* Intellectual property belongs to IRD/UMR DIADE.
-
-* Written by Clothilde Chenal and Christine Tranchant-Dubreuil
-
-* Copyright 2021

README.rst

+frangiPANe was developed as a modular and interactive application to
+simplify the construction of a panreference using the map-then-assembly
+approach. It consists in a Jupyter Notebook application that centralizes
+code,documentation and interactive visualizations together
+
+### Requirements
+
+-  Docker : https://docs.docker.com/get-docker/
+
+-  Python3 (v3.9.7) : https://www.python.org/
+
+-  biopython : https://biopython.org/
+
+-  panel : https://panel.holoviz.org/
+
+-  abyss : https://github.com/bcgsc/abyss/blob/master/README.md
+
+-  bwa (v. 0.7.17) : https://github.com/lh3/bwa/blob/master/README.md
+
+-  ea-utils (fastq-stats, v 1.01) :
+   https://expressionanalysis.github.io/ea-utils/
+
+-  samtools (v1.10) : http://www.htslib.org/
+
+-  assembly-stats : https://github.com/sanger-pathogens/assembly-stats
+
+-  cd-hit : https://github.com/weizhongli/cdhit/blob/master/README
+
+-  mnimap2
+
+-  girafe
+
+How to use FrangiPANe ?
+=======================
+
+Clone the git repository
+------------------------
+
+::
+
+   git clone ...
+
+Run FrangiPANe
+--------------
+
+::
+
+    snakemake -r -c1
+
+-  Download a dataset to test frangiPANe
+
+::
+
+   wget https://itrop.ird.fr/frangiPANe/data_test.tar.gz
+   tar zxvf data_test.tar.gz
+
+Licence
+=======
+
+-  Licencied under CeCill-C
+   (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and
+   GPLv3
+
+-  Intellectual property belongs to IRD/UMR DIADE.
+
+-  Written by Clothilde Chenal and Christine Tranchant-Dubreuil
+
+-  Copyright 2021

pyproject.toml

+#Build system backend to create package to upload on pypi
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools>=68.2.0",
+    "setuptools_scm[toml]>=8.0.0",
+    "build>=1.0.0"
+]
+
+# configuration of setuptools_scm to use tag version autoincrementation
+# used last TAG version dernier
+[tool.setuptools_scm]
+write_to = "frangiPANe/_version.py"  #TODO: SEB 17/11 => creer automatiquement mais à ajouter dans .gitignore
+version_scheme = "release-branch-semver"
+tag_regex = "^(\\d.\\d.\\d)-*\\w*\\d*$"
+local_scheme = "no-local-version"
+
+# define Project settings
+[project]
+name = "frangiPANe" #"culebrONT"
+dynamic = ["version"]
+description = """blablabla"""
+authors = [
+    { name = "Tranchant-Dubreuil Christine (IRD)", email = "christine.tranchant@ird.fr" },
+]
+maintainers = [
+    { name = "Tranchant-Dubreuil Christine (IRD)", email = "christine.tranchant@ird.fr" },
+]
+dependencies = ["pandas",       #TODO: SEB 17/11 => actualiser avec packages python / rules etc.
+                "matplotlib",
+                "tabulate",
+                "ipython",
+                "biopython",
+                "pysam",
+                "numpy",
+                "snakecdysis>=0.1.0",
+                "setuptools>=68.2.0",
+                "nbformat"
+]
+requires-python = ">=3.8"
+readme = "README.rst"
+license = { file = "LICENCE" }
+keywords = ["snakemake", "assembly", "workflow", "HPC"]
+classifiers = [
+            'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
+            'License :: CeCILL-C Free Software License Agreement (CECILL-C)',
+            'License :: Free for non-commercial use',
+            'Development Status :: 5 - Production/Stable',
+            'Intended Audience :: Developers',
+            'Intended Audience :: End Users/Desktop',
+            'Operating System :: POSIX :: Linux',
+            'Programming Language :: Python :: 3.6',
+            'Programming Language :: Python :: 3.7',
+            'Programming Language :: Python :: 3.8',
+            'Programming Language :: Python :: 3.9',
+            'Programming Language :: R',
+            'Natural Language :: English',
+            'Topic :: Scientific/Engineering',
+            'Topic :: Scientific/Engineering :: Bio-Informatics',
+            'Topic :: Software Development :: Assemblers'
+]
+
+[project.urls]
+Homepage = "https://forge.ird.fr/diade/culebront_pipeline"
+Downloads = "https://forge.ird.fr/diade/culebront_pipeline/archive/"
+"Bug Tracker" = "https://forge.ird.fr/diade/culebront_pipeline/issues"
+Documentation = "https://snakecdysis.readthedocs.io/en/latest/"
+"Source Code" = "https://forge.ird.fr/diade/culebront_pipeline"
+
+[project.optional-dependencies]
+dev = [
+    "sphinx_click",
+    "sphinx_copybutton",
+    "sphinx_rtd_theme",
+    "tox",
+]
+
+# setup scripts links
+[project.scripts]
+culebrONT = "culebrONT.main:main"
+
+[project.entry-points.culebrONT]
+culebrONT = "__init__"
+
+# Try to link sphinx to file
+[tool.sphinx]
+source-dir = "docs/source"
+build-dir = "docs/build"
+config-dir = "docs/source"
+