From 2e215f9c68840f1657339c277f92106d84b25e2d Mon Sep 17 00:00:00 2001
From: Gertjan Bisschop <gertjanbisschop@gmail.com>
Date: Tue, 12 Sep 2023 17:12:35 +0100
Subject: [PATCH] restructure

---
 gimbleprep => gimbleprep.py       | 0
 {cli => gimbleprep}/__init__.py   | 0
 {cli => gimbleprep}/interface.py  | 2 +-
 {cli => gimbleprep}/preprocess.py | 2 +-
 {lib => gimbleprep}/runargs.py    | 0
 lib/__init__.py                   | 0
 setup.py                          | 9 ++++-----
 7 files changed, 6 insertions(+), 7 deletions(-)
 rename gimbleprep => gimbleprep.py (100%)
 rename {cli => gimbleprep}/__init__.py (100%)
 rename {cli => gimbleprep}/interface.py (96%)
 rename {cli => gimbleprep}/preprocess.py (99%)
 rename {lib => gimbleprep}/runargs.py (100%)
 delete mode 100644 lib/__init__.py

diff --git a/gimbleprep b/gimbleprep.py
similarity index 100%
rename from gimbleprep
rename to gimbleprep.py
diff --git a/cli/__init__.py b/gimbleprep/__init__.py
similarity index 100%
rename from cli/__init__.py
rename to gimbleprep/__init__.py
diff --git a/cli/interface.py b/gimbleprep/interface.py
similarity index 96%
rename from cli/interface.py
rename to gimbleprep/interface.py
index fb074d4..cfdd422 100644
--- a/cli/interface.py
+++ b/gimbleprep/interface.py
@@ -22,7 +22,7 @@
 from timeit import default_timer as timer
 
 RUNNER_BY_MODULE = {
-    'preprocess': 'cli.preprocess', 
+    'preprocess': 'gimbleprep.preprocess', 
 }
 MODULES = RUNNER_BY_MODULE.keys()
 
diff --git a/cli/preprocess.py b/gimbleprep/preprocess.py
similarity index 99%
rename from cli/preprocess.py
rename to gimbleprep/preprocess.py
index 3bbde68..00e4e6d 100644
--- a/cli/preprocess.py
+++ b/gimbleprep/preprocess.py
@@ -15,7 +15,7 @@
         -h, --help                       Show this
 """
 
-import lib.runargs
+import gimbleprep.runargs
 import numpy as np
 import tempfile
 import pathlib
diff --git a/lib/runargs.py b/gimbleprep/runargs.py
similarity index 100%
rename from lib/runargs.py
rename to gimbleprep/runargs.py
diff --git a/lib/__init__.py b/lib/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/setup.py b/setup.py
index 4752833..58540b1 100644
--- a/setup.py
+++ b/setup.py
@@ -2,17 +2,16 @@
 
 setup(
     name='gimbleprep',
-    version='0.0.2b3',
+    version='0.0.2b4',
     description='Preprocess fasta, bam and vcf files ready to be used by gimble',
     url='http://github.com/LohseLab/gimbleprep',
     author='Lohse Lab',
     author_email='',
     license='GPLv3',
-    packages=["cli", "lib"],
+    packages=["gimbleprep"],
     package_dir={
         "": ".",
-        "cli": "./cli",
-        "lib": "./lib",
+        "gimbleprep": "./gimbleprep",
     },
     install_requires=[
         "docopt",
@@ -29,7 +28,7 @@
     ],
     entry_points={
         'console_scripts': [
-            'gimbleprep = cli.interface:main',
+            'gimbleprep = gimbleprep.interface:main',
         ]
     }
 )