From 18159df26d36b4d69a806b02aa6a7ba07093b179 Mon Sep 17 00:00:00 2001
From: Hugo Madge Leon <hugo.madgeleon@stud.unibas.ch>
Date: Fri, 9 Dec 2022 16:26:30 +0000
Subject: [PATCH] Small changes overall
---
requirements.txt | 5 ++++-
setup.py | 10 ++++++----
terminal-fragment-selector/__init__.py | 1 +
terminal-fragment-selector/{main.py => cli.py} | 4 +---
4 files changed, 12 insertions(+), 8 deletions(-)
create mode 100644 terminal-fragment-selector/__init__.py
rename terminal-fragment-selector/{main.py => cli.py} (99%)
diff --git a/requirements.txt b/requirements.txt
index a238d56..70de6eb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1,4 @@
-'random','argparse 1.4.0', 'check_positive', 'arghelper 0.4.2', 'fragmentation_v2', 'numpy 1.23.4', 'pandas 1.5'
\ No newline at end of file
+argparse
+biopython >= 1.78
+numpy >= 1.23.3
+pandas >= 1.4.4
\ No newline at end of file
diff --git a/setup.py b/setup.py
index e806894..abcfdb7 100644
--- a/setup.py
+++ b/setup.py
@@ -1,16 +1,18 @@
"""Set up project."""
from setuptools import setup, find_packages
from pathlib import Path
+
project_root_dir = Path(__file__).parent.resolve()
with open(project_root_dir / "requirements.txt",
- "r", encoding="utf-8") as _file:
- INSTALL_REQUIRES = _file.read().splitlines()
+ "r", encoding="utf-8") as f:
+ INSTALL_REQUIRES = f.read().splitlines()
+url = 'https://git.scicore.unibas.ch/zavolan_group/tools/terminal-fragment-selector'
setup(
- name='terminal-fragment-selection',
+ name='terminal-fragment-selector',
version='0.1.1',
- url='https://git.scicore.unibas.ch/zavolan_group/tools/terminal-fragment-selector',
+ url=url,
license='MIT',
author='Hugo Madge Leon, Sunho Kim, Tanya Nandan',
author_email='hmadge@ethz.ch',
diff --git a/terminal-fragment-selector/__init__.py b/terminal-fragment-selector/__init__.py
new file mode 100644
index 0000000..bb7d5f3
--- /dev/null
+++ b/terminal-fragment-selector/__init__.py
@@ -0,0 +1 @@
+"""Initialise package."""
diff --git a/terminal-fragment-selector/main.py b/terminal-fragment-selector/cli.py
similarity index 99%
rename from terminal-fragment-selector/main.py
rename to terminal-fragment-selector/cli.py
index 73368a1..1585025 100644
--- a/terminal-fragment-selector/main.py
+++ b/terminal-fragment-selector/cli.py
@@ -61,9 +61,7 @@ def file_validation(fasta_file: str,
"""
with open(fasta_file, "r") as handle:
fasta = SeqIO.parse(handle, "fasta")
- try:
- any(fasta)
- except Exception:
+ if not any(fasta):
logger.exception("Input FASTA file is either empty or \
incorrect file type.")
--
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