From dc6c48865bd326e56c8ed19e382865ec3e3326e1 Mon Sep 17 00:00:00 2001
From: ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Mon, 23 Sep 2019 11:47:33 -0500
Subject: [PATCH] allow running tacos with 'path/to/python -m tacos --help'
---
README.md | 4 ++++
tacos/__main__.py | 4 ++++
tacos/cli.py | 6 ++++--
3 files changed, 12 insertions(+), 2 deletions(-)
create mode 100644 tacos/__main__.py
diff --git a/README.md b/README.md
index c23171f..34c8f78 100644
--- a/README.md
+++ b/README.md
@@ -25,6 +25,10 @@ Run the application:
$ conda activate <path/tacos_env> # if not already activated
$ tacos --help
```
+or
+```
+$ <path/tacos_env>/bin/python -m tacos --help # no need to activate the environment
+```
To run the tests:
```
diff --git a/tacos/__main__.py b/tacos/__main__.py
new file mode 100644
index 0000000..53b8076
--- /dev/null
+++ b/tacos/__main__.py
@@ -0,0 +1,4 @@
+from tacos import cli
+
+if __name__ == "__main__":
+ cli.tacos()
\ No newline at end of file
diff --git a/tacos/cli.py b/tacos/cli.py
index 96d076e..9f1ea35 100644
--- a/tacos/cli.py
+++ b/tacos/cli.py
@@ -8,6 +8,7 @@ from tacos.distance import hamming_pool
@click.group()
def tacos():
pass
+
@tacos.command()
@click.option('--ignore_gap', 'ignore_gap', is_flag=True, help='enable coding gaps(i.e indels) as missing values')
@click.option('-d','--separator', 'sep', default='\t', help='field separator [default: TAB]')
@@ -123,5 +124,6 @@ def distance_matrix(ignore_gap, adjust, n_jobs, type, input_, output):
f.write('\n')
click.echo('Finished! Computed {} pairwise distances for {} genomes.'.format(len(genome_pairs), nr_genomes))
-if __name__ == '__main__':
- tacos()
\ No newline at end of file
+
+#if __name__ == '__main__':
+# tacos()
\ No newline at end of file
--
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