update rest of structure to move cli functionality to separate package

move testutils inside chanjo

chanjo/cli/__init__.py

@@ -2,3 +2,6 @@
 from .calculate import calculate
 from .sex import sex
 from .load import link, load
+from .sambamba import sambamba
+from .db import db_cmd
+from .init import init

chanjo/store/cli.py → chanjo/cli/db.py

@@ -3,42 +3,42 @@
 
 import click
 
-from .api import ChanjoDB
-from .models import Sample
+from chanjo.store.api import ChanjoDB
+from chanjo.store.models import Sample
 
-log = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
 
 
-@click.group()
+@click.group('db')
 @click.pass_context
-def db(context):
+def db_cmd(context):
     """Interact with the database for maintainance tasks."""
     context.obj['db'] = ChanjoDB(uri=context.obj['database'])
 
 
-@db.command()
+@db_cmd.command()
 @click.option('--reset', is_flag=True, help='tear down existing db')
 @click.pass_context
 def setup(context, reset):
     """Initialize a new datbase from scratch."""
     if reset:
-        log.info('tearing down existing database')
+        LOG.info('tearing down existing database')
         context.obj['db'].tear_down()
-    log.info('setting up new database')
+    LOG.info('setting up new database')
     context.obj['db'].set_up()
 
 
-@db.command()
+@db_cmd.command()
 @click.argument('sample_id', type=str)
 @click.pass_context
 def remove(context, sample_id):
     """Remove all traces of a sample from the database."""
-    db = context.obj['db']
-    log.debug('find sample in database with id: %s', sample_id)
+    store = context.obj['db']
+    LOG.debug('find sample in database with id: %s', sample_id)
     sample_obj = Sample.query.get(sample_id)
     if sample_obj is None:
-        log.warn('sample (%s) not found in database', sample_id)
+        LOG.warning('sample (%s) not found in database', sample_id)
         context.abort()
-    log.info('delete sample (%s) from database', sample_id)
-    db.session.delete(sample_obj)
-    db.save()
+    LOG.info('delete sample (%s) from database', sample_id)
+    store.session.delete(sample_obj)
+    store.save()

chanjo/init/cli.py → chanjo/cli/init.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
 import codecs
+from distutils.spawn import find_executable
 import logging
 
 import click
 from path import Path
 import ruamel.yaml
-from distutils.spawn import find_executable
 
 from chanjo.store.api import ChanjoDB
-from .bootstrap import pull, BED_NAME, DB_NAME
-from .demo import setup_demo, DEMO_BED_NAME
+from chanjo.init.bootstrap import pull, BED_NAME, DB_NAME
+from chanjo.init.demo import setup_demo, DEMO_BED_NAME
 
-log = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
 
 
 @click.command()
@@ -25,29 +25,29 @@ def init(context, force, demo, auto, root_dir):
     is_bootstrapped = False
     root_path = Path(root_dir)
 
-    log.info("setting up chanjo under: %s", root_path)
+    LOG.info("setting up chanjo under: %s", root_path)
     db_uri = context.obj.get('database')
     db_uri = db_uri or "sqlite:///{}".format(root_path.joinpath(DB_NAME).abspath())
 
     # test setup of sambamba
     sambamba_bin = find_executable('sambamba')
     if sambamba_bin is None:  # pragma: no cover
-        log.warn("'sambamba' command not found")
+        LOG.warning("'sambamba' command not found")
     else:
-        log.debug("'sambamba' found: %s", sambamba_bin)
+        LOG.debug("'sambamba' found: %s", sambamba_bin)
 
     if demo:
-        log.info("copying demo files: %s", root_dir)
+        LOG.info("copying demo files: %s", root_dir)
         setup_demo(root_dir, force=force)
 
-        log.info("configure new chanjo database: %s", db_uri)
+        LOG.info("configure new chanjo database: %s", db_uri)
         chanjo_db = ChanjoDB(db_uri)
         chanjo_db.set_up()
         is_bootstrapped = True
     elif auto or click.confirm('Bootstrap HGNC transcript BED?'):
         pull(root_dir, force=force)
 
-        log.info("configure new chanjo database: %s", db_uri)
+        LOG.info("configure new chanjo database: %s", db_uri)
         chanjo_db = ChanjoDB(db_uri)
         chanjo_db.set_up()
         is_bootstrapped = True
@@ -58,7 +58,7 @@ def init(context, force, demo, auto, root_dir):
     with codecs.open(conf_path, 'w', encoding='utf-8') as conf_handle:
         data = {'database': db_uri}
         data_str = ruamel.yaml.dump(data, Dumper=ruamel.yaml.RoundTripDumper)
-        log.info("writing config file: %s", conf_path)
+        LOG.info("writing config file: %s", conf_path)
         conf_handle.write(data_str)
 
     if is_bootstrapped:

chanjo/sambamba/cli.py → chanjo/cli/sambamba.py

@@ -1,10 +1,11 @@
 # -*- coding: utf-8 -*-
-import click
 import logging
 
-from .run import run_sambamba
+import click
+
+from chanjo.sambamba import run_sambamba
 
-log = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
 
 
 @click.command()
@@ -21,9 +22,9 @@
 @click.pass_context
 def sambamba(context, bam_file, regions, cov_thresholds, outfile):
     """Run Sambamba from chanjo."""
-    log.info("Running chanjo sambamba")
+    LOG.info("Running chanjo sambamba")
     try:
         run_sambamba(bam_file, regions, outfile, cov_thresholds)
     except Exception:
-        log.exception('something went really wrong :_(')
+        LOG.exception('something went really wrong :_(')
         context.abort()

tests/init/test_utils.py → chanjo/testutils.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import os
 
 

setup.py

@@ -94,10 +94,10 @@ def run_tests(self):
             'chanjo = chanjo.cli:root',
         ],
         'chanjo.subcommands.4': [
-            'init = chanjo.init.cli:init',
+            'init = chanjo.cli:init',
             'sex = chanjo.cli:sex',
-            'sambamba = chanjo.sambamba.cli:sambamba',
-            'db = chanjo.store.cli:db',
+            'sambamba = chanjo.cli:sambamba',
+            'db = chanjo.cli:db_cmd',
             'load = chanjo.cli:load',
             'link = chanjo.cli:link',
             'calculate = chanjo.cli:calculate',

tests/init/test_init_cli.py → tests/cli/test_cli_init.py

@@ -1,11 +1,10 @@
 # -*- coding: utf-8 -*-
-from __future__ import absolute_import
 from tempfile import gettempdir
 
 from mock import patch
 import ruamel.yaml
 
-from test_utils import FakeZipFile, fake_urlretrieve
+from chanjo.testutils import FakeZipFile, fake_urlretrieve
 
 
 def test_init_demo(tmpdir, invoke_cli):

tests/init/test_init_bootstrap.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
-from __future__ import absolute_import
 import os
+
 from mock import patch
-from chanjo.init import bootstrap
 
-from test_utils import FakeZipFile, fake_urlretrieve
+from chanjo.init import bootstrap
+from chanjo.testutils import FakeZipFile, fake_urlretrieve
 
 
 @patch('urllib.request.urlretrieve', fake_urlretrieve)