Merge branch 'master' of https://github.com/4dn-dcic/tibanna

4dn-dcic · Oct 8, 2019 · 42eb976 · 42eb976
2 parents 0091ed2 + f5591be
commit 42eb976
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Showing 235 changed files with 3 additions and 16,958 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -19,12 +19,11 @@ jobs:
     install:
     - pip install six
     - python setup.py install
-    - pip install -U -r requirements-4dn.txt
     - pip install -U -r requirements-test.txt
     - pip install codacy-coverage
     script:
     - if [ "$TRAVIS_BRANCH" != "doc" ]; then
-      invoke test --no-flake --no-post; fi  # temporarily ignore test_webdev which uses tibanna_pony
+      invoke test --no-flake; fi
     after_success:
     - echo "finished running tests on repo"
     - python-codacy-coverage -r coverage.xml

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,9 +1,5 @@
 include README.md
 include LICENSE.txt
 include requirements.txt
-include requirements-4dn.txt
-include requirements-cgap.txt
 include requirements-test.txt
 include tibanna/lambdas/*
-include tibanna_4dn/lambdas/*
-include tibanna_cgap/lambdas/*
diff --git a/requirements-4dn.txt b/requirements-4dn.txt
diff --git a/requirements-cgap.txt b/requirements-cgap.txt
diff --git a/setup.cfg b/setup.cfg
@@ -21,7 +21,6 @@ omit =
     */.eggs/*
 include =
     */tibanna/*
-    */tibanna_4dn/*
 [aliases]
 test=check
 

diff --git a/setup.py b/setup.py
@@ -42,7 +42,7 @@
     description='Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.',
     long_description=long_description,
     long_description_content_type='text/markdown',
-    packages=['tibanna', 'tibanna_ffcommon', 'tibanna_4dn', 'tibanna_cgap'],
+    packages=['tibanna'],
     zip_safe=False,
     author='4DN Team at Harvard Medical School',
     author_email='[email protected], [email protected], [email protected]',
@@ -61,8 +61,6 @@
     entry_points={
         'console_scripts': [
              'tibanna = tibanna.__main__:main',
-             'tibanna_4dn = tibanna_4dn.__main__:main',
-             'tibanna_cgap = tibanna_cgap.__main__:main',
         ]
     }
 )
diff --git a/tasks.py b/tasks.py
@@ -27,13 +27,6 @@ def test(ctx, watch=False, last_failing=False, no_flake=False, k='',  extra='',
     if ignore:
         args.append('--ignore')
         args.append(ignore)
-    if ignore_pony:
-        args.append('--ignore')
-        args.append('tests/tibanna/pony')
-    if no_post:
-        args.append('--ignore')  # skip tests that posts items to portal
-        args.append('tests/tibanna/pony/test_pony_utils_post.py')
-        args.append('tests/tibanna/zebra/test_zebra_utils_post.py')
     args.append('tests/tibanna/')
     retcode = pytest.main(args)
     if retcode != 0:

diff --git a/test_json/pony/add-hic-normvector-to-mcool_jin.json b/test_json/pony/add-hic-normvector-to-mcool_jin.json
diff --git a/test_json/pony/add-hic-normvector-to-mcool_rao12.json b/test_json/pony/add-hic-normvector-to-mcool_rao12.json
diff --git a/test_json/pony/add-hic-normvector-to-mcool_rao13.json b/test_json/pony/add-hic-normvector-to-mcool_rao13.json
diff --git a/test_json/pony/add-hic-normvector-to-mcool_selveraj.json b/test_json/pony/add-hic-normvector-to-mcool_selveraj.json
diff --git a/test_json/pony/addfrag.json b/test_json/pony/addfrag.json
diff --git a/test_json/pony/addnormtohic_jin.json b/test_json/pony/addnormtohic_jin.json
diff --git a/test_json/pony/addnormtohic_rao12.json b/test_json/pony/addnormtohic_rao12.json
diff --git a/test_json/pony/addnormtohic_rao13.json b/test_json/pony/addnormtohic_rao13.json
diff --git a/test_json/pony/addnormtohic_selveraj.json b/test_json/pony/addnormtohic_selveraj.json
diff --git a/test_json/pony/bed2beddb.json b/test_json/pony/bed2beddb.json
diff --git a/test_json/pony/bg2bw.json b/test_json/pony/bg2bw.json