Adding codecov

.travis.yml

@@ -4,7 +4,10 @@ env:
   global:
     - PYTHON_VERSION=2.7
   matrix:
-    - TEST_ADD_STUDIES=False
+    - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_db
+    - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_pet
+    - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_core
+    - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_ware
     - TEST_ADD_STUDIES=True
 before_install:
   - redis-server --version
@@ -27,7 +30,7 @@ install:
     'pandas>=0.18' 'matplotlib>=1.1.0' 'scipy>0.13.0' 'numpy>=1.7' 'h5py>=2.3.1'
   - source activate qiita
   - pip install -U pip
-  - pip install sphinx sphinx-bootstrap-theme coveralls 'ipython[all]==2.4.1' nose-timer
+  - pip install sphinx sphinx-bootstrap-theme 'ipython[all]==2.4.1' nose-timer codecov
   - travis_retry pip install . --process-dependency-links
   - 'echo "backend: Agg" > matplotlibrc'
   # Install the biom plugin so we can run the analysis tests
@@ -56,7 +59,7 @@ script:
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then test_data_studies/commands.sh ; fi
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then qiita-cron-job ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then qiita-test-install ; fi
-  - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage --with-timer -v --cover-package=qiita_db,qiita_pet,qiita_core,qiita_ware; fi
+  - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests $COVER_PACKAGE --with-doctest --with-coverage --with-timer -v --cover-package=$COVER_PACKAGE; fi
   - flake8 qiita_* setup.py scripts/*
   - ls -R /home/travis/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_pet/support_files/doc/
   - qiita pet webserver
@@ -66,4 +69,4 @@ services:
   - redis-server
   - postgresql
 after_success:
-  - if [ ${TEST_ADD_STUDIES} == "False" ]; then coveralls ; fi
+  - if [ ${TEST_ADD_STUDIES} == "False" ]; then codecov ; fi

README.rst

@@ -80,7 +80,7 @@ future.
 
 .. |Build Status| image:: https://travis-ci.org/biocore/qiita.png?branch=master
    :target: https://travis-ci.org/biocore/qiita
-.. |Coverage Status| image:: https://coveralls.io/repos/biocore/qiita/badge.png?branch=master
-   :target: https://coveralls.io/r/biocore/qiita
+.. |Coverage Status| image:: https://codecov.io/gh/biocore/qiita/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/biocore/qiita
 .. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg
    :target: https://gitter.im/biocore/qiita?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

qiita_db/util.py

@@ -821,6 +821,10 @@ def move_filepaths_to_upload_folder(study_id, filepaths):
     """
     with qdb.sql_connection.TRN:
         uploads_fp = join(get_mountpoint("uploads")[0][1], str(study_id))
+
+        if not exists(uploads_fp):
+            makedirs(uploads_fp)
+
         path_builder = partial(join, uploads_fp)
 
         # We can now go over and remove all the filepaths

qiita_pet/test/test_download.py

@@ -183,9 +183,9 @@ def test_download_raw_data(self):
         self.assertEqual(response.code, 200)
 
         exp = (
-            '- 0 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
+            '- 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
             'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
-            '- 0 /protected/raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz '
+            '- 58 /protected/raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz '
             'raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
             '- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
             'mapping_files/1_mapping_file.txt\n'

qiita_ware/test/test_ebi.py

@@ -45,13 +45,6 @@ def setUp(self):
         self.study_id = None
 
     def tearDown(self):
-        for f in self.files_to_remove:
-            if exists(f):
-                if isdir(f):
-                    rmtree(f)
-                else:
-                    remove(f)
-
         if self.study_id and Study.exists("Test EBI study"):
             study = Study(self.study_id)
             for a in study.artifacts():
@@ -61,6 +54,13 @@ def tearDown(self):
             SampleTemplate.delete(self.study_id)
             Study.delete(self.study_id)
 
+        for f in self.files_to_remove:
+            if exists(f):
+                if isdir(f):
+                    rmtree(f)
+                else:
+                    remove(f)
+
     def test_init(self):
         artifact_id = 3
         action = 'ADD'