Merge pull request #71 from josenavas/py3

Adding py3 to travis

.travis.yml

@@ -1,12 +1,24 @@
 language: python
-python:
-  - "2.7"
+env:
+  - PYTHON_VERSION=3.4
+  - PYTHON_VERSION=2.7
+before_install:
+  - wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/anaconda/bin:$PATH
+  # Update conda itself
+  - conda update --yes conda
 install:
+  - conda create --yes -n env_name python=$PYTHON_VERSION pip nose pep8
+  - source activate env_name
+  - pip 
   - pip install coveralls
   - pip install .
 script:
   - qiita_db make_test_env
-  - nosetests
+  - nosetests --with-doctest
+  - pep8 qiita_db qiita_core qiita_pet setup.py
   # we need to run the test suite from setup.py for coveralls to grab the info
   - coverage run setup.py test
   - coverage report -m

INSTALL.md

@@ -3,21 +3,26 @@ Dependencies
 
 Qiita is a python package, with support for python 2.7 and 3.2, that depends on the following python libraries (all of them can be installed using pip):
 
+<!--
 * [tornado 3.1.1](http://www.tornadoweb.org/en/stable/)
 * [redis 2.8.0](https://pypi.python.org/pypi/redis/)
 * [tornado-redis](https://pypi.python.org/pypi/tornado-redis)
-* [Psycopg2](http://initd.org/psycopg/download/)
 * [pgbouncer](http://pgfoundry.org/projects/pgbouncer)
-* [pyqi 0.3](https://github.com/bipy/pyqi)
 * [IPython](https://github.com/ipython/ipython)
 * [QIIME](https://github.com/qiime/qiime)
 * [NumPy](https://github.com/numpy/numpy)
-* [PyCogent](http://pycogent.org)
+-->
+
+* [Psycopg2](http://initd.org/psycopg/download/)
+* [pyqi 0.3](https://github.com/bipy/pyqi)
 
 And on the following packages:
 
 * [PostgresSQL 9.3](http://www.postgresql.org/download/)
+
+<!--
 * [redis-server](http://redis.io)
+-->
 
 Install
 -------
@@ -26,7 +31,5 @@ The easiest way to install Qiita is to run the following commands:
 
 
 ```bash
-pip install numpy
-pip install cogent
 pip install https://github.com/biocore/qiita/archive/master.zip
 ```

qiita_core/configuration_manager.py

@@ -7,7 +7,13 @@
 # -----------------------------------------------------------------------------
 
 from os.path import join, dirname, abspath
-from ConfigParser import ConfigParser, NoOptionError
+
+try:
+    # Python 2
+    from ConfigParser import ConfigParser, NoOptionError
+except ImportError:
+    # Python 3
+    from configparser import ConfigParser, NoOptionError
 
 
 class ConfigurationManager(object):

qiita_db/__init__.py

@@ -9,4 +9,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.0.1-dev"
+__version__ = "0.0.1-dev"

qiita_db/metadata_template.py

@@ -22,8 +22,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-from itertools import izip
-from string import lower
+from future.builtins import zip
 
 from .base import QiitaStatusObject
 from .exceptions import QiitaDBNotImplementedError
@@ -100,7 +99,7 @@ def create(cls, md_template, study_id):
 
         # Get the column names paired with its datatype for SQL
         columns = []
-        for column_name, datatype in izip(sql_safe_column_names, datatypes):
+        for column_name, datatype in zip(sql_safe_column_names, datatypes):
             columns.append('%s %s' % (column_name, datatype))
         # Get the columns in a comma-separated string
         columns = ", ".join(columns)
@@ -114,10 +113,10 @@ def create(cls, md_template, study_id):
                                       " values ('" + str(study_id) +
                                       "', %s, %s)")
         # The column names should be lowercase and quoted
-        quoted_lc_headers = [quote_data_value(lower(h)) for h in headers]
+        quoted_lc_headers = [quote_data_value(h.lower()) for h in headers]
         # Pair up the column names with its datatype
         sql_args_list = [(column_name, datatype) for column_name, datatype in
-                         izip(quoted_lc_headers, datatypes)]
+                         zip(quoted_lc_headers, datatypes)]
         conn_handler.executemany(column_tables_sql_template,
                                  sql_args_list)
 

qiita_db/sql_connection.py

@@ -40,7 +40,7 @@ def get_postgres_cursor(self):
         try:
             with self._connection.cursor(cursor_factory=DictCursor) as cur:
                 yield cur
-        except PostgresError, e:
+        except PostgresError as e:
             raise QiitaDBConnectionError("Cannot get postgres cursor! %s" % e)
 
     def _check_sql_args(self, sql_args):
@@ -87,7 +87,6 @@ def _sql_executor(self, sql, sql_args=None, many=False):
         else:
             self._check_sql_args(sql_args)
 
-
         # Execute the query
         with self.get_postgres_cursor() as cur:
             try:
@@ -97,7 +96,7 @@ def _sql_executor(self, sql, sql_args=None, many=False):
                     cur.execute(sql, sql_args)
                 yield cur
                 self._connection.commit()
-            except PostgresError, e:
+            except PostgresError as e:
                 self._connection.rollback()
                 try:
                     err_sql = cur.mogrify(sql, sql_args)

qiita_db/support_files/populate_test_db.sql

@@ -47,16 +47,16 @@ INSERT INTO qiita.investigation_study (investigation_id, study_id) VALUES (1, 1)
 INSERT INTO qiita.study_experimental_factor (study_id, efo_id) VALUES (1, 1);
 
 -- Insert the raw data filepaths for study 1
-INSERT INTO qiita.filepath (filepath, filepath_type_id) VALUES ('$QIITA_TEST_FOLDER/s_G1_L001_sequences.fastq.gz', 1), ('$QIITA_TEST_FOLDER/s_G1_L001_sequences_barcodes.fastq.gz', 2);
+INSERT INTO qiita.filepath (filepath, filepath_type_id) VALUES ('s_G1_L001_sequences.fastq.gz', 1), ('s_G1_L001_sequences_barcodes.fastq.gz', 2), ('sequences.fastq.gz', 1), ('sequences_barcodes.fastq.gz', 2);
 
 -- Insert the raw data information for study 1
-INSERT INTO qiita.raw_data (filetype_id, submitted_to_insdc) VALUES (2, FALSE);
+INSERT INTO qiita.raw_data (filetype_id, submitted_to_insdc) VALUES (2, FALSE), (2, TRUE);
 
 -- Insert (link) the raw data with the raw filepaths
-INSERT INTO qiita.raw_filepath (raw_data_id, filepath_id) VALUES (1, 1), (1, 2);
+INSERT INTO qiita.raw_filepath (raw_data_id, filepath_id) VALUES (1, 1), (1, 2), (1, 3), (1, 4);
 
 -- Insert (link) the study with the raw data
-INSERT INTO qiita.study_raw_data (study_id, raw_data_id) VALUES (1, 1);
+INSERT INTO qiita.study_raw_data (study_id, raw_data_id) VALUES (1, 1), (1, 2);
 
 -- Add the required_sample_info for study 1
 INSERT INTO qiita.required_sample_info (study_id, sample_id, physical_location, has_physical_specimen, has_extracted_data, sample_type, required_sample_info_status_id, collection_date, host_subject_id, description) VALUES
@@ -281,31 +281,31 @@ INSERT INTO qiita.prep_1 (sample_id, BarcodeSequence, LIBRARY_CONSTRUCTION_PROTO
 	('SKM9.640192', 'AGCAGGCACGAA', 'This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to Ê1,500 samples per lane, and both PCR primers contain sequencer adapter regions.', 'GTGCCAGCMGCCGCGGTAA', 'V4', '16S rRNA', 'ANL', 's_G1_L001_sequences', '8/1/12', 'ANL', 'micro biome of soil and rhizosphere of cannabis plants from CA', 'Cannabis Soil Microbiome', 'Illumina', '.25,g', 'Sequencing by synthesis', 'MiSeq', 'ANL', 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT', 'CCME');
 
 -- Insert preprocessed information for raw data 1
-INSERT INTO qiita.preprocessed_data (raw_data_id, preprocessed_params_table, preprocessed_params_id) VALUES (1, 'preprocessed_sequence_illumina_params', 1);
+INSERT INTO qiita.preprocessed_data (raw_data_id, preprocessed_params_table, preprocessed_params_id) VALUES (1, 'preprocessed_sequence_illumina_params', 1), (1, 'preprocessed_sequence_illumina_params', 2);
 
 -- Insert (link) preprocessed information to study 1
-INSERT INTO qiita.study_preprocessed_data (preprocessed_data_id, study_id) VALUES (1, 1);
+INSERT INTO qiita.study_preprocessed_data (preprocessed_data_id, study_id) VALUES (1, 1), (2, 1);
 
 -- Insert the preprocessed filepath for raw data 1
-INSERT INTO qiita.filepath (filepath, filepath_type_id) VALUES ('$QIITA_TEST_FOLDER/seqs.fna', 4), ('$QIITA_TEST_FOLDER/seqs.qual', 5);
+INSERT INTO qiita.filepath (filepath, filepath_type_id) VALUES ('seqs.fna', 4), ('seqs.qual', 5);
 
 -- Insert (link) the preprocessed data with the preprocessed filepaths
 INSERT INTO qiita.preprocessed_filepath (preprocessed_data_id, filepath_id) VALUES (1, 3), (1, 4);
 
 -- Insert the preprocessed illumina params used for raw data 1
-INSERT INTO qiita.preprocessed_sequence_illumina_params (trim_length) VALUES (151);
+INSERT INTO qiita.preprocessed_sequence_illumina_params (trim_length) VALUES (151), (100);
 
 -- Insert processed information for study 0 and processed data 1
 INSERT INTO qiita.processed_data (preprocessed_data_id, processed_params_table, processed_params_id, processed_date) VALUES (1, 'processed_params_uclust', 1, 'Mon Oct 1 09:30:27 2012');
 
 -- Populate the reference table
-INSERT INTO qiita.reference (reference_name, reference_version, sequence_filepath, taxonomy_filepath, tree_filepath) VALUES ('GreenGenes', '4feb2011', '$QIITA_TEST_FOLDER/gg_97_otus_4feb2011.fasta', '$QIITA_TEST_FOLDER/greengenes_tax.txt', '$QIITA_TEST_FOLDER/gg_97_otus_4feb2011.tre');
+INSERT INTO qiita.reference (reference_name, reference_version, sequence_filepath, taxonomy_filepath, tree_filepath) VALUES ('GreenGenes', '4feb2011', 'gg_97_otus_4feb2011.fasta', 'greengenes_tax.txt', 'gg_97_otus_4feb2011.tre');
 
 -- Insert the processed params uclust used for preprocessed data 1
 INSERT INTO qiita.processed_params_uclust (similarity, enable_rev_strand_match, suppress_new_clusters, reference_id) VALUES (0.97, TRUE, TRUE, 1);
 
 -- Insert the biom table filepath for processed data 1
-INSERT INTO qiita.filepath (filepath, filepath_type_id) VALUES ('$QIITA_TEST_FOLDER/study_1001_closed_reference_otu_table.biom', 6);
+INSERT INTO qiita.filepath (filepath, filepath_type_id) VALUES ('study_1001_closed_reference_otu_table.biom', 6);
 
 -- Insert (link) the processed data with the processed filepath
 INSERT INTO qiita.processed_filepath (processed_data_id, filepath_id) VALUES (1, 5);

qiita_db/test/__init__.py

@@ -9,4 +9,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.0.1-dev"
+__version__ = "0.0.1-dev"