Use external SampleSource package

.circleci/config.yml

@@ -1,7 +1,27 @@
 version: 2
 
+# Common steps for building server Docker images
+pypi_step: &pypi_step
+  name: Init .pypirc
+  command: |
+    echo -e "[distutils]" >> ~/.pypirc
+    echo -e "index-servers =" >> ~/.pypirc
+    echo -e "    pypi" >> ~/.pypirc
+    echo -e "    longtailbio" >> ~/.pypirc
+    echo -e "" >> ~/.pypirc
+    echo -e "[pypi]" >> ~/.pypirc
+    echo -e "" >> ~/.pypirc
+    echo -e "[longtailbio]" >> ~/.pypirc
+    echo -e "repository: https://pypi.longtailbio.com" >> ~/.pypirc
+    echo -e "username: $LT_PYPI_USERNAME" >> ~/.pypirc
+    echo -e "password: $LT_PYPI_PASSWORD" >> ~/.pypirc
+    mkdir ~/.pip
+    echo -e "[global]" >> ~/.pip/pip.conf
+    echo -e "extra-index-url = https://pypi.longtailbio.com/simple/" >> ~/.pip/pip.conf
+
+
 jobs:
-  build:
+  test_package:
     docker:
       - image: themattrix/tox
 
@@ -12,6 +32,8 @@ jobs:
 
       - checkout
 
+      - run: *pypi_step
+
       - run:
           name: Run tests with py35
           command: tox -e py35
@@ -28,3 +50,60 @@ jobs:
           name: Run pylint
           command: tox -e pylint
           when: always
+
+  deploy:
+    docker:
+      - image: circleci/python:3.6.3-jessie
+
+    steps:
+      - checkout
+
+      # Download and cache dependencies
+      - restore_cache:
+          keys:
+          - v1-dependencies-{{ checksum "requirements.txt" }}
+          # fallback to using the latest cache if no exact match is found
+          - v1-dependencies-
+
+      - run:
+          name: Install Python Dependencies
+          command: |
+            python3 -m venv venv
+            . venv/bin/activate
+            pip install -r requirements.txt
+
+      - save_cache:
+          paths:
+            - ./venv
+          key: v1-dependencies-{{ checksum "requirements.txt" }}
+
+      - run: *pypi_step
+
+      - run:
+          name: Build package
+          command: |
+            . venv/bin/activate
+            python setup.py bdist_wheel --universal
+
+      - run:
+          name: Upload to Longtail PyPi
+          command: |
+            . venv/bin/activate
+            pip install twine
+            twine upload -r longtailbio dist/*
+
+
+
+workflows:
+  version: 2
+  build_and_deploy:
+    jobs:
+      - test_package:
+          context: longtail-pypi
+      - deploy:
+          context: longtail-pypi
+          filters:
+            branches:
+              only: master
+          requires:
+            - test_package

README.md

@@ -13,6 +13,7 @@ Simply run:
 
     $ pipsi install .
 
+**Note:** this relies packages from the Longtail Bio PyPi index. See [`pangea-modules`](https://github.com/LongTailBio/pangea-modules/tree/develop#pangea-modules) for instructions on setting that up.
 
 ### Usage
 

metagenscope_cli/cli/upload_cli.py

@@ -3,8 +3,7 @@
 from sys import stderr
 import click
 
-from metagenscope_cli.sample_sources.data_super_source import DataSuperSource
-from metagenscope_cli.sample_sources.file_source import FileSource
+from pangea_modules.sample_source import DataSuperSource, FileSystemSource
 
 from .utils import batch_upload, add_authorization, parse_metadata
 
@@ -52,7 +51,7 @@ def datasuper(uploader, group, group_name):
 @click.argument('result_files', nargs=-1)
 def files(uploader, group, result_files):
     """Upload all samples from llist of tool result files."""
-    sample_source = FileSource(files=result_files)
+    sample_source = FileSystemSource(files=result_files)
     samples = sample_source.get_sample_payloads()
 
     batch_upload(uploader, samples, group_uuid=group)

metagenscope_cli/cli/utils.py

@@ -7,10 +7,10 @@
 
 import click
 from requests.exceptions import HTTPError
+from pangea_modules.sample_source.parser import parse_metadata_from_csv
 
 from metagenscope_cli.network import Knex, Uploader
 from metagenscope_cli.network.token_auth import TokenAuth
-from metagenscope_cli.tools.parse_metadata import parse_metadata_from_csv
 
 
 def parse_metadata(filename, sample_names):

metagenscope_cli/config.py

@@ -9,7 +9,7 @@
 TOKEN_OPTION_KEY = 'token'
 
 
-class MetagenscopeConfiguration(object):
+class MetagenscopeConfiguration:
     """MetaGenScope configuration."""
 
     def __init__(self, filename, dirname='~'):

metagenscope_cli/network/knex.py

@@ -5,7 +5,7 @@
 from metagenscope_cli.constants import DEFAULT_HOST
 
 
-class Knex(object):
+class Knex:
     """Knex wraps MetaGenScope requests requiring authentication."""
 
     def __init__(self, token_auth, host=None, headers=None):

metagenscope_cli/network/token_auth.py

@@ -15,7 +15,7 @@ def __init__(self, jwt_token=None):
         if self.jwt_token is None:
             try:
                 self.jwt_token = config.get_token()
-            except KeyError:
+            except KeyError:  # pylint: disable=try-except-raise
                 # No saved token
                 raise