Merge eca3a7c into 0803225

EdinburghGenomics · Jun 12, 2017 · 9fdf872 · 9fdf872
2 parents 0803225 + eca3a7c
commit 9fdf872
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Showing 38 changed files with 1,670 additions and 2,758 deletions.
diff --git a/.gitignore b/.gitignore
@@ -10,7 +10,5 @@ docs/_sources/
 docs/.doctrees/
 docs/_templates/
 docs/*.html
-.fabfilerc
-scripts/*.csv
-scripts/*.log
-scripts/*.out
+
+
diff --git a/.travis.yml b/.travis.yml
@@ -1,11 +1,15 @@
 language: python
 python:
   - "2.7"
-  - "3.3"
   - "3.4"
-  - "3.5"
-install: "pip install -r requirements.txt"
-script: PYTHONPATH=. py.test
+  - "3.6"
+install:
+  - "pip install -r requirements.txt"
+  - "pip install python-coveralls pytest-cov"
+  - "python setup.py install"
+script: PYTHONPATH=. py.test tests/ --doctest-modules  -v --cov pyclarity_lims --cov-report term-missing
+after_success:
+  - coveralls
 notifications:
   email:
     on_success: never 

diff --git a/Changelogs.md b/Changelogs.md
@@ -0,0 +1,5 @@
+Changelog for Pyclarity-Lims
+============================
+
+0.4 (unreleased)
+----------------
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,11 @@
+include *.md
+include *.txt
+include *.yml
+include CHANGELOG
+recursive-include etc *.html
+recursive-include etc *.yaml
+recursive-include tests *.gz
+recursive-include tests *.log
+recursive-include tests *.py
+recursive-include tests *.sh
+recursive-include tests *.txt
diff --git a/README.md b/README.md
@@ -1,17 +1,17 @@
-## Python interface to the GenoLogics LIMS server via its REST API.
+## Python interface to the BaseSpace Clarity LIMS server via its REST API.
 
 [![PyPI version](https://badge.fury.io/py/genologics.svg)](http://badge.fury.io/py/genologics)
 
-A basic module for interacting with the GenoLogics LIMS server via
+A basic module for interacting with the BaseSpace LIMS server via
 its REST API. The goal is to provide simple access to the most common
 entities and their attributes in a reasonably Pythonic fashion.
 
 Supported python versions :
 
-2.6
-2.7 (recommended)
+2.7
 3.4
 3.5
+3.6 (recommended)
 
 ### Design
 
@@ -32,14 +32,9 @@ instance to the database.
 ### Installation
 
 ```
-pip install genologics
+pip install pyclarity-lims
 ```
 
-or for the cutting edge version:
-
-```
-pip install https://github.com/SciLifeLab/genologics/tarball/master
-```
 
 ### Usage
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -218,7 +218,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'genologics', u'Genologics Documentation',
+    ('index', 'pyclarity_lims', u'Genologics Documentation',
      [u'Per Kraulis, Johannes Alneberg'], 1)
 ]
 

diff --git a/examples/attach_delivery_report.py b/examples/attach_delivery_report.py
diff --git a/examples/epp_script.py b/examples/epp_script.py
diff --git a/examples/get_application.py b/examples/get_application.py
diff --git a/examples/get_artifacts.py b/examples/get_artifacts.py
diff --git a/examples/get_containers.py b/examples/get_containers.py
diff --git a/examples/get_labs.py b/examples/get_labs.py
diff --git a/examples/get_processes.py b/examples/get_processes.py