Merge pull request #7 from matthiaskoenig/develop

changes for v0.2.0
matthiaskoenig · Jul 30, 2019 · 6ef6d87 · 6ef6d87
2 parents 0f21cc0 + 9c178a7
commit 6ef6d87
Show file tree

Hide file tree

Showing 15 changed files with 2,611 additions and 727 deletions.
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+brendapy/resources/brenda_download.txt filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,3 @@ brendapy.egg-info
 .tox
 dist
 
-brendapy/resources/brenda_download.txt
-brendapy/resources/brenda_download_2019-07-29.zip
-tmp
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,15 @@
+language: python
+cache: pip
+python:
+  - "3.6"
+  - "3.7"
+sudo: required
+
+install:
+  pip install -r requirements-develop.txt
+
+script:
+  pytest --cov=brendapy
+
+after_success:
+   pip install codecov; codecov
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,5 +1,7 @@
 include requirements.txt
 include README.md
+include README.rst
+
 
 include brendapy/resources/README.md
 include brendapy/resources/brenda_download_2019-07-29.zip

diff --git a/README.md b/README.md
diff --git a/README.rst b/README.rst
@@ -0,0 +1,22 @@
+brendapy: BRENDA in python
+====================================
+
+The ``brendapy`` package provides a python parser for
+`BRENDA <https://www.brenda-enzymes.org/index.php>`__
+enzyme information. The parser extracts the protein information from the
+database flat file and makes it accessible in a simple manner.
+
+This package was developed in the context of building kinetic pathway models
+with source code at https://github.com/matthiaskoenig/brendapy
+
+``brendapy`` support has been tested on ``py36`` and ``py37``.
+
+If you use this package cite `BRENDA <https://www.brenda-enzymes.org/index.php>`__
+
+::
+
+    BRENDA in 2019: a European ELIXIR core data resource
+    Jeske L., Placzek S., Schomburg I., Chang A., Schomburg D., Nucleic Acids Res., in print (2019)
+
+
+© 2019 Matthias König
diff --git a/brendapy/_version.py b/brendapy/_version.py
@@ -1,7 +1,4 @@
 """
 Definition of version string.
 """
-__version__ = "0.1.2"
-
-PROGRAM_VERSION = __version__
-PROGRAM_NAME = 'brendapy'
+__version__ = "0.2.0"
diff --git a/brendapy/examples.py b/brendapy/examples.py
@@ -11,11 +11,11 @@ def parse_proteins_for_ec():
     """
     brenda = BrendaParser()
     ec = "1.1.1.1"
-    proteins = brenda.parse_proteins(ec)
+    proteins = brenda.get_proteins(ec)
 
     print(f"{len(proteins)} proteins for EC {ec} in BRENDA")
     print(f"Protein identifier: {proteins.keys()}")
-    print("-"*80)
+    print("-" * 80)
     for p in proteins.values():
         if p.organism == "Homo sapiens":
             print(p)