Reorganize repository and make new output

README.rst

@@ -1,18 +1,25 @@
-Semi-automated Curation Results
+Semi-Automated Curation Results
 ===============================
 This repository contains the results of semi-automated curation in the Human Brain Pharmacome project.
 
 Installation
 ------------
-This repository requires a particular package structure and can currently only be installed with pip in development
-mode using the following command:
+This repository can be installed from GitHub using pip with the following command:
 
 .. code-block:: sh
 
-    $ git clone https://github.com/pharmacome/semi-automated-curation.git
-    $ cd semi-automated-curation
+    $ pip install git+https://github.com/pharmacome/semi-automated-curation.git
+
+For developers, this repository can be cloned and installd with the following commands:
+
+.. code-block:: sh
+
+    $ git clone https://github.com/pharmacome/semi-automated-curation.git hbp-semi-automated-curation
+    $ cd hbp-semi-automated-curation
     $ pip install -e .
 
+Usage
+-----
 It can be imported and used with the following. Note that it installs at a different name than the GitHub repository.
 
 .. code-block:: python
@@ -21,6 +28,10 @@ It can be imported and used with the following. Note that it installs at a diffe
     >>> graph = repository.get_graph()
     >>> graph.summarize()
 
+Content
+-------
+The curation can be found in the `src/curation` folder.
+
 License
 -------
 - BEL scripts in this repository are licensed under the CC BY 4.0 license.

setup.cfg

@@ -3,7 +3,7 @@
 ##########################
 [metadata]
 name = hbp_semi_automated_curation
-version = 0.0.1-dev
+version = attr: src.hbp_semi_automated_curation.__init__.VERSION
 description = Semi-automated curation for the Human Brain Pharmacome project
 long_description = file: README.rst
 
@@ -20,7 +20,7 @@ maintainer = Charles Tapley Hoyt
 maintainer_email = charles.hoyt@scai.fraunhofer.de
 
 # License Information
-license = MIT License
+license = MIT
 license_file = LICENSE
 
 # Search tags
@@ -47,15 +47,18 @@ keywords =
 
 [options]
 install_requires =
-    bel_enrichment
+    bel_enrichment>=0.0.3
 
 # Random options
 python_requires = >=3.6
 zip-safe = false
 include-package-data = true
+packages = find:
+package_dir =
+    = src
 
-# Where is my code
-py_modules = hbp_semi_automated_curation
+[options.packages.find]
+where = src
 
 [options.entry_points]
 console_scripts =

hbp_semi_automated_curation.py → src/hbp_semi_automated_curation/__init__.py

@@ -30,11 +30,13 @@
 
 # Folder pointers
 HERE = os.path.abspath(os.path.dirname(__file__))
-GENES_DIRECTORY = os.path.join(HERE, 'genes')
+CURATION_DIRECTORY = os.path.join(HERE, 'curation')
+
+VERSION = '0.1.1'
 
 metadata = BELMetadata(
-    name='HBP Semi-automated Curation',
-    version='0.1.0',
+    name='HBP Semi-Automated Curation',
+    version=VERSION,
     description="This knowledge graph contains content generated with the semi-automated curation workflow"
                 "in the Human Brain Pharmacome project.",
     authors=AUTHOR_STRING,
@@ -43,11 +45,9 @@
 )
 
 repository = BELSheetsRepository(
-    directory=GENES_DIRECTORY,
+    directory=CURATION_DIRECTORY,
+    output_directory=HERE,
     metadata=metadata,
 )
 
 main = repository.build_cli()
-
-if __name__ == '__main__':
-    main()

src/hbp_semi_automated_curation/__main__.py

@@ -0,0 +1,4 @@
+from hbp_semi_automated_curation import main
+
+if __name__ == '__main__':
+    main()