Merge pull request #11 from BONSAMURAIS/issue-9

Issue 9

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

CHANGELOG.md

@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [0.5.0] - 2020-07-01
+### Added
+- package is published to pypi repository
 ### Changed
 - new command line syntax:
 ```

README.md

@@ -1,6 +1,7 @@
 # YSTAFDB
 
-YSTAFDB creates turtle files of the istances of data based on an ontology. The turtle files are needed for the BONSAI knowledge graph. 
+YSTAFDB creates turtle files of the istances of data based on an ontology.
+The turtle files are needed for the BONSAI knowledge graph.
 
 The turtle files generated are stored in the BONSAI [rdf repository](https://github.com/BONSAMURAIS/rdf).
 
@@ -10,9 +11,14 @@ Currently generates the following:
 
 ## Installation
 
-### with package managers [pip or conda]
+### with package manager pip from pypi
+
+Installable via `pip`:
+
+```
+pip install ystafdb
+```
 
-Installable via `pip`
 ### manual
 
 Clone git repo
@@ -24,11 +30,24 @@ Enter cloned repo
 ```
 $ cd ystafdb
 ```
-##### Download Base Data 
-Before progressing the installation, the base ystafdb data must be downloaded, and placed in a folder of your choosing, inside the repo.
+
+Now install package
+
+```
+$ python setup.py install
+```
+
+## Usage
+
+You must first download the Base Data, and then use `ystafdb-cli` to produce the ttl/nt/xml files.
+
+### Download Base Data
+
 The data can be downloaded [here](https://www.sciencebase.gov/catalog/file/get/5b9a7c28e4b0d966b485d915?f=__disk__0f%2F58%2Fa7%2F0f58a74db669ee5418f36a698bc85781e867e0ab) as a zip file.
-Extract the zip file and move relevant files to a folder. As an example, the data can be placed under `/ystafdb/data/`.
-The following ystafdb files are mandatory to have in the folder:
+
+Extract the contents of the zip file. As an example, the data can be placed under `ystafdb-input`.
+The following files from the Base Data are _mandatory_ to have in the folder (`ystafdb-input` in our example):
+
 - `material_names.csv`
 - `subsystems.csv`
 - `flows.csv`
@@ -37,63 +56,59 @@ The following ystafdb files are mandatory to have in the folder:
 - `reference_materials.csv`
 - `reference_timeframes.csv`
 
-##### Create env and install dependencies
-Either 1) create new virtualenv and enter shell or 2) enter already existing virtualenv and install dependencies
-##### Option 1)
-```
-$ pipenv install
-$ pipenv shell
-```
 
-##### Option 2)
+Under a Linux terminal, you can acomplish the previous two operations with:
+
 ```
-$ source path/to/environment/bin/activate
-$ pip install -r requirements.txt
+curl -L "https://www.sciencebase.gov/catalog/file/get/5b9a7c28e4b0d966b485d915?f=__disk__0f%2F58%2Fa7%2F0f58a74db669ee5418f36a698bc85781e867e0ab" -o YSTAFDB_CSV_files.zip
+unzip -d ystafdb-input YSTAFDB_CSV_files.zip
 ```
 
-Now install package
+### Generate the ttl or nt or xml files
+
+If the package is correctly installed, you can use the command line tool `ystafdb-cli` to produce the rdfs as follows:
+
 ```
-$ python setup.py install
+$ ystafdb-cli -i <inputdir> -o <outputdir>
 ```
 
 
-## Usage
-
-### As a command line tool
+Where:
++ `<inputdir>` is the location of the ystafdb csv files, and 
++ `<outputdir>` is the directory where the output triples graphs will be placed. This is optional,
+  if not supplied, the output directory will be `output`
 
-If the package is correctly installed, you can use the command line tool `ystafdb-cli` to produce the rdfs as follows:
+In the Linux terminal example from above, this would be done with:
 
 ```
-$ ystafdb-cli -i <input/dir> -o  <output/dir>
+ystafdb-cli -i ystafdb-input
 ```
 
-Where `<input/dir>` is the location of the ystafdb csv files, and `<output/dir>` is the directory where the output triples graphs will be placed. 
-The `<output/dir>` directory will have the following content:
+The `<outputdir>` directory will have the following contents:
 
 ```
 output
-├── activitytype
-│   └── ystafdb
-│       └── ystafdb.ttl
-├── flowobject
-│   └── ystafdb
-│       └── ystafdb.ttl
-├── location
-│   └── ystafdb
-│       └── ystafdb.ttl
-├── foaf
-│   └── ystafdb
-│       └── ystafdb.ttl
-└── prov
-|   └── ystafdb
-|       └── ystafdb.ttl
-└── flow
-    └── ystafdb
-        └── huse
-            └── huse.ttl
-
+├── [ 4.0K]  activitytype
+│   └── [ 4.0K]  ystafdb
+│       └── [ 249K]  ystafdb.ttl
+├── [ 4.0K]  flow
+│   └── [ 4.0K]  ystafdb
+│       └── [ 4.0K]  huse
+│           └── [  41M]  huse.ttl
+├── [ 4.0K]  flowobject
+│   └── [ 4.0K]  ystafdb
+│       └── [  63K]  ystafdb.ttl
+├── [ 4.0K]  foaf
+│   └── [ 4.0K]  ystafdb
+│       └── [ 1.4K]  ystafdb.ttl
+├── [ 4.0K]  location
+│   └── [ 4.0K]  ystafdb
+│       └── [ 158K]  ystafdb.ttl
+└── [ 4.0K]  prov
+    └── [ 4.0K]  ystafdb
+        └── [ 1.0M]  ystafdb.ttl
 ```
 
-
 ## Contributing
-All contributions should be via pull request, do not edit this package directly! We actually use it for stuff.
+All contributions should be via pull request, do not edit this package directly! We actually use it for stuff.
+

setup.py

@@ -16,64 +16,54 @@
 
 
 # Probably should be changed, __init__.py is no longer required for Python 3
-for dirpath, dirnames, filenames in os.walk('ystafdb'):
-    # Ignore dirnames that start with '.'
-    if '__init__.py' in filenames:
-        pkg = dirpath.replace(os.path.sep, '.')
+for dirpath, dirnames, filenames in os.walk("ystafdb"):
+    # Ignore dirnames that start with "."
+    if "__init__.py" in filenames:
+        pkg = dirpath.replace(os.path.sep, ".")
         if os.path.altsep:
-            pkg = pkg.replace(os.path.altsep, '.')
+            pkg = pkg.replace(os.path.altsep, ".")
         packages.append(pkg)
 
 
 def package_files(directory):
     paths = []
     for (path, directories, filenames) in os.walk(directory):
         for filename in filenames:
-            paths.append(os.path.join('..', path, filename))
+            paths.append(os.path.join("..", path, filename))
     return paths
 
 
 setup(
-    name='ystafdb',
-    version="0.5",
+    name="ystafdb",
+    version="0.5.0",
     packages=packages,
+    description="CLI tool to parse YSTAFDB and produce ttl/nt/xml.",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
     author="Emil Riis Hansen",
     author_email="emilrh@cs.aau.dk",
-    license=open('LICENSE').read(),
-    package_data={'ystafdb': package_files(os.path.join('ystafdb', 'data'))},
+    package_data={"ystafdb": package_files(os.path.join("ystafdb", "data"))},
     # Only if you have non-python data (CSV, etc.). Might need to change the directory name as well.
-    # package_data={'your_name_here': package_files(os.path.join('your_library_name', 'data'))},
-    entry_points = {
-        'console_scripts': [
-            'ystafdb-cli = ystafdb.bin.ystafdb:main',
-        ]
-    },
-    install_requires=[
-        'appdirs',
-        'docopt',
-        'rdflib',
-        'pandas'
-    ],
+    # package_data={"your_name_here": package_files(os.path.join("your_library_name", "data"))},
+    entry_points={"console_scripts": ["ystafdb-cli = ystafdb.bin.ystafdb:main",]},
+    install_requires=["appdirs", "docopt", "rdflib", "pandas"],
     url="https://github.com/BONSAMURAIS/ystafdb/",
-    long_description_content_type='text/markdown',
-    long_description=open('README.md').read(),
-    description='',
     classifiers=[
-        'Intended Audience :: End Users/Desktop',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: Microsoft :: Windows',
-        'Operating System :: POSIX',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Topic :: Scientific/Engineering :: Information Analysis',
-        'Topic :: Scientific/Engineering :: Mathematics',
-        'Topic :: Scientific/Engineering :: Visualization',
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: MacOS :: MacOS X",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: POSIX",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.5",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+        "Topic :: Scientific/Engineering :: Mathematics",
+        "Topic :: Scientific/Engineering :: Visualization",
     ],
 )