Add README + better structure

README.md

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+Janis - Unix tools

janis_unix/__init__.py

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+from janis_unix.data_types import *
+from janis_unix.tools import *

janis_unix/data_types/__init__.py

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+from .csv import Csv
+from .json import JsonFile
+from .tarfile import TarFile
+from .tsv import Tsv
+from .zipfile import ZipFile

data_types/csv.py → janis_unix/data_types/csv.py

@@ -1,4 +1,4 @@
-from janis import File
+from janis_core import File
 
 
 class Csv(File):

data_types/json.py → janis_unix/data_types/json.py

@@ -1,4 +1,4 @@
-from janis import File
+from janis_core import File
 
 
 class JsonFile(File):

data_types/tarfile.py → janis_unix/data_types/tarfile.py

@@ -1,4 +1,4 @@
-from janis.types.common_data_types import File
+from janis_core import File
 
 
 class TarFile(File):

data_types/tsv.py → janis_unix/data_types/tsv.py

@@ -1,4 +1,4 @@
-from janis import File
+from janis_core import File
 
 
 class Tsv(File):

data_types/zipfile.py → janis_unix/data_types/zipfile.py

@@ -1,4 +1,4 @@
-from janis.types.common_data_types import File
+from janis_core import File
 
 
 class ZipFile(File):

janis_unix/tools/__init__.py

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+from .cat import Cat
+from .compile import Compile
+from .echo import Echo
+from .merge import Merge
+from .tar import Tar
+from .untar import Untar

tools/cat.py → janis_unix/tools/cat.py

@@ -1,8 +1,5 @@
-from janis import ToolOutput, Stdout
-
-from janis.tool.commandtool import ToolInput
-from janis.types.common_data_types import Array, File
-from janis.unix.tools.unixtool import UnixTool
+from janis_core import ToolInput, ToolOutput, Stdout, Array, File
+from .unixtool import UnixTool
 
 
 class Cat(UnixTool):

tools/compile.py → janis_unix/tools/compile.py

@@ -4,9 +4,8 @@
 
 from typing import List
 
-from janis import ToolInput, ToolOutput, ToolArgument, WildcardSelector, File
-from janis.unix.tools.unixtool import UnixTool
-
+from janis_core import ToolInput, ToolOutput, ToolArgument, WildcardSelector, File
+from .unixtool import UnixTool
 
 class Compile(UnixTool):
     @staticmethod

tools/echo.py → janis_unix/tools/echo.py

@@ -1,5 +1,5 @@
-from janis import String, ToolInput, ToolOutput, Stdout
-from janis.unix.tools.unixtool import UnixTool
+from janis_core import String, ToolInput, ToolOutput, Stdout
+from .unixtool import UnixTool
 
 
 class Echo(UnixTool):

tools/merge.py → janis_unix/tools/merge.py

@@ -1,5 +1,5 @@
-from janis import File, Array, ToolInput, ToolOutput, Stdout
-from janis.unix.tools.unixtool import UnixTool
+from janis_core import File, Array, ToolInput, ToolOutput, Stdout
+from .unixtool import UnixTool
 
 
 class Merge(UnixTool):

tools/tar.py → janis_unix/tools/tar.py

@@ -1,9 +1,8 @@
 #
 # Untar a file
-from janis import Array, ToolInput, ToolOutput, InputSelector, File, Filename
-from janis.unix.data_types.tarfile import TarFile
-from janis.unix.tools.unixtool import UnixTool
-
+from janis_core import Array, ToolInput, ToolOutput, InputSelector, File, Filename
+from ..data_types.tarfile import TarFile
+from .unixtool import UnixTool
 
 class Tar(UnixTool):
     @staticmethod

tools/unixtool.py → janis_unix/tools/unixtool.py

@@ -1,6 +1,6 @@
 from abc import ABC
 
-from janis import CommandTool
+from janis_core import CommandTool
 
 
 class UnixTool(CommandTool, ABC):

tools/untar.py → janis_unix/tools/untar.py

@@ -1,6 +1,6 @@
-from janis import Array, ToolInput, ToolOutput, WildcardSelector, File
-from janis.unix.data_types.tarfile import TarFile
-from janis.unix.tools.unixtool import UnixTool
+from janis_core import Array, ToolInput, ToolOutput, WildcardSelector, File
+from ..data_types.tarfile import TarFile
+from .unixtool import UnixTool
 
 
 class Untar(UnixTool):

setup.py

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+from setuptools import setup, find_packages
+
+# Version information is found in the __init__ file of `janiscore/`
+DESCRIPTION = "Contains UNIX classes"
+
+######## SHOULDN'T NEED EDITS BELOW THIS LINE ########
+
+with open("./README.md") as readme:
+    long_description = readme.read()
+
+__version__ = "v0.1.0"
+
+
+setup(
+    name="janis-pipelines.unix",
+    version=__version__,
+    description=DESCRIPTION,
+    url="",
+    author="Michael Franklin, Evan Thomas, Mohammad Bhuyan",
+    author_email="[email protected]",
+    license="GNU",
+    keywords=["pipelines", "bioinformatics", "workflows"],
+    packages=["janis_unix"]
+    + ["janis_unix." + p for p in sorted(find_packages("./janis_unix"))],
+    install_requires=[
+        "janis-pipelines.core"
+    ],
+    entry_points={"janis.extension": ["unix=janis_unix"]},
+    zip_safe=False,
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    classifiers=[
+        "Development Status :: 2 - Pre-Alpha",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
+)