From a1b41be271b655daf74905798169ba5bba0a1bcc Mon Sep 17 00:00:00 2001
From: Michael Franklin <michael.franklin@petermac.org>
Date: Mon, 22 Jul 2019 14:05:27 +1000
Subject: [PATCH] Add README + better structure

---
 README.md                                     |   1 +
 __init__.py                                   |   2 -
 data_types/__init__.py                        |   7 ----
 janis_unix/__init__.py                        |   2 +
 .../__pycache__/__init__.cpython-37.pyc       | Bin 0 -> 216 bytes
 janis_unix/data_types/__init__.py             |   5 +++
 .../__pycache__/__init__.cpython-37.pyc       | Bin 0 -> 338 bytes
 .../data_types/__pycache__/csv.cpython-37.pyc | Bin 0 -> 589 bytes
 .../__pycache__/json.cpython-37.pyc           | Bin 0 -> 604 bytes
 .../__pycache__/tarfile.cpython-37.pyc        | Bin 0 -> 610 bytes
 .../data_types/__pycache__/tsv.cpython-37.pyc | Bin 0 -> 587 bytes
 .../__pycache__/zipfile.cpython-37.pyc        | Bin 0 -> 614 bytes
 {data_types => janis_unix/data_types}/csv.py  |   2 +-
 {data_types => janis_unix/data_types}/json.py |   2 +-
 .../data_types}/tarfile.py                    |   2 +-
 {data_types => janis_unix/data_types}/tsv.py  |   2 +-
 .../data_types}/zipfile.py                    |   2 +-
 janis_unix/tools/__init__.py                  |   6 +++
 .../tools/__pycache__/__init__.cpython-37.pyc | Bin 0 -> 360 bytes
 .../tools/__pycache__/cat.cpython-37.pyc      | Bin 0 -> 1230 bytes
 .../tools/__pycache__/compile.cpython-37.pyc  | Bin 0 -> 1527 bytes
 .../tools/__pycache__/echo.cpython-37.pyc     | Bin 0 -> 1123 bytes
 .../tools/__pycache__/merge.cpython-37.pyc    | Bin 0 -> 1146 bytes
 .../tools/__pycache__/tar.cpython-37.pyc      | Bin 0 -> 1413 bytes
 .../tools/__pycache__/unixtool.cpython-37.pyc | Bin 0 -> 657 bytes
 .../tools/__pycache__/untar.cpython-37.pyc    | Bin 0 -> 1250 bytes
 {tools => janis_unix/tools}/cat.py            |   7 +---
 {tools => janis_unix/tools}/compile.py        |   5 +--
 {tools => janis_unix/tools}/echo.py           |   4 +-
 {tools => janis_unix/tools}/merge.py          |   4 +-
 {tools => janis_unix/tools}/tar.py            |   7 ++--
 {tools => janis_unix/tools}/unixtool.py       |   2 +-
 {tools => janis_unix/tools}/untar.py          |   6 +--
 setup.py                                      |  39 ++++++++++++++++++
 tools/__init__.py                             |   7 ----
 35 files changed, 73 insertions(+), 41 deletions(-)
 create mode 100644 README.md
 delete mode 100644 __init__.py
 delete mode 100644 data_types/__init__.py
 create mode 100644 janis_unix/__init__.py
 create mode 100644 janis_unix/__pycache__/__init__.cpython-37.pyc
 create mode 100644 janis_unix/data_types/__init__.py
 create mode 100644 janis_unix/data_types/__pycache__/__init__.cpython-37.pyc
 create mode 100644 janis_unix/data_types/__pycache__/csv.cpython-37.pyc
 create mode 100644 janis_unix/data_types/__pycache__/json.cpython-37.pyc
 create mode 100644 janis_unix/data_types/__pycache__/tarfile.cpython-37.pyc
 create mode 100644 janis_unix/data_types/__pycache__/tsv.cpython-37.pyc
 create mode 100644 janis_unix/data_types/__pycache__/zipfile.cpython-37.pyc
 rename {data_types => janis_unix/data_types}/csv.py (82%)
 rename {data_types => janis_unix/data_types}/json.py (83%)
 rename {data_types => janis_unix/data_types}/tarfile.py (96%)
 rename {data_types => janis_unix/data_types}/tsv.py (82%)
 rename {data_types => janis_unix/data_types}/zipfile.py (75%)
 create mode 100644 janis_unix/tools/__init__.py
 create mode 100644 janis_unix/tools/__pycache__/__init__.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/cat.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/compile.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/echo.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/merge.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/tar.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/unixtool.cpython-37.pyc
 create mode 100644 janis_unix/tools/__pycache__/untar.cpython-37.pyc
 rename {tools => janis_unix/tools}/cat.py (69%)
 rename {tools => janis_unix/tools}/compile.py (83%)
 rename {tools => janis_unix/tools}/echo.py (77%)
 rename {tools => janis_unix/tools}/merge.py (76%)
 rename {tools => janis_unix/tools}/tar.py (78%)
 rename {tools => janis_unix/tools}/unixtool.py (84%)
 rename {tools => janis_unix/tools}/untar.py (70%)
 create mode 100644 setup.py
 delete mode 100644 tools/__init__.py

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..ded6e60
--- /dev/null
+++ b/README.md
@@ -0,0 +1 @@
+Janis - Unix tools
diff --git a/__init__.py b/__init__.py
deleted file mode 100644
index 43705fa..0000000
--- a/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-from .data_types import *
-from .tools import *
diff --git a/data_types/__init__.py b/data_types/__init__.py
deleted file mode 100644
index 9c5a3ba..0000000
--- a/data_types/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-from os.path import dirname, basename, isfile
-import glob
-
-modules = glob.glob(dirname(__file__) + "/*.py")
-__all__ = [
-    basename(f)[:-3] for f in modules if isfile(f) and not f.endswith("__init__.py")
-]
diff --git a/janis_unix/__init__.py b/janis_unix/__init__.py
new file mode 100644
index 0000000..310b70f
--- /dev/null
+++ b/janis_unix/__init__.py
@@ -0,0 +1,2 @@
+from janis_unix.data_types import *
+from janis_unix.tools import *
diff --git a/janis_unix/__pycache__/__init__.cpython-37.pyc b/janis_unix/__pycache__/__init__.cpython-37.pyc
new file mode 100644
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diff --git a/janis_unix/data_types/__init__.py b/janis_unix/data_types/__init__.py
new file mode 100644
index 0000000..4335b08
--- /dev/null
+++ b/janis_unix/data_types/__init__.py
@@ -0,0 +1,5 @@
+from .csv import Csv
+from .json import JsonFile
+from .tarfile import TarFile
+from .tsv import Tsv
+from .zipfile import ZipFile
\ No newline at end of file
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diff --git a/data_types/csv.py b/janis_unix/data_types/csv.py
similarity index 82%
rename from data_types/csv.py
rename to janis_unix/data_types/csv.py
index fdfef2f..cf72f50 100644
--- a/data_types/csv.py
+++ b/janis_unix/data_types/csv.py
@@ -1,4 +1,4 @@
-from janis import File
+from janis_core import File
 
 
 class Csv(File):
diff --git a/data_types/json.py b/janis_unix/data_types/json.py
similarity index 83%
rename from data_types/json.py
rename to janis_unix/data_types/json.py
index 76d3b4d..35dea4e 100644
--- a/data_types/json.py
+++ b/janis_unix/data_types/json.py
@@ -1,4 +1,4 @@
-from janis import File
+from janis_core import File
 
 
 class JsonFile(File):
diff --git a/data_types/tarfile.py b/janis_unix/data_types/tarfile.py
similarity index 96%
rename from data_types/tarfile.py
rename to janis_unix/data_types/tarfile.py
index 7692c81..1632d50 100644
--- a/data_types/tarfile.py
+++ b/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):
diff --git a/data_types/tsv.py b/janis_unix/data_types/tsv.py
similarity index 82%
rename from data_types/tsv.py
rename to janis_unix/data_types/tsv.py
index a8dfb7e..7cf99fa 100644
--- a/data_types/tsv.py
+++ b/janis_unix/data_types/tsv.py
@@ -1,4 +1,4 @@
-from janis import File
+from janis_core import File
 
 
 class Tsv(File):
diff --git a/data_types/zipfile.py b/janis_unix/data_types/zipfile.py
similarity index 75%
rename from data_types/zipfile.py
rename to janis_unix/data_types/zipfile.py
index f5d0529..b39ef0f 100644
--- a/data_types/zipfile.py
+++ b/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):
diff --git a/janis_unix/tools/__init__.py b/janis_unix/tools/__init__.py
new file mode 100644
index 0000000..2ad3520
--- /dev/null
+++ b/janis_unix/tools/__init__.py
@@ -0,0 +1,6 @@
+from .cat import Cat
+from .compile import Compile
+from .echo import Echo
+from .merge import Merge
+from .tar import Tar
+from .untar import Untar
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diff --git a/tools/cat.py b/janis_unix/tools/cat.py
similarity index 69%
rename from tools/cat.py
rename to janis_unix/tools/cat.py
index a621c56..b3aa917 100644
--- a/tools/cat.py
+++ b/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):
diff --git a/tools/compile.py b/janis_unix/tools/compile.py
similarity index 83%
rename from tools/compile.py
rename to janis_unix/tools/compile.py
index bd357b7..5c500c4 100644
--- a/tools/compile.py
+++ b/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
diff --git a/tools/echo.py b/janis_unix/tools/echo.py
similarity index 77%
rename from tools/echo.py
rename to janis_unix/tools/echo.py
index cea543b..ccc0936 100644
--- a/tools/echo.py
+++ b/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):
diff --git a/tools/merge.py b/janis_unix/tools/merge.py
similarity index 76%
rename from tools/merge.py
rename to janis_unix/tools/merge.py
index 10efa51..074f057 100644
--- a/tools/merge.py
+++ b/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):
diff --git a/tools/tar.py b/janis_unix/tools/tar.py
similarity index 78%
rename from tools/tar.py
rename to janis_unix/tools/tar.py
index b049be6..0ee5197 100644
--- a/tools/tar.py
+++ b/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
diff --git a/tools/unixtool.py b/janis_unix/tools/unixtool.py
similarity index 84%
rename from tools/unixtool.py
rename to janis_unix/tools/unixtool.py
index 8476d52..8cc1282 100644
--- a/tools/unixtool.py
+++ b/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):
diff --git a/tools/untar.py b/janis_unix/tools/untar.py
similarity index 70%
rename from tools/untar.py
rename to janis_unix/tools/untar.py
index 918363e..7164029 100644
--- a/tools/untar.py
+++ b/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):
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..5df1f36
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,39 @@
+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="michael.franklin@petermac.org",
+    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",
+    ],
+)
diff --git a/tools/__init__.py b/tools/__init__.py
deleted file mode 100644
index 9c5a3ba..0000000
--- a/tools/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-from os.path import dirname, basename, isfile
-import glob
-
-modules = glob.glob(dirname(__file__) + "/*.py")
-__all__ = [
-    basename(f)[:-3] for f in modules if isfile(f) and not f.endswith("__init__.py")
-]