Merge pull request #7 from Athanaseus/MDGA

update binary

.travis/py2.docker

@@ -5,3 +5,4 @@ RUN pip install --upgrade pip setuptools
 ADD . /code
 WORKDIR /code
 RUN pip install .[python-numpy,pytest]
+RUN drasticali -h

.travis/py3.docker

@@ -10,3 +10,4 @@ RUN docker-apt-install \
 ADD . /code
 WORKDIR /code
 RUN pip3 install .[python-numpy,testing]
+RUN drasticali -h

MANIFEST.in

@@ -1,5 +1,5 @@
 include LICENSE
-include README.md
+include README.rst
 recursive-include recipes *.json
 recursive-include recipes/input *.txt
-recursive-include drastic *.ipynb
+recursive-include drasticali *.ipynb

README.rst

@@ -9,7 +9,7 @@ drasticali
 
 Diverse Radio Astronomy Software Tools for Imaging and Calibration
 
-Main website: https://github.com/Athanaseus/Drastic/wiki
+Main website: https://github.com/Athanaseus/drasticali/wiki
 
 ==============
 Introduction
@@ -28,7 +28,7 @@ working directory where source is checked out
   
     $ pip install .
 
-This package will soon be available on *PYPI*, allowing
+This package is available on *PYPI*, allowing
 
 .. code-block:: bash
   
@@ -47,19 +47,19 @@ Contribute
 Contributions are always welcome! Please ensure that you adhere to our coding
 standards pep8_.
 
-.. |Pypi Version| image:: https://img.shields.io/pypi/v/aimfast.svg
-                  :target: https://pypi.python.org/pypi/aimfast
+.. |Pypi Version| image:: https://img.shields.io/pypi/v/drasticali.svg
+                  :target: https://pypi.python.org/pypi/drasticali
                   :alt:
-.. |Build Version| image:: https://travis-ci.com/Athanaseus/Drastic.svg?branch=master
-                  :target: https://travis-ci.com/Athanaseus/Drastic
+.. |Build Version| image:: https://travis-ci.org/Athanaseus/drasticali.svg?branch=master
+                  :target: https://travis-ci.org/Athanaseus/drasticali
                   :alt:
 
-.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/aimfast.svg
-                     :target: https://pypi.python.org/pypi/aimfast/
+.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/drasticali.svg
+                     :target: https://pypi.python.org/pypi/drasticali/
                      :alt:
 
 .. |Project License| image:: https://img.shields.io/badge/license-GPL-blue.svg
-                     :target: https://github.com/Athanaseus/Drastic/blob/master/LICENSE
+                     :target: https://github.com/Athanaseus/drasticali/blob/master/LICENSE
                      :alt:
 
 .. _source: https://github.com/Athanaseus/Drastic

bin/drasticali

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 
+import os
+import time
 import argparse
 from functools import partial
 
@@ -8,16 +10,62 @@ def get_argparser():
     """Get argument parser."""
     parser = argparse.ArgumentParser(
         description=("Diverse Radio Astronomy Tools for Imaging and Calibration"))
+    subparsers = parser.add_subparsers(help='commands')
+    list_parser = subparsers.add_parser('run', help='Run notebook server')
+    list_parser.add_argument('--port', action='store', help='Notebook server port')
     argument = partial(parser.add_argument)
+    argument("-gn", "--generate_notebooks",
+             default=False, action='store_true',
+             help='Generate default notebook files (.ipynb format)')
     return parser
 
-def pull():
-    """Use stimela to pull docker images"""
-    pass
+def generate_notebooks():
+    """Generate drasticali notebooks"""
+    time_start_load = time.time()
+    from shutil import copyfile
+    import drasticali
+    print("## Getting notebook files.")
+    drasticali_files = ['drasticali-add.ipynb',
+                        'drasticali-edit.ipynb',
+                        'drasticali-run.ipynb',
+                        'drasticali-inspect.ipynb']
+    DRASTICALI_PATH = os.path.dirname(os.path.dirname(os.path.abspath(drasticali.__file__)))
+    copyfile('{}/{}/{}'.format(DRASTICALI_PATH, 'drasticali', drasticali_files[0]),
+             drasticali_files[0])
+    print(drasticali_files[0])
+    copyfile('{}/{}/{}'.format(DRASTICALI_PATH, 'drasticali', drasticali_files[1]),
+             drasticali_files[1])
+    print(drasticali_files[1])
+    copyfile('{}/{}/{}'.format(DRASTICALI_PATH, 'drasticali', drasticali_files[2]),
+             drasticali_files[2])
+    print(drasticali_files[2])
+    copyfile('{}/{}/{}'.format(DRASTICALI_PATH, 'drasticali', drasticali_files[3]),
+             drasticali_files[3])
+    print(drasticali_files[3])
+    print("## Done ({0:.3f}s)".format(time.time() - time_start_load))
+
+def run_notebook(port):
+    """Run the notebooks"""
+    import subprocess
+    bashCommand1 = "jupyter-nbextension enable --py widgetsnbextension --sys-prefix"
+    bashCommand2 = "jupyter-nbextension install --py jupyter_dashboards --sys-prefix"
+    bashCommand3 = "jupyter-nbextension enable --py jupyter_dashboards --sys-prefix"
+    bashCommand4 = "jupyter-notebook --NotebookApp.iopub_data_rate_limit=1000000000 --port={} --no-browser".format(port)
+    process = subprocess.Popen(bashCommand1.split(), stdout=subprocess.PIPE, shell=True)
+    process = subprocess.Popen(bashCommand2.split(), stdout=subprocess.PIPE, shell=True)
+    process = subprocess.Popen(bashCommand3.split(), stdout=subprocess.PIPE, shell=True)
+    process = subprocess.Popen(bashCommand4.split(), stdout=subprocess.PIPE, shell=True)
 
 def main():
     """Main function."""
     parser = get_argparser()
     args = parser.parse_args()
+    if args.generate_notebooks:
+        generate_notebooks()
+    port = getattr(args, 'port', 0)
+    if port:
+       run_notebook(port)
+    elif port is None:
+       run_notebook('8888')
 
 main()

drasticali/drasticali-add.ipynb

@@ -41,9 +41,9 @@
     "import os\n",
     "import json\n",
     "import stimela\n",
-    "import drastic\n",
+    "import drasticali\n",
     "import pkg_resources\n",
-    "from drastic import natural_keys, remove_cab\n",
+    "from drasticali import natural_keys, remove_cab\n",
     "from ipywidgets import widgets, interact\n",
     "from IPython.display import Javascript"
    ]
@@ -333,10 +333,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "reload(drastic)\n",
     "cab_num = cab_number.value\n",
     "cab_func_name = cab.value\n",
-    "cab_func = getattr(drastic, cab_func_name, None)\n",
+    "cab_func = getattr(drasticali, cab_func_name, None)\n",
     "for key, val in PAR.items():\n",
     "    if val.value in ['None']:\n",
     "        continue\n",
@@ -420,7 +419,7 @@
    },
    "outputs": [],
    "source": [
-    "drastic.run_all(recipe, recipe_file.value)"
+    "drasticali.run_all(recipe, recipe_file.value)"
    ]
   },
   {
@@ -436,7 +435,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = drastic.get_data(recipe_file.value)\n",
+    "data = drasticali.get_data(recipe_file.value)\n",
     "recipe.jobs = []\n",
     "data_keys = data.keys()\n",
     "data_keys.sort(key=natural_keys)\n",

drasticali/drasticali-edit.ipynb

@@ -41,9 +41,9 @@
     "import os\n",
     "import json\n",
     "import stimela\n",
-    "import drastic\n",
+    "import drasticali\n",
     "import pkg_resources\n",
-    "from drastic import natural_keys\n",
+    "from drasticali import natural_keys\n",
     "from ipywidgets import widgets, interact\n",
     "from IPython.display import Javascript"
    ]
@@ -181,7 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = drastic.get_data(recipe_file.value)\n",
+    "data = drasticali.get_data(recipe_file.value)\n",
     "recipe.jobs = []"
    ]
   },
@@ -335,7 +335,7 @@
     "\n",
     "c = DATA[cab_func_name]\n",
     "params = c['parameters']\n",
-    "cab_func = getattr(drastic, cab_func_name, None)\n",
+    "cab_func = getattr(drasticali, cab_func_name, None)\n",
     "for key, val in PAR.items():\n",
     "    key = str(key)\n",
     "    if val.value in ['None', '', \"''\"]:\n",
@@ -391,7 +391,7 @@
    },
    "outputs": [],
    "source": [
-    "drastic.run_all(recipe, recipe_file.value)"
+    "drasticali.run_all(recipe, recipe_file.value)"
    ]
   }
  ],

drasticali/drasticali-run.ipynb

@@ -41,9 +41,9 @@
     "import os\n",
     "import json\n",
     "import stimela\n",
-    "import drastic\n",
+    "import drasticali\n",
     "import pkg_resources\n",
-    "from drastic import natural_keys\n",
+    "from drasticali import natural_keys\n",
     "from ipywidgets import widgets, interact\n",
     "from IPython.display import Javascript"
    ]
@@ -176,7 +176,7 @@
    "source": [
     "Im = []\n",
     "recipe.jobs = []\n",
-    "data = drastic.get_data(recipe_file.value)\n",
+    "data = drasticali.get_data(recipe_file.value)\n",
     "cb_cont = widgets.HBox(background_color='red',height='200px',width='100%')\n",
     "data_keys = data.keys()\n",
     "data_keys.sort(key=natural_keys)\n",
@@ -217,7 +217,7 @@
     "    new_cab_params = dict()\n",
     "    cab_num = cab_value.split('_')[0]\n",
     "    cab_name = cab_value.split('{}_'.format(cab_num))[-1]\n",
-    "    cab_func = getattr(drastic, 'cab_function', None)\n",
+    "    cab_func = getattr(drasticali, 'cab_function', None)\n",
     "    for c in cb_cont.children:\n",
     "        if c.description == cab_value:\n",
     "            if c.value:\n",
@@ -227,7 +227,7 @@
     "                                                          else cab_param_value)\n",
     "                cab_func(recipe, name=cab_name, num=cab_num, parameters=new_cab_params,\n",
     "                         recipes_file=recipe_file.value, dump=False)\n",
-    "drastic.run_all(recipe, recipe_file.value)"
+    "drasticali.run_all(recipe, recipe_file.value)"
    ]
   },
   {
@@ -260,7 +260,7 @@
    "source": [
     "cab_ids, times = [], []\n",
     "prefix = recipe_file.value.split('/')[-1].split('.')[0]\n",
-    "data = drastic.get_data('{}_time-it.json'.format(prefix))\n",
+    "data = drasticali.get_data('{}_time-it.json'.format(prefix))\n",
     "data_keys = data.keys()\n",
     "data_keys.sort(key=natural_keys)\n",
     "for key in data_keys:\n",

requirements.txt

@@ -1,2 +1,3 @@
 aimfast
+ipywidgets
 stimela

setup.py

@@ -2,7 +2,7 @@
 from setuptools import setup, find_packages
 
 pkg = 'drasticali'
-__version__ = '0.0.7'
+__version__ = '0.0.8'
 
 build_root = os.path.dirname(__file__)
 scripts = ["bin/" + j for j in os.listdir("bin") ]
@@ -26,7 +26,7 @@ def requirements():
       author="Athanaseus Ramaila",
       author_email="[email protected]",
       packages=find_packages(),
-      url="https://github.com/Athanaseus/Drastic",
+      url="https://github.com/Athanaseus/drasticali",
       license="GNU GPL 3",
       classifiers=["Intended Audience :: Developers",
                    "Programming Language :: Python :: 3",