Merge pull request #92 from EarthCubeInGeo/develop

[MNT]: Release v2021.1.0

HISTORY.rst

@@ -1,6 +1,12 @@
 
 .. :changelog:
 
+2021.1.0 (2021-08-11)
++++++++++++++++++++++
+
+- Update start jupyter command so that resen works with jupyter lab 3
+- Fixes #85, a bug which caused downloading images to fail on windows computer because progress bars were not generated in a system agnostic way
+
 2020.2.1 (2020-11-12)
 +++++++++++++++++++++
 

README.rst

@@ -18,7 +18,7 @@ Resen requires both python 3 and docker to be installed.
 
 1. Install `Python 3 <https://www.python.org/>`_
 2. Install `docker <https://docs.docker.com/install/>`_
-3. Install Resen with pip ``pip install git+https://github.com/EarthCubeInGeo/resen.git@v2020.2.1``
+3. Install Resen with pip ``pip install git+https://github.com/EarthCubeInGeo/resen.git@v2021.1.0``
 
 Please refer to the :ref:`installation documentation <installation>` for more detailed instructions.
 

docs/installation/installation.general.rst

@@ -35,4 +35,4 @@ Resen
 
 Install Resen from a python 3 environment using ``pip``::
 
- pip install git+https://github.com/EarthCubeInGeo/resen.git@v2020.2.0
+ pip install git+https://github.com/EarthCubeInGeo/resen.git@v2021.1.0

docs/tutorials.rst

@@ -13,26 +13,28 @@ The InGeO team has collected a variety of `tutorials <https://github.com/EarthCu
 
 4. Copy/paste the appropriate fetching command from the table below to download the tutorial, for example::
 
- $ wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/GetStartedWithPython.ipynb
+ $ wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/GetStartedWithPython.ipynb
 
 After downloading completes, the tutorial notebook should be visible in the navigation toolbar. By double-clicking, you can launch the jupyter notebook, read through descriptions, try example code, and even modify the notebook to try new things.
 
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
 | Tutorials | Fetch Command |
 +========================================================================================================================================+========================================================================================================================+
-| `GetStartedWithPython.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/GetStartedWithPython.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/GetStartedWithPython.ipynb`` |
+| `GetStartedWithPython.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/GetStartedWithPython.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/GetStartedWithPython.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `GetStartedWithJupyter.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/GetStartedWithJupyter.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/GetStartedWithJupyter.ipynb`` |
+| `GetStartedWithJupyter.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/GetStartedWithJupyter.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/GetStartedWithJupyter.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `GetStartedWithResen.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/GetStartedWithReSEn.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/GetStartedWithReSEn.ipynb`` |
+| `GetStartedWithResen.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/GetStartedWithResen.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/GetStartedWithResen.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `GeospacePackagesInResen.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/GeospacePackagesInResen.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/GeospacePackagesInResen.ipynb`` |
+| `GeospacePackagesInResen.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/GeospacePackagesInResen.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/GeospacePackagesInResen.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `CaseStudy.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/CaseStudy.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/CaseStudy.ipynb`` |
+| `CaseStudy.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/CaseStudy.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/CaseStudy.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `Intro-Swarm-viresclient.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/Intro-Swarm-viresclient.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/Intro-Swarm-viresclient.ipynb`` |
+| `Intro-Swarm-viresclient.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/Intro-Swarm-viresclient.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/Intro-Swarm-viresclient.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `ICON-Data-Demo.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/ICON-Data-Demo.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/ICON-Data-Demo.ipynb`` |
+| `ICON-Data-Demo.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/ICON-Data-Demo.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/ICON-Data-Demo.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
-| `CitationHelper.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2020.2.1/tutorials/CitationHelper.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2020.2.1/tutorials/CitationHelper.ipynb`` |
+| `EmpiricalModels.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/EmpiricalModels.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/EmpiricalModels.ipynb`` |
++----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+
+| `CitationHelper.ipynb <https://github.com/EarthCubeInGeo/resen-core/blob/v2021.1.0/tutorials/CitationHelper.ipynb>`_ | ``wget https://raw.githubusercontent.com/EarthCubeInGeo/resen-core/v2021.1.0/tutorials/CitationHelper.ipynb`` |
 +----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+

docs/usage.rst

@@ -12,7 +12,7 @@ This will open the resen tool::
  | / _|\__ \ _|| .` |
  |_|_\___|___/___|_|\_|
 
- Resen 2020.2.1 -- Reproducible Software Environment
+ Resen 2021.1.0 -- Reproducible Software Environment
 
  [resen] >>>
 
@@ -66,8 +66,8 @@ Setup a New Bucket
  Next, the user is asked to specify the version of resen-core to use::
 
  Please choose a version of resen-core.
- Available versions: 2019.1.0, 2020.1.0, 2020.2.0
- >>> Select a version: 2020.2.0
+ Available versions: 2019.1.0, 2020.1.0, 2021.1.0
+ >>> Select a version: 2021.1.0
 
  Optionally, one may then specify a local directory to :ref:`mount <mounting>` into the bucket at ``/home/jovyan/mount``::
 
@@ -100,7 +100,7 @@ Setup a New Bucket
  amber
  =====
 
- Resen-core Version: 2020.2.0
+ Resen-core Version: 2021.1.0
  Status: running
  Jupyter Token: e7a11fc1ea42a445807b4e24146b9908e1abff82bacbf6f2
  Jupyter Port: 9002
@@ -122,7 +122,7 @@ Work with a Bucket
 
  [resen] >>> list
  Bucket Name Docker Image Status
- amber 2020.2.0 running
+ amber 2021.1.0 running
 
  If a bucket is running, it will consume system resources accordingly.
 
@@ -134,7 +134,7 @@ Work with a Bucket
 
  [resen] >>> list
  Bucket Name Docker Image Status
- amber 2020.2.0 exited
+ amber 2021.1.0 exited
 
  The bucket will still exist and can be restarted at any time, even after quitting and restarting resen.
 
@@ -146,7 +146,7 @@ Work with a Bucket
 
  [resen] >>> status
  Bucket Name Docker Image Status
- amber 2020.2.0 running
+ amber 2021.1.0 running
 
 4. Export bucket ``amber``::
 

docs/version_update.py

@@ -5,7 +5,7 @@
 import fileinput
 
 old_version = '2020.2.0'
-new_version = '2020.2.1'
+new_version = '2021.1.0'
 
 for root, dirs, files in os.walk('..'):
  for fn in files:

resen/DockerHelper.py

@@ -129,7 +129,8 @@ def truncate_secs(delta_time, fmt=":%.2d"):
  # get terminal dimensions
  def get_terminal_dims():
  """Returns integers rows and columns of the terminal."""
- return [int(x) for x in os.popen('stty size', 'r').read().split()]
+ terminal_size = os.get_terminal_size()
+ return terminal_size.lines, terminal_size.columns
 
  # progress bar
  def update_bar(sum_total,accumulated,t0,current_time, init_bar_chars=34):

resen/Resen.py

@@ -43,6 +43,7 @@
 from subprocess import Popen, PIPE # used for selinux detection
 import platform # NEEDED FOR WINDOWS QUICK FIX
 import requests
+import glob
 
 
 from .DockerHelper import DockerHelper
@@ -571,9 +572,10 @@ def stop_jupyter(self,bucket_name):
 
  # form python command to stop jupyter and execute it
  port = bucket['jupyter']['port']
- python_cmd = 'from notebook.notebookapp import shutdown_server, list_running_servers; '
- python_cmd += 'svrs = [x for x in list_running_servers() if x[\\\"port\\\"] == %s]; ' % (port)
- python_cmd += 'sts = True if len(svrs) == 0 else shutdown_server(svrs[0]); print(sts)'
+ python_cmd = 'exec(\\\"try: from jupyter_server.serverapp import shutdown_server, list_running_servers\\n'
+ python_cmd += 'except: from notebook.notebookapp import shutdown_server, list_running_servers\\n'
+ python_cmd += 'svrs = [x for x in list_running_servers() if x[\\\\\\"port\\\\\\"] == %s]; ' % (port)
+ python_cmd += 'sts = True if len(svrs) == 0 else shutdown_server(svrs[0]); print(sts)\\\")'
  command = "bash -cl '%s/bin/python -c \"%s \"'" % (envpath,python_cmd)
  status = self.execute_command(bucket_name,command,detach=False)
 
@@ -862,13 +864,15 @@ def __get_valid_cores(self):
  self.update_core_list()
 
  # for each JSON file in core directory, read in list of cores
+ json_files = glob.glob(os.path.join(core_dir, '*.json'))
+
  cores = []
- for fn in os.listdir(core_dir):
+ for filename in sorted(json_files):
  try:
- with open(os.path.join(core_dir,fn),'r') as f:
+ with open(filename) as f:
  cores.extend(json.load(f))
- except json.decoder.JSONDecodeError:
- print('WARNING: {} is not a valid JSON file! Skiping this file.'.format(fn))
+ except:
+ print(f'WARNING: Problem reading {filename}. Skipping.')
 
  return cores
 

resen/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '2020.2.1'
+__version__ = '2021.1.0'
 
 from .Resen import Resen