Merge pull request #51 from materials-data-facility/forge-dev

Merge Forge dev to master

Author: blaiszik

.travis.yml

@@ -3,6 +3,7 @@ python:
 - '3.5'
 - '3.6'
 - '3.7'
+- '3.8'
 install:
 - pip install --upgrade pip
 - pip install -e .

README.md

@@ -28,9 +28,7 @@ Tutorials and examples can be found in the `docs` directory. The Jupyter noteboo
 * To access data in the MDF, you must have an account recognized by Globus Auth (including Google, ORCiD, many academic institutions, or a [free Globus ID](https://www.globusid.org/create)).
 
 # Contributions
-If you find a bug or want a feature, feel free to open an issue here on GitHub (and please tag it accordingly). If you want to contribute code yourself, we're more than happy to accept merge requests.
-
-
+If you find a bug or want a feature, feel free to open an issue here on GitHub (and please tag it accordingly). If you want to contribute code yourself, we're more than happy to accept pull requests. Please direct these pull requests to the `forge-dev` branch
 
 # Support
 This work was performed under financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the [Center for Hierarchical Material Design (CHiMaD)](http://chimad.northwestern.edu). This work was performed under the following financial assistance award 70NANB19H005 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD). This work was also supported by the National Science Foundation as part of the [Midwest Big Data Hub](http://midwestbigdatahub.org) under NSF Award Number: 1636950 "BD Spokes: SPOKE: MIDWEST: Collaborative: Integrative Materials Design (IMaD): Leverage, Innovate, and Disseminate".

mdf_forge/__init__.py

@@ -1 +1,2 @@
 from .forge import Forge  # noqa: F401
+from .version import __version__   # noqa: F401

mdf_forge/forge.py

@@ -5,10 +5,10 @@
 import globus_sdk
 import mdf_toolbox
 import requests
-
-
 from tqdm import tqdm
 
+from .version import __version__
+
 # Maximum recommended number of HTTP file transfers
 #  Large transfers are much better suited for Globus Transfer
 HTTP_NUM_LIMIT = 50
@@ -70,6 +70,14 @@ def __init__(self, index=__default_index, local_ep=None, anonymous=False,
                     to overwrite the default for accessing the MDF NCSA endpoint.
             petrel_authorizer (globus_sdk.GlobusAuthorizer): An authenticated GlobusAuthorizer
                     to override the default.
+            no_local_server (bool): Disable spinning up a local server to automatically
+                    copy-paste the auth code. THIS IS REQUIRED if you are on a remote server.
+                    When used locally with no_local_server=False, the domain is localhost with
+                    a randomly chosen open port number.
+                    **Default**: ``False``.
+            no_browser (bool): Do not automatically open the browser for the Globus Auth URL.
+                    Display the URL instead and let the user navigate to that location manually.
+                    **Default**: ``False``.
         """
         self.__anonymous = anonymous
         self.local_ep = local_ep
@@ -82,7 +90,9 @@ def __init__(self, index=__default_index, local_ep=None, anonymous=False,
             if services:
                 clients = mdf_toolbox.login(services=services, app_name=self.__app_name,
                                             client_id=self.__client_id,
-                                            clear_old_tokens=clear_old_tokens)
+                                            clear_old_tokens=clear_old_tokens,
+                                            no_local_server=kwargs.get("no_local_server", False),
+                                            no_browser=kwargs.get("no_browser", False))
             else:
                 clients = {}
 
@@ -97,6 +107,10 @@ def __init__(self, index=__default_index, local_ep=None, anonymous=False,
         super().__init__(index=index, search_client=search_client,
                          scroll_field=self.__scroll_field, **kwargs)
 
+    @property
+    def version(self):
+        return __version__
+
     # ***********************************************
     # * Field-specific helpers
     # ***********************************************
@@ -636,7 +650,7 @@ def http_download(self, results, dest=".", preserve_dir=False, verbose=True):
             }
 
     def globus_download(self, results, dest=".", dest_ep=None, preserve_dir=False,
-                        inactivity_time=None, download_datasets=False, verbose=True):
+                        download_datasets=False, verbose=True, **kwargs):
         """Download data files from the provided results using Globus Transfer.
         This method requires Globus Connect to be installed on the destination endpoint.
 
@@ -651,9 +665,6 @@ def globus_download(self, results, dest=".", dest_ep=None, preserve_dir=False,
                     will be relative to the ``dest`` path
                     If ``False``, only the data files themselves will be saved.
                     **Default:** ``False``.
-            inactivity_time (int): Number of seconds the Transfer is allowed to go without progress
-                    before being cancelled.
-                    **Default:** ``self.__inactivity_time``.
             download_datasets (bool): If ``True``, will download the full dataset for any dataset
                     entries given.
                     If ``False``, will skip dataset entries with a notification.
@@ -668,7 +679,14 @@ def globus_download(self, results, dest=".", dest_ep=None, preserve_dir=False,
                     and errors will prompt for continuation confirmation.
                     If ``False``, only error messages will be printed,
                     and the Transfer will always continue.
-                    **Default:** ``True``.
+                    **Default:** ``False``.
+
+        Keyword Arguments:
+            inactivity_time (int): Number of seconds the Transfer is allowed to go without progress
+                    before being cancelled.
+                    **Default:** ``self.__inactivity_time``.
+            interval (int): Time in seconds to wait between checking transfer status.
+                            **Default:** ``self.__transfer_interval``
 
         Returns:
             list of str: The task IDs of the Globus transfers.
@@ -679,6 +697,9 @@ def globus_download(self, results, dest=".", dest_ep=None, preserve_dir=False,
                 "success": False,
                 "message": "Anonymous Globus Transfer not supported."
                 }
+        inactivity_time = kwargs.get("inactivity_time", self.__inactivity_time)
+        interval = kwargs.get('interval', self.__transfer_interval)
+
         dest = os.path.abspath(dest)
         # If results have info attached, remove it
         if type(results) is tuple:
@@ -687,8 +708,6 @@ def globus_download(self, results, dest=".", dest_ep=None, preserve_dir=False,
             if not self.local_ep:
                 self.local_ep = globus_sdk.LocalGlobusConnectPersonal().endpoint_id
             dest_ep = self.local_ep
-        if not inactivity_time:
-            inactivity_time = self.__inactivity_time
 
         # Assemble the transfer data
         tasks = {}
@@ -772,7 +791,7 @@ def globus_download(self, results, dest=".", dest_ep=None, preserve_dir=False,
         for task_ep, task_paths in tqdm(tasks.items(), desc="Transferring data",
                                         disable=(not verbose)):
             transfer = mdf_toolbox.custom_transfer(self.__transfer_client, task_ep, dest_ep,
-                                                   task_paths, interval=self.__transfer_interval,
+                                                   task_paths, interval=interval,
                                                    inactivity_time=inactivity_time)
             cont = True
             # Prime loop

mdf_forge/version.py

@@ -0,0 +1,2 @@
+# Single source of truth for package version
+__version__ = "0.7.6"

setup.py

@@ -1,8 +1,15 @@
+import os
 from setuptools import setup
 
+# Single source of truth for version
+version_ns = {}
+with open(os.path.join("mdf_forge", "version.py")) as f:
+    exec(f.read(), version_ns)
+version = version_ns['__version__']
+
 setup(
     name='mdf_forge',
-    version='0.7.5',
+    version=version,
     packages=['mdf_forge'],
     description='Materials Data Facility python package',
     long_description=("Forge is the Materials Data Facility Python package"