Add partial type annotations

.isort.cfg

@@ -0,0 +1,12 @@
+[settings]
+combine_as_imports=true
+force_alphabetical_sort_within_sections=true
+# Override force_grid_wrap value from profile=black, but black is still happy
+force_grid_wrap=2
+# Same line length as for black
+line_length=120
+no_lines_before=LOCALFOLDER
+profile=black
+reverse_relative=true
+skip_gitignore=true
+src_paths=src

MANIFEST.in

@@ -1,2 +1,2 @@
 graft src
-include *.rst LICENSE
+include *.rst LICENSE src/ephemeris/py.typed

Makefile

@@ -1,7 +1,7 @@
 # Default tests run with make test and make quick-tests
 NOSE_TESTS?=tests ephemeris
 # Default environment for make tox
-ENV?=py27
+ENV?=py37
 # Extra arguments supplied to tox command
 ARGS?=
 # Location of virtualenv used for development.

src/ephemeris/__init__.py

@@ -1,26 +1,28 @@
-
 # -*- coding: utf-8 -*-
 
 import yaml
 from bioblend import galaxy
 
-__version__ = '0.10.7'
+__version__ = "0.10.7"
 
 PROJECT_NAME = "ephemeris"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/ephemeris"
-PROJECT_AUTHOR = 'Galaxy Project and Community'
-PROJECT_EMAIL = 'jmchilton@gmail.com'
+PROJECT_AUTHOR = "Galaxy Project and Community"
+PROJECT_EMAIL = "jmchilton@gmail.com"
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
-    PROJECT_USERAME, PROJECT_NAME
+    PROJECT_USERAME,
+    PROJECT_NAME,
 )
 
 
 def check_url(url, log=None):
-    if not url.startswith('http'):
+    if not url.startswith("http"):
         if log:
-            log.warning('URL should start with http:// or https://. https:// chosen by default.')
-        url = 'https://' + url
+            log.warning(
+                "URL should start with http:// or https://. https:// chosen by default."
+            )
+        url = "https://" + url
     return url
 
 
@@ -35,25 +37,29 @@ def get_galaxy_connection(args, file=None, log=None, login_required=True):
     else:
         file_content = dict()
 
-    url = args.galaxy or file_content.get('galaxy_instance')
+    url = args.galaxy or file_content.get("galaxy_instance")
     galaxy_url = check_url(url, log)
-    api_key = args.api_key or file_content.get('api_key')
+    api_key = args.api_key or file_content.get("api_key")
 
     if args.user and args.password:
-        return galaxy.GalaxyInstance(url=galaxy_url, email=args.user, password=args.password)
+        return galaxy.GalaxyInstance(
+            url=galaxy_url, email=args.user, password=args.password
+        )
     elif api_key:
         return galaxy.GalaxyInstance(url=galaxy_url, key=api_key)
     elif not login_required:
         return galaxy.GalaxyInstance(url=galaxy_url)
     else:
-        raise ValueError("Missing api key or user & password combination, in order to make a galaxy connection.")
+        raise ValueError(
+            "Missing api key or user & password combination, in order to make a galaxy connection."
+        )
 
 
 def load_yaml_file(filename):
     """
     Load YAML from the `tool_list_file` and return a dict with the content.
     """
-    with open(filename, 'r') as f:
+    with open(filename, "r") as f:
         dictionary = yaml.safe_load(f)
     return dictionary
 
@@ -62,5 +68,5 @@ def dump_to_yaml_file(content, file_name):
     """
     Dump YAML-compatible `content` to `file_name`.
     """
-    with open(file_name, 'w') as f:
+    with open(file_name, "w") as f:
         yaml.dump(content, f, default_flow_style=False)

src/ephemeris/common_parser.py

@@ -4,29 +4,36 @@
 
 
 def get_common_args(login_required=True, log_file=False):
-
     parser = argparse.ArgumentParser(add_help=False)
-    general_group = parser.add_argument_group('General options')
-    general_group.add_argument("-v", "--verbose", help="Increase output verbosity.", action="store_true")
+    general_group = parser.add_argument_group("General options")
+    general_group.add_argument(
+        "-v", "--verbose", help="Increase output verbosity.", action="store_true"
+    )
     if log_file:
-        general_group.add_argument("--log_file",
-                                   dest="log_file",
-                                   help="Where the log file should be stored. "
-                                   "Default is a file in your system's temp folder",
-                                   default=None)
+        general_group.add_argument(
+            "--log_file",
+            dest="log_file",
+            help="Where the log file should be stored. "
+            "Default is a file in your system's temp folder",
+            default=None,
+        )
 
-    con_group = parser.add_argument_group('Galaxy connection')
-    con_group.add_argument("-g", "--galaxy",
-                           help="Target Galaxy instance URL/IP address",
-                           default="http://localhost:8080")
+    con_group = parser.add_argument_group("Galaxy connection")
+    con_group.add_argument(
+        "-g",
+        "--galaxy",
+        help="Target Galaxy instance URL/IP address",
+        default="http://localhost:8080",
+    )
 
     if login_required:
-        con_group.add_argument("-u", "--user",
-                               help="Galaxy user email address")
-        con_group.add_argument("-p", "--password",
-                               help="Password for the Galaxy user")
-        con_group.add_argument("-a", "--api_key",
-                               dest="api_key",
-                               help="Galaxy admin user API key (required if not defined in the tools list file)")
+        con_group.add_argument("-u", "--user", help="Galaxy user email address")
+        con_group.add_argument("-p", "--password", help="Password for the Galaxy user")
+        con_group.add_argument(
+            "-a",
+            "--api_key",
+            dest="api_key",
+            help="Galaxy admin user API key (required if not defined in the tools list file)",
+        )
 
     return parser

src/ephemeris/ephemeris_log.py

@@ -7,21 +7,22 @@ class ProgressConsoleHandler(logging.StreamHandler):
     A handler class which allows the cursor to stay on
     one line for selected messages
     """
+
     on_same_line = False
 
     def emit(self, record):
         try:
             msg = self.format(record)
             stream = self.stream
-            same_line = hasattr(record, 'same_line')
+            same_line = hasattr(record, "same_line")
             if self.on_same_line and not same_line:
-                stream.write('\r\n')
+                stream.write("\r\n")
             stream.write(msg)
             if same_line:
-                stream.write('.')
+                stream.write(".")
                 self.on_same_line = True
             else:
-                stream.write('\r\n')
+                stream.write("\r\n")
                 self.on_same_line = False
             self.flush()
         except (KeyboardInterrupt, SystemExit):
@@ -32,16 +33,16 @@ def emit(self, record):
 
 def disable_external_library_logging():
     # Omit (most of the) logging by external libraries
-    logging.getLogger('bioblend').setLevel(logging.ERROR)
-    logging.getLogger('requests').setLevel(logging.ERROR)
+    logging.getLogger("bioblend").setLevel(logging.ERROR)
+    logging.getLogger("requests").setLevel(logging.ERROR)
     try:
         logging.captureWarnings(True)  # Capture HTTPS warngings from urllib3
     except AttributeError:
         pass
 
 
 def setup_global_logger(name, log_file=None):
-    formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s')
+    formatter = logging.Formatter("%(asctime)s %(levelname)-5s - %(message)s")
     progress = ProgressConsoleHandler()
     console = logging.StreamHandler()
     console.setFormatter(formatter)