Update formatting

Author: mikecormier

ggd/__main__.py

@@ -14,10 +14,13 @@
 from .uninstall import add_uninstall
 
 if sys.version_info[0] < 3:
-    print("\n:ggd:WARNING: Python 2 is no longer maintained by python developers."
-          " GGD will not maintain support for python 2 past December 31, 2020."
-          " Python 2 may still work, but continued maintenance and support will"
-          " be focused on python >=  3\n")
+    print(
+        "\n:ggd:WARNING: Python 2 is no longer maintained by python developers."
+        " GGD will not maintain support for python 2 past December 31, 2020."
+        " Python 2 may still work, but continued maintenance and support will"
+        " be focused on python >=  3\n"
+    )
+
 
 def main(args=None):
     if args is None:

ggd/check_recipe.py

@@ -90,7 +90,6 @@ def check_ggd_recipe(ggd_recipe, ggd_channel):
 
     package_list = search_packages(jdict, [ggd_recipe])
 
-
     if ggd_recipe in package_list:
         print(
             "\n:ggd:install: %s exists in the ggd-%s channel"
@@ -251,9 +250,9 @@ def install_from_cached(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix
     True if successful install
     """
     from .utils import (
+        ChecksumError,
         bypass_satsolver_on_install,
         update_installed_pkg_metadata,
-        ChecksumError,
     )
 
     conda_channel = "ggd-" + ggd_channel
@@ -339,9 +338,9 @@ def conda_install(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix=None)
     True if successful install
     """
     from .utils import (
+        ChecksumError,
         get_required_conda_version,
         update_installed_pkg_metadata,
-        ChecksumError,
     )
 
     ## Get the target prefix
@@ -351,8 +350,7 @@ def conda_install(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix=None)
     conda_version, equals = get_required_conda_version()
 
     ## create install string
-    conda_install_str = "{}conda{}{}{}".format("\"", equals, conda_version, "\"")
-
+    conda_install_str = "{}conda{}{}{}".format('"', equals, conda_version, '"')
 
     try:
         ## py3 *args. (Syntax error in py2)
@@ -529,11 +527,12 @@ def install_checksum(pkg_names, ggd_jdict, prefix=conda_root()):
     2) raises "ChecksumError" if fails
     """
     import tarfile
+
     from .utils import (
-        get_conda_package_list,
-        get_checksum_dict_from_tar,
-        data_file_checksum,
         ChecksumError,
+        data_file_checksum,
+        get_checksum_dict_from_tar,
+        get_conda_package_list,
     )
 
     print("\n:ggd:install: Initiating data file content validation using checksum")
@@ -698,12 +697,12 @@ def install(parser, args):
 
         ## Check that the package is set up for installation into a different prefix if one is provided
         if diff_prefix and conda_prefix != conda_root():
-            assert (
-                "final-files" in ggd_jsonDict["packages"][pkg]["tags"]
-            ), ("\n\n:ggd:install: !!ERROR!! the --prefix flag was set but the '{}' data package is not set up" 
+            assert "final-files" in ggd_jsonDict["packages"][pkg]["tags"], (
+                "\n\n:ggd:install: !!ERROR!! the --prefix flag was set but the '{}' data package is not set up"
                 " to be installed into a different prefix. GGD is unable to fulfill the install request. Remove the"
                 " --prefix flag to install this data package. Notify the ggd team if you would like this recipe"
-                " to be updated for --prefix install compatibility").format(pkg)
+                " to be updated for --prefix install compatibility"
+            ).format(pkg)
 
         ## Check if the recipe is already installed
         if check_if_installed(pkg, ggd_jsonDict, conda_prefix) == False:

ggd/install.py

@@ -55,10 +55,7 @@ def add_list_files(p):
         default=None,
         help="(Optional) The name or the full directory path to an conda environment where a ggd recipe is stored. (Only needed if not getting file paths for files in the current conda environment)",
     )
-    c.add_argument(
-        "name",
-        help="recipe name"
-    )
+    c.add_argument("name", help="recipe name")
     c.set_defaults(func=list_files)
 
 
@@ -117,7 +114,6 @@ def in_ggd_channel(ggd_recipe, ggd_channel):
     if len(json_dict["packages"].keys()) > 0:
         package_list = search_packages(json_dict, [ggd_recipe])
 
-
     if ggd_recipe in package_list:
         species = json_dict["packages"][ggd_recipe]["identifiers"]["species"]
         build = json_dict["packages"][ggd_recipe]["identifiers"]["genome-build"]
@@ -140,6 +136,7 @@ def list_files(parser, args):
     """Main method. Method used to list files for an installed ggd-recipe"""
 
     import glob
+
     from .utils import (
         conda_root,
         get_conda_prefix_path,

ggd/list_files.py

@@ -15,7 +15,7 @@
 ## Argument Parser
 # -------------------------------------------------------------------------------------------------------------
 def add_list_installed_packages(p):
-    
+
     import argparse
 
     c = p.add_parser(
@@ -33,11 +33,7 @@ def add_list_installed_packages(p):
         default=None,
         help="(Optional) The name or the full directory path to a conda environment where a ggd recipe is stored. (Only needed if listing data files not in the current environment)",
     )
-    c.add_argument(
-        "--reset",
-        action="store_true",
-        help=argparse.SUPPRESS
-    )
+    c.add_argument("--reset", action="store_true", help=argparse.SUPPRESS)
     c.set_defaults(func=list_installed_packages)
 
 
@@ -123,7 +119,7 @@ def list_pkg_info(pkg_names, pkgs_dict, env_vars, conda_list, prefix, prefix_set
     ]
 
     missing_in_conda = False
-    missing_message = " [WARNING: Present in GGD but missing from Conda]" 
+    missing_message = " [WARNING: Present in GGD but missing from Conda]"
     ## Iterate over each package in pkg_names
     for pkg in pkg_names:
 
@@ -141,7 +137,7 @@ def list_pkg_info(pkg_names, pkgs_dict, env_vars, conda_list, prefix, prefix_set
             missing_in_conda = True
             build = missing_message
             channel = ""
-            
+
         ## Get env_vars
         env_variables = []
         if (
@@ -202,11 +198,15 @@ def list_pkg_info(pkg_names, pkgs_dict, env_vars, conda_list, prefix, prefix_set
 
     ## Print message if a package is missing from conda metadata
     if missing_in_conda:
-        print(("#\n# NOTE: Packages with the '{}' messages represent packages where the ggd"
-              " packages is installed, but the package metadata has been removed from conda storage. This happens when"
-              " the packages is uninstalled using conda rather then ggd. The package is still available for use and is"
-              " in the same state as before the 'conda uninstall'. To fix the problem on conda's side, uninstall"
-              " the package with 'ggd uninstall' and re-install with 'ggd install'.\n").format(missing_message))
+        print(
+            (
+                "#\n# NOTE: Packages with the '{}' messages represent packages where the ggd"
+                " packages is installed, but the package metadata has been removed from conda storage. This happens when"
+                " the packages is uninstalled using conda rather then ggd. The package is still available for use and is"
+                " in the same state as before the 'conda uninstall'. To fix the problem on conda's side, uninstall"
+                " the package with 'ggd uninstall' and re-install with 'ggd install'.\n"
+            ).format(missing_message)
+        )
 
 
 def list_installed_packages(parser, args):
@@ -221,8 +221,8 @@ def list_installed_packages(parser, args):
 
     from .utils import (
         conda_root,
-        get_conda_prefix_path,
         get_conda_package_list,
+        get_conda_prefix_path,
         prefix_in_conda,
         update_installed_pkg_metadata,
     )
@@ -234,14 +234,18 @@ def list_installed_packages(parser, args):
         else conda_root()
     )
 
-    ## If reset list 
+    ## If reset list
     if args.reset:
-        print("\n:ggd:list: The --reset flag was set. RESETTING ggd installed list metadata.")
+        print(
+            "\n:ggd:list: The --reset flag was set. RESETTING ggd installed list metadata."
+        )
         update_installed_pkg_metadata(args.prefix)
-        print("\n:ggd:list: Run 'ggd list' without --reset to see a list of installed ggd data packages")
+        print(
+            "\n:ggd:list: Run 'ggd list' without --reset to see a list of installed ggd data packages"
+        )
         print("\nDONE\n")
         sys.exit(0)
-        
+
     ggd_info_path = os.path.join(CONDA_ROOT, GGD_INFO)
 
     ## Check that the ggd info dir exists. If not, create it

ggd/list_installed_pkgs.py

@@ -107,16 +107,20 @@ def get_meta_yaml_info(tarball_info_object, ggd_recipe, ggd_channel):
 
     """
     import glob
+
     import yaml
-    from .utils import literal_block, add_yaml_literal_block
+
+    from .utils import add_yaml_literal_block, literal_block
 
     dash = "     " + "-" * 100
     print("\n\n", dash)
 
     yaml_dict = yaml.safe_load(tarball_info_object)
     ## Add literal block if needed
     if "genome_file" in yaml_dict["extra"]:
-        yaml_dict["extra"]["genome_file"]["commands"] = utils.literal_block(yaml_dict["extra"]["genome_file"]["commands"])
+        yaml_dict["extra"]["genome_file"]["commands"] = utils.literal_block(
+            yaml_dict["extra"]["genome_file"]["commands"]
+        )
         utils.add_yaml_literal_block(yaml)
 
     species = yaml_dict["about"]["identifiers"]["species"]
@@ -211,7 +215,15 @@ def get_meta_yaml_info(tarball_info_object, ggd_recipe, ggd_channel):
                 + "Approximate Data File Sizes:"
                 + "\033[0m"
                 + " {}".format(
-                    "\n\t\t" + "\n\t\t".join(["{}: {}".format(x,yaml_dict["about"]["tags"]["final-file-sizes"][x]) for x in yaml_dict["about"]["tags"]["final-file-sizes"]])
+                    "\n\t\t"
+                    + "\n\t\t".join(
+                        [
+                            "{}: {}".format(
+                                x, yaml_dict["about"]["tags"]["final-file-sizes"][x]
+                            )
+                            for x in yaml_dict["about"]["tags"]["final-file-sizes"]
+                        ]
+                    )
                 )
             )
 
@@ -285,6 +297,7 @@ def get_pkg_info(ggd_recipe, ggd_channel, show_recipe):
     3) show_recipe: A bool value, where if true will print the recipe.sh script
     """
     import tarfile
+
     from .utils import get_conda_package_list
 
     ## Get a list of installed ggd packages using conda list

ggd/list_pkg_info.py

@@ -80,9 +80,9 @@ def add_make_bash(p):
     c2.add_argument(
         "-dv",
         "--data-version",
-        help="The version of the data (itself) being downloaded and processed (EX: dbsnp-127)" +
-        " If there is no data version apparent we recommend you use the date associated with the files" +
-        " or something else that can uniquely identify the 'version' of the data",
+        help="The version of the data (itself) being downloaded and processed (EX: dbsnp-127)"
+        + " If there is no data version apparent we recommend you use the date associated with the files"
+        + " or something else that can uniquely identify the 'version' of the data",
         required=True,
     )
     c2.add_argument(
@@ -135,6 +135,7 @@ def make_bash(parser, args):
 
     import shutil
     import sys
+
     import yaml
 
     name = (
@@ -163,7 +164,8 @@ def make_bash(parser, args):
     assert (
         args.summary.strip() != ""
     ), "Please provide a thorough summary of the data package"
-    print("\n:ggd:make-recipe: Name of recipe: {0}-{1}-{2}-v{3}\n".format(
+    print(
+        "\n:ggd:make-recipe: Name of recipe: {0}-{1}-{2}-v{3}\n".format(
             args.genome_build.lower(),
             args.name.lower(),
             data_provider.lower(),
@@ -237,22 +239,19 @@ def make_bash(parser, args):
         )
     )
 
-
-
     from .search import load_json
     from .utils import get_channel_data
 
     ## Get a list of ggd packages
     ggd_packages = set()
     for channel in CHANNEL_LIST:
-        channel = channel.decode("utf-8") if not isinstance(channel,str) else channel
+        channel = channel.decode("utf-8") if not isinstance(channel, str) else channel
         json_dict = load_json(get_channel_data(channel))
         ggd_packages.update(json_dict["packages"].keys())
 
-    ## Get non-ggd dependencies 
+    ## Get non-ggd dependencies
     non_ggd_deps = [x for x in deps if x not in ggd_packages]
 
-
     extra_files = []
     for f in args.extra_file:
         flist = f.strip().split(".")
@@ -262,9 +261,7 @@ def make_bash(parser, args):
     ## Check coordinates
     assert (
         args.coordinate_base in GENOMIC_COORDINATE_LIST
-    ), "{c} is not an acceptable genomic coordinate base".format(
-        c=args.coordinate_base
-    )
+    ), "{c} is not an acceptable genomic coordinate base".format(c=args.coordinate_base)
     # ("Please provide a genomic coordinate base from the follow list: {}".format(", ".join(GENOMIC_COORDINATE_LIST)))
 
     ## Check data version

ggd/make_bash.py

@@ -68,8 +68,8 @@ def get_ggd_metadata(ggd_channel):
     1) GGD metadata as a dictionary
 
     """
-    from .utils import check_for_internet_connection, get_channeldata_url
     from .search import load_json_from_url
+    from .utils import check_for_internet_connection, get_channeldata_url
 
     json_dict = {"channeldata_version": 1, "packages": {}}
     if check_for_internet_connection(3):
@@ -88,6 +88,7 @@ def predict_path(parser, args):
     """ Main method. Method used to predict the installed data file path for a data file that has not bee installed yet"""
     import os
     import re
+
     from .utils import conda_root, get_conda_prefix_path, prefix_in_conda
 
     ## get prefix
@@ -166,5 +167,3 @@ def predict_path(parser, args):
         file_name,
     )
     print(path)
-
-