Merge pull request #33 from vinisalazar/dev

Merge v0.1.18

.gitignore

@@ -1,5 +1,6 @@
 # BioProv
 bioprov/db.json
+bioprov/provstore_api.txt
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

CHANGELOG.md

@@ -3,16 +3,18 @@
 ### To-do
 * Fix documentation issues [ ]
     * Add subpackage docstrings [ ]
-* Add subparsers for CLI commands [ ]
-* Add support for ProvStore API (#23) [ ]
-* Make File inherit from pathlib.Path [ ]
-* Add Directories class to Files module [ ]
-    * Support globbing Directory outputs [ ]
-* Make config.threads an integer to support manipulation [ ]
 * Create methods for Sample and Project
     * .describe []
-    * .iter_programs and .iter_files [ ]
-    * .write_paths_to_file and .copy_files_to_dir()
+    * .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir()
+
+### v0.1.18
+* Add support for ProvStore API (#23) [x]
+* Add subparsers for CLI commands [x]
+* Add Directories class to Files module [x]
+    * Support globbing Directory outputs [x]
+* Increase test coverage [x]
+* Added more example data [x]
+* Make config.threads an integer to support operations [x]
 
 ### v0.1.17
 * Add more database methods [x]

bioprov/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.17"
+__version__ = "0.1.18"
 
 
 """
@@ -12,7 +12,7 @@
 """
 
 from .src.config import config, EnvProv, BioProvDB
-from .src.files import File, SeqFile
+from .src.files import File, SeqFile, Directory
 from .src.main import (
     Program,
     PresetProgram,

bioprov/bioprov

@@ -3,7 +3,7 @@ __author__ = "Vini Salazar"
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.17"
+__version__ = "0.1.18"
 
 """
 Executable that goes in $PATH. Code for the command-line is on the bioprov.py module.

bioprov/bioprov.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.17"
+__version__ = "0.1.18"
 
 """
 BioProv command-line application. This module holds the main executable.
@@ -19,6 +19,7 @@
     KaijuWorkflow,
 )
 from bioprov.utils import parser_help, dict_to_string
+from pathlib import Path
 
 
 def main(args=None):
@@ -39,6 +40,16 @@ def main(args=None):
     commands.add_argument(
         "--show_config", help="Show location of config file.", action="store_true"
     )
+    commands.add_argument(
+        "--show_provstore",
+        help="Show location of ProvStore credentials file.",
+        action="store_true",
+    )
+    commands.add_argument(
+        "--create_provstore",
+        help="Create ProvStore file credentials file.",
+        action="store_true",
+    )
     commands.add_argument(
         "--show_db", help="Show location of database file.", action="store_true"
     )
@@ -69,42 +80,78 @@ def main(args=None):
         else:
             args = bioprov_parser.parse_args()  # no cover
 
-    # TODO: Must improve this if/else loop. Use a dictionary.
-    if args.show_config:
+    for command, value in args.__dict__.items():
+        if value:
+            try:
+                getattr(CommandOptionsParser, command)()
+            except AttributeError:
+                pass
+    parser = WorkflowOptionsParser()  # no cover
+    try:
+        parser.parse_options(args)  # no cover
+    except KeyError:
+        parser_help(bioprov_parser)
+
+
+class CommandOptionsParser:
+    def __init__(self):
+        pass
+
+    @classmethod
+    def show_config(cls):
         print(
             "This is the location of the config module.\n"
             "Edit it to alter your BioProv settings.\n\n",
             f"'{bp_config_module.__file__}'\n",
         )
         print("These are your configuration settings:")
-        print(dict_to_string(config.__dict__))
+        print(dict_to_string(config.serializer()))
+
+        sys.exit(0)
+
+    @classmethod
+    def show_provstore(cls):
+        print(
+            "This is the location of your ProvStore credentials file.\n"
+            "Edit it to alter your BioProv settings.\n\n",
+            f"{config.provstore_file}\n",
+        )
+        if not Path(config.provstore_file).is_file():
+            print("It does not exist, but you can create one with the command:")
+            print("  $ bioprov --create_provstore")
 
         sys.exit(0)
 
-    elif args.show_db:
+    @classmethod
+    def create_provstore(cls):  # no cover
+        config.create_provstore_file()
+        sys.exit(0)
+
+    @classmethod
+    def show_db(cls):
         print(
             "This is the location of your BioProv database file.\n"
             f"'{config.db_path}'\n",
         )
         sys.exit(0)
 
-    elif args.version:
+    @classmethod
+    def version(cls):
         print(f"Local BioProv version is v{__version__}")
         sys.exit(0)
 
-    elif args.list:
+    @classmethod
+    def list(cls):
         tags = [f"'{project['tag']}'" for project in config.db.all()]
         print(f"You have {len(tags)} Projects in your database.")
         if tags:
             print("\n".join(tags))
         sys.exit(0)
 
-    elif args.clear_db:  # no cover
-        config.db.clear_db()  # no cover
-        sys.exit(0)  # no cover
-
-    parser = WorkflowOptionsParser()
-    parser.parse_options(args)
+    @classmethod
+    def clear_db(cls):  # no cover
+        config.db.clear_db()
+        sys.exit(0)
 
 
 if __name__ == "__main__":

bioprov/data/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.17"
+__version__ = "0.1.18"
 
 
 """

bioprov/data/datasets/picocyano.csv

@@ -1,3 +1,6 @@
 sample-id,assembly,taxon
-GCF_000010065.1_ASM1006v1,bioprov/data/genomes/GCF_000010065.1_ASM1006v1_genomic.fna,Synechococcus elongatus PCC 6301
-GCF_000007925.1_ASM792v1,bioprov/data/genomes/GCF_000007925.1_ASM792v1_genomic.fna,Prochlorococcus marinus CCMP1375
+GCF_000010065.1,bioprov/data/genomes/GCF_000010065.1_ASM1006v1_genomic.fna,Synechococcus elongatus PCC 6301
+GCF_000007925.1,bioprov/data/genomes/GCF_000007925.1_ASM792v1_genomic.fna,Prochlorococcus marinus CCMP1375
+GCA_000316515.1,bioprov/data/genomes/GCF_000316515.1_ASM31651v1_genomic.fna,Cyanobium gracile PCC 6307
+GCF_000012625.1,bioprov/data/genomes/GCF_000012625.1_ASM1262v1_genomic.fna,Parasynechococcus africanus CC9605
+GCF_000011485.1,bioprov/data/genomes/GCF_000011485.1_ASM1148v1_genomic.fna,Thaumococcus swingsii MIT9313