Merge v0.1.22

CHANGELOG.md

@@ -8,11 +8,20 @@
     * .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir() [ ]
 * Add logger calls when saving to JSON and uploading to ProvStore [ ]
 
+### v0.1.22
+* Simplify `bp.load_project()` function [x]
+* Fix user and env PROV relationships [x]
+* Add Run attributes as Program class properties (will consume from the last run) [x]
+* Add sequence dunder methods for Project class [x]
+* Improve run methods [x]
+* Allow specifying sequence format to PresetProgram outputs [x]
+* Update env file to Py 3.9 [x]
+
 ### v0.1.21
 * Add _config argument to `bp.load_project()` (this is a temporary fix) [x]
 * Add db property to Config class (prevents bug when setting DB path) [x]
 * Improve a few docstrings [x]
-* Refactor sha1 as sha256 [x]  
+* Refactor sha1 as sha256 [x]   
 * Add add and radd dunder methods for Directory and File [x]  
 * Package workflows in single module [x]
 * Add FastTree PresetProgram [x]

bioprov/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 """

bioprov/bioprov.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 """
 BioProv command-line application. This module holds the main executable.

bioprov/data/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 """

bioprov/programs/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 from .programs import (

bioprov/programs/programs.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 """
@@ -60,8 +60,8 @@ def prodigal(sample=None, input_tag="assembly", extra_flags=None):
         sample=sample,
         input_files={"-i": input_tag},
         output_files={
-            "-a": ("proteins", "_proteins.faa"),
-            "-d": ("genes", "_genes.fna"),
+            "-a": ("proteins", "_proteins.faa", "fasta"),
+            "-d": ("genes", "_genes.fna", "fasta"),
             "-s": ("scores", "_scores.cds"),
         },
         preffix_tag=input_tag,

bioprov/src/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 """

bioprov/src/config.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 """
@@ -274,10 +274,19 @@ def __init__(self):
         self.user = None
         self.env_namespace = None
         self.update()
+        self._actedOnBehalfOf = False
 
     def __repr__(self):
         return self.env_hash
 
+    @property
+    def actedOnBehalfOf(self):
+        return self._actedOnBehalfOf
+
+    @actedOnBehalfOf.setter
+    def actedOnBehalfOf(self, value):
+        self._actedOnBehalfOf = value
+
     def update(self):
         """
         Checks current environment and updates attributes using the os.environ module.

bioprov/src/files.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.21"
+__version__ = "0.1.22"
 
 
 """