Logo (#175)

* Physlr logo

two logos:
- one is transparent
- one has a wider frame

* v1.0.1

README.md

@@ -1,6 +1,8 @@
 [![Published in DNA](https://img.shields.io/badge/Published%20in-DNA-blue.svg)](https://www.mdpi.com/2673-8856/2/2/9)
 [![Release](https://img.shields.io/github/release/bcgsc/physlr.svg)](https://github.com/bcgsc/physlr/releases)
 
+![Logo](https://github.com/bcgsc/physlr/blob/logo/physlr-logo-wide.png)
+
 # Physlr: Next-generation Physical Maps
 
 Physlr constructs a *de novo* physical map using linked reads from 10X Genomics or MGI stLFR. This physical map can then be used to scaffold an existing assembly to yield chromosome-level contiguity.

bin/physlr-make

@@ -238,7 +238,7 @@ help:
 	@echo "To ensure that the pipeline runs correctly, make sure that the following tools are in your PATH: ntCard, ntHits, and Quast."
 
 version:
-	@echo "physlr 1.0.0"
+	@echo "physlr 1.0.1"
 
 ################################################################################
 # Test m=1 prune_branches=1 prune_bridges=1

data/profile-physlr.Rmd

@@ -235,7 +235,7 @@ if (dim(df)[1] == 0) {
     labs(
       title = "Physlr - time Gantt chart",
       subtitle = paste("path:", ldir),
-      caption = "physlr version: 0.2.0"
+      caption = "physlr version: 1.0.1"
     ) +
     theme(
       plot.title = element_text(color = "black", face = "bold"),
@@ -271,7 +271,7 @@ if (dim(df)[1] == 0) {
     labs(
       title = "Physlr - memory usage",
       subtitle = paste("path:", ldir),
-      caption = "physlr version: 0.2.0"
+      caption = "physlr version: 1.0.1"
     ) +
     theme(
       plot.title = element_text(color = "black", face = "bold"),

physlr/physlr.py

@@ -2799,7 +2799,7 @@ def parse_arguments():
             "-V", "--verbose", action="store", dest="verbose", type=int, default="2",
             help="the level of verbosity: 0:silent, 1:periodic, 2:progress, 3:verbose [2]")
         argparser.add_argument(
-            "--version", action="version", version="physlr 0.1.0")
+            "--version", action="version", version="physlr 1.0.1")
         argparser.add_argument(
             "command",
             help="A command")

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="physlr",
-    version="1.0.0",
+    version="1.0.1",
     author="Amirhossein Afshinfard",
     author_email="aafshinfard@bcgsc.ca",
     description="Next-generation Physical Maps using Linked Reads",