From f4d52601a93c916b0a660a7acf7ded2ed342a7d0 Mon Sep 17 00:00:00 2001
From: John Davey <johnomics@gmail.com>
Date: Thu, 30 May 2019 19:43:43 +0100
Subject: [PATCH] v0.9.3 add CSS, fix assembly write bug, add conda to README

---
 README.md            | 15 +++++++++++----
 setup.py             |  4 ++--
 tapestry/_version.py |  2 +-
 tapestry/assembly.py |  3 ++-
 4 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index bdfc7f5..5c6d531 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,19 @@ The report is intended to be shared with collaborators to explain the genome ass
 Tapestry is designed for use with small eukaryotic genome assemblies, perhaps less than 50 Mb and less than 100 contigs. It will run on larger genomes (particularly with the -n option, see below), but it may be slow.
 
 ## Getting started
+
+### Installation
+Tapestry is in the [Bioconda](https://bioconda.github.io) repository. If you are set up to use Bioconda (see [Install conda](https://bioconda.github.io/#install-conda) and [Set up channels](https://bioconda.github.io/#set-up-channels)), install with `conda`:
+
+```
+conda install tapestry
+```
+
+
 ### Requirements
 
+Tapestry requires the following packages and tools (which will be installed by `conda` automatically):
+
 - Linux or macOS
 - Python 3.6 or later
 
@@ -31,10 +42,6 @@ Python packages:
 - sqlalchemy
 - tqdm
 
-### Installation
-```
-git clone https://github.com/johnomics/tapestry
-```
 
 ### Basic usage
 
diff --git a/setup.py b/setup.py
index 1fa90dc..9d96cf2 100644
--- a/setup.py
+++ b/setup.py
@@ -2,14 +2,14 @@
 
 setup(
     name="tapestry",
-    version="0.9.1",
+    version="0.9.3",
     author="John Davey",
     author_email="johnomics@gmail.com",
     description="Validate and edit small eukaryotic genome assemblies",
     url="https://github.com/johnomics/tapestry",
     packages=['tapestry'],
     package_data={
-        'tapestry': ['report/template.html', 'report/static/*.js'],
+        'tapestry': ['report/template.html', 'report/static/*.js', 'report/static/*.css'],
     },
     test_suite = 'test',
     scripts=['weave', 'clean'],
diff --git a/tapestry/_version.py b/tapestry/_version.py
index a2fecb4..c598173 100644
--- a/tapestry/_version.py
+++ b/tapestry/_version.py
@@ -1 +1 @@
-__version__ = "0.9.2"
+__version__ = "0.9.3"
diff --git a/tapestry/assembly.py b/tapestry/assembly.py
index 7b603c5..008a831 100644
--- a/tapestry/assembly.py
+++ b/tapestry/assembly.py
@@ -160,7 +160,8 @@ def load_assembly(self):
                     SeqIO.write(rec, assembly_out, "fasta")
 
             assembly_in.close()
-            assembly_out.close()
+            if not assembly_found:
+                assembly_out.close()
 
             if len(contigs) == 0:
                 log.error(f"Could not load any contigs from {self.assemblyfile}. Is this a valid FASTA file?")