Merge pull request #1 from Edinburgh-Genome-Foundry/dev

Add symbols

README.rst

@@ -1,7 +1,7 @@
 .. raw:: html
 
     <p align="center">
-    <img alt="caravagene Logo" title="lala Logo" src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/logo.png" width="500">
+    <img alt="Caravagene logo" title="Caravagene logo" src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/logo.png" width="500">
     <br /><br />
     </p>
 
@@ -45,19 +45,19 @@ showing multiple constructs:
         title="My constructs",
         constructs=[
             Construct(name="ASM1", parts=[
-                Part('HA1', category='homology-arm'),
-                Part('rc1', category='recombinase-recognition-sequence'),
-                Part('my promoter', category='promoter'),
-                Part('RNA stability', category='rna-stability-sequence'),
-                Part('<i>acs</i>', category='CDS'),
-                Part('PolyA', category='terminator'),
-                Part('I1', category='insulator'),
+                Part(label='HA1', category='homology-arm'),
+                Part(label='rc1', category='recombinase-recognition-sequence'),
+                Part(label='my promoter', category='promoter'),
+                Part(label='RNA stability', category='rna-stability-sequence'),
+                Part(label='<i>acs</i>', category='CDS'),
+                Part(label='PolyA', category='terminator'),
+                Part(label='I1', category='insulator'),
             ]),
             Construct(name="ASM2", parts=[
-                Part('my promoter', category='promoter'),
-                Part('gene with a very very long name', category='CDS'),
-                Part('PolyA', category='terminator'),
-                Part('I1', category='insulator')
+                Part(label='my promoter', category='promoter'),
+                Part(label='gene with a very very long name', category='CDS'),
+                Part(label='PolyA', category='terminator'),
+                Part(label='I1', category='insulator')
             ])
         ]
     )
@@ -130,7 +130,7 @@ You can install caravagene through PIP:
 
 .. code:: shell
 
-    sudo pip install caravagene
+    pip install caravagene
 
 Alternatively, you can unzip the source code in a folder and type:
 

caravagene/caravagene.py

@@ -235,9 +235,11 @@ def __init__(
             if title == "auto":
                 self.title = os.path.splitext(os.path.basename(constructs))[0]
                 self.title = self.title.replace("_", " ")
-            sheet_names = pandas.ExcelFile(constructs).sheet_names
+            sheet_names = pandas.ExcelFile(constructs, engine="openpyxl").sheet_names
             if "options" in sheet_names:
-                df = pandas.read_excel(constructs, sheet_name="options")
+                df = pandas.read_excel(
+                    constructs, sheet_name="options", engine="openpyxl"
+                )
                 self.__dict__.update(
                     {
                         row.field: row.value
@@ -255,7 +257,10 @@ def __init__(
                     }
                 )
             constructs = [
-                Construct(pandas.read_excel(constructs, sheet_name=sheet), name=sheet)
+                Construct(
+                    pandas.read_excel(constructs, sheet_name=sheet, engine="openpyxl"),
+                    name=sheet,
+                )
                 for sheet in sheet_names
                 if sheet != "options"
             ]

caravagene/version.py

@@ -1 +1 @@
-__version__ = "0.1.5"
+__version__ = "0.1.6"

setup.py

@@ -15,7 +15,7 @@
     license="MIT",
     keywords="SBOL DNA assembly plot",
     scripts=["scripts/caravagene"],
-    install_requires=["docopt", "xlrd", "jinja2", "pandas"],
+    install_requires=["docopt", "openpyxl", "jinja2", "pandas"],
     include_package_data=True,
     packages=find_packages(exclude="docs"),
 )