Merge pull request #7 from Edinburgh-Genome-Foundry/dev

Dev
Edinburgh-Genome-Foundry · Dec 11, 2020 · ef1d525 · ef1d525
2 parents 5208b96 + 59b8d2b
commit ef1d525
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Showing 8 changed files with 18 additions and 12 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -2,3 +2,4 @@ include pypi-readme.rst
 include ez_setup.py
 include *.txt
 recursive-include examples *.txt *.py
+recursive-include dnacauldron/report_assets *
diff --git a/README.rst b/README.rst
@@ -41,6 +41,7 @@ Cauldron, you'll get the same results at the bench.
     <br /><br />
     </p>
 
+
 Usage tutorial
 --------------
 
@@ -67,6 +68,7 @@ time by setting ``topology='linear'``, ``topology='circular'``, or for instance
 ``topology='default_to_linear'`` to use the topology specified by each Genbank and
 default to linear if none is specified.
 
+
 Parts assembly
 ~~~~~~~~~~~~~~
 
@@ -108,6 +110,7 @@ Now you can explore the results of the simulation:
 DNA Cauldron aims at generating reports as useful as possible to help you
 pinpoint any problem when you don't get the expected number of assemblies.
 
+
 Assembly Plans
 ~~~~~~~~~~~~~~
 
@@ -144,15 +147,15 @@ The simulation and reporting on an assembly plan is very similar to that of a si
 
 
 Installation
--------------
+------------
 
-You can install DnaCauldron through PIP:
+You can install DNA Cauldron through PIP:
 
 .. code:: shell
 
     sudo pip install dnacauldron
 
-The full installation using `dnacauldron[reports]` is required for report generation.
+The full installation using ``dnacauldron[reports]`` is required for report generation.
 Alternatively, you can unzip the sources in a folder and type:
 
 .. code:: shell
@@ -163,19 +166,20 @@ Alternatively, you can unzip the sources in a folder and type:
 How it works
 ------------
 
-Dna Cauldron predicts circular constructs by finding circular paths in parts
+DNA Cauldron predicts circular constructs by finding circular paths in part
 homology graphs, an idea first described in
-`Pereira et al. Bioinf. 2015 <http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0544-x>`_ .
+`Pereira et al. (2015) <http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0544-x>`_,
 and used in the Python library `PyDNA <https://github.com/BjornFJohansson/pydna>`_.
 
 
 Contribute!
 -----------
 
-Dna Cauldron is an open-source software originally written at the `Edinburgh Genome Foundry
+DNA Cauldron is an open-source software originally written at the `Edinburgh Genome Foundry
 <http://www.genomefoundry.io>`_ by `Zulko <https://github.com/Zulko>`_
-and `released on Github <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron>`_ under the MIT licence (Copyright Edinburgh Genome Foundry).
-Everyone is welcome to contribute !
+and `released on Github <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron>`_ under the MIT licence (Copyright 2020 Edinburgh Genome Foundry).
+Everyone is welcome to contribute!
+
 
 More biology software
 ----------------------

diff --git a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
@@ -301,7 +301,7 @@ def _write_assembly_plan_spreadsheets(self, report_root):
                 file_name = self._get_file_name(file_name)
             f = report_root._file(file_name)
             lines = [",".join([c] + parts) for c, parts in construct_parts]
-            f.write("\n".join(["construct, parts"] + lines))
+            f.write("\n".join(["construct,parts"] + lines))
 
     def _calculate_simulation_info(self):
         stats_dict = self.compute_stats()

diff --git a/...on/report_assets/domestication_report.pug → ...ldron/report_assets/simulation_report.pug b/...on/report_assets/domestication_report.pug → ...ldron/report_assets/simulation_report.pug
diff --git a/dnacauldron/reports.py b/dnacauldron/reports.py
@@ -13,7 +13,7 @@
 
 THIS_PATH = os.path.dirname(os.path.realpath(__file__))
 ASSETS_PATH = os.path.join(THIS_PATH, "report_assets")
-DOMESTICATION_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "domestication_report.pug")
+DOMESTICATION_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "simulation_report.pug")
 STYLESHEET = os.path.join(ASSETS_PATH, "report_style.css")
 
 

diff --git a/dnacauldron/version.py b/dnacauldron/version.py
@@ -1 +1 @@
-__version__ = "2.0.3"
+__version__ = "2.0.4"
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -23,7 +23,7 @@ Gibson Assembly Plan
 
 .. literalinclude:: ../examples/gibson_assembly/gibson_assembly.py
 
-Hierarichical BioBrick assembly
+Hierarchical BioBrick assembly
 ++++++++++++++++++++++++++++++++++++++++++
 
 .. literalinclude:: ../examples/hierarchical_biobrick/hierarchical_biobrick.py

diff --git a/setup.py b/setup.py
@@ -17,6 +17,7 @@
     keywords="DNA assembly cloning simulator synthetic biology",
     scripts=["scripts/dnacauldron"],
     packages=find_packages(exclude="docs"),
+    include_package_data=True,
     install_requires=[
         "Biopython",
         "numpy",