From 1195f73bfe5802affd8b8973cd38c1986328263c Mon Sep 17 00:00:00 2001 From: Peter Vegh Date: Sun, 18 Oct 2020 14:35:56 +0100 Subject: [PATCH 1/6] Typo fixes --- README.rst | 2 +- docs/examples.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 3bdfeed..ef851cb 100644 --- a/README.rst +++ b/README.rst @@ -152,7 +152,7 @@ You can install DnaCauldron through PIP: 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 diff --git a/docs/examples.rst b/docs/examples.rst index 607a66e..1e1c8d2 100644 --- 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 From e4445fa1a3072049862ec3ca111c965d97263c40 Mon Sep 17 00:00:00 2001 From: Peter Vegh Date: Thu, 10 Dec 2020 20:11:14 +0000 Subject: [PATCH 2/6] Fix header line (extra space) in output csv plan --- dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py index d39e22f..27f7247 100644 --- 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() From 41508d8e3790de8dc65c26dfc4ca781e73bc445a Mon Sep 17 00:00:00 2001 From: Peter Vegh Date: Thu, 10 Dec 2020 20:21:57 +0000 Subject: [PATCH 3/6] Fix readme typos and formatting --- README.rst | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index ef851cb..381f966 100644 --- a/README.rst +++ b/README.rst @@ -41,6 +41,7 @@ Cauldron, you'll get the same results at the bench.

+ 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 ~~~~~~~~~~~~~~ @@ -144,9 +147,9 @@ 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 @@ -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 `_ . +`Pereira et al. (2015) `_, and used in the Python library `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 `_ by `Zulko `_ -and `released on Github `_ under the MIT licence (Copyright Edinburgh Genome Foundry). -Everyone is welcome to contribute ! +and `released on Github `_ under the MIT licence (Copyright 2020 Edinburgh Genome Foundry). +Everyone is welcome to contribute! + More biology software ---------------------- From 716c57673b52f1c68e68735df07d3e9346f20f42 Mon Sep 17 00:00:00 2001 From: Peter Vegh Date: Thu, 10 Dec 2020 20:30:46 +0000 Subject: [PATCH 4/6] Rename report pug template file --- .../{domestication_report.pug => simulation_report.pug} | 0 dnacauldron/reports.py | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename dnacauldron/report_assets/{domestication_report.pug => simulation_report.pug} (100%) diff --git a/dnacauldron/report_assets/domestication_report.pug b/dnacauldron/report_assets/simulation_report.pug similarity index 100% rename from dnacauldron/report_assets/domestication_report.pug rename to dnacauldron/report_assets/simulation_report.pug diff --git a/dnacauldron/reports.py b/dnacauldron/reports.py index 57463a9..1015c43 100644 --- 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") From 10e3274aadf6e7492f49d6d3cb6eb7e8998ca884 Mon Sep 17 00:00:00 2001 From: Peter Vegh Date: Thu, 10 Dec 2020 21:10:10 +0000 Subject: [PATCH 5/6] v2.0.4 --- dnacauldron/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dnacauldron/version.py b/dnacauldron/version.py index 5fa9130..f6bb6f4 100644 --- a/dnacauldron/version.py +++ b/dnacauldron/version.py @@ -1 +1 @@ -__version__ = "2.0.3" +__version__ = "2.0.4" From 59b8d2b9bae925cbfe002be7c207c1621b0f2e48 Mon Sep 17 00:00:00 2001 From: Peter Vegh Date: Thu, 10 Dec 2020 21:10:43 +0000 Subject: [PATCH 6/6] Add pug template to package --- MANIFEST.in | 1 + setup.py | 1 + 2 files changed, 2 insertions(+) diff --git a/MANIFEST.in b/MANIFEST.in index 3f2613e..90c1a3b 100644 --- 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/setup.py b/setup.py index b91c084..9ac8878 100644 --- 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",