From 4d86906de3958b1609b5e74ab8c446505bc7e0ff Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Tue, 22 Sep 2020 12:40:30 +0100
Subject: [PATCH 01/10] License fix in setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1e7cf88..d2be687 100644
--- a/setup.py
+++ b/setup.py
@@ -13,7 +13,7 @@
     url="https://github.com/Edinburgh-Genome-Foundry/DnaCauldron",
     description="Cloning simulation for DNA assembly (Golden Gate, Gibson...)",
     long_description=open("pypi-readme.rst").read(),
-    license="see LICENSE.txt",
+    license="MIT",
     keywords="DNA assembly cloning simulator synthetic biology",
     scripts=["scripts/dnacauldron"],
     packages=find_packages(exclude="docs"),

From 98dd3ceac8fdc850ca81ff1e2250a5ca5979c557 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Thu, 1 Oct 2020 13:52:47 +0100
Subject: [PATCH 02/10] Black & docstrings

---
 .../AssemblyReportWriter.py                   | 54 +++++++------------
 1 file changed, 19 insertions(+), 35 deletions(-)

diff --git a/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py b/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py
index 520f77f..82c4414 100644
--- a/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py
+++ b/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py
@@ -6,9 +6,9 @@
 
 
 class AssemblyReportWriter(AssemblyReportPlotsMixin):
-    """Class to configure assembly simulation reports writing.
+    """Class to configure assembly simulation report writing.
 
-    Responsible to write the final sequence(s) of the assembly in Genbank
+    Responsible for writing the final sequence(s) of the assembly in Genbank
     format as well as a .csv report on all assemblies produced and PDF figures
     to allow a quick overview or diagnostic.
 
@@ -28,32 +28,31 @@ class AssemblyReportWriter(AssemblyReportPlotsMixin):
     include_part_plots
       Either True/False/"on_error" to plot schemas of the parts used, possibly
       with restriction sites relevant to the AssemblyMix.
+
     include_mix_graphs
-      Either True/False/"on_error" to plot representations of fragments
+      Either True/False/"on_error" to plot representations of fragment
       connectivity in the AssemblyMix created during the simulation.
 
     include_part_records
       True/False to include the parts records in the simulation results (makes
-      for larger folders and zips, but is better for traceability)
+      for larger folders and zips, but is better for traceability).
 
     include_assembly_plots
       True/False to include assembly schemas in the reports (makes the
       report generation slower, but makes it easier to check assemblies at a
-      glance)
-    
+      glance).
+
     show_overhangs_in_graph
       If true, the AssemblyMix graph representations will display the sequence
-      of all fragments overhangs.
-    
+      of all fragment overhangs.
+
     include_errors_spreadsheet
       If true and there are errors, an errors spreadsheet will be added to the
-      report
-    
+      report.
+
     include_warnings_spreadsheet
       If true and there are warnings, a warnings spreadsheet will be added to
-      the report
-
-
+      the report.
     """
 
     def __init__(
@@ -114,20 +113,12 @@ def _write_records_plots(self, assembly_simulation, report_root):
                 construct_record = construct_record.as_biopython_record()
             self.plot_construct(construct_record, plots_dir)
 
-    def _write_errors_spreadsheet(
-        self, simulation, report_root, error_type="error"
-    ):
-        errors = (
-            simulation.errors if error_type == "error" else simulation.warnings
-        )
+    def _write_errors_spreadsheet(self, simulation, report_root, error_type="error"):
+        errors = simulation.errors if error_type == "error" else simulation.warnings
         if len(errors) > 0:
-            columns = ";".join(
-                ["assembly_name", "message", "suggestion", "data"]
-            )
+            columns = ";".join(["assembly_name", "message", "suggestion", "data"])
             all_error_rows = [
-                ";".join(
-                    [err.assembly.name, err.message, err.data_as_string(),]
-                )
+                ";".join([err.assembly.name, err.message, err.data_as_string(),])
                 for err in errors
             ]
             filename = "%s.csv" % error_type
@@ -153,9 +144,7 @@ def write_report(self, assembly_simulation, target):
 
         self._write_records(assembly_simulation, report_root)
         if self.include_part_records:
-            self._write_part_records(
-                assembly_simulation, part_records, report_root
-            )
+            self._write_part_records(assembly_simulation, part_records, report_root)
         if self.include_assembly_plots:
             self._write_records_plots(assembly_simulation, report_root)
 
@@ -165,9 +154,7 @@ def write_report(self, assembly_simulation, target):
         if plot_options["parts_plots"]:
             enzymes = assembly.enzymes if hasattr(assembly, "enzymes") else []
             self.plot_provided_parts(
-                report_root=report_root,
-                parts_records=part_records,
-                enzymes=enzymes,
+                report_root=report_root, parts_records=part_records, enzymes=enzymes,
             )
         if plot_options["fragment_plots"]:
             for mix in assembly_simulation.mixes:
@@ -180,9 +167,7 @@ def write_report(self, assembly_simulation, target):
                     with_overhangs=self.show_overhangs_in_graph,
                 )
         if len(assembly_simulation.construct_records):
-            self._write_constructs_spreadsheet(
-                assembly_simulation, report_root
-            )
+            self._write_constructs_spreadsheet(assembly_simulation, report_root)
         if self.include_errors_spreadsheet:
             self._write_errors_spreadsheet(
                 assembly_simulation, report_root, error_type="error"
@@ -191,7 +176,6 @@ def write_report(self, assembly_simulation, target):
             self._write_errors_spreadsheet(
                 assembly_simulation, report_root, error_type="warnings"
             )
-        
 
         if target == "@memory":
             return report_root._close()

From 6d08ddaab015a2b62f7355e4b1a633653972a48e Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Thu, 1 Oct 2020 13:58:09 +0100
Subject: [PATCH 03/10] Black & docstrings

---
 .../AssemblyPlan/AssemblyPlanSimulation.py    | 44 +++++++------------
 1 file changed, 15 insertions(+), 29 deletions(-)

diff --git a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
index 521189d..462c4e3 100644
--- a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
+++ b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
@@ -1,9 +1,7 @@
 from flametree import file_tree
 import proglog
 import pandas
-from ..tools import (
-    format_data_dicts_records_for_spreadsheet
-)
+from ..tools import format_data_dicts_records_for_spreadsheet
 from ..biotools import write_record
 from ..Assembly.AssemblyReportWriter import AssemblyReportWriter
 from .plot_leveled_graph import plot_leveled_graph
@@ -73,7 +71,7 @@ def compute_summary_dataframe(self):
         return pandas.DataFrame(data, columns=columns)
 
     def compute_stats(self):
-        """Return a dictionnary of stats.
+        """Return a dictionary of stats.
 
         For instance {"cancelled_assemblies": 2, "errored_assemblies": 1,
         "valid_assemblies": 5}.
@@ -94,7 +92,7 @@ def write_report(
         logger="bar",
         include_original_parts_records=True,
     ):
-        """Write a comprehensive report to a folder or zip file
+        """Write a comprehensive report to a folder or zip file.
 
         Parameters
         ----------
@@ -102,33 +100,29 @@ def write_report(
         target
           Either a path to a folder, to a zip file, or ``"@memory"`` to write
           into a virtual zip file whose raw data is then returned.
-        
+
         folder_name
           Name of the folder created inside the target to host the report (yes,
           it is a folder inside a folder, which can be very practical).
-        
+
         assembly_report_writer
           Either the "default" or any AssemblyReportWriter instance.
-        
+
         logger
           Either "bar" for a progress bar, or None, or any Proglog logger.
 
         include_original_parts_records
           If true, the original provided part records will be included in the
-          report (creates larger file sizes, but better for traceability). 
-        """ 
+          report (creates larger file sizes, but better for traceability).
+        """
         if assembly_report_writer == "default":
             # We'll write all records into one folder for the whole plan
-            assembly_report_writer = AssemblyReportWriter(
-                include_part_records=False
-            )
+            assembly_report_writer = AssemblyReportWriter(include_part_records=False)
         logger = proglog.default_bar_logger(logger)
         if folder_name == "auto":
             folder_name = self.assembly_plan.name + "_simulation"
         report_root = file_tree(target)._dir(folder_name, replace=True)
-        self._write_assembly_reports(
-            report_root, assembly_report_writer, logger=logger
-        )
+        self._write_assembly_reports(report_root, assembly_report_writer, logger=logger)
         self._write_errors_spreadsheet(report_root, error_type="error")
         self._write_errors_spreadsheet(report_root, error_type="warning")
 
@@ -164,8 +158,7 @@ def _write_cancelled_assemblies(self, report_root):
         filename = self._get_file_name("cancelled_assemblies.csv")
         columns = ",".join(["cancelled_assembly", "failed_parent_assembly"])
         cancelled = [
-            ",".join([c.assembly_name, c.failed_dependency])
-            for c in self.cancelled
+            ",".join([c.assembly_name, c.failed_dependency]) for c in self.cancelled
         ]
         report_root._file(filename).write("\n".join([columns] + cancelled))
 
@@ -179,9 +172,7 @@ def parts_sort_key(name):
                 return 1000000
             return indices[0]
 
-        all_parts = (
-            self.list_all_original_parts_used() + self.assembly_plan.all_parts
-        )
+        all_parts = self.list_all_original_parts_used() + self.assembly_plan.all_parts
         all_parts = sorted(set(all_parts), key=parts_sort_key)
 
         def sort_key(name):
@@ -199,9 +190,7 @@ def draw_node(x, y, node, ax):
             text = node.replace("_", " ")
             ax.text(x, y, text, bbox={"facecolor": "white"})
 
-        _, ax = plot_leveled_graph(
-            levels=levels, edges=edges, draw_node=draw_node
-        )
+        _, ax = plot_leveled_graph(levels=levels, edges=edges, draw_node=draw_node)
         target = report_root._file("assembly_plan_graph.pdf")
         ax.figure.savefig(target.open("wb"), format="pdf")
         plt.close(ax.figure)
@@ -211,9 +200,7 @@ def _write_errors_spreadsheet(self, report_root, error_type="error"):
             error
             for simulation in self.assembly_simulations
             for error in (
-                simulation.errors
-                if error_type == "error"
-                else simulation.warnings
+                simulation.errors if error_type == "error" else simulation.warnings
             )
         ]
         if len(all_errors) > 0:
@@ -260,8 +247,7 @@ def list_all_original_parts_used(self):
             for part in simulation.list_all_parts_used()
         ]
         assemblies = [
-            simulation.assembly.name
-            for simulation in self.assembly_simulations
+            simulation.assembly.name for simulation in self.assembly_simulations
         ]
         parts_that_arent_assembled = set(all_parts).difference(set(assemblies))
         return sorted(parts_that_arent_assembled)

From 7bc87cc9db1924e593c7ec27978f4ae9653aedd6 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Thu, 1 Oct 2020 16:10:13 +0100
Subject: [PATCH 04/10] PDF report generation  draft

`AssemblyReportWriter()` parameter `include_pdf_report=False` added.
---
 .../AssemblyReportWriter.py                   |   5 ++
 .../AssemblyPlan/AssemblyPlanSimulation.py    |  18 +++++++
 dnacauldron/__init__.py                       |   3 ++
 .../report_assets/domestication_report.pug    |  34 ++++++++++++++
 dnacauldron/report_assets/imgs/logo.png       | Bin 0 -> 19541 bytes
 dnacauldron/report_assets/report_style.css    |  29 ++++++++++++
 dnacauldron/reports.py                        |  44 ++++++++++++++++++
 7 files changed, 133 insertions(+)
 create mode 100644 dnacauldron/report_assets/domestication_report.pug
 create mode 100644 dnacauldron/report_assets/imgs/logo.png
 create mode 100644 dnacauldron/report_assets/report_style.css
 create mode 100644 dnacauldron/reports.py

diff --git a/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py b/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py
index 82c4414..0210047 100644
--- a/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py
+++ b/dnacauldron/Assembly/AssemblyReportWriter/AssemblyReportWriter.py
@@ -53,6 +53,9 @@ class AssemblyReportWriter(AssemblyReportPlotsMixin):
     include_warnings_spreadsheet
       If true and there are warnings, a warnings spreadsheet will be added to
       the report.
+
+    include_pdf_report
+      If true, a PDF report file is also generated.
     """
 
     def __init__(
@@ -66,6 +69,7 @@ def __init__(
         annotate_parts_homologies=True,
         include_errors_spreadsheet=True,
         include_warnings_spreadsheet=True,
+        include_pdf_report=False,
     ):
         self.include_fragment_plots = include_fragment_plots
         self.include_part_plots = include_part_plots
@@ -76,6 +80,7 @@ def __init__(
         self.annotate_parts_homologies = annotate_parts_homologies
         self.include_errors_spreadsheet = include_errors_spreadsheet
         self.include_warnings_spreadsheet = include_warnings_spreadsheet
+        self.include_pdf_report = include_pdf_report
 
     def _write_constructs_spreadsheet(self, simulation, report_root):
         dataframe = simulation.compute_summary_dataframe()
diff --git a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
index 462c4e3..13583d9 100644
--- a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
+++ b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
@@ -7,6 +7,14 @@
 from .plot_leveled_graph import plot_leveled_graph
 import matplotlib.pyplot as plt
 
+try:
+    import pdf_reports
+
+    PDF_REPORTS_AVAILABLE = True
+except ImportError:
+    PDF_REPORTS_AVAILABLE = False
+from ..reports import write_pdf_domestication_report
+
 
 class AssemblyPlanSimulation:
     def __init__(
@@ -136,6 +144,16 @@ def write_report(
             self._write_all_required_parts_records(report_root)
         if not self.has_single_level:
             self._plot_assembly_graph(report_root)
+
+        if assembly_report_writer.include_pdf_report:
+            if not PDF_REPORTS_AVAILABLE:
+                raise ImportError(
+                    "Could not load PDF Reports. Install with `pip install pdf_reports`"
+                    "to generate a PDF report."
+                )
+            print("PDF record will be included.")
+            write_pdf_domestication_report(report_root._file("Report.pdf"))
+
         if target == "@memory":
             return report_root._close()
 
diff --git a/dnacauldron/__init__.py b/dnacauldron/__init__.py
index 2b9a805..a6097cf 100644
--- a/dnacauldron/__init__.py
+++ b/dnacauldron/__init__.py
@@ -46,6 +46,9 @@
     write_record,
     autoselect_enzyme,
 )
+
+from .reports import write_pdf_domestication_report
+
 from .utils import (
     swap_donor_vector_part,
     insert_parts_on_backbones,
diff --git a/dnacauldron/report_assets/domestication_report.pug b/dnacauldron/report_assets/domestication_report.pug
new file mode 100644
index 0000000..bc97304
--- /dev/null
+++ b/dnacauldron/report_assets/domestication_report.pug
@@ -0,0 +1,34 @@
+#sidebar: p {{sidebar_text}}
+
+.logos
+  img(src="file:///{{ dc_logo_url }}")
+  img(src="file:///{{ egf_logo_url }}")
+
+hr
+h1 DNA assembly simulation report
+hr
+
+p.
+  The 'all_construct_records' folder contains the final assemblies and 'part_records'
+  (if generated) contains the original input Genbank files of all parts provided for
+  the assembly. There is one folder for each assembly, which contains:
+ul
+  li The Genbank file of the assembly (.gb)
+  li A CSV file about the assembly
+  li PDF files with schematic views of how the parts assemble together
+  li Genbank files of the parts ('provided_parts_records' folder)
+
+p.
+  In addition, various summary text/csv files are provided about the simulation.
+
+
+h2  Summary table
+
+{{ summary_table }}
+
+//- h2 Domesticators
+
+//- each domesticator in domesticators
+//-   .ui.segment.raised
+//-     .ui.title.ribbon.label.teal {{domesticator.name}}
+//-     .description {{ domesticator.html_details() }}
diff --git a/dnacauldron/report_assets/imgs/logo.png b/dnacauldron/report_assets/imgs/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..28207d6e9a0d11ff07d09bfd40a8bdf5cf6a5714
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HcmV?d00001

diff --git a/dnacauldron/report_assets/report_style.css b/dnacauldron/report_assets/report_style.css
new file mode 100644
index 0000000..2186452
--- /dev/null
+++ b/dnacauldron/report_assets/report_style.css
@@ -0,0 +1,29 @@
+.logos {
+  margin: 0 auto;
+}
+
+h1.appendix {
+  page-break-before: always;
+}
+
+h1 {
+  text-align: center;
+}
+
+.ribbon {
+  margin-left: -2.3em !important;
+}
+
+.description {
+  margin-top: 1em;
+}
+
+table {
+  font-size: 0.6em !important;
+}
+
+table img {
+  width: 1.5em;
+  /* height: 1em; */
+  margin-right: 1em
+}
diff --git a/dnacauldron/reports.py b/dnacauldron/reports.py
new file mode 100644
index 0000000..1ba1cbf
--- /dev/null
+++ b/dnacauldron/reports.py
@@ -0,0 +1,44 @@
+from datetime import datetime
+import os
+import hashlib
+from copy import deepcopy
+
+from Bio import SeqIO
+import matplotlib.pyplot as plt
+import pandas
+import jinja2
+import weasyprint
+
+import flametree
+from pdf_reports import (
+    write_report,
+    pug_to_html,
+    dataframe_to_html,
+    style_table_rows,
+    add_css_class,
+)
+
+from .version import __version__
+
+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")
+STYLESHEET = os.path.join(ASSETS_PATH, "report_style.css")
+
+
+def dnacauldron_pug_to_html(template, **context):
+    now = datetime.now().strftime("%Y-%m-%d")
+    defaults = {
+        "sidebar_text": "Generated on %s by DNA Cauldron version %s"
+        % (now, __version__),
+        "dc_logo_url": os.path.join(ASSETS_PATH, "imgs", "logo.png"),
+    }
+    for k in defaults:
+        if k not in context:
+            context[k] = defaults[k]
+    return pug_to_html(template, **context)
+
+
+def write_pdf_domestication_report(target):
+    html = dnacauldron_pug_to_html(DOMESTICATION_REPORT_TEMPLATE,)
+    write_report(html, target, extra_stylesheets=(STYLESHEET,))

From 35fde2e1fb0be5ae2dfe3578d7762547ce7e6a11 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Fri, 2 Oct 2020 14:50:01 +0100
Subject: [PATCH 05/10] Fix Travis CI

Removed unused imports Install pdf_reports
---
 .travis.yml            |  2 +-
 dnacauldron/reports.py | 12 ------------
 2 files changed, 1 insertion(+), 13 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index e425cd7..d8dfd98 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,7 +3,7 @@ python:
   - "3.6"
 # command to install dependencies
 install:
-  - pip install coveralls geneblocks pytest-cov==2.6 pytest==3.2.3
+  - pip install coveralls geneblocks pdf_reports pytest-cov==2.6 pytest==3.2.3
   - pip install -e .
   - sudo apt-get install ncbi-blast+
 # command to run tests
diff --git a/dnacauldron/reports.py b/dnacauldron/reports.py
index 1ba1cbf..c1df653 100644
--- a/dnacauldron/reports.py
+++ b/dnacauldron/reports.py
@@ -1,21 +1,9 @@
 from datetime import datetime
 import os
-import hashlib
-from copy import deepcopy
 
-from Bio import SeqIO
-import matplotlib.pyplot as plt
-import pandas
-import jinja2
-import weasyprint
-
-import flametree
 from pdf_reports import (
     write_report,
     pug_to_html,
-    dataframe_to_html,
-    style_table_rows,
-    add_css_class,
 )
 
 from .version import __version__

From ad33addd9114af0cb9a84f09ff3f6b1932d57a9c Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Fri, 2 Oct 2020 15:53:50 +0100
Subject: [PATCH 06/10] Test pdf report generation

---
 tests/test_reports.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 tests/test_reports.py

diff --git a/tests/test_reports.py b/tests/test_reports.py
new file mode 100644
index 0000000..214ad23
--- /dev/null
+++ b/tests/test_reports.py
@@ -0,0 +1,26 @@
+import os
+import dnacauldron as dc
+
+this_directory = os.path.join("tests", "test_hierarchical_type2s")
+parts_folder = os.path.join(this_directory, "parts")
+
+
+def test_single_assembly(tmpdir):
+    repository = dc.SequenceRepository()
+    repository.import_records(folder=parts_folder, use_file_names_as_ids=True)
+    assembly_plan = dc.AssemblyPlan.from_spreadsheet(
+        assembly_class=dc.Type2sRestrictionAssembly,
+        path=os.path.join(this_directory, "type2s_two-level.csv"),
+    )
+    plan_simulation = assembly_plan.simulate(sequence_repository=repository)
+    stats = plan_simulation.compute_stats()
+    report_writer = dc.AssemblyReportWriter(
+        include_fragment_plots=False,
+        include_part_plots=False,
+        include_mix_graphs=False,
+        include_assembly_plots=False,
+        show_overhangs_in_graph=False,
+        annotate_parts_homologies=False,
+        include_pdf_report=True,
+    )
+    plan_simulation.write_report(target="@memory", assembly_report_writer=report_writer)

From 049e70692fc8aff7b64f6980750f476b699313c5 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Fri, 2 Oct 2020 16:51:36 +0100
Subject: [PATCH 07/10] Added summary table to pdf report (draft)

Added AssemblyPlanSimulation()._calculate_simulation_info()
Also renamed
write_pdf_domestication_report() to write_simulation_pdf_report()
---
 .../AssemblyPlan/AssemblyPlanSimulation.py    | 29 +++++++++++++++++--
 dnacauldron/__init__.py                       |  2 +-
 dnacauldron/reports.py                        | 10 +++++--
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
index 13583d9..f69f9a5 100644
--- a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
+++ b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
@@ -13,7 +13,7 @@
     PDF_REPORTS_AVAILABLE = True
 except ImportError:
     PDF_REPORTS_AVAILABLE = False
-from ..reports import write_pdf_domestication_report
+from ..reports import write_simulation_pdf_report
 
 
 class AssemblyPlanSimulation:
@@ -149,10 +149,14 @@ def write_report(
             if not PDF_REPORTS_AVAILABLE:
                 raise ImportError(
                     "Could not load PDF Reports. Install with `pip install pdf_reports`"
-                    "to generate a PDF report."
+                    " to generate a PDF report."
                 )
             print("PDF record will be included.")
-            write_pdf_domestication_report(report_root._file("Report.pdf"))
+
+            simulation_info = self._calculate_simulation_info()
+            write_simulation_pdf_report(
+                report_root._file("Report.pdf"), simulation_info
+            )
 
         if target == "@memory":
             return report_root._close()
@@ -299,3 +303,22 @@ def _write_assembly_plan_spreadsheets(self, report_root):
             f = report_root._file(file_name)
             lines = [",".join([c] + parts) for c, parts in construct_parts]
             f.write("\n".join(["construct, parts"] + lines))
+
+    def _calculate_simulation_info(self):
+        stats_dict = self.compute_stats()
+        stats_dict_series = {
+            "Outcome": pandas.Series(
+                ["Valid assemblies", "Cancelled assemblies", "Errored assemblies"]
+            ),
+            "Number": pandas.Series(
+                [
+                    stats_dict["valid_assemblies"],
+                    stats_dict["errored_assemblies"],
+                    stats_dict["errored_assemblies"],
+                ]
+            ),
+        }
+
+        stats_df = pandas.DataFrame(stats_dict_series)
+
+        return stats_df
diff --git a/dnacauldron/__init__.py b/dnacauldron/__init__.py
index a6097cf..b1b4453 100644
--- a/dnacauldron/__init__.py
+++ b/dnacauldron/__init__.py
@@ -47,7 +47,7 @@
     autoselect_enzyme,
 )
 
-from .reports import write_pdf_domestication_report
+from .reports import write_simulation_pdf_report
 
 from .utils import (
     swap_donor_vector_part,
diff --git a/dnacauldron/reports.py b/dnacauldron/reports.py
index c1df653..1213c46 100644
--- a/dnacauldron/reports.py
+++ b/dnacauldron/reports.py
@@ -2,8 +2,9 @@
 import os
 
 from pdf_reports import (
-    write_report,
+    dataframe_to_html,
     pug_to_html,
+    write_report,
 )
 
 from .version import __version__
@@ -27,6 +28,9 @@ def dnacauldron_pug_to_html(template, **context):
     return pug_to_html(template, **context)
 
 
-def write_pdf_domestication_report(target):
-    html = dnacauldron_pug_to_html(DOMESTICATION_REPORT_TEMPLATE,)
+def write_simulation_pdf_report(target, simulation_info):
+    summary_table = dataframe_to_html(simulation_info, extra_classes=("definition",))
+    html = dnacauldron_pug_to_html(
+        DOMESTICATION_REPORT_TEMPLATE, summary_table=summary_table
+    )
     write_report(html, target, extra_stylesheets=(STYLESHEET,))

From 7e27ac0b09cd06237802c670959d62dd39b5f804 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Fri, 16 Oct 2020 12:24:26 +0100
Subject: [PATCH 08/10] pdf_reports dependency added

---
 README.rst | 8 +++++---
 setup.py   | 1 +
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/README.rst b/README.rst
index a25fd4f..3bdfeed 100644
--- a/README.rst
+++ b/README.rst
@@ -142,22 +142,24 @@ The simulation and reporting on an assembly plan is very similar to that of a si
    # Write a detailed report on each assembly and on the plan as a whole
    plan_simulation.write_report("my_assembly_simulation.zip")
 
+
 Installation
 -------------
 
-You can install DnaCauldron through PIP
-
+You can install DnaCauldron through PIP:
 
 .. code:: shell
 
     sudo pip install dnacauldron
 
-Alternatively, you can unzip the sources in a folder and type
+The full installation using `dnacauldron[reports]` is required for report generation.
+Alternatively, you can unzip the sources in a folder and type:
 
 .. code:: shell
 
     sudo python setup.py install
 
+
 How it works
 ------------
 
diff --git a/setup.py b/setup.py
index d2be687..b91c084 100644
--- a/setup.py
+++ b/setup.py
@@ -34,4 +34,5 @@
         "python-Levenshtein",
         "xlrd",
     ],
+    extras_require={"reports": ["pdf_reports"]},
 )

From 4e3689d68508a08708c4391261cf7ec100fddb58 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Fri, 16 Oct 2020 16:16:21 +0100
Subject: [PATCH 09/10] Finalise report formatting

---
 .../AssemblyPlan/AssemblyPlanSimulation.py      |  9 +++------
 .../report_assets/domestication_report.pug      |  6 +++---
 dnacauldron/reports.py                          | 17 +++++++++++++++++
 3 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
index f69f9a5..d39e22f 100644
--- a/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
+++ b/dnacauldron/AssemblyPlan/AssemblyPlanSimulation.py
@@ -151,7 +151,6 @@ def write_report(
                     "Could not load PDF Reports. Install with `pip install pdf_reports`"
                     " to generate a PDF report."
                 )
-            print("PDF record will be included.")
 
             simulation_info = self._calculate_simulation_info()
             write_simulation_pdf_report(
@@ -307,13 +306,11 @@ def _write_assembly_plan_spreadsheets(self, report_root):
     def _calculate_simulation_info(self):
         stats_dict = self.compute_stats()
         stats_dict_series = {
-            "Outcome": pandas.Series(
-                ["Valid assemblies", "Cancelled assemblies", "Errored assemblies"]
-            ),
-            "Number": pandas.Series(
+            "Outcome": pandas.Series(["Valid", "Cancelled", "Errored"]),
+            "Number of assemblies": pandas.Series(
                 [
                     stats_dict["valid_assemblies"],
-                    stats_dict["errored_assemblies"],
+                    stats_dict["cancelled_assemblies"],
                     stats_dict["errored_assemblies"],
                 ]
             ),
diff --git a/dnacauldron/report_assets/domestication_report.pug b/dnacauldron/report_assets/domestication_report.pug
index bc97304..a83584f 100644
--- a/dnacauldron/report_assets/domestication_report.pug
+++ b/dnacauldron/report_assets/domestication_report.pug
@@ -15,11 +15,11 @@ p.
 ul
   li The Genbank file of the assembly (.gb)
   li A CSV file about the assembly
-  li PDF files with schematic views of how the parts assemble together
-  li Genbank files of the parts ('provided_parts_records' folder)
+  li PDF files with schematic views of how the parts assemble together (if generated)
+  li Genbank files of the parts, in the 'provided_parts_records' folder
 
 p.
-  In addition, various summary text/csv files are provided about the simulation.
+  In addition, various summary text and csv files are provided about the simulation.
 
 
 h2  Summary table
diff --git a/dnacauldron/reports.py b/dnacauldron/reports.py
index 1213c46..57463a9 100644
--- a/dnacauldron/reports.py
+++ b/dnacauldron/reports.py
@@ -3,6 +3,8 @@
 
 from pdf_reports import (
     dataframe_to_html,
+    style_table_rows,
+    add_css_class,
     pug_to_html,
     write_report,
 )
@@ -30,6 +32,21 @@ def dnacauldron_pug_to_html(template, **context):
 
 def write_simulation_pdf_report(target, simulation_info):
     summary_table = dataframe_to_html(simulation_info, extra_classes=("definition",))
+
+    def tr_modifier(tr):
+        tds = list(tr.find_all("td"))
+        if len(tds) == 0:
+            return
+        outcome, number = tds
+        if outcome.text == "Valid":
+            if number.text == "0":
+                add_css_class(tr, "negative")
+            else:
+                add_css_class(tr, "positive")
+        elif number.text != "0":
+            add_css_class(tr, "negative")
+
+    summary_table = style_table_rows(summary_table, tr_modifier)
     html = dnacauldron_pug_to_html(
         DOMESTICATION_REPORT_TEMPLATE, summary_table=summary_table
     )

From 8f45aa4a1bbdd548d4137db14402f5ab267fefb6 Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Fri, 16 Oct 2020 16:17:29 +0100
Subject: [PATCH 10/10] v2.0.3

Added `AssemblyReportWriter()` parameter `include_pdf_report=False`.
If `True`, then a PDF summary is created.
---
 dnacauldron/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dnacauldron/version.py b/dnacauldron/version.py
index 0309ae2..5fa9130 100644
--- a/dnacauldron/version.py
+++ b/dnacauldron/version.py
@@ -1 +1 @@
-__version__ = "2.0.2"
+__version__ = "2.0.3"