Snapshot release for colonies paper

.dockerignore

@@ -3,6 +3,7 @@
 /.idea
 /docs
 /user
+/stubs
 
 # Compiled source #
 ###################
@@ -29,6 +30,7 @@ coverage.xml
 nosetests.xml
 nosetests.*.xml
 .pytest_cache
+/unittests.xml
 
 # IPython notebook files #
 ##########################
@@ -44,7 +46,9 @@ cached
 
 # Fixtures #
 ############
-/fixtures/
+fixtures/sim/*
+fixtures/kb/*
+fixtures/test/*
 
 # C extensions #
 ################

.gcloudignore

@@ -0,0 +1 @@
+#!include:.dockerignore

.gitignore

@@ -1,6 +1,10 @@
+# A temporary copy to upload to Cloud Build. Don't .dockerignore it.
+/cloud/docker/runtime/requirements.txt
+
 # Compiled source #
 ###################
 *.pyc
+__pycache__
 
 # OS generated files #
 ######################
@@ -22,18 +26,16 @@ coverage.xml
 nosetests.xml
 nosetests.*.xml
 .pytest_cache
+/unittests.xml
 
 # IPython notebook files #
 ##########################
 .ipynb_checkpoints
 
 # Output files #
 ################
-out
-out/*
-!out/out.txt
-!out/images.html
-!out/makeHtml.py
+/out
+/colony/out
 
 # Cached sim data #
 ###################
@@ -72,23 +74,23 @@ user/*
 # kernprof.py output #
 ######################
 *.lprof
+*.prof
 
 # pyenv python version #
 ########################
 .python-version
 
-# files created from templates #
-################################
-/my_launchpad*.yaml
-/my_qadapter*.yaml
+# personal config files #
+#########################
+/*.yaml
 
 # Fireworks output #
 ####################
 launcher_*
 block_*
 FW.json
 
-# Fitter output #
+# Parca output #
 #################
 reconstruction/ecoli/dataclasses/process/equilibrium_odes.py
 reconstruction/ecoli/dataclasses/process/two_component_system_odes.py
@@ -107,7 +109,11 @@ reconstruction/ecoli/dataclasses/process/two_component_system_odes_fitter.py
 *.pickle
 *.log
 *.hdf
+*.tar.gz
 /build/
+/.pytype/
+/.mypy_cache/
+secrets.*
 
 # PyCharm files #
 #################
@@ -120,6 +126,7 @@ reconstruction/ecoli/dataclasses/process/two_component_system_odes_fitter.py
 .idea/libraries
 .idea/codeStyleSettings.xml
 .idea/codeStyles/codeStyleConfig.xml
+.idea/inspectionProfiles/profiles_settings.xml
 
 # Potentially OK if editing it to project-jdk-name="Python 2.7" works:
 .idea/misc.xml
@@ -135,7 +142,16 @@ reconstruction/ecoli/dataclasses/process/two_component_system_odes_fitter.py
 
 # Gradle:
 .idea/gradle.xml
-.idea/libraries
 
 # Mongo Explorer plugin:
 .idea/mongoSettings.xml
+
+# LaTeX compilation files #
+###########################
+*.aux
+*.bbl
+*.blg
+*.fdb_latexmk
+*.fls
+*.synctex.gz
+

Makefile

@@ -1,15 +1,23 @@
-.PHONY: compile, clean
+.PHONY: compile, clean, recompile
 
 compile:
-	python2.7 setup.py build_ext --inplace
+	python setup.py build_ext --inplace
 	rm -fr build
 
+# The reconstruction/ecoli/dataclasses/process/*.py files were generated by
+#  write_ode_file.py in Parca code.
+# Fireworks writes launcher_20* and block_20*.
 clean:
 	rm -fr fixtures
 	(cd reconstruction/ecoli/dataclasses/process && rm -f equilibrium_odes.py two_component_system_odes*.py)
-	find . -not \( -path ./out -prune \) -not \( -path ./.git -prune \) -name "*.cPickle" -exec rm -fr {} \;
 	find . -name "*.pyc" -exec rm -rf {} \;
 	find . -name "*.o" -exec rm -fr {} \;
 	find . -name "*.so" -exec rm -fr {} \;
 	rm -fr build
 	rm -fr launcher_20* block_20*
+
+# Delete just the *.so libraries then (re)compile them.
+# This is useful when switching to a different Python virtualenv.
+recompile:
+	find . -name "*.so" -delete
+	make compile