ageorgou · cthoyt · Jan 23, 2022 · Sep 9, 2022
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,319 @@
-/results
-/test
-/models/results
-__pycache*
+# Created by https://www.toptal.com/developers/gitignore/api/macos,linux,pycharm,python,windows
+# Edit at https://www.toptal.com/developers/gitignore?templates=macos,linux,pycharm,python,windows
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### PyCharm ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### PyCharm Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+# https://plugins.jetbrains.com/plugin/7973-sonarlint
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator-enh.xml
+.idea/**/markdown-navigator/
+
+# Cache file creation bug
+# See https://youtrack.jetbrains.com/issue/JBR-2257
+.idea/$CACHE_FILE$
+
+# CodeStream plugin
+# https://plugins.jetbrains.com/plugin/12206-codestream
+.idea/codestream.xml
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+pytestdebug.log
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+doc/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+pythonenv*
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# profiling data
+.prof
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.toptal.com/developers/gitignore/api/macos,linux,pycharm,python,windows
+
+scratch/
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta:__legacy__"
diff --git a/setup.cfg b/setup.cfg
@@ -0,0 +1,20 @@
+[metadata]
+name = proppa
+version = 1.0.0
+
+[options]
+install_requires =
+    numpy
+    scipy
+    matplotlib
+    # be careful about recent release of PyParsing
+    pyparsing<3.0
+    docopt
+
+# Where is my code
+packages = find:
+package_dir =
+    = src
+
+[options.packages.find]
+where = src
diff --git a/__init__.py → src/proppa/__init__.py b/__init__.py → src/proppa/__init__.py
diff --git a/abc_sampler.py → src/proppa/abc_sampler.py b/abc_sampler.py → src/proppa/abc_sampler.py
diff --git a/enhanced_abc_sampler.py → src/proppa/enhanced_abc_sampler.py b/enhanced_abc_sampler.py → src/proppa/enhanced_abc_sampler.py
diff --git a/finite_metropolis_sampler.py → src/proppa/finite_metropolis_sampler.py b/finite_metropolis_sampler.py → src/proppa/finite_metropolis_sampler.py
diff --git a/finite_state_gibbs.py → src/proppa/finite_state_gibbs.py b/finite_state_gibbs.py → src/proppa/finite_state_gibbs.py
diff --git a/finite_state_solution.py → src/proppa/finite_state_solution.py b/finite_state_solution.py → src/proppa/finite_state_solution.py
diff --git a/fluid_sampler.py → src/proppa/fluid_sampler.py b/fluid_sampler.py → src/proppa/fluid_sampler.py
diff --git a/lna_sampler.py → src/proppa/lna_sampler.py b/lna_sampler.py → src/proppa/lna_sampler.py
diff --git a/mh.py → src/proppa/mh.py b/mh.py → src/proppa/mh.py
diff --git a/model_utilities.py → src/proppa/model_utilities.py b/model_utilities.py → src/proppa/model_utilities.py
diff --git a/models/SIR.proppa → src/proppa/models/SIR.proppa b/models/SIR.proppa → src/proppa/models/SIR.proppa
diff --git a/models/__init__.py → src/proppa/models/__init__.py b/models/__init__.py → src/proppa/models/__init__.py
diff --git a/models/config_SIR → src/proppa/models/config_SIR b/models/config_SIR → src/proppa/models/config_SIR
diff --git a/models/config_predPrey → src/proppa/models/config_predPrey b/models/config_predPrey → src/proppa/models/config_predPrey
diff --git a/models/config_rumour → src/proppa/models/config_rumour b/models/config_rumour → src/proppa/models/config_rumour
diff --git a/models/obs_SIR → src/proppa/models/obs_SIR b/models/obs_SIR → src/proppa/models/obs_SIR
diff --git a/models/obs_predPrey → src/proppa/models/obs_predPrey b/models/obs_predPrey → src/proppa/models/obs_predPrey
diff --git a/models/obs_rumour → src/proppa/models/obs_rumour b/models/obs_rumour → src/proppa/models/obs_rumour
diff --git a/models/predPrey.proppa → src/proppa/models/predPrey.proppa b/models/predPrey.proppa → src/proppa/models/predPrey.proppa
diff --git a/models/rumour.proppa → src/proppa/models/rumour.proppa b/models/rumour.proppa → src/proppa/models/rumour.proppa
diff --git a/models/testExperiments.py → src/proppa/models/testExperiments.py b/models/testExperiments.py → src/proppa/models/testExperiments.py
diff --git a/ode_simulator.py → src/proppa/ode_simulator.py b/ode_simulator.py → src/proppa/ode_simulator.py
diff --git a/proppa.py → src/proppa/proppa.py b/proppa.py → src/proppa/proppa.py
diff --git a/roulette.py → src/proppa/roulette.py b/roulette.py → src/proppa/roulette.py
diff --git a/roulette_gibbs_sampler.py → src/proppa/roulette_gibbs_sampler.py b/roulette_gibbs_sampler.py → src/proppa/roulette_gibbs_sampler.py
diff --git a/roulette_metropolis_sampler.py → src/proppa/roulette_metropolis_sampler.py b/roulette_metropolis_sampler.py → src/proppa/roulette_metropolis_sampler.py
diff --git a/samplers.py → src/proppa/samplers.py b/samplers.py → src/proppa/samplers.py
diff --git a/simulate_from_dist.py → src/proppa/simulate_from_dist.py b/simulate_from_dist.py → src/proppa/simulate_from_dist.py
diff --git a/simulate_ode_from_dist.py → src/proppa/simulate_ode_from_dist.py b/simulate_ode_from_dist.py → src/proppa/simulate_ode_from_dist.py
diff --git a/transient.py → src/proppa/transient.py b/transient.py → src/proppa/transient.py
diff --git a/utilities.py → src/proppa/utilities.py b/utilities.py → src/proppa/utilities.py
diff --git a/tests/__init__.py b/tests/__init__.py
diff --git a/tests/test_import.py b/tests/test_import.py
@@ -0,0 +1,13 @@
+"""Tests for importing ProPPA."""
+
+import unittest
+
+
+class TestTrivial(unittest.TestCase):
+    """A trivial test case."""
+
+    def test_import(self):
+        """Test that proppa can be imported."""
+        import proppa
+
+        self.assertIsNotNone(proppa)
diff --git a/tox.ini b/tox.ini
@@ -0,0 +1,25 @@
+[tox]
+# To use PEP-517 build-backend, you are required to configure
+# tox to use an isolated build. See: https://tox.readthedocs.io/en/latest/example/package.html
+isolated_build = true
+
+# These environments are run in order if you run `tox`
+envlist =
+    py
+
+[testenv]
+commands =
+    pytest tests/
+deps =
+    pytest
+description = Run unit tests.
+
+[testenv:lint]
+deps =
+    black
+    isort
+skip_install = true
+commands =
+    black src/ tests/
+    isort src/ tests/
+description = Run linters.