Cleanup (#142)

* docs * docs * docs * docs * inference * executable docs * more comments, added BayesianModel * Remove MaybeT and use ExceptT * remove vscode and update gitignore * delete additional changes: Failure * delete broken files * update test for enumerator * tips on inference * more pipes * update docs * update docs * cleanup SMC.hs * more cleanup, and explicit imports * remove Rejection * update docs * build docs manually * insegel theme * stanford theme * lint * lint * ormulo * nix ormolu fixes: git push * docs * trying to fix mathjax * remove empirical * notebooks * remove helpers * formatting * yaml * prepare for PR * address warnings * review * more warnings fixed * less warnings * update ghc version stated in cabal * remove warnings * fix build * version bump * remove safe * fix rmsmc bug you introduced * fix bug * linter * 1980 -> 2022 Co-authored-by: Reuben Cohn-Gordon <reubencohn-gordon@Reubens-MacBook-Air.local> Co-authored-by: System Administrator <root@Reubens-MacBook-Air.local>
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diff --git a/.gitignore b/.gitignore
@@ -18,6 +18,7 @@
 .ghc.environment.*
 .hpc
 .hsenv
+.vscode
 .stack-work/
 cabal-dev
 cabal.project.local

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,23 @@
 
 - No unreleased changes so far.
 
+# 0.1.1.2 (2021-06-08)
+
+Clean up of unused functions and broken code
+
+- remove unused functions in `Weighted` and `Population`
+- remove broken models in `models`
+- explicit imports
+- added some global language extensions
+
+# 0.1.1.1 (2021-06-08)
+
+Add documentation
+
+- docs written in markdown
+- docs built by sphinx
+
+
 # 0.1.1.0 (2020-04-08)
 
 - New exported function: `Control.Monad.Bayes.Class` now exports `discrete`.

diff --git a/README.md b/README.md
@@ -1,22 +1,20 @@
 # monad-bayes
 
-[![Hackage](https://img.shields.io/hackage/v/monad-bayes.svg)](https://hackage.haskell.org/package/monad-bayes)
+<!-- [![Hackage](https://img.shields.io/hackage/v/monad-bayes.svg)](https://hackage.haskell.org/package/monad-bayes)
 [![Stackage](http://stackage.org/package/monad-bayes/badge/lts)](http://stackage.org/lts/package/monad-bayes)
 [![Hackage Deps](https://img.shields.io/hackage-deps/v/monad-bayes.svg)](http://packdeps.haskellers.com/reverse/monad-bayes)
-[![Build status](https://badge.buildkite.com/147af088063e8619fcf52ecf93fa7dd3353a2e8a252ef8e6ad.svg?branch=master)](https://buildkite.com/tweag-1/monad-bayes)
+[![Build status](https://badge.buildkite.com/147af088063e8619fcf52ecf93fa7dd3353a2e8a252ef8e6ad.svg?branch=master)](https://buildkite.com/tweag-1/monad-bayes) -->
 
-A library for **probabilistic programming in Haskell** using probability
-monads. The emphasis is on composition of inference algorithms implemented in
-terms of monad transformers.
+A library for **probabilistic programming in Haskell**. The emphasis is on composition of inference algorithms, and is implemented in terms of monad transformers.
 
-Created by [Adam Scibior][adam-web] ([@adscib][adam-github]), maintained by
-[Tweag I/O][tweagio].
+See the [documentation](https://monad-bayes.netlify.app/) for a quick-start user guide and a reference overview of how it all works.
+
+Created by [Adam Scibior][adam-web] ([@adscib][adam-github]), documentation by [Reuben][reuben-web], maintained by [Tweag I/O][tweagio].
 
 ## Project status
 
 Now that `monad-bayes` has been released on Hackage, we will focus on improving
-documentation. In the meantime, see the [`models` folder][models] for examples.
-
+documentation, adding a variety of applications, improving the API, and making inference more easily customizable.
 ## Background
 
 The basis for the code in this repository is the ICFP 2018 paper [2]. For the
@@ -49,6 +47,7 @@ Now you can use `stack build`, `stack test` and `stack ghci`.
 
 [adam-github]: https://github.com/adscib
 [adam-web]: https://www.cs.ubc.ca/~ascibior/
+[reuben-web]: https://reubencohngordon.com/
 [haskell2015-doi]: https://doi.org/10.1145/2804302.2804317
 [haskell2015-tag]: https://github.com/tweag/monad-bayes/tree/haskell2015
 [icfp2018-doi]: https://doi.org/10.1145/3236778

diff --git a/benchmark/SSM.hs b/benchmark/SSM.hs
@@ -1,14 +1,14 @@
 module Main where
 
-import Control.Monad.Bayes.Inference.PMMH as PMMH
-import Control.Monad.Bayes.Inference.RMSMC
-import Control.Monad.Bayes.Inference.SMC
-import Control.Monad.Bayes.Inference.SMC2 as SMC2
-import Control.Monad.Bayes.Population
-import Control.Monad.Bayes.Sampler
-import Control.Monad.Bayes.Weighted
-import Control.Monad.IO.Class
-import NonlinearSSM
+import Control.Monad.Bayes.Inference.PMMH as PMMH (pmmh)
+import Control.Monad.Bayes.Inference.RMSMC (rmsmcLocal)
+import Control.Monad.Bayes.Inference.SMC (smcMultinomial)
+import Control.Monad.Bayes.Inference.SMC2 as SMC2 (smc2)
+import Control.Monad.Bayes.Population (runPopulation)
+import Control.Monad.Bayes.Sampler (sampleIO)
+import Control.Monad.Bayes.Weighted (prior)
+import Control.Monad.IO.Class (MonadIO (liftIO))
+import NonlinearSSM (generateData, model, param)
 
 main :: IO ()
 main = sampleIO $ do

diff --git a/benchmark/Single.hs b/benchmark/Single.hs
@@ -1,3 +1,6 @@
+{-# LANGUAGE DerivingStrategies #-}
+{-# LANGUAGE ImportQualifiedPost #-}
+
 import Control.Monad.Bayes.Class
 import Control.Monad.Bayes.Inference.RMSMC
 import Control.Monad.Bayes.Inference.SMC
@@ -6,14 +9,14 @@ import Control.Monad.Bayes.Sampler
 import Control.Monad.Bayes.Traced
 import Control.Monad.Bayes.Weighted
 import Data.Time
-import qualified HMM
-import qualified LDA
-import qualified LogReg
+import HMM qualified
+import LDA qualified
+import LogReg qualified
 import Options.Applicative
 import System.Random.MWC (createSystemRandom)
 
 data Model = LR Int | HMM Int | LDA (Int, Int)
-  deriving (Show, Read)
+  deriving stock (Show, Read)
 
 parseModel :: String -> Maybe Model
 parseModel s =
@@ -36,7 +39,7 @@ getModel model = (size model, program model)
     program (LDA (d, w)) = show <$> synthesize (LDA.syntheticData d w) LDA.lda
 
 data Alg = SMC | MH | RMSMC
-  deriving (Read, Show)
+  deriving stock (Read, Show)
 
 runAlg :: Model -> Alg -> SamplerIO String
 runAlg model alg =

diff --git a/benchmark/Speed.hs b/benchmark/Speed.hs
@@ -1,26 +1,37 @@
+{-# LANGUAGE DerivingStrategies #-}
+{-# LANGUAGE ImportQualifiedPost #-}
 {-# OPTIONS_GHC -Wall #-}
 
 module Main (main) where
 
-import Control.Monad.Bayes.Class
-import Control.Monad.Bayes.Inference.RMSMC
-import Control.Monad.Bayes.Inference.SMC
-import Control.Monad.Bayes.Population
-import Control.Monad.Bayes.Sampler
-import Control.Monad.Bayes.Traced
-import Control.Monad.Bayes.Weighted
+import Control.Monad.Bayes.Class (MonadInfer)
+import Control.Monad.Bayes.Inference.RMSMC (rmsmcLocal)
+import Control.Monad.Bayes.Inference.SMC (smcSystematic)
+import Control.Monad.Bayes.Population (runPopulation)
+import Control.Monad.Bayes.Sampler (SamplerIO, sampleIOwith)
+import Control.Monad.Bayes.Traced (mh)
+import Control.Monad.Bayes.Weighted (prior)
 import Criterion.Main
-import Criterion.Types
-import qualified HMM
-import qualified LDA
-import qualified LogReg
+  ( Benchmark,
+    Benchmarkable,
+    bench,
+    defaultConfig,
+    defaultMainWith,
+    nfIO,
+  )
+import Criterion.Types (Config (csvFile, rawDataFile))
+import Data.Functor (void)
+import HMM qualified
+import LDA qualified
+import LogReg qualified
+import System.Process.Typed (runProcess)
 import System.Random.MWC (GenIO, createSystemRandom)
 
 -- | Environment to execute benchmarks in.
 newtype Env = Env {rng :: GenIO}
 
 data ProbProgSys = MonadBayes
-  deriving (Show)
+  deriving stock (Show)
 
 data Model = LR [(Double, Bool)] | HMM [Double] | LDA [[String]]
 
@@ -59,11 +70,11 @@ prepareBenchmark e MonadBayes model alg =
   bench (show MonadBayes ++ sep ++ show model ++ sep ++ show alg) $
     prepareBenchmarkable (rng e) MonadBayes model alg
   where
-    sep = "_"
+    sep = "_" :: String
 
 -- | Checks if the requested benchmark is implemented.
 supported :: (ProbProgSys, Model, Alg) -> Bool
-supported (_, _, RMSMC _ _) = False
+supported (_, _, RMSMC _ _) = True
 supported _ = True
 
 systems :: [ProbProgSys]
@@ -74,9 +85,9 @@ systems =
 lengthBenchmarks :: Env -> [(Double, Bool)] -> [Double] -> [[String]] -> [Benchmark]
 lengthBenchmarks e lrData hmmData ldaData = benchmarks
   where
-    lrLengths = 10 : map (* 100) [1 .. 10]
-    hmmLengths = 10 : map (* 100) [1 .. 10]
-    ldaLengths = 5 : map (* 50) [1 .. 10]
+    lrLengths = 10 : map (* 100) [1 :: Int .. 10]
+    hmmLengths = 10 : map (* 100) [1 :: Int .. 10]
+    ldaLengths = 5 : map (* 50) [1 :: Int .. 10]
     models =
       map (LR . (`take` lrData)) lrLengths
         ++ map (HMM . (`take` hmmData)) hmmLengths
@@ -98,9 +109,9 @@ lengthBenchmarks e lrData hmmData ldaData = benchmarks
 samplesBenchmarks :: Env -> [(Double, Bool)] -> [Double] -> [[String]] -> [Benchmark]
 samplesBenchmarks e lrData hmmData ldaData = benchmarks
   where
-    lrLengths = [50]
-    hmmLengths = [20]
-    ldaLengths = [10]
+    lrLengths = [50 :: Int]
+    hmmLengths = [20 :: Int]
+    ldaLengths = [10 :: Int]
     models =
       map (LR . (`take` lrData)) lrLengths
         ++ map (HMM . (`take` hmmData)) hmmLengths
@@ -120,6 +131,9 @@ samplesBenchmarks e lrData hmmData ldaData = benchmarks
 main :: IO ()
 main = do
   g <- createSystemRandom
+  writeFile "speed-length.csv" ""
+  writeFile "speed-samples.csv" ""
+  writeFile "raw.dat" ""
   let e = Env g
   lrData <- sampleIOwith (LogReg.syntheticData 1000) g
   hmmData <- sampleIOwith (HMM.syntheticData 1000) g
@@ -128,3 +142,4 @@ main = do
   defaultMainWith configLength (lengthBenchmarks e lrData hmmData ldaData)
   let configSamples = defaultConfig {csvFile = Just "speed-samples.csv", rawDataFile = Just "raw.dat"}
   defaultMainWith configSamples (samplesBenchmarks e lrData hmmData ldaData)
+  void $ runProcess "python plots.py"
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/probprog.doctree b/docs/build/doctrees/probprog.doctree
diff --git a/docs/build/doctrees/usage.doctree b/docs/build/doctrees/usage.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ab9c3aee1cef2c7b4cb6a54bc1a416ce
+config: acd02203342909cc9f295870ee4d239a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle
diff --git a/docs/build/html/.doctrees/index 2.doctree b/docs/build/html/.doctrees/index 2.doctree
diff --git a/docs/build/html/.doctrees/index.doctree b/docs/build/html/.doctrees/index.doctree
diff --git a/docs/build/html/.doctrees/probprog.doctree b/docs/build/html/.doctrees/probprog.doctree
diff --git a/docs/build/html/.doctrees/usage.doctree b/docs/build/html/.doctrees/usage.doctree
diff --git a/docs/build/html/_sources/probprog.md.txt b/docs/build/html/_sources/probprog.md.txt
@@ -1,6 +1,5 @@
 # User Guide
 
-
 Probabilistic programming is all about being able to write probabilistic models as programs. For instance, here is a Bayesian linear regression model:
 
 ```haskell