├── .gitignore
├── .gitmodules
├── LICENSE
├── README.md
├── setup.sh
└── test.sh


/.gitignore:
--------------------------------------------------------------------------------
 1 | # Prerequisites
 2 | *.d
 3 | 
 4 | # Compiled Object files
 5 | *.slo
 6 | *.lo
 7 | *.o
 8 | *.obj
 9 | 
10 | # Precompiled Headers
11 | *.gch
12 | *.pch
13 | 
14 | # Compiled Dynamic libraries
15 | *.so
16 | *.dylib
17 | *.dll
18 | 
19 | # Fortran module files
20 | *.mod
21 | *.smod
22 | 
23 | # Compiled Static libraries
24 | *.lai
25 | *.la
26 | *.a
27 | *.lib
28 | 
29 | # Executables
30 | *.exe
31 | *.out
32 | *.app
33 | 
34 | *~
35 | 


--------------------------------------------------------------------------------
/.gitmodules:
--------------------------------------------------------------------------------
1 | [submodule "stan"]
2 | 	path = stan
3 | 	url = https://github.com/stan-dev/stan
4 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | BSD 3-Clause License
 2 | 
 3 | Copyright (c) 2021, Daniel Lee
 4 | All rights reserved.
 5 | 
 6 | Redistribution and use in source and binary forms, with or without
 7 | modification, are permitted provided that the following conditions are met:
 8 | 
 9 | 1. Redistributions of source code must retain the above copyright notice, this
10 |    list of conditions and the following disclaimer.
11 | 
12 | 2. Redistributions in binary form must reproduce the above copyright notice,
13 |    this list of conditions and the following disclaimer in the documentation
14 |    and/or other materials provided with the distribution.
15 | 
16 | 3. Neither the name of the copyright holder nor the names of its
17 |    contributors may be used to endorse or promote products derived from
18 |    this software without specific prior written permission.
19 | 
20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | # Reimplementation of Stan algorithms
 2 | 
 3 | This project is a collaborative effort to rewrite the Stan algorithms.
 4 | 
 5 | 
 6 | The goals we have are to:
 7 | 
 8 | 1. tbd
 9 | 2. tbd
10 | 
11 | 
12 | If you'd like to join, please find us on Discourse (FIXME: more details).
13 | 
14 | We are reimplementing the algorithms in [Stan v2.28.2](https://github.com/stan-dev/stan/tree/v2.28.2) (`4383f846f`). Although the algorithms code does not change very quickly, it's good to have a target version we are implementing against.
15 | 
16 | 
17 | ## Setup
18 | 
19 | ```
20 | ./setup.sh
21 | ```
22 | 
23 | There's a script for one-time setup. This will:
24 | 
25 | 1. Update the git submodules for Stan.
26 | 2. Download the appropriate version of `stan/bin/stanc` that is compatible with this version of Stan.
27 | 
28 | Once this script is run, the tests can run.
29 | 
30 | ### Git Submodule for Stan v2.28.2
31 | 
32 | The `stan` source code is included as a git submodule located in the `stan/` folder.
33 | 
34 | 
35 | ## Testing
36 | 
37 | ```
38 | ./test.sh
39 | ```
40 | 
41 | Currently this runs the services tests in the Stan submodule.
42 | 
43 | 


--------------------------------------------------------------------------------
/setup.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | set -e
 3 | 
 4 | ## 1. Update submodules
 5 | 
 6 | git submodule update --init --recursive
 7 | 
 8 | 
 9 | ## 2. Download appropriate stanc3 v2.18.1
10 | mkdir -p stan/bin
11 | 
12 | if [[ "$OSTYPE" == "linux-gnu"* ]]; then
13 |     OS_TAG=linux
14 | elif [[ "$OSTYPE" == "darwin"* ]]; then
15 |     OS_TAG=mac
16 | else
17 |     echo "Not downloading stan/bin/stanc for OS type: $OSTYPE"
18 |     error 1
19 | fi
20 | 
21 | echo "Downloading stanc3 version: v2.18.1"
22 | 
23 | curl -L "https://github.com/stan-dev/stanc3/releases/download/v2.28.1/${OS_TAG}-stanc" -o stan/bin/stanc --retry 5 --retry-delay 10
24 | 
25 | chmod +x stan/bin/stanc
26 | 


--------------------------------------------------------------------------------
/test.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | set -e
3 | 
4 | pushd stan
5 | 
6 | ./runTests.py src/test/unit/services
7 | 
8 | popd
9 | 


--------------------------------------------------------------------------------