update ai changes to Julia 1.0

.travis.yml

@@ -3,8 +3,10 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
 notifications:
   email: false
 script:
-  - julia -e 'Pkg.clone(pwd()); Pkg.build("ForneyLab"); Pkg.test("ForneyLab"; coverage=true)'
+  - julia -e 'mv("_Project.toml", "Project.toml")'
+  - julia -e 'import Pkg; Pkg.build(); Pkg.test()'

CONTRIB.md

@@ -1,6 +1,13 @@
 Contribution guidelines
 =======================
 
+
+Workflow
+--------
+
+We use the standard [GitHub Flow](https://guides.github.com/introduction/flow/) in which all contributions are added through pull requests. To contribute, [fork](https://guides.github.com/activities/forking/) the repository, commit your contributions to your fork and then create a pull request on the ForneyLab.jl repository.
+
+
 File structure
 --------------
 - `/demo/`: demos in Jupyter (iJulia) notebook format (`.ipynb`)
@@ -12,11 +19,12 @@ File structure
     + `engines/`: render message passing schedules to executable code
         * `julia/`: Julia engine and update rule implementations
     + `factor_nodes/`: all node-specific files
-    + `update_rules/`: message passing update rules 
+    + `update_rules/`: message passing update rules
 - `/test/`: test files with similar directory structure as `/src/`.
 
 File and directory names are always in `snake_case`, except for `REQUIRE` and markdown files in the root directory.
 
+
 Pre-commit hook for demos
 -------------------------
 

Manifest.toml

@@ -0,0 +1,116 @@
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[BinDeps]]
+deps = ["Compat", "Libdl", "SHA", "URIParser"]
+git-tree-sha1 = "12093ca6cdd0ee547c39b1870e0c9c3f154d9ca9"
+uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee"
+version = "0.8.10"
+
+[[BinaryProvider]]
+deps = ["Libdl", "Pkg", "SHA", "Test"]
+git-tree-sha1 = "b530fbeb6f41ab5a83fbe3db1fcbe879334bcd2d"
+uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
+version = "0.4.2"
+
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "ae262fa91da6a74e8937add6b613f58cd56cdad4"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "1.1.0"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[Distributed]]
+deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[InteractiveUtils]]
+deps = ["LinearAlgebra", "Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[SpecialFunctions]]
+deps = ["BinDeps", "BinaryProvider", "Compat", "Libdl"]
+git-tree-sha1 = "d12f8917be3782f4b800ba16003b8d0d4858c2e5"
+uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
+version = "0.7.0"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[URIParser]]
+deps = ["Test", "Unicode"]
+git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"
+uuid = "30578b45-9adc-5946-b283-645ec420af67"
+version = "0.4.0"
+
+[[UUIDs]]
+deps = ["Random"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

README.md

@@ -1,6 +1,8 @@
 ForneyLab.jl
 ============
 
+[![Build Status](https://travis-ci.org/biaslab/ForneyLab.jl.svg?branch=master)](https://travis-ci.org/biaslab/ForneyLab.jl)
+
 ForneyLab.jl is a Julia package for automatic generation of (Bayesian) inference algorithms. Given a probabilistic model, ForneyLab generates efficient Julia code for message-passing based inference. It uses the model structure to generate an algorithm that consists of a sequence of local computations on a Forney-style factor graph (FFG) representation of the model. For an excellent introduction to message passing and FFGs, see [The Factor Graph Approach to Model-Based Signal Processing](https://ieeexplore.ieee.org/document/4282128/) by Loeliger et al. (2007).
 
 We designed ForneyLab with a focus on flexible and modular modeling of time-series data. ForneyLab enables a user to:
@@ -11,32 +13,29 @@ We designed ForneyLab with a focus on flexible and modular modeling of time-seri
 
 The current version supports [belief propagation](https://en.wikipedia.org/wiki/Belief_propagation) (sum-product message passing), [variational message passing](https://en.wikipedia.org/wiki/Variational_message_passing) and [expectation propagation](https://en.wikipedia.org/wiki/Expectation_propagation).
 
-For a more detailed introduction we refer to the [demos](https://github.com/biaslab/ForneyLab.jl/tree/master/demo).
+The [ForneyLab project page](http://forneylab.org) provides more background on ForneyLab as well as pointers to related literature and talks. For a practical introduction, have a look at [the demos](https://github.com/biaslab/ForneyLab.jl/tree/master/demo).
+
 
 Installation
 ============
 
-Add the ForneyLab package to your Julia installation:
+Install ForneyLab through the Julia package manager:
 ```jl
-Pkg.clone("https://github.com/biaslab/ForneyLab.jl.git")
+] add ForneyLab
 ```
-To update, use:
-```jl
-Pkg.update()
-```
-If you want to be able to use the graph visualization functions, you'll also need to have [GraphViz](http://www.graphviz.org/) installed. On Linux, just use `apt-get install graphviz` or `yum install graphviz`. On Windows, run the installer and afterwards manually add the path of the GraphViz installation to the `PATH` system variable. The command `dot -?` should work from the command line.
+If you want to be able to use the graph visualization functions, you will also need to have [GraphViz](http://www.graphviz.org/) installed. On Linux, just use `apt-get install graphviz` or `yum install graphviz`. On Windows, run the installer and afterwards manually add the path of the GraphViz installation to the `PATH` system variable. On MacOS, use for example `brew install graphviz`. The `dot` command should work from the command line.
+
+Some demos use the [PyPlot](https://github.com/stevengj/PyPlot.jl) plotting module. Install it using `] add PyPlot`.
+
+Optionally, use `] test ForneyLab` to validate the installation by running the test suite.
 
-Some demos use the [PyPlot](https://github.com/stevengj/PyPlot.jl) plotting module. Install it using `Pkg.add("PyPlot")`.
 
 Getting started
 ===============
 
-Import ForneyLab:
-```jl
-using ForneyLab
-```
-
 There are [demos](https://github.com/biaslab/ForneyLab.jl/tree/master/demo) available to get you started.
+Additionally, the [ForneyLab project page](http://forneylab.org) contains a talk and other resources that might be helpful.
+
 
 License
 =======

REQUIRE

@@ -1,2 +1,2 @@
-julia 0.6
+julia 0.7
 SpecialFunctions

_Project.toml

@@ -0,0 +1,13 @@
+name = "ForneyLab"
+uuid = "9fc3f58a-c2cc-5bff-9419-6a294fefdca9"
+version = "0.9.0"
+
+[deps]
+Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"