Updated Changelog.

Author: iancze

README.md

@@ -62,12 +62,14 @@ inside of your `.bashrc` or `.zshrc` file. Finally,
 
     $ source ~/.zshrc
 
-To check that you have properly added the scripts, you can try in your system shell
+To check that you have properly added the scripts (and check that you installed the correct version), you can try in your system shell
 
-    $ JudithInitialize.jl --test
+    $ JudithInitialize.jl --version
     Your JudithExcalibur scripts are successfully linked.
+    You are running JudithExcalibur 0.1.1
     Exiting
 
+
 Second, most of the scripts and IO routines require Python and several Python packages. Please install the following packages via your own package manager or a distribution like anaconda:
 
 * numpy

docs/changelog.md

@@ -4,28 +4,43 @@ The following are the changes that have been implemented since the previous vers
 
 # Version 0.1.1
 
-Now includes a cookbook example for AK Sco.
+## Model specification
 
-New implemenation of models. Created the `AbstractParameters` type, with subtypes `ParametersStandard` and `ParametersTruncated`. Added new parameters type
+New implementation of models through parameter types in `model.jl`. Instead of separate model files for each new parameterization, which duplicated a lot of code and made things difficult to maintain, we are now collating all model types in `model.jl` by their parameters. We have created the `AbstractParameters` umbrella type, with subtypes `ParametersStandard`, `ParametersTruncated`, and `ParametersCavity`. Previous model specification routines like `Sigma(r::Float64, pars::Parameters)` (surface density) are now have overloaded methods for different models based upon these parameter types
+
+    Sigma(r::Float64, pars::ParametersStandard)
+    Sigma(r::Float64, pars::ParametersTruncated)
+    Sigma(r::Float64, pars::ParametersCavity)
+
+And routines that are general to all models (e.g. velocity specification) are denoted by
+
+    velocity{T}(r::T, pars::AbstractParameters)
 
 Note that model types `cavity` and `truncated` are still experimental and likely to change.
 
-Updated the `config.yaml` format to include new fields like `model: standard`. Changed the items in the `parameters` dictionary to be a single Float64 number, not an array of `[starting, jump]` like it was previously. An example is `assets/config.yaml`.
+To go along with this change, I have updated the automatic generation of the `config.yaml` file to include new fields like `model: standard`. Within the `config.yaml` file, items in the `parameters` dictionary are now simply a single Float64 number, not an array of `[starting, jump]` like it was previously.
+
+`model.jl` now handles the implementation of priors, that dispatch off of the parameter types. This greatly streamlines the function `fprob` in `venus.jl`.
+
+
+## One-off model synthesis and plotting
 
-Simplified synthesizing and plotting of models. Split `plot_model.jl` into `synthesize_model.jl` and separately `plot_chmaps.jl`.
+I've simplified synthesizing and plotting of models. What was previously `plot_model.jl` is now split into `synthesize_model.jl` and `plot_chmaps.jl`.
 
-Added new `plot_moments.jl` script which plots zeroth-moment.
+Added new `plot_moments.jl` script which plots the zeroth-moment image. Soon it will plot first moment as well.
 
-Created `InitializeWalkers.ipynb` that is copied to new directory to help specify walker starting positions.
+## MCMC Sampling
 
-Streamlined various model implementations into the `venus.jl` code.
+The specification of parameter types allowed me to greatly simplify the MCMC sampling code into a single script, `venus.jl`. I have moved previous sampling scripts to the `attic/` directory.
 
-`model.jl` now handles the implementation of priors. This greatly streamlines the function `fprob` in `venus.jl`.
+Created `InitializeWalkers.ipynb` that is copied to new directory to help specify walker starting positions. The user edits this with a Jupyter/IPython notebook.
 
-`plot_walkers.py` now includes ability to determine highest density interval for quoting credible intervals.
+## Cookbook
 
+We now have a [cookbook example](docs/cookbook.md) for AK Sco, check it out to get started!
 
+`plot_walkers.py` now includes ability to determine highest density interval for quoting credible intervals and should automatically label the parameters after reading from `config.yaml`.
 
 # Version 0.1.0
 
-Initial commit.
+Initial commit on the new versioning roadmap.

scripts/JudithInitialize.jl

@@ -8,8 +8,8 @@ using ArgParse
 
 s = ArgParseSettings(description="Initialize a new project directory with the appropriate files. Can also be used to update RADMC-3D input files after making changes to config.yaml")
 @add_arg_table s begin
-    "--test"
-    help = "Print a test message to see you linked things correctly"
+    "--version"
+    help = "Print a the version number and exit."
     action = :store_true
     "--new-project"
     help = "Copy a stock configuration file to this directory. Can be 'standard', 'truncated', 'cavity'"
@@ -36,12 +36,6 @@ parsed_args = parse_args(ARGS, s)
 
 assets_dir = Pkg.dir("JudithExcalibur") * "/assets/"
 
-# This is just for new users to test that the package is successfully installed.
-if parsed_args["test"]
-    println("Your JudithExcalibur scripts are successfully linked.")
-    println("Exiting")
-    quit()
-end
 
 # The user is going to start modeling a new disk, so copy in the new configuration file.
 if parsed_args["new-project"] != "no"
@@ -63,6 +57,14 @@ using HDF5
 using JudithExcalibur.constants
 using JudithExcalibur.model
 
+# This is just for new users to test that the package is successfully installed.
+if parsed_args["version"]
+    println("Your JudithExcalibur scripts are successfully linked.")
+    println("You are running JudithExcalibur $JUDITHEXCALIBUR_VERSION")
+    println("Exiting")
+    quit()
+end
+
 # Create an output directory that will be useful for the results.
 out_base = config["out_base"]
 if !ispath(out_base)

src/constants.jl

@@ -3,6 +3,9 @@
 module constants
 
 export M_sun, M_earth, AU, pc, G, kB, amu, c_ang, cc, c_kms, mu_gas, m_H, m_CO, m_12CO, m_13CO, m_C18O, number_densities, molnames, arcsec, deg, fftspace, MCO, lam0_12CO, lam0_13CO, lam0_C18O, lam0s, nyquist_factor, r_out_factor, Av_sigmaH
+export JUDITHEXCALIBUR_VERSION
+
+JUDITHEXCALIBUR_VERSION = v"0.1.1"
 
 # Conversion from astronomical units to CGS units
 M_sun = 1.99e33 # [g]