From 8f08b1eff0ec42c071f6f3427820fc77b0c3e9a4 Mon Sep 17 00:00:00 2001
From: Jonathan Doucette <jdoucette@physics.ubc.ca>
Date: Thu, 3 Mar 2022 11:36:56 -0800
Subject: [PATCH] update external api for DECAES v0.4.3

---
 api/decaes.m  |  2 +-
 api/decaes.py | 25 +++++++++++++++++++++++--
 api/decaes.sh |  6 ++++--
 3 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/api/decaes.m b/api/decaes.m
index 071fa40..c931326 100644
--- a/api/decaes.m
+++ b/api/decaes.m
@@ -92,7 +92,7 @@
 % 
 %   Note the separation of the Matlab-specific flags from the DECAES settings file.
 % 
-% This version of decaes.m was written for DECAES v0.4.2.
+% This version of decaes.m was written for DECAES v0.4.3.
 % DECAES was written by Jonathan Doucette (jdoucette@physics.ubc.ca).
 % Original MATLAB implementation is by Thomas Prasloski (tprasloski@gmail.com).
 
diff --git a/api/decaes.py b/api/decaes.py
index 089dc28..49fed36 100644
--- a/api/decaes.py
+++ b/api/decaes.py
@@ -1,3 +1,24 @@
+"""
+Load the DECAES.jl Julia package from python.
+DECAES.jl will be installed automatically, if necessary.
+
+This module requires the julia Python package to be installed.
+See the following documentation for instructions:
+
+    https://github.com/JuliaPy/pyjulia#quick-usage
+
+Quick usage:
+
+    import decaes
+    decaes.initialize()
+    from decaes import DECAES
+
+    # Call methods from the DECAES module as usual, e.g.
+    DECAES.T2mapSEcorr(image; kwargs...)
+
+This version of decaes.py was written for DECAES v0.4.3.
+"""
+
 import julia
 import os
 import subprocess
@@ -39,13 +60,13 @@ def install(
     # Install DECAES.jl
     decaes_install_script = """try
             @info "Trying to import DECAES..."
-            import DECAES
+            @eval import DECAES
         catch e
             @error "`import DECAES` failed" exception=(e, catch_backtrace())
             @info "Installing DECAES..."
             import Pkg
             Pkg.add("DECAES")
-            import DECAES
+            @eval import DECAES
         end
         """.replace("        ", "")
 
diff --git a/api/decaes.sh b/api/decaes.sh
index 58176dc..33df987 100755
--- a/api/decaes.sh
+++ b/api/decaes.sh
@@ -16,10 +16,12 @@ parser = argparse.ArgumentParser(
 
     Example:
 
-        Start Julia with 8 threads and run DECAES using parameters specified by the
+        Start Julia with multiple threads and run DECAES using parameters specified by the
         settings file 'decaes_settings_file.txt':
 
-            python decaes.py --threads=8 @/path/to/decaes_settings_file.txt
+            python decaes.py @/path/to/decaes_settings_file.txt
+
+    This version of decaes.sh was written for DECAES v0.4.3.
     """,
     formatter_class = argparse.RawDescriptionHelpFormatter,
 )