From aeffebed783a8bd48925891c33946c76df73a6ae Mon Sep 17 00:00:00 2001
From: Marco Matthies <71844+marcom@users.noreply.github.com>
Date: Thu, 18 Jan 2024 02:40:54 +0100
Subject: [PATCH] Improve overriding energy parameter dirs via env vars

Always ensure the DATAPATH, CYCLEFOLD_DATAPATH env vars are pointing
to the correct path from the `RNAstructure_jll` binary package.

These paths can be overridden with the RNASTRUCTURE_JL_DATAPATH,
RNASTRUCTURE_JLCYCLEFOLD_DATAPATH env vars if necessary.

Don't warn if the DATAPATH, CYCLEFOLD_DATAPATH env vars are already
set to the correct directories.  This avoids unnecessary warnings when
running the tests.

Fixes #4.
---
 README.md           | 17 +++++++++++++++++
 src/RNAstructure.jl | 27 ++++++++++++++++++---------
 test/runtests.jl    |  1 +
 3 files changed, 36 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index d13ce2a..a986fa6 100644
--- a/README.md
+++ b/README.md
@@ -39,6 +39,23 @@ for more details.
 Some programs make exceptions to these rules, check the manual pages
 of the RNAstructure programs for details on any differences.
 
+### Note: Overriding energy parameter directories
+
+The environment variables `RNASTRUCTURE_JL_DATAPATH` can be set to
+override the directory where energy parameters are read from. For the
+`cyclefold_*` functions the environment variable is called
+`RNASTRUCTURE_JL_CYCLEFOLD_DATAPATH`.
+
+In the original RNAstructure program these environment variables are
+called `DATAPATH` and `CYCLEFOLD_DATAPATH`. `RNAstructure.jl` (this
+package) sets these environment variables automatically to the
+corresponding installation directory of the `RNAstructure_jll` binary
+package.  The names of the env vars were changed to avoid clashes with
+possible settings you might already have in your shell startup files
+from a pre-existing manual RNAstructure installation, which could be a
+different version and have different parameters. In this way, you can
+be sure that this package uses the correct parameters, while still
+allowing to override them if necessary.
 
 ### Minimum free energy (MFE) and structure
 
diff --git a/src/RNAstructure.jl b/src/RNAstructure.jl
index e1e6c37..da6361a 100644
--- a/src/RNAstructure.jl
+++ b/src/RNAstructure.jl
@@ -18,16 +18,25 @@ include("pairtable-to-dbn.jl")
 include("plot.jl")
 
 function __init__()
-    if !haskey(ENV, "DATAPATH")
-        ENV["DATAPATH"] = joinpath(RNAstructure_jll.artifact_dir, "data_tables")
-    else
-        @info "RNAstructure: energy params already set, DATAPATH=$(ENV["DATAPATH"])"
-    end
-    if !haskey(ENV, "CYCLEFOLD_DATAPATH")
-        ENV["CYCLEFOLD_DATAPATH"] = joinpath(RNAstructure_jll.artifact_dir, "CycleFold", "datafiles")
-    else
-        @info "RNAstructure: CycleFold energy params already set, CYCLEFOLD_DATAPATH=$(ENV["CYCLEFOLD_DATAPATH"])"
+    datapath = joinpath(RNAstructure_jll.artifact_dir, "data_tables")
+    cyclefold_datapath = joinpath(RNAstructure_jll.artifact_dir, "CycleFold", "datafiles")
+
+    # set env vars DATAPATH, CYCLEFOLD_DATAPATH needed for RNAstructure_jll
+    # these can be overridden with RNASTRUCTURE_JL_DATAPATH, RNASTRUCTURE_JL_CYCLEFOLD_DATAPATH
+    for (env_varname, default_path) in [("DATAPATH", datapath), ("CYCLEFOLD_DATAPATH", cyclefold_datapath)]
+        if haskey(ENV, "RNASTRUCTURE_JL_$(env_varname)")
+            @info "Setting ENV[\"$(env_varname)\"] = ENV[\"RNASTRUCTURE_JL_$(env_varname)\"]"
+            ENV[env_varname] = ENV["RNASTRUCTURE_JL_$(env_varname)"]
+        else
+            if haskey(ENV, env_varname) && ENV[env_varname] != default_path
+                # only warn if env var is set to non-default path
+                @warn ("RNAstructure: $(env_varname) env var set, replacing with $default_path\n"
+                       * "To override $(env_varname) used by RNAstructure, set the RNASTRUCTURE_JL_$(env_varname) env var")
+            end
+            ENV[env_varname] = default_path
+        end
     end
+
     # TODO: set OMP_NUM_THREADS env var for smp programs (number of threads to use)
     return nothing
 end
diff --git a/test/runtests.jl b/test/runtests.jl
index a3be9cb..91b17f5 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -14,6 +14,7 @@ showtestset() = println(" "^(2 * Test.get_testset_depth()), "testing ",
 @testset verbose=true "RNAstructure" begin
     showtestset()
     include("aqua.jl")
+    include("init-env-vars.jl")
     include("ct-format.jl")
     include("plot.jl")
     include("RNAstructure.jl")