From fa6d7e3b5a427c4ea64783fcaed87726a606671b Mon Sep 17 00:00:00 2001
From: Marco Matthies <71844+marcom@users.noreply.github.com>
Date: Thu, 18 Jan 2024 13:50:36 +0100
Subject: [PATCH] Improve overriding energy parameter dirs via env vars (#5)
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/init-env-vars.jl | 64 +++++++++++++++++++++++++++++++++++++++++++
test/runtests.jl | 1 +
4 files changed, 100 insertions(+), 9 deletions(-)
create mode 100644 test/init-env-vars.jl
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/init-env-vars.jl b/test/init-env-vars.jl
new file mode 100644
index 0000000..c2f3ee7
--- /dev/null
+++ b/test/init-env-vars.jl
@@ -0,0 +1,64 @@
+@testset "__init__ env vars" begin
+ showtestset()
+
+ upstream_env_vars = [
+ "DATAPATH",
+ "CYCLEFOLD_DATAPATH",
+ ]
+ our_env_vars = ["RNASTRUCTURE_JL_" * e for e in upstream_env_vars]
+ env_var_mapping = Dict(e => "RNASTRUCTURE_JL_" * e for e in upstream_env_vars)
+ all_env_vars = [upstream_env_vars..., our_env_vars...]
+
+ function delete_all_env_vars()
+ for e in all_env_vars
+ delete!(ENV, e);
+ end
+ end
+
+ # save relevant ENV vars so that we can change them here for
+ # testing and then restore them later
+ saved_env_vars = Dict{String,String}()
+ for e in all_env_vars
+ if haskey(ENV, e)
+ saved_env_vars[e] = ENV[e]
+ delete!(ENV, e)
+ end
+ end
+
+ @test RNAstructure.__init__() == nothing
+ delete_all_env_vars()
+
+ # setting DATAPATH, etc
+ for e in upstream_env_vars
+ ENV[e] = "non-existent-dir-path"
+ warn_msg = ("RNAstructure: $e env var set, replacing with $(saved_env_vars[e])\n"
+ * "To override $e used by RNAstructure, set the RNASTRUCTURE_JL_$e env var")
+ @test (@test_logs (:warn, (warn_msg)) RNAstructure.__init__()) == nothing
+ delete_all_env_vars()
+ end
+
+ # setting RNASTRUCTURE_JL_*
+ for (upstream_env, our_env) in env_var_mapping
+ ENV[our_env] = "non-existent-dir-path"
+ info_msg = ("Setting ENV[\"$upstream_env\"] = ENV[\"$our_env\"]")
+ @test (@test_logs (:info, (info_msg)) RNAstructure.__init__()) == nothing
+ delete_all_env_vars()
+ end
+
+ # setting both upstream_env_vars and our_env_vars, our_env_vars
+ # should have precedence
+ for (upstream_env, our_env) in env_var_mapping
+ ENV[upstream_env] = "non-existent-dir-path"
+ ENV[our_env] = "non-existent-dir-path"
+ info_msg = ("Setting ENV[\"$upstream_env\"] = ENV[\"$our_env\"]")
+ @test (@test_logs (:info, (info_msg)) RNAstructure.__init__()) == nothing
+ delete_all_env_vars()
+ end
+
+ # restore env vars that we previously unset
+ for e in all_env_vars
+ if haskey(saved_env_vars, e)
+ ENV[e] = saved_env_vars[e]
+ end
+ end
+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")