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Merged
ramez17khaled merged 1 commit into from
Apr 16, 2026
Merged

split rptools #271

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6 changes: 4 additions & 2 deletions tools/rptools/rpcompletion.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<requirements>
<requirement type="package" version="6.8.4">rpcompletion</requirement>
</requirements>
<stdio>
<exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
<exit_code range="2" level="fatal" description="ValueError returned" />
Expand All @@ -22,7 +24,7 @@
#set sinkfile=$sink.sinkfile
#end if

python -m rptools.rpcompletion
python -m rpcompletion
'$rp2_pathways'
$sinkfile
'$rp2paths_compounds'
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6 changes: 4 additions & 2 deletions tools/rptools/rpextractsink.xml
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Expand Up @@ -4,15 +4,17 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<requirements>
<requirement type="package" version="6.8.2">rpextractsink</requirement>
</requirements>
<stdio>
<regex match="Could not retreive any species in the compartment" level="fatal" />
</stdio>
<command detect_errors="exit_code"><![CDATA[
TMPDIR="\${TMPDIR:-.}/rr_cache" &&
mkdir -p "\${TMPDIR}" &&

python -m rptools.rpextractsink
python -m rpextractsink
'$input'
'$sink'
--compartment-id '$compartment_id'
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6 changes: 4 additions & 2 deletions tools/rptools/rpthermo.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,17 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<requirements>
<requirement type="package" version="6.8.4">rpthermo</requirement>
</requirements>
<stdio>
<regex match="WARNING:" level="warning" />
<regex match="ERROR:" level="fatal" />
<regex match="ERROR:root:ChemAxon" level="warning" />
</stdio>
<command detect_errors="exit_code"><![CDATA[
export XDG_CACHE_HOME="\${TMPDIR:-.}" ;
python -m rptools.rpthermo
python -m rpthermo
'$input'
'$pathway_with_thermo'
--pH '$adv.ph'
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