Mercurial > repos > muon-spectroscopy-computational-project > muspinsim

changeset 2:136ed45d1ea9 draft

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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author muon-spectroscopy-computational-project
date Fri, 03 Feb 2023 15:39:01 +0000
parents b30217097125
children e002cee8f707
files muspinsim.xml test-data/celio.in test-data/celio.log test-data/fitting_data.dat test-data/fitting_fit_report.txt test-data/fitting_fitreport.txt test-data/hfine.dat test-data/hfine_powder.dat
diffstat 8 files changed, 169 insertions(+), 137 deletions(-) [+]
line wrap: on
line diff
--- a/muspinsim.xml	Thu Sep 15 10:23:28 2022 +0000
+++ b/muspinsim.xml	Fri Feb 03 15:39:01 2023 +0000
@@ -1,28 +1,29 @@
-<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
+<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
     <description>perform spin dynamics calculations for muon science experiments</description>
     <macros>
         <!-- version of underlying tool (PEP 440) -->
-        <token name="@TOOL_VERSION@">1.1.0</token>
+        <token name="@TOOL_VERSION@">2.0.2</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">1</token>
+        <token name="@WRAPPER_VERSION@">0</token>
         <!-- citation should be updated with every underlying tool version -->
         <!-- typical fields to update are version, month, year, and doi -->
         <token name="@TOOL_CITATION@">
             @software{muspinsim,
-                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
+                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and Davies, Joel and Wilkinson, John and {Muon Spectroscopy Computational Project}},
                 license = {MIT},
                 title = {{muspinsim}},
                 url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
-                version = {v1.1.0},
-                month = {5},
-                year = {2022},
-                doi = {10.5281/zenodo.6563074}
+                version = {v2.0.2},
+                month = {1},
+                year = {2023}
+                doi = {10.5281/zenodo.7568830}
             }
         </token>
     </macros>
     <creator>
         <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
         <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
+        <person givenName="Joel" familyName="Davies" url="https://github.com/joelvdavies" identifier="https://orcid.org/0000-0002-4153-6819"/>
         <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
     </creator>
     <requirements>
@@ -30,29 +31,31 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ## remove spaces in names
-        mu_sim_name=\$(sed 's/ //g' <<< "$mu_sim.name") &&
+        mu_sim_name=\$(sed 's/ //g' <<< '$mu_sim.name') &&
+        ## input file name without extension
+        mu_in_name=\${mu_sim_name%.*} &&
         ## create links
-        ln -s $mu_sim \$mu_sim_name &&
+        ln -s '$mu_sim' \$mu_sim_name &&
         ## grab 'name' field from input file, if it doesn't exist, set name as 'muspinsim'
         mu_out=\$(grep -A1 '^name' \$mu_sim_name | grep -v 'name' | sed -e 's/^[ \t]*//') &&
-        fitreport_out=\${mu_out:-"fitting_data"}_fitreport.txt &&
+        fit_report_out=\${mu_in_name:-"fitting_data"}_fit_report.txt &&
         mu_out=\${mu_out:-"muspinsim"} &&
         log_out=\$(echo \$mu_sim_name | cut -d '.' -f1).log &&
         ## if fitting data required, check if fitting data exists
         ## create symlink and change filepath in input file to point to symlink
-        if grep '^fitting_data' $mu_sim; then
+        if grep '^fitting_data' '$mu_sim'; then
             if [[ '$mu_exp_in.name' != 'None' ]]; then
-                mu_exp_in_name=\$(sed 's/ //g' <<< "$mu_exp_in.name") &&
-                ln -s $mu_exp_in \$mu_exp_in_name &&
+                mu_exp_in_name=\$(sed 's/ //g' <<< '$mu_exp_in.name') &&
+                ln -s '$mu_exp_in' \$mu_exp_in_name &&
                 sed -iE "/^fitting_data/{n;s/([^)]*)/(\"\$mu_exp_in_name\")/g}" \$mu_sim_name;
             else
-                echo "fitting data required, but no experiment data given" && exit 64;
+                echo "Fitting data required, but no experiment data given" && exit 64;
             fi;
         fi &&
         muspinsim \$mu_sim_name &&
         mkdir data &&
         mv \$mu_out*.dat data &&
-        if test -f \$fitreport_out; then mv -f \$fitreport_out fit_report.txt; fi &&
+        if test -f \$fit_report_out; then mv -f \$fit_report_out fit_report.txt; fi &&
         mv \$log_out log_out.log
     ]]></command>
     <inputs>
@@ -74,7 +77,7 @@
         <test expect_num_outputs="2">
             <param name="mu_sim" value="hfine.in" ftype="txt"/>
             <output_collection name="muspinsim_results" type="list">
-                <element name="hfine.dat" file="hfine.dat" ftype="txt" lines_diff="4"/>
+                <element name="hfine.dat" file="hfine.dat" ftype="txt" compare="re_match"/>
             </output_collection>
             <output name="log_out" file="hfine.log" ftype="txt" compare="re_match"/>
         </test>
@@ -89,10 +92,17 @@
             </output_collection>
             <output name="log_out" file="hfine_powder.log" ftype="txt" compare="re_match">
                 <assert_contents>
-                    <has_size value="802"/>
+                    <has_size value="803" delta="2"/>
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="2">
+            <param name="mu_sim" value="celio.in" ftype="txt"/>
+            <output_collection name="muspinsim_results" type="list">
+                <element name="celio.dat" file="generic_out.dat" ftype="txt" compare="re_match_multiline"/>
+            </output_collection>
+            <output name="log_out" file="celio.log" ftype="txt" compare="re_match"/>
+        </test>
         <test expect_num_outputs="3">
             <param name="mu_sim" value="fitting.in" ftype="txt"/>
             <param name="mu_exp_in" value="fitting_input.dat" ftype="txt"/>
@@ -104,7 +114,7 @@
                     <has_size value="17145"/>
                 </assert_contents>
             </output>
-            <output name="fit_report" file="fitting_fitreport.txt" ftype="txt" lines_diff="4"/>
+            <output name="fit_report" file="fitting_fit_report.txt" ftype="txt" lines_diff="2"/>
         </test>
         <test expect_num_outputs="2">
             <param name="mu_sim" value="multi_out.in" ftype="txt"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/celio.in	Fri Feb 03 15:39:01 2023 +0000
@@ -0,0 +1,12 @@
+name
+   celio
+spins
+   mu F F
+dipolar 1 2
+   0 0 1
+dipolar 1 3
+   0 0 -1
+celio
+   8 4
+time
+   range(0, 10, 100)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/celio.log	Fri Feb 03 15:39:01 2023 +0000
@@ -0,0 +1,10 @@
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Launching MuSpinSim calculation from file: celio.in
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Using X axis:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		t => 100 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Created spin system with spins:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		mu F F
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding dipolar term to spins 1-2
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding dipolar term to spins 1-3
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to simulate: 1
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to average: 1
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Simulation completed in [\d\.]+ seconds
\ No newline at end of file
--- a/test-data/fitting_data.dat	Thu Sep 15 10:23:28 2022 +0000
+++ b/test-data/fitting_data.dat	Fri Feb 03 15:39:01 2023 +0000
@@ -1,5 +1,5 @@
-# MUSPINSIM v.1.0.3
-# Output file written on Thu Mar 31 18:26:46 2022
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
 # Parameters used:
 # 
 0.000000000000000000e+00 5.000000000000000000e-01
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting_fit_report.txt	Fri Feb 03 15:39:01 2023 +0000
@@ -0,0 +1,11 @@
+Fitting process for fitting_data completed
+Success achieved: True
+Final absolute error <|f-f_targ|>: 0.004596737036516675
+Number of simulations: 40
+Number of iterations: 20
+
+====================
+
+Values found for fitting variables:
+
+	g = 3.0368750000000104
\ No newline at end of file
--- a/test-data/fitting_fitreport.txt	Thu Sep 15 10:23:28 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-Fitting process for fitting_data completed
-Success achieved: True
-Final absolute error <|f-f_targ|>: 0.0
-Number of simulations: 40
-Number of iterations: 20
-
-====================
-
-Values found for fitting variables:
-
-	g = 3.0368750000000104
\ No newline at end of file
--- a/test-data/hfine.dat	Thu Sep 15 10:23:28 2022 +0000
+++ b/test-data/hfine.dat	Fri Feb 03 15:39:01 2023 +0000
@@ -1,104 +1,104 @@
-# MUSPINSIM v.1.0.3
-# Output file written on Thu Mar 31 15:40:40 2022
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
 # Parameters used:
-# 
-0.000000000000000000e+00 4.999999999999998890e-01
-1.010101010101010100e-03 4.994966691179709706e-01
-2.020202020202020200e-03 4.979887032076987241e-01
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+#
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+1\.0000000000000\d{5}e-01 4\.9999999999999\d{5}e-01
\ No newline at end of file
--- a/test-data/hfine_powder.dat	Thu Sep 15 10:23:28 2022 +0000
+++ b/test-data/hfine_powder.dat	Fri Feb 03 15:39:01 2023 +0000
@@ -1,5 +1,5 @@
-# MUSPINSIM v.1.0.3
-# Output file written on Thu Mar 31 15:53:05 2022
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
 # Parameters used:
 # 
 0.000000000000000000e+00 4.999999999999978906e-01