| Previous changeset 2:2d9b2ffec9d5 (2023-02-03) Next changeset 4:84fe9136c8c8 (2024-07-26) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c |
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modified:
muon_macros.xml pm_yaml_config.xml |
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| diff -r 2d9b2ffec9d5 -r 03f4f2aaa91c muon_macros.xml --- a/muon_macros.xml Fri Feb 03 15:40:12 2023 +0000 +++ b/muon_macros.xml Tue Jul 18 13:27:20 2023 +0000 |
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| @@ -17,4 +17,13 @@ <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> </param> </xml> + <!-- version of underlying tool (PEP 440) --> + <!-- citation should be updated with every underlying tool version --> + <!-- concept is not updated, and should only be used for referencing the idea of the software --> + <token name="@MUSPINSIM_VERSION@">2.2.1</token> + <token name="@MUSPINSIM_CITATION@">10.5281/zenodo.7733979</token> + <token name="@MUSPINSIM_CONCEPT@">10.5281/zenodo.6517626</token> + <token name="@PYMUONSUITE_VERSION@">0.3.0</token> + <token name="@PYMUONSUITE_CITATION@">10.5281/zenodo.8026711</token> + <token name="@PYMUONSUITE_CONCEPT@">10.5281/zenodo.7025643</token> </macros> \ No newline at end of file |
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| diff -r 2d9b2ffec9d5 -r 03f4f2aaa91c pm_yaml_config.xml --- a/pm_yaml_config.xml Fri Feb 03 15:40:12 2023 +0000 +++ b/pm_yaml_config.xml Tue Jul 18 13:27:20 2023 +0000 |
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| b'@@ -4,75 +4,103 @@\n <!-- version of underlying tool (PEP 440) -->\n <!-- this wrapper doesn\'t have pymuonsuite as a dependency, but it will change according\n to the pymuonsuite interface, so follow the same versioning pattern -->\n- <token name="@TOOL_VERSION@">0.2.3</token>\n+ <token name="@TOOL_VERSION@">0.3.0</token>\n <!-- version of this tool wrapper (integer) -->\n <token name="@WRAPPER_VERSION@">0</token>\n <!-- citation should be updated with every underlying tool version -->\n- <!-- typical fields to update are version, month, year, and doi -->\n- <token name="@TOOL_CITATION@">\n- @software{Sturniolo_pymuon-suite_2022,\n- author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},\n- license = {GPL-3.0},\n- month = {8},\n- title = {{pymuon-suite}},\n- url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n- version = {v0.2.3},\n- doi = {10.5281/zenodo.7025644},\n- year = {2022}\n- }\n- </token>\n+ <token name="@TOOL_CITATION@">10.5281/zenodo.8026711</token>\n <import>muon_macros.xml</import>\n </macros>\n <creator>\n <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>\n <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>\n+ <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>\n <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>\n </creator>\n <requirements>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- touch outputx.yaml &&\n- ([[ ! -z \'$general_params.poisson_r\' ]] && printf \'poisson_r: $general_params.poisson_r\\n\'>>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) &&\n- ([[ ! -z \'$general_params.name\' ]] && printf \'name: $general_params.name\\n\'>>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) &&\n- ([[ ! -z \'$general_params.charged\' ]] && printf \'charged: $general_params.charged\\n\'>>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) &&\n- ([[ ! -z \'$general_params.geom_steps\' ]] && printf \'geom_steps: $general_params.geom_steps\\n\'>>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) &&\n- ([[ ! -z \'$general_params.vdw_scale\' ]] && printf \'vdw_scale: $general_params.vdw_scale\\n\'>>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) &&\n- ([[ ! -z \'$calculator_params.calculator_cond.calculator\' ]] && printf \'calculator: $calculator_params.calculator_cond.calculator\\n\'>>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) &&\n- ([[ ! -z \'$general_params.geom_force_tol\' ]] && printf \'geom_force_tol: $general_params.geom_force_tol\\n\'>>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) &&\n- ([[ ! -z \'$general_params.out_folder\' ]] && printf \'out_folder: $general_params.out_folder\\n\'>>outputx.yaml || printf "out_folder: muon-airss-out\\n">>outputx.yaml) &&\n- ([[ ! -z \'$general_params.random_seed\' ]] && printf \'random_seed: $general_params.random_seed\\n\'>>outputx.yaml || ( echo "random_seed empty")) &&\n- ([[ ! -z \'$clustering_params.supercell\' ]] && (printf \'supercell: $clustering_params.supercell\\n\' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>outputx.yaml || ( >&2 echo "supercell empty" && exit 2)) &&\n- ([[ ! -z \'$clustering_params.k_points_grid\' ]] && (printf \'k_points_grid: $clustering_params.k_points_grid\\n\' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) '..b'$clustering_params.clustering.clustering_hier_t\n+#else if str($clustering_params.clustering.clustering_method)=="kmeans":\n+clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k\n+#end if</configfile>\n+ </configfiles>\n <inputs>\n <section name="general_params" expanded="true" title="General Parameters">\n <param type="float" argument="poisson_r" value="0.8" min="0.0" label="Poisson radius" help=" Poisson sphere radius to use for random generation. No two starting muon positions will be closer than this distance. Smaller values make for bigger structure sets."/>\n@@ -82,7 +110,7 @@\n <param type="float" argument="vdw_scale" value="0.5" min="0.0" label="Van der Waals scale" help="Van der Waals scaling factor to use when generating muon sites to avoid existing atoms. Smaller values will allow muons to get closer to the other ions."/>\n <param type="text" argument="out_folder" optional="true" value="muon-airss-out" label="Output folder name" help="Name to call the output folder used to store the files that the script generates."/>\n <param type="float" argument="geom_force_tol" value="0.05" min="0.0" label="Geometry optimization tolerance" help="Tolerance on geometry optimisation in units of eV/\xc3\x85."/>\n- <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Random seed for pymuonsuite."/>\n+ <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Seed used to randomise the positions of the muons in the generated structures."/>\n </section>\n <section name="calculator_params" expanded="true" title="Calculator parameters">\n <conditional name="calculator_cond">\n@@ -137,7 +165,7 @@\n </section>\n </inputs>\n <outputs>\n- <data label="Configuration for $general_params.name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/>\n+ <data label="Configuration for $general_params.name" name="out_yaml" format="yaml"/>\n </outputs>\n <tests>\n <test expect_num_outputs="1">\n@@ -166,7 +194,7 @@\n <param name="k_points_grid" value="[1,1,1]"/>\n <param name="max_scc_steps" value="200"/>\n </section>\n- <output name="out_yaml" file="config.yaml" ftype="yaml" delta="100"/>\n+ <output name="out_yaml" file="config.yaml" ftype="yaml"/>\n </test>\n <test expect_num_outputs="1">\n <section name="general_params">\n@@ -175,7 +203,7 @@\n </section>\n <section name="clustering_params">\n </section>\n- <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/>\n+ <output name="out_yaml" file="config-default.yaml" ftype="yaml"/>\n </test>\n <test expect_num_outputs="1">\n <section name="general_params">\n@@ -187,7 +215,7 @@\n </section>\n <section name="clustering_params">\n </section>\n- <output name="out_yaml" file="config-dftb.yaml" ftype="yaml" delta="100"/>\n+ <output name="out_yaml" file="config-dftb.yaml" ftype="yaml"/>\n </test>\n <test expect_num_outputs="1">\n <section name="general_params">\n@@ -199,7 +227,7 @@\n </section>\n <section name="clustering_params">\n </section>\n- <output name="out_yaml" file="config-all.yaml" ftype="yaml" delta="100"/>\n+ <output name="out_yaml" file="config-all.yaml" ftype="yaml"/>\n </test>\n <test expect_failure="true">\n <section name="general_params">\n@@ -237,8 +265,6 @@\n +------------+-------------------------------------+-----------------------------------+\n ]]></help>\n <citations>\n- <citation type="bibtex">\n- @TOOL_CITATION@\n- </citation>\n+ <citation type="doi">@TOOL_CITATION@</citation>\n </citations>\n </tool>\n' |