From 3aa892dbec7e8204ad32c922bc42dc7bc46c511e Mon Sep 17 00:00:00 2001 From: ehennestad Date: Tue, 1 Jul 2025 15:05:24 +0200 Subject: [PATCH 01/15] Move files from"code" to "src/did" --- {code => src/did}/+did/+common/PathConstants.m | 0 {code => src/did}/+did/+common/getCache.m | 0 {code => src/did}/+did/+datastructures/cell2str.m | 0 {code => src/did}/+did/+datastructures/celloritem.m | 0 {code => src/did}/+did/+datastructures/colvec.m | 0 .../did}/+did/+datastructures/emptystruct.m | 0 {code => src/did}/+did/+datastructures/eqemp.m | 0 {code => src/did}/+did/+datastructures/eqlen.m | 0 {code => src/did}/+did/+datastructures/eqtot.m | 0 {code => src/did}/+did/+datastructures/equnique.m | 0 .../did}/+did/+datastructures/fieldsearch.m | 0 .../did}/+did/+datastructures/findclosest.m | 0 .../did}/+did/+datastructures/isfullfield.m | 0 .../did}/+did/+datastructures/jsonencodenan.m | 0 {code => src/did}/+did/+datastructures/sizeeq.m | 0 .../did}/+did/+datastructures/structmerge.m | 0 .../did}/+did/+db/struct_name_value_search.m | 0 {code => src/did}/+did/+db/tableCrossJoin.m | 0 {code => src/did}/+did/+file/binaryTable.m | 0 {code => src/did}/+did/+file/checkout_lock_file.m | 0 {code => src/did}/+did/+file/dumbjsondb.m | 0 {code => src/did}/+did/+file/fileCache.m | 0 {code => src/did}/+did/+file/fileid_value.m | 0 {code => src/did}/+did/+file/fileobj.m | 0 {code => src/did}/+did/+file/filesepconversion.m | 0 {code => src/did}/+did/+file/fullfilename.m | 0 {code => src/did}/+did/+file/isfilepathroot.m | 0 {code => src/did}/+did/+file/isurl.m | 0 .../did}/+did/+file/mustBeValidMachineFormat.m | 0 .../did}/+did/+file/mustBeValidPermission.m | 0 {code => src/did}/+did/+file/readlines.m | 0 {code => src/did}/+did/+file/readonly_fileobj.m | 0 {code => src/did}/+did/+file/release_lock_file.m | 0 {code => src/did}/+did/+file/str2text.m | 0 {code => src/did}/+did/+file/string2filestring.m | 0 {code => src/did}/+did/+file/text2cellstr.m | 0 {code => src/did}/+did/+fun/docs2graph.m | 0 {code => src/did}/+did/+fun/findalldependencies.m | 0 .../did}/+did/+fun/finddocs_missing_dependencies.m | 0 .../did}/+did/+fun/plotinteractivedocgraph.m | 0 .../did}/+did/+implementations/binarydoc_matfid.m | 0 {code => src/did}/+did/+implementations/doc2sql.m | 0 .../did}/+did/+implementations/matlabdumbjsondb.m | 0 {code => src/did}/+did/+implementations/sqldb.m | 0 {code => src/did}/+did/+implementations/sqlitedb.m | 0 {code => src/did}/+did/binarydoc.m | 0 {code => src/did}/+did/database.m | 0 {code => src/did}/+did/document.m | 0 {code => src/did}/+did/documentservice.m | 0 {code => src/did}/+did/filesep.m | 0 {code => src/did}/+did/ido.m | 0 {code => src/did}/+did/query.m | 0 {code => src/did}/+did/toolboxdir.m | 0 {code => src/did}/Contents.m | 0 {code => src/did}/example_schema/.gitkeep | 0 .../did}/example_schema/demo_schema1/.gitkeep | 0 .../GenBankControlledVocabulary-info.txt | 0 .../GenBankControlledVocabulary.tsv.gz | Bin .../controlled_vocabulary/genbank_commonname.json | 0 .../controlled_vocabulary/scientific_name.json | 0 .../demo_schema1/database_documents/base.json | 0 .../demo_schema1/database_documents/base.md | 0 .../demo_schema1/database_documents/demoA.json | 0 .../demo_schema1/database_documents/demoB.json | 0 .../demo_schema1/database_documents/demoC.json | 0 .../demo_schema1/database_documents/demoFile.json | 0 .../did_document_animalsubject.json | 0 .../database_documents/did_document_app.json | 0 .../database_documents/did_document_element.json | 0 .../did_document_element_epoch.json | 0 .../database_documents/did_document_epochid.json | 0 .../database_documents/did_document_subject.json | 0 .../database_documents/did_document_subject.md | 0 .../database_documents/did_validate_config.json | 0 .../ndi_document_element_epoch.json | 0 .../demo_schema1/database_schema/base.schema.json | 0 .../demo_schema1/database_schema/demoA.schema.json | 0 .../demo_schema1/database_schema/demoB.schema.json | 0 .../demo_schema1/database_schema/demoC.schema.json | 0 .../database_schema/demoFile.schema.json | 0 .../old/did_document_animalsubject_schema.json | 0 .../old/did_document_app_schema.json | 0 .../old/did_document_element_schema.json | 0 .../old/did_document_epochid_schema.json | 0 .../database_schema/old/did_document_schema.json | 0 .../old/did_document_subject_schema.json | 0 .../old/did_validate_config_schema.json | 0 87 files changed, 0 insertions(+), 0 deletions(-) rename {code => src/did}/+did/+common/PathConstants.m (100%) rename {code => src/did}/+did/+common/getCache.m (100%) rename {code => src/did}/+did/+datastructures/cell2str.m (100%) rename {code => src/did}/+did/+datastructures/celloritem.m (100%) rename {code => src/did}/+did/+datastructures/colvec.m (100%) rename {code => src/did}/+did/+datastructures/emptystruct.m (100%) rename {code => src/did}/+did/+datastructures/eqemp.m (100%) rename {code => src/did}/+did/+datastructures/eqlen.m (100%) rename {code => src/did}/+did/+datastructures/eqtot.m (100%) rename {code => src/did}/+did/+datastructures/equnique.m (100%) rename {code => src/did}/+did/+datastructures/fieldsearch.m (100%) rename {code => src/did}/+did/+datastructures/findclosest.m (100%) rename {code => src/did}/+did/+datastructures/isfullfield.m (100%) rename {code => src/did}/+did/+datastructures/jsonencodenan.m (100%) rename {code => src/did}/+did/+datastructures/sizeeq.m (100%) rename {code => src/did}/+did/+datastructures/structmerge.m (100%) rename {code => src/did}/+did/+db/struct_name_value_search.m (100%) rename {code => src/did}/+did/+db/tableCrossJoin.m (100%) rename {code => src/did}/+did/+file/binaryTable.m (100%) rename {code => src/did}/+did/+file/checkout_lock_file.m (100%) rename {code => src/did}/+did/+file/dumbjsondb.m (100%) rename {code => src/did}/+did/+file/fileCache.m (100%) rename {code => src/did}/+did/+file/fileid_value.m (100%) rename {code => src/did}/+did/+file/fileobj.m (100%) rename {code => src/did}/+did/+file/filesepconversion.m (100%) rename {code => src/did}/+did/+file/fullfilename.m (100%) rename {code => src/did}/+did/+file/isfilepathroot.m (100%) rename {code => src/did}/+did/+file/isurl.m (100%) rename {code => src/did}/+did/+file/mustBeValidMachineFormat.m (100%) rename {code => src/did}/+did/+file/mustBeValidPermission.m (100%) rename {code => src/did}/+did/+file/readlines.m (100%) rename {code => src/did}/+did/+file/readonly_fileobj.m (100%) rename {code => src/did}/+did/+file/release_lock_file.m (100%) rename {code => src/did}/+did/+file/str2text.m (100%) rename {code => src/did}/+did/+file/string2filestring.m (100%) rename {code => src/did}/+did/+file/text2cellstr.m (100%) rename {code => src/did}/+did/+fun/docs2graph.m (100%) rename {code => src/did}/+did/+fun/findalldependencies.m (100%) rename {code => src/did}/+did/+fun/finddocs_missing_dependencies.m (100%) rename {code => src/did}/+did/+fun/plotinteractivedocgraph.m (100%) rename {code => src/did}/+did/+implementations/binarydoc_matfid.m (100%) rename {code => src/did}/+did/+implementations/doc2sql.m (100%) rename {code => src/did}/+did/+implementations/matlabdumbjsondb.m (100%) rename {code => src/did}/+did/+implementations/sqldb.m (100%) rename {code => src/did}/+did/+implementations/sqlitedb.m (100%) rename {code => src/did}/+did/binarydoc.m (100%) rename {code => src/did}/+did/database.m (100%) rename {code => src/did}/+did/document.m (100%) rename {code => src/did}/+did/documentservice.m (100%) rename {code => src/did}/+did/filesep.m (100%) rename {code => src/did}/+did/ido.m (100%) rename {code => src/did}/+did/query.m (100%) rename {code => src/did}/+did/toolboxdir.m (100%) rename {code => src/did}/Contents.m (100%) rename {code => src/did}/example_schema/.gitkeep (100%) rename {code => src/did}/example_schema/demo_schema1/.gitkeep (100%) rename {code => src/did}/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary-info.txt (100%) rename {code => src/did}/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary.tsv.gz (100%) rename {code => src/did}/example_schema/demo_schema1/controlled_vocabulary/genbank_commonname.json (100%) rename {code => src/did}/example_schema/demo_schema1/controlled_vocabulary/scientific_name.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/base.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/base.md (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/demoA.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/demoB.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/demoC.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/demoFile.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_animalsubject.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_app.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_element.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_element_epoch.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_epochid.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_subject.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_document_subject.md (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/did_validate_config.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_documents/ndi_document_element_epoch.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/base.schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/demoA.schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/demoB.schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/demoC.schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/demoFile.schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_document_animalsubject_schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_document_app_schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_document_element_schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_document_epochid_schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_document_schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_document_subject_schema.json (100%) rename {code => src/did}/example_schema/demo_schema1/database_schema/old/did_validate_config_schema.json (100%) diff --git a/code/+did/+common/PathConstants.m b/src/did/+did/+common/PathConstants.m similarity index 100% rename from code/+did/+common/PathConstants.m rename to src/did/+did/+common/PathConstants.m diff --git a/code/+did/+common/getCache.m b/src/did/+did/+common/getCache.m similarity index 100% rename from code/+did/+common/getCache.m rename to src/did/+did/+common/getCache.m diff --git a/code/+did/+datastructures/cell2str.m b/src/did/+did/+datastructures/cell2str.m similarity index 100% rename from code/+did/+datastructures/cell2str.m rename to src/did/+did/+datastructures/cell2str.m diff --git a/code/+did/+datastructures/celloritem.m b/src/did/+did/+datastructures/celloritem.m similarity index 100% rename from code/+did/+datastructures/celloritem.m rename to src/did/+did/+datastructures/celloritem.m diff --git a/code/+did/+datastructures/colvec.m b/src/did/+did/+datastructures/colvec.m similarity index 100% rename from code/+did/+datastructures/colvec.m rename to src/did/+did/+datastructures/colvec.m diff --git a/code/+did/+datastructures/emptystruct.m b/src/did/+did/+datastructures/emptystruct.m similarity index 100% rename from code/+did/+datastructures/emptystruct.m rename to src/did/+did/+datastructures/emptystruct.m diff --git a/code/+did/+datastructures/eqemp.m b/src/did/+did/+datastructures/eqemp.m similarity index 100% rename from code/+did/+datastructures/eqemp.m rename to src/did/+did/+datastructures/eqemp.m diff --git a/code/+did/+datastructures/eqlen.m b/src/did/+did/+datastructures/eqlen.m similarity index 100% rename from code/+did/+datastructures/eqlen.m rename to src/did/+did/+datastructures/eqlen.m diff --git a/code/+did/+datastructures/eqtot.m b/src/did/+did/+datastructures/eqtot.m similarity index 100% rename from code/+did/+datastructures/eqtot.m rename to src/did/+did/+datastructures/eqtot.m diff --git a/code/+did/+datastructures/equnique.m b/src/did/+did/+datastructures/equnique.m similarity index 100% rename from code/+did/+datastructures/equnique.m rename to src/did/+did/+datastructures/equnique.m diff --git a/code/+did/+datastructures/fieldsearch.m b/src/did/+did/+datastructures/fieldsearch.m similarity index 100% rename from code/+did/+datastructures/fieldsearch.m rename to src/did/+did/+datastructures/fieldsearch.m diff --git a/code/+did/+datastructures/findclosest.m b/src/did/+did/+datastructures/findclosest.m similarity index 100% rename from code/+did/+datastructures/findclosest.m rename to src/did/+did/+datastructures/findclosest.m diff --git a/code/+did/+datastructures/isfullfield.m b/src/did/+did/+datastructures/isfullfield.m similarity index 100% rename from code/+did/+datastructures/isfullfield.m rename to src/did/+did/+datastructures/isfullfield.m diff --git a/code/+did/+datastructures/jsonencodenan.m b/src/did/+did/+datastructures/jsonencodenan.m similarity index 100% rename from code/+did/+datastructures/jsonencodenan.m rename to src/did/+did/+datastructures/jsonencodenan.m diff --git a/code/+did/+datastructures/sizeeq.m b/src/did/+did/+datastructures/sizeeq.m similarity index 100% rename from code/+did/+datastructures/sizeeq.m rename to src/did/+did/+datastructures/sizeeq.m diff --git a/code/+did/+datastructures/structmerge.m b/src/did/+did/+datastructures/structmerge.m similarity index 100% rename from code/+did/+datastructures/structmerge.m rename to src/did/+did/+datastructures/structmerge.m diff --git a/code/+did/+db/struct_name_value_search.m b/src/did/+did/+db/struct_name_value_search.m similarity index 100% rename from code/+did/+db/struct_name_value_search.m rename to src/did/+did/+db/struct_name_value_search.m diff --git a/code/+did/+db/tableCrossJoin.m b/src/did/+did/+db/tableCrossJoin.m similarity index 100% rename from code/+did/+db/tableCrossJoin.m rename to src/did/+did/+db/tableCrossJoin.m diff --git a/code/+did/+file/binaryTable.m b/src/did/+did/+file/binaryTable.m similarity index 100% rename from code/+did/+file/binaryTable.m rename to src/did/+did/+file/binaryTable.m diff --git a/code/+did/+file/checkout_lock_file.m b/src/did/+did/+file/checkout_lock_file.m similarity index 100% rename from code/+did/+file/checkout_lock_file.m rename to src/did/+did/+file/checkout_lock_file.m diff --git a/code/+did/+file/dumbjsondb.m b/src/did/+did/+file/dumbjsondb.m similarity index 100% rename from code/+did/+file/dumbjsondb.m rename to src/did/+did/+file/dumbjsondb.m diff --git a/code/+did/+file/fileCache.m b/src/did/+did/+file/fileCache.m similarity index 100% rename from code/+did/+file/fileCache.m rename to src/did/+did/+file/fileCache.m diff --git a/code/+did/+file/fileid_value.m b/src/did/+did/+file/fileid_value.m similarity index 100% rename from code/+did/+file/fileid_value.m rename to 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a/code/+did/+file/mustBeValidMachineFormat.m b/src/did/+did/+file/mustBeValidMachineFormat.m similarity index 100% rename from code/+did/+file/mustBeValidMachineFormat.m rename to src/did/+did/+file/mustBeValidMachineFormat.m diff --git a/code/+did/+file/mustBeValidPermission.m b/src/did/+did/+file/mustBeValidPermission.m similarity index 100% rename from code/+did/+file/mustBeValidPermission.m rename to src/did/+did/+file/mustBeValidPermission.m diff --git a/code/+did/+file/readlines.m b/src/did/+did/+file/readlines.m similarity index 100% rename from code/+did/+file/readlines.m rename to src/did/+did/+file/readlines.m diff --git a/code/+did/+file/readonly_fileobj.m b/src/did/+did/+file/readonly_fileobj.m similarity index 100% rename from code/+did/+file/readonly_fileobj.m rename to src/did/+did/+file/readonly_fileobj.m diff --git a/code/+did/+file/release_lock_file.m b/src/did/+did/+file/release_lock_file.m similarity index 100% rename from code/+did/+file/release_lock_file.m rename to src/did/+did/+file/release_lock_file.m diff --git a/code/+did/+file/str2text.m b/src/did/+did/+file/str2text.m similarity index 100% rename from code/+did/+file/str2text.m rename to src/did/+did/+file/str2text.m diff --git a/code/+did/+file/string2filestring.m b/src/did/+did/+file/string2filestring.m similarity index 100% rename from code/+did/+file/string2filestring.m rename to src/did/+did/+file/string2filestring.m diff --git a/code/+did/+file/text2cellstr.m b/src/did/+did/+file/text2cellstr.m similarity index 100% rename from code/+did/+file/text2cellstr.m rename to src/did/+did/+file/text2cellstr.m diff --git a/code/+did/+fun/docs2graph.m b/src/did/+did/+fun/docs2graph.m similarity index 100% rename from code/+did/+fun/docs2graph.m rename to src/did/+did/+fun/docs2graph.m diff --git a/code/+did/+fun/findalldependencies.m b/src/did/+did/+fun/findalldependencies.m similarity index 100% rename from code/+did/+fun/findalldependencies.m rename to 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a/code/+did/+implementations/matlabdumbjsondb.m b/src/did/+did/+implementations/matlabdumbjsondb.m similarity index 100% rename from code/+did/+implementations/matlabdumbjsondb.m rename to src/did/+did/+implementations/matlabdumbjsondb.m diff --git a/code/+did/+implementations/sqldb.m b/src/did/+did/+implementations/sqldb.m similarity index 100% rename from code/+did/+implementations/sqldb.m rename to src/did/+did/+implementations/sqldb.m diff --git a/code/+did/+implementations/sqlitedb.m b/src/did/+did/+implementations/sqlitedb.m similarity index 100% rename from code/+did/+implementations/sqlitedb.m rename to src/did/+did/+implementations/sqlitedb.m diff --git a/code/+did/binarydoc.m b/src/did/+did/binarydoc.m similarity index 100% rename from code/+did/binarydoc.m rename to src/did/+did/binarydoc.m diff --git a/code/+did/database.m b/src/did/+did/database.m similarity index 100% rename from code/+did/database.m rename to src/did/+did/database.m diff --git a/code/+did/document.m 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a/code/example_schema/.gitkeep b/src/did/example_schema/.gitkeep similarity index 100% rename from code/example_schema/.gitkeep rename to src/did/example_schema/.gitkeep diff --git a/code/example_schema/demo_schema1/.gitkeep b/src/did/example_schema/demo_schema1/.gitkeep similarity index 100% rename from code/example_schema/demo_schema1/.gitkeep rename to src/did/example_schema/demo_schema1/.gitkeep diff --git a/code/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary-info.txt b/src/did/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary-info.txt similarity index 100% rename from code/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary-info.txt rename to src/did/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary-info.txt diff --git a/code/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary.tsv.gz b/src/did/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary.tsv.gz similarity index 100% rename from code/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary.tsv.gz rename to src/did/example_schema/demo_schema1/controlled_vocabulary/GenBankControlledVocabulary.tsv.gz diff --git a/code/example_schema/demo_schema1/controlled_vocabulary/genbank_commonname.json b/src/did/example_schema/demo_schema1/controlled_vocabulary/genbank_commonname.json similarity index 100% rename from code/example_schema/demo_schema1/controlled_vocabulary/genbank_commonname.json rename to src/did/example_schema/demo_schema1/controlled_vocabulary/genbank_commonname.json diff --git a/code/example_schema/demo_schema1/controlled_vocabulary/scientific_name.json b/src/did/example_schema/demo_schema1/controlled_vocabulary/scientific_name.json similarity index 100% rename from code/example_schema/demo_schema1/controlled_vocabulary/scientific_name.json rename to src/did/example_schema/demo_schema1/controlled_vocabulary/scientific_name.json diff --git a/code/example_schema/demo_schema1/database_documents/base.json b/src/did/example_schema/demo_schema1/database_documents/base.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/base.json rename to src/did/example_schema/demo_schema1/database_documents/base.json diff --git a/code/example_schema/demo_schema1/database_documents/base.md b/src/did/example_schema/demo_schema1/database_documents/base.md similarity index 100% rename from code/example_schema/demo_schema1/database_documents/base.md rename to src/did/example_schema/demo_schema1/database_documents/base.md diff --git a/code/example_schema/demo_schema1/database_documents/demoA.json b/src/did/example_schema/demo_schema1/database_documents/demoA.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/demoA.json rename to src/did/example_schema/demo_schema1/database_documents/demoA.json diff --git a/code/example_schema/demo_schema1/database_documents/demoB.json b/src/did/example_schema/demo_schema1/database_documents/demoB.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/demoB.json rename to src/did/example_schema/demo_schema1/database_documents/demoB.json diff --git a/code/example_schema/demo_schema1/database_documents/demoC.json b/src/did/example_schema/demo_schema1/database_documents/demoC.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/demoC.json rename to src/did/example_schema/demo_schema1/database_documents/demoC.json diff --git a/code/example_schema/demo_schema1/database_documents/demoFile.json b/src/did/example_schema/demo_schema1/database_documents/demoFile.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/demoFile.json rename to src/did/example_schema/demo_schema1/database_documents/demoFile.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_animalsubject.json b/src/did/example_schema/demo_schema1/database_documents/did_document_animalsubject.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_animalsubject.json rename to src/did/example_schema/demo_schema1/database_documents/did_document_animalsubject.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_app.json b/src/did/example_schema/demo_schema1/database_documents/did_document_app.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_app.json rename to src/did/example_schema/demo_schema1/database_documents/did_document_app.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_element.json b/src/did/example_schema/demo_schema1/database_documents/did_document_element.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_element.json rename to src/did/example_schema/demo_schema1/database_documents/did_document_element.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_element_epoch.json b/src/did/example_schema/demo_schema1/database_documents/did_document_element_epoch.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_element_epoch.json rename to src/did/example_schema/demo_schema1/database_documents/did_document_element_epoch.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_epochid.json b/src/did/example_schema/demo_schema1/database_documents/did_document_epochid.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_epochid.json rename to src/did/example_schema/demo_schema1/database_documents/did_document_epochid.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_subject.json b/src/did/example_schema/demo_schema1/database_documents/did_document_subject.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_subject.json rename to src/did/example_schema/demo_schema1/database_documents/did_document_subject.json diff --git a/code/example_schema/demo_schema1/database_documents/did_document_subject.md b/src/did/example_schema/demo_schema1/database_documents/did_document_subject.md similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_document_subject.md rename to src/did/example_schema/demo_schema1/database_documents/did_document_subject.md diff --git a/code/example_schema/demo_schema1/database_documents/did_validate_config.json b/src/did/example_schema/demo_schema1/database_documents/did_validate_config.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/did_validate_config.json rename to src/did/example_schema/demo_schema1/database_documents/did_validate_config.json diff --git a/code/example_schema/demo_schema1/database_documents/ndi_document_element_epoch.json b/src/did/example_schema/demo_schema1/database_documents/ndi_document_element_epoch.json similarity index 100% rename from code/example_schema/demo_schema1/database_documents/ndi_document_element_epoch.json rename to src/did/example_schema/demo_schema1/database_documents/ndi_document_element_epoch.json diff --git a/code/example_schema/demo_schema1/database_schema/base.schema.json b/src/did/example_schema/demo_schema1/database_schema/base.schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/base.schema.json rename to src/did/example_schema/demo_schema1/database_schema/base.schema.json diff --git a/code/example_schema/demo_schema1/database_schema/demoA.schema.json b/src/did/example_schema/demo_schema1/database_schema/demoA.schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/demoA.schema.json rename to src/did/example_schema/demo_schema1/database_schema/demoA.schema.json diff --git a/code/example_schema/demo_schema1/database_schema/demoB.schema.json b/src/did/example_schema/demo_schema1/database_schema/demoB.schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/demoB.schema.json rename to src/did/example_schema/demo_schema1/database_schema/demoB.schema.json diff --git a/code/example_schema/demo_schema1/database_schema/demoC.schema.json b/src/did/example_schema/demo_schema1/database_schema/demoC.schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/demoC.schema.json rename to src/did/example_schema/demo_schema1/database_schema/demoC.schema.json diff --git a/code/example_schema/demo_schema1/database_schema/demoFile.schema.json b/src/did/example_schema/demo_schema1/database_schema/demoFile.schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/demoFile.schema.json rename to src/did/example_schema/demo_schema1/database_schema/demoFile.schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_document_animalsubject_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_document_animalsubject_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_document_animalsubject_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_document_animalsubject_schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_document_app_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_document_app_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_document_app_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_document_app_schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_document_element_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_document_element_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_document_element_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_document_element_schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_document_epochid_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_document_epochid_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_document_epochid_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_document_epochid_schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_document_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_document_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_document_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_document_schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_document_subject_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_document_subject_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_document_subject_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_document_subject_schema.json diff --git a/code/example_schema/demo_schema1/database_schema/old/did_validate_config_schema.json b/src/did/example_schema/demo_schema1/database_schema/old/did_validate_config_schema.json similarity index 100% rename from code/example_schema/demo_schema1/database_schema/old/did_validate_config_schema.json rename to src/did/example_schema/demo_schema1/database_schema/old/did_validate_config_schema.json From 24990098b922d336bb697c7cc75604ebcf29743f Mon Sep 17 00:00:00 2001 From: ehennestad Date: Tue, 1 Jul 2025 15:08:27 +0200 Subject: [PATCH 02/15] Update did_Init.m Changed "code" to "src/did" to reflect new folder organization --- did_Init.m | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/did_Init.m b/did_Init.m index f6f09cb..2dc80c2 100644 --- a/did_Init.m +++ b/did_Init.m @@ -10,4 +10,4 @@ rmpath(pathstoremove); % Add the code subdirectory to MATLAB's search path -pathstoadd = addpath(genpath(fullfile(mydidpath, 'code'))); +pathstoadd = addpath(genpath(fullfile(mydidpath, 'src', 'did'))); From 5686f7173bc45f29ecc651b60ce757fccdc6ba59 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Tue, 1 Jul 2025 15:16:16 +0200 Subject: [PATCH 03/15] Move "tests" from "tools" to root directory --- {tools/tests => tests}/+did/+test/+fixture/PathConstantFixture.m | 0 .../tests => tests}/+did/+test/+helper/+branch/add_branch_nodes.m | 0 .../+did/+test/+helper/+branch/delete_random_branch.m | 0 .../+did/+test/+helper/+branch/verify_branch_node_structure.m | 0 .../+did/+test/+helper/+branch/verify_branch_nodes.m | 0 .../tests => tests}/+did/+test/+helper/+documents/add_doc_tree.m | 0 .../tests => tests}/+did/+test/+helper/+documents/make_doc_tree.m | 0 .../+did/+test/+helper/+documents/make_doc_tree_invalid.m | 0 .../tests => tests}/+did/+test/+helper/+documents/rm_doc_tree.m | 0 .../+did/+test/+helper/+documents/verify_db_document_structure.m | 0 .../+did/+test/+helper/+utility/addrm_docs_to_branches.m | 0 .../tests => tests}/+did/+test/+helper/+utility/apply_didquery.m | 0 {tools/tests => tests}/+did/+test/+helper/+utility/get_demoType.m | 0 .../+did/+test/+helper/+utility/get_docs_expected.m | 0 {tools/tests => tests}/+did/+test/+helper/+utility/make_tree.m | 0 {tools/tests => tests}/+did/+test/+helper/+utility/name_tree.m | 0 .../+did/+test/+helper/+utility/number_to_alpha_label.m | 0 {tools/tests => tests}/+did/+test/_old/+file/binaryTable.m | 0 {tools/tests => tests}/+did/+test/_old/+file/fileCache.m | 0 {tools/tests => tests}/+did/+test/_old/parfor_test.m | 0 {tools/tests => tests}/+did/+test/_old/test_did_document.m | 0 {tools/tests => tests}/+did/+test/_old/test_did_sqlitedb.m | 0 {tools/tests => tests}/+did/+test/_old/test_did_validator.m | 0 .../tests => tests}/+did/+unittest/+abstract/TestModification.m | 0 {tools/tests => tests}/+did/+unittest/BranchTest.m | 0 {tools/tests => tests}/+did/+unittest/DatastructuresTest.m | 0 {tools/tests => tests}/+did/+unittest/DocumentAndBranchTest.m | 0 {tools/tests => tests}/+did/+unittest/DocumentTest.m | 0 {tools/tests => tests}/+did/+unittest/DocumentTestClearMex.m | 0 {tools/tests => tests}/+did/+unittest/SimpleBranchTest.m | 0 {tools/tests => tests}/+did/+unittest/TestDbQueries.m | 0 {tools/tests => tests}/+did/+unittest/TestFileDocument.m | 0 {tools/tests => tests}/+did/+unittest/TestInvalidModification.m | 0 {tools/tests => tests}/+did/+unittest/TestTableCrossJoin.m | 0 {tools/tests => tests}/+did/+unittest/TestValidModification.m | 0 35 files changed, 0 insertions(+), 0 deletions(-) rename {tools/tests => tests}/+did/+test/+fixture/PathConstantFixture.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+branch/add_branch_nodes.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+branch/delete_random_branch.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+branch/verify_branch_node_structure.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+branch/verify_branch_nodes.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+documents/add_doc_tree.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+documents/make_doc_tree.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+documents/make_doc_tree_invalid.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+documents/rm_doc_tree.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+documents/verify_db_document_structure.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/addrm_docs_to_branches.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/apply_didquery.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/get_demoType.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/get_docs_expected.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/make_tree.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/name_tree.m (100%) rename {tools/tests => tests}/+did/+test/+helper/+utility/number_to_alpha_label.m (100%) rename {tools/tests => tests}/+did/+test/_old/+file/binaryTable.m (100%) rename {tools/tests => tests}/+did/+test/_old/+file/fileCache.m (100%) rename {tools/tests => tests}/+did/+test/_old/parfor_test.m (100%) rename {tools/tests => tests}/+did/+test/_old/test_did_document.m (100%) rename {tools/tests => tests}/+did/+test/_old/test_did_sqlitedb.m (100%) rename {tools/tests => tests}/+did/+test/_old/test_did_validator.m (100%) rename {tools/tests => tests}/+did/+unittest/+abstract/TestModification.m (100%) rename {tools/tests => tests}/+did/+unittest/BranchTest.m (100%) rename {tools/tests => tests}/+did/+unittest/DatastructuresTest.m (100%) rename {tools/tests => tests}/+did/+unittest/DocumentAndBranchTest.m (100%) rename {tools/tests => tests}/+did/+unittest/DocumentTest.m (100%) rename {tools/tests => tests}/+did/+unittest/DocumentTestClearMex.m (100%) rename {tools/tests => tests}/+did/+unittest/SimpleBranchTest.m (100%) rename {tools/tests => tests}/+did/+unittest/TestDbQueries.m (100%) rename {tools/tests => tests}/+did/+unittest/TestFileDocument.m (100%) rename {tools/tests => tests}/+did/+unittest/TestInvalidModification.m (100%) rename {tools/tests => tests}/+did/+unittest/TestTableCrossJoin.m (100%) rename {tools/tests => tests}/+did/+unittest/TestValidModification.m (100%) diff --git a/tools/tests/+did/+test/+fixture/PathConstantFixture.m b/tests/+did/+test/+fixture/PathConstantFixture.m similarity index 100% rename from tools/tests/+did/+test/+fixture/PathConstantFixture.m rename to tests/+did/+test/+fixture/PathConstantFixture.m diff --git a/tools/tests/+did/+test/+helper/+branch/add_branch_nodes.m b/tests/+did/+test/+helper/+branch/add_branch_nodes.m similarity index 100% rename from tools/tests/+did/+test/+helper/+branch/add_branch_nodes.m rename to tests/+did/+test/+helper/+branch/add_branch_nodes.m diff --git a/tools/tests/+did/+test/+helper/+branch/delete_random_branch.m b/tests/+did/+test/+helper/+branch/delete_random_branch.m similarity index 100% rename from tools/tests/+did/+test/+helper/+branch/delete_random_branch.m rename to tests/+did/+test/+helper/+branch/delete_random_branch.m diff --git a/tools/tests/+did/+test/+helper/+branch/verify_branch_node_structure.m b/tests/+did/+test/+helper/+branch/verify_branch_node_structure.m similarity index 100% rename from tools/tests/+did/+test/+helper/+branch/verify_branch_node_structure.m rename to tests/+did/+test/+helper/+branch/verify_branch_node_structure.m diff --git a/tools/tests/+did/+test/+helper/+branch/verify_branch_nodes.m b/tests/+did/+test/+helper/+branch/verify_branch_nodes.m similarity index 100% rename from tools/tests/+did/+test/+helper/+branch/verify_branch_nodes.m rename to tests/+did/+test/+helper/+branch/verify_branch_nodes.m diff --git a/tools/tests/+did/+test/+helper/+documents/add_doc_tree.m b/tests/+did/+test/+helper/+documents/add_doc_tree.m similarity index 100% rename from tools/tests/+did/+test/+helper/+documents/add_doc_tree.m rename to tests/+did/+test/+helper/+documents/add_doc_tree.m diff --git a/tools/tests/+did/+test/+helper/+documents/make_doc_tree.m b/tests/+did/+test/+helper/+documents/make_doc_tree.m similarity index 100% rename from tools/tests/+did/+test/+helper/+documents/make_doc_tree.m rename to tests/+did/+test/+helper/+documents/make_doc_tree.m diff --git a/tools/tests/+did/+test/+helper/+documents/make_doc_tree_invalid.m b/tests/+did/+test/+helper/+documents/make_doc_tree_invalid.m similarity index 100% rename from tools/tests/+did/+test/+helper/+documents/make_doc_tree_invalid.m rename to tests/+did/+test/+helper/+documents/make_doc_tree_invalid.m diff --git a/tools/tests/+did/+test/+helper/+documents/rm_doc_tree.m b/tests/+did/+test/+helper/+documents/rm_doc_tree.m similarity index 100% rename from tools/tests/+did/+test/+helper/+documents/rm_doc_tree.m rename to tests/+did/+test/+helper/+documents/rm_doc_tree.m diff --git a/tools/tests/+did/+test/+helper/+documents/verify_db_document_structure.m b/tests/+did/+test/+helper/+documents/verify_db_document_structure.m similarity index 100% rename from tools/tests/+did/+test/+helper/+documents/verify_db_document_structure.m rename to tests/+did/+test/+helper/+documents/verify_db_document_structure.m diff --git a/tools/tests/+did/+test/+helper/+utility/addrm_docs_to_branches.m b/tests/+did/+test/+helper/+utility/addrm_docs_to_branches.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/addrm_docs_to_branches.m rename to tests/+did/+test/+helper/+utility/addrm_docs_to_branches.m diff --git a/tools/tests/+did/+test/+helper/+utility/apply_didquery.m b/tests/+did/+test/+helper/+utility/apply_didquery.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/apply_didquery.m rename to tests/+did/+test/+helper/+utility/apply_didquery.m diff --git a/tools/tests/+did/+test/+helper/+utility/get_demoType.m b/tests/+did/+test/+helper/+utility/get_demoType.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/get_demoType.m rename to tests/+did/+test/+helper/+utility/get_demoType.m diff --git a/tools/tests/+did/+test/+helper/+utility/get_docs_expected.m b/tests/+did/+test/+helper/+utility/get_docs_expected.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/get_docs_expected.m rename to tests/+did/+test/+helper/+utility/get_docs_expected.m diff --git a/tools/tests/+did/+test/+helper/+utility/make_tree.m b/tests/+did/+test/+helper/+utility/make_tree.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/make_tree.m rename to tests/+did/+test/+helper/+utility/make_tree.m diff --git a/tools/tests/+did/+test/+helper/+utility/name_tree.m b/tests/+did/+test/+helper/+utility/name_tree.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/name_tree.m rename to tests/+did/+test/+helper/+utility/name_tree.m diff --git a/tools/tests/+did/+test/+helper/+utility/number_to_alpha_label.m b/tests/+did/+test/+helper/+utility/number_to_alpha_label.m similarity index 100% rename from tools/tests/+did/+test/+helper/+utility/number_to_alpha_label.m rename to tests/+did/+test/+helper/+utility/number_to_alpha_label.m diff --git a/tools/tests/+did/+test/_old/+file/binaryTable.m b/tests/+did/+test/_old/+file/binaryTable.m similarity index 100% rename from tools/tests/+did/+test/_old/+file/binaryTable.m rename to tests/+did/+test/_old/+file/binaryTable.m diff --git a/tools/tests/+did/+test/_old/+file/fileCache.m b/tests/+did/+test/_old/+file/fileCache.m similarity index 100% rename from tools/tests/+did/+test/_old/+file/fileCache.m rename to tests/+did/+test/_old/+file/fileCache.m diff --git a/tools/tests/+did/+test/_old/parfor_test.m b/tests/+did/+test/_old/parfor_test.m similarity index 100% rename from tools/tests/+did/+test/_old/parfor_test.m rename to tests/+did/+test/_old/parfor_test.m diff --git a/tools/tests/+did/+test/_old/test_did_document.m b/tests/+did/+test/_old/test_did_document.m similarity index 100% rename from tools/tests/+did/+test/_old/test_did_document.m rename to tests/+did/+test/_old/test_did_document.m diff --git a/tools/tests/+did/+test/_old/test_did_sqlitedb.m b/tests/+did/+test/_old/test_did_sqlitedb.m similarity index 100% rename from tools/tests/+did/+test/_old/test_did_sqlitedb.m rename to tests/+did/+test/_old/test_did_sqlitedb.m diff --git a/tools/tests/+did/+test/_old/test_did_validator.m b/tests/+did/+test/_old/test_did_validator.m similarity index 100% rename from tools/tests/+did/+test/_old/test_did_validator.m rename to tests/+did/+test/_old/test_did_validator.m diff --git a/tools/tests/+did/+unittest/+abstract/TestModification.m b/tests/+did/+unittest/+abstract/TestModification.m similarity index 100% rename from tools/tests/+did/+unittest/+abstract/TestModification.m rename to tests/+did/+unittest/+abstract/TestModification.m diff --git a/tools/tests/+did/+unittest/BranchTest.m b/tests/+did/+unittest/BranchTest.m similarity index 100% rename from tools/tests/+did/+unittest/BranchTest.m rename to tests/+did/+unittest/BranchTest.m diff --git a/tools/tests/+did/+unittest/DatastructuresTest.m b/tests/+did/+unittest/DatastructuresTest.m similarity index 100% rename from tools/tests/+did/+unittest/DatastructuresTest.m rename to tests/+did/+unittest/DatastructuresTest.m diff --git a/tools/tests/+did/+unittest/DocumentAndBranchTest.m b/tests/+did/+unittest/DocumentAndBranchTest.m similarity index 100% rename from tools/tests/+did/+unittest/DocumentAndBranchTest.m rename to tests/+did/+unittest/DocumentAndBranchTest.m diff --git a/tools/tests/+did/+unittest/DocumentTest.m b/tests/+did/+unittest/DocumentTest.m similarity index 100% rename from tools/tests/+did/+unittest/DocumentTest.m rename to tests/+did/+unittest/DocumentTest.m diff --git a/tools/tests/+did/+unittest/DocumentTestClearMex.m b/tests/+did/+unittest/DocumentTestClearMex.m similarity index 100% rename from tools/tests/+did/+unittest/DocumentTestClearMex.m rename to tests/+did/+unittest/DocumentTestClearMex.m diff --git a/tools/tests/+did/+unittest/SimpleBranchTest.m b/tests/+did/+unittest/SimpleBranchTest.m similarity index 100% rename from tools/tests/+did/+unittest/SimpleBranchTest.m rename to tests/+did/+unittest/SimpleBranchTest.m diff --git a/tools/tests/+did/+unittest/TestDbQueries.m b/tests/+did/+unittest/TestDbQueries.m similarity index 100% rename from tools/tests/+did/+unittest/TestDbQueries.m rename to tests/+did/+unittest/TestDbQueries.m diff --git a/tools/tests/+did/+unittest/TestFileDocument.m b/tests/+did/+unittest/TestFileDocument.m similarity index 100% rename from tools/tests/+did/+unittest/TestFileDocument.m rename to tests/+did/+unittest/TestFileDocument.m diff --git a/tools/tests/+did/+unittest/TestInvalidModification.m b/tests/+did/+unittest/TestInvalidModification.m similarity index 100% rename from tools/tests/+did/+unittest/TestInvalidModification.m rename to tests/+did/+unittest/TestInvalidModification.m diff --git a/tools/tests/+did/+unittest/TestTableCrossJoin.m b/tests/+did/+unittest/TestTableCrossJoin.m similarity index 100% rename from tools/tests/+did/+unittest/TestTableCrossJoin.m rename to tests/+did/+unittest/TestTableCrossJoin.m diff --git a/tools/tests/+did/+unittest/TestValidModification.m b/tests/+did/+unittest/TestValidModification.m similarity index 100% rename from tools/tests/+did/+unittest/TestValidModification.m rename to tests/+did/+unittest/TestValidModification.m From 7e6f36a57f969a70343caa3341ae27c9af4fffc2 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Tue, 1 Jul 2025 15:21:15 +0200 Subject: [PATCH 04/15] Update test workflow to use reusable workflow from matbox-actions --- .github/workflows/run_tests.yml | 32 -------------------------------- .github/workflows/test-code.yml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 30 insertions(+), 32 deletions(-) delete mode 100644 .github/workflows/run_tests.yml create mode 100644 .github/workflows/test-code.yml diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml deleted file mode 100644 index f41d6b4..0000000 --- a/.github/workflows/run_tests.yml +++ /dev/null @@ -1,32 +0,0 @@ -name: Run tests - -on: - # Triggers the workflow on push or pull request events for the "main" branch - push: - branches: [ "main" ] - paths-ignore: - - '*.md' - - '.github/workflows/**' - pull_request: - branches: [ "main" ] - paths-ignore: - - '*.md' - - '.github/workflows/**' - - # Allows for manually running this workflow from the Actions tab - workflow_dispatch: - -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true - -jobs: - call-reusable-test-toolbox-workflow: - name: Test and analyse code - uses: ehennestad/matbox/.github/workflows/reusable_test_workflow.yml@v0.9 - with: - matlab_release: R2021b - matlab_use_cache: true - matlab_products: Statistics_and_Machine_Learning_Toolbox - secrets: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/test-code.yml b/.github/workflows/test-code.yml new file mode 100644 index 0000000..7826dd9 --- /dev/null +++ b/.github/workflows/test-code.yml @@ -0,0 +1,30 @@ +name: Test code + +on: + push: + branches: main + paths-ignore: + - '*.md' + - '.github/**' + + pull_request: + branches: main + paths-ignore: + - '*.md' + - '.github/**' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + test-code: + if: github.run_number > 1 + name: Analyse and test code + uses: ehennestad/matbox-actions/.github/workflows/test-code-workflow.yml@v1 + with: + matlab_release: R2021b + matlab_use_cache: true + matlab_products: Statistics_and_Machine_Learning_Toolbox + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} From 9f7d8e0bf1284034280f6ad6d29cba8790688eda Mon Sep 17 00:00:00 2001 From: ehennestad Date: Tue, 1 Jul 2025 15:28:14 +0200 Subject: [PATCH 05/15] Update prepare-release.yml --- .github/workflows/prepare-release.yml | 20 ++++---------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/.github/workflows/prepare-release.yml b/.github/workflows/prepare-release.yml index f433fbc..8a847bf 100644 --- a/.github/workflows/prepare-release.yml +++ b/.github/workflows/prepare-release.yml @@ -12,24 +12,12 @@ on: type: string jobs: - reuse-workflow-release: + prepare-release: name: Prepare toolbox release - uses: ehennestad/matbox/.github/workflows/reusable_release_workflow.yml@make-release-workflow-reusable + uses: ehennestad/matbox-actions/.github/workflows/prepare-release-workflow.yml@v1 with: - # Do not change - version: ${{ inputs.version }} - - # Do not change - ref_name: ${{ github.ref_name }} - - # Path to directory containing source code. This directory will be packaged - # into the toolbox. Important: This should not be a namespace directory - code_directory: code - - # Path to directory containing tools and MLToolboxInfo.json. Used for finding - # unit tests, running customized MatBox tasks, and determining toolbox metadata - tools_directory: tools - + version: ${{ inputs.version }} # Do not change + ref_name: ${{ github.ref_name }} # Do not change matlab_products: Statistics_and_Machine_Learning_Toolbox secrets: From c44a598882db9ee6a1bc9fbc16e7708c880cd947 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Tue, 1 Jul 2025 15:29:30 +0200 Subject: [PATCH 06/15] Update test-code.yml --- .github/workflows/test-code.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test-code.yml b/.github/workflows/test-code.yml index 7826dd9..2eb5556 100644 --- a/.github/workflows/test-code.yml +++ b/.github/workflows/test-code.yml @@ -19,7 +19,6 @@ concurrency: jobs: test-code: - if: github.run_number > 1 name: Analyse and test code uses: ehennestad/matbox-actions/.github/workflows/test-code-workflow.yml@v1 with: From 2c3b804cbcf57846dd808f7ac63d6ec55e6fddfe Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 4 Jul 2025 11:08:10 +0200 Subject: [PATCH 07/15] Update testToolbox.m Need to specify tests folder --- tools/tasks/testToolbox.m | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tools/tasks/testToolbox.m b/tools/tasks/testToolbox.m index d7a359b..8dad761 100644 --- a/tools/tasks/testToolbox.m +++ b/tools/tasks/testToolbox.m @@ -1,5 +1,8 @@ function testToolbox(varargin) projectRootDirectory = didtools.projectdir(); matbox.installRequirements(projectRootDirectory) - matbox.tasks.testToolbox(projectRootDirectory, "CreateBadge", false, varargin{:}) + matbox.tasks.testToolbox(projectRootDirectory, ... + "CreateBadge", false, ... + "TestsFolderName", 'tests', ... + varargin{:}) end From 69cafb466e6b893e834d6f8df25b5c841c7b0484 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 4 Jul 2025 18:26:52 +0200 Subject: [PATCH 08/15] Update testToolbox.m --- tools/tasks/testToolbox.m | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/tasks/testToolbox.m b/tools/tasks/testToolbox.m index 8dad761..ad1dc34 100644 --- a/tools/tasks/testToolbox.m +++ b/tools/tasks/testToolbox.m @@ -3,6 +3,7 @@ function testToolbox(varargin) matbox.installRequirements(projectRootDirectory) matbox.tasks.testToolbox(projectRootDirectory, ... "CreateBadge", false, ... + "SourceFolderName", 'src', ... "TestsFolderName", 'tests', ... varargin{:}) end From 0aab8aa0bc6dde83d396f6c5a56e4fd6ea4a4059 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 4 Jul 2025 19:57:25 +0200 Subject: [PATCH 09/15] Update testToolbox.m --- tools/tasks/testToolbox.m | 1 - 1 file changed, 1 deletion(-) diff --git a/tools/tasks/testToolbox.m b/tools/tasks/testToolbox.m index ad1dc34..0cf9245 100644 --- a/tools/tasks/testToolbox.m +++ b/tools/tasks/testToolbox.m @@ -2,7 +2,6 @@ function testToolbox(varargin) projectRootDirectory = didtools.projectdir(); matbox.installRequirements(projectRootDirectory) matbox.tasks.testToolbox(projectRootDirectory, ... - "CreateBadge", false, ... "SourceFolderName", 'src', ... "TestsFolderName", 'tests', ... varargin{:}) From 824a416be85e4a628b2105bad32cf8916ce80e1f Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 25 Jul 2025 12:04:26 +0200 Subject: [PATCH 10/15] Delete badges from reports directory --- docs/reports/badge/code_issues.json | 1 - docs/reports/badge/tests.json | 1 - 2 files changed, 2 deletions(-) delete mode 100644 docs/reports/badge/code_issues.json delete mode 100644 docs/reports/badge/tests.json diff --git a/docs/reports/badge/code_issues.json b/docs/reports/badge/code_issues.json deleted file mode 100644 index 0341ffe..0000000 --- a/docs/reports/badge/code_issues.json +++ /dev/null @@ -1 +0,0 @@ -{"schemaVersion":1,"label":"code issues","message":"1664","color":"green"} \ No newline at end of file diff --git a/docs/reports/badge/tests.json b/docs/reports/badge/tests.json deleted file mode 100644 index c26e77d..0000000 --- a/docs/reports/badge/tests.json +++ /dev/null @@ -1 +0,0 @@ -{"schemaVersion":1,"label":"tests","message":"81 passed","color":"green"} \ No newline at end of file From a8086a293cc2a619b68949c04d8d2707e7cb959e Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 25 Jul 2025 12:40:45 +0200 Subject: [PATCH 11/15] Fix source directory in prepare-release workflow --- .github/workflows/prepare-release.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/prepare-release.yml b/.github/workflows/prepare-release.yml index 8a847bf..0628a4f 100644 --- a/.github/workflows/prepare-release.yml +++ b/.github/workflows/prepare-release.yml @@ -19,6 +19,7 @@ jobs: version: ${{ inputs.version }} # Do not change ref_name: ${{ github.ref_name }} # Do not change matlab_products: Statistics_and_Machine_Learning_Toolbox + source_directory: src secrets: # SSH deploy key for pushing to protected branches. Required for creating From 06fe3692097d2b039a40195d6352a22172471a25 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 25 Jul 2025 13:01:26 +0200 Subject: [PATCH 12/15] Delete packageToolbox.m --- tools/tasks/packageToolbox.m | 9 --------- 1 file changed, 9 deletions(-) delete mode 100644 tools/tasks/packageToolbox.m diff --git a/tools/tasks/packageToolbox.m b/tools/tasks/packageToolbox.m deleted file mode 100644 index 4202452..0000000 --- a/tools/tasks/packageToolbox.m +++ /dev/null @@ -1,9 +0,0 @@ -function [newVersion, mltbxPath] = packageToolbox(releaseType, versionString) - arguments - releaseType {mustBeTextScalar,mustBeMember(releaseType,["build","major","minor","patch","specific"])} = "build" - versionString {mustBeTextScalar} = ""; - end - projectRootDirectory = didtools.projectdir(); - [newVersion, mltbxPath] = matbox.tasks.packageToolbox(projectRootDirectory, ... - releaseType, versionString, "ToolboxShortName", "DID_MATLAB"); -end From 02d336ddd8b6bc5fe67552508c7847a07fd0b762 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 25 Jul 2025 13:03:41 +0200 Subject: [PATCH 13/15] Update testToolbox.m --- tools/tasks/testToolbox.m | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/tasks/testToolbox.m b/tools/tasks/testToolbox.m index 0cf9245..787d223 100644 --- a/tools/tasks/testToolbox.m +++ b/tools/tasks/testToolbox.m @@ -4,5 +4,6 @@ function testToolbox(varargin) matbox.tasks.testToolbox(projectRootDirectory, ... "SourceFolderName", 'src', ... "TestsFolderName", 'tests', ... + "CreateBadge", false, ... varargin{:}) end From 7784d371e797433ac6f8af5a456bc8d9451875d1 Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 25 Jul 2025 13:47:32 +0200 Subject: [PATCH 14/15] Update testToolbox.m --- tools/tasks/testToolbox.m | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tools/tasks/testToolbox.m b/tools/tasks/testToolbox.m index 787d223..980a56d 100644 --- a/tools/tasks/testToolbox.m +++ b/tools/tasks/testToolbox.m @@ -2,8 +2,9 @@ function testToolbox(varargin) projectRootDirectory = didtools.projectdir(); matbox.installRequirements(projectRootDirectory) matbox.tasks.testToolbox(projectRootDirectory, ... + varargin{:}, ... "SourceFolderName", 'src', ... "TestsFolderName", 'tests', ... - "CreateBadge", false, ... - varargin{:}) + "CreateBadge", false ... + ) end From 46516e5c4d3f8f9b50ab148720d7020eeb06a0dd Mon Sep 17 00:00:00 2001 From: ehennestad Date: Fri, 25 Jul 2025 17:03:31 +0200 Subject: [PATCH 15/15] Removed unused files --- .github/badges/v0.7.9/tested_with.json | 1 - .github/workflows/create_release.yml | 148 ------------------------- 2 files changed, 149 deletions(-) delete mode 100644 .github/badges/v0.7.9/tested_with.json delete mode 100644 .github/workflows/create_release.yml diff --git a/.github/badges/v0.7.9/tested_with.json b/.github/badges/v0.7.9/tested_with.json deleted file mode 100644 index 616bddd..0000000 --- a/.github/badges/v0.7.9/tested_with.json +++ /dev/null @@ -1 +0,0 @@ -{"schemaVersion":1,"label":"tested with","message":"R2024b | R2024a | R2023b | R2023a | R2022b | R2022a | R2021b | R2021a | R2020b","color":"green"} \ No newline at end of file diff --git a/.github/workflows/create_release.yml b/.github/workflows/create_release.yml deleted file mode 100644 index 49d4c66..0000000 --- a/.github/workflows/create_release.yml +++ /dev/null @@ -1,148 +0,0 @@ -# Test the toolbox across all supported releases of MATLAB, package toolbox, create release -# Adapted from: https://github.com/mathworks/climatedatastore/blob/main/.github/workflows/release.yml - -name: Create new release - -# Run workflow when a tag is created -on: - push: - tags: - - 'v*' - -jobs: - # This workflow contains: - # 1. a matrixed test job run across a bunch of releases of MATLAB - # 2. a reporting job that summarizes the tests, and updates release badge - test: - strategy: - fail-fast: false - matrix: - MATLABVersion: [R2020b, R2021a, R2021b, R2022a, R2022b, R2023a, R2023b, R2024a, R2024b] - # The type of runner that the job will run on - runs-on: ubuntu-latest - - steps: - # Checks-out the repository under $GITHUB_WORKSPACE, so the job can access it - - uses: actions/checkout@v4 - - - name: Set up MATLAB - uses: matlab-actions/setup-matlab@v2 - with: - release: ${{ matrix.MATLABVersion }} - products: Statistics_and_Machine_Learning_Toolbox - - # Runs all tests in the project. Put results in a version specific subdirectory - - name: Run tests - uses: matlab-actions/run-command@v2 - with: - command: addpath(genpath("tools")), testToolbox('ReportSubdirectory',"${{ matrix.MATLABVersion }}") - - # Upload code coverage information to Codecov - - name: Upload code coverage report to Codecov - uses: codecov/codecov-action@v4 - if: always() - with: - token: ${{ secrets.CODECOV_TOKEN }} - files: docs/reports/codecoverage.xml - env_vars: ${{ matrix.MATLABVersion }} - - # Save the contents of the report directory from each release into an artifact. - - name: Save Report Directory - uses: actions/upload-artifact@v4 - if: always() - with: - name: reports-${{ matrix.MATLABVersion }} - path: docs/reports - - # Report on what releases tested successfully. - # Generate a draft release based on the tag - # Recreate the tag with the final version of JSON files - release: - needs: test - if: always() - runs-on: ubuntu-latest - - steps: - # Todo: change ref to: refs/heads/main - - uses: actions/checkout@v4 - with: - ref: main_v080_refactor - - - name: Set up MATLAB - uses: matlab-actions/setup-matlab@v2 - - # Copy all the reports down into the container - - uses: actions/download-artifact@v4 - with: - pattern: reports-* - path: docs/reports - merge-multiple: true - - # Generate the JSON for the releases tested badge - - name: Generate tested with badge - uses: matlab-actions/run-command@v2 - with: - command: addpath(genpath("tools")), createTestedWithBadgeforToolbox("${{ github.ref_name }}") - - # Publish test results from all the releases - - name: Publish Test Results - uses: EnricoMi/publish-unit-test-result-action@v2 - if: always() - with: - junit_files: "docs/reports/*/test-results.xml" - - # Package the MLTBX - - name: Package Toolbox - uses: matlab-actions/run-command@v2 - with: - command: addpath(genpath("tools")), packageToolbox("specific","${{ github.ref_name }}") - - # Define the versionNumber using underscores, as this is used in the MLTBX - - name: Set version number - id: set_version - run: | - versionNumber=$(echo "${{ github.ref_name }}" | sed 's/\./_/g') - echo "versionNumber=$versionNumber" >> $GITHUB_ENV - - - # Save the MLTBX. - - name: Save Packaged Toolbox - uses: actions/upload-artifact@v4 - with: - name: DID_MATLAB_${{ env.versionNumber }}.mltbx - path: releases/DID_MATLAB_${{ env.versionNumber }}.mltbx - - # Commit the JSON for the MATLAB releases badge and ToolboxPackaging.prj - - name: commit changed files - continue-on-error: true - run: | - git config user.name "${{ github.workflow }} by ${{ github.actor }}" - git config user.email "<>" - git status - git add code/Contents.m - git add .github/badges/${{ github.ref_name }}/tested_with.json - git commit -m "Final checkins for release ${{ github.ref_name }}" - git fetch - git push - - # Retag the repo so that the updated files are included in the release tag - - name: update tag - if: always() - continue-on-error: true - run: | - git config user.name "${{ github.workflow }} by ${{ github.actor }}" - git config user.email "<>" - git tag -d "${{ github.ref_name }}" - git push --delete origin ${{ github.ref_name }} - git tag -m "Release ${{ github.ref_name }}" ${{ github.ref_name }} - git push --tag - - # Create the release - - name: Create GitHub Release - uses: ncipollo/release-action@v1 - with: - draft: true - artifacts: "releases/DID_MATLAB_${{ env.versionNumber }}.mltbx" - generateReleaseNotes: true - body: "![MATLAB Versions Tested](https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2F${{ github.repository }}%2Fmain_v080_refactor%2F.github%2Fbadges%2F${{ github.ref_name }}%2Ftested_with.json)" -