diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 8cdcf209..e96e5fb1 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -30,8 +30,8 @@ A more detailed explanation or comments can be left in the commit description. * Once the newer version for any external software (BLAST+, DIAMOND, HMMER) is available, identify the newest version which is simultaneously available for macOS, Unix/Linux and Windows * Create a separate branch from the `devel` branch and name it e.g. `chore/updateBinaries` * Commit the changes for each program and operating system separately, e.g. `chore: update HMMER (Win) to 3.2.1` -* As soon as all binaries for particular program are updated through commits, update the corresponding license file, if available and place it in e.g. `software/blast+` directory. -* Update the version number in `RAVENdir/software/version.txt` file. +* As soon as all binaries for particular program are updated through commits, update the corresponding license file, if available and place it in e.g. `src/external/blast+` directory. +* Update the version number in `RAVENdir/src/external/version.txt` file. * Do some testing to ensure that the new binaries are working correctly. Upon successful tests, create a Pull Request to the `devel` branch. ### Pull Requests diff --git a/.github/scripts/assemble_offline_software.py b/.github/scripts/assemble_offline_software.py index 0d0384d1..4193fcf2 100644 --- a/.github/scripts/assemble_offline_software.py +++ b/.github/scripts/assemble_offline_software.py @@ -1,8 +1,8 @@ #!/usr/bin/env python -"""Populate RAVEN's software/ with every platform's external binaries. +"""Populate RAVEN's src/external/ with every platform's external binaries. Downloads the per-platform binary ZIPs from raven-data and lays them out under -``/software//`` using RAVEN's suffix scheme — bare name = Linux, +``/src/external//`` using RAVEN's suffix scheme — bare name = Linux, ``.mac`` = macOS, ``.exe`` = Windows. With all platforms present in one tree, the whole RAVEN checkout can be zipped into a single **OS-independent** offline distribution (see the release-bundle workflow). @@ -50,7 +50,7 @@ def _extract(zip_bytes: bytes, dest: Path, rename: dict[str, str]) -> None: def assemble(raven: Path) -> None: - soft = raven / "software" + soft = raven / "src" / "external" for subdir, bundle, vmap, exes in CLI_TOOLS: dest = soft / subdir for plat, suffix in PLATFORMS.items(): diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 3c7183aa..c280ae19 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -1,8 +1,8 @@ name: Documentation -# Regenerate doc/ from the function help texts and commit the result. +# Regenerate docs/html/ from the function help texts and commit the result. # -# doc/ is generated output that is nevertheless tracked, so it drifts as soon +# docs/html/ is generated output that is nevertheless tracked, so it drifts as soon # as anyone edits a docstring or adds/removes a function without remembering to # run updateDocumentation. Running it here instead means nobody has to. # @@ -34,7 +34,7 @@ concurrency: jobs: update-documentation: - name: Regenerate doc/ + name: Regenerate docs/html/ runs-on: ubuntu-latest timeout-minutes: 20 @@ -71,11 +71,11 @@ jobs: - name: Commit regenerated documentation run: | - # updateDocumentation deletes and rebuilds doc/, so stage first: + # updateDocumentation deletes and rebuilds docs/html/, so stage first: # a plain "git diff" would not see added or removed pages. - git add -A doc - if git diff --cached --quiet -- doc; then - echo "doc/ is already up to date." + git add -A docs/html + if git diff --cached --quiet -- docs/html; then + echo "docs/html/ is already up to date." exit 0 fi git config user.name "github-actions[bot]" diff --git a/.github/workflows/release-bundle.yml b/.github/workflows/release-bundle.yml index fdcf3a5c..418a379f 100644 --- a/.github/workflows/release-bundle.yml +++ b/.github/workflows/release-bundle.yml @@ -1,7 +1,7 @@ name: Offline binary bundle # Build the OS-independent offline RAVEN distribution: the full repo with -# software/ populated with every platform's external binaries, so an air-gapped +# src/external/ populated with every platform's external binaries, so an air-gapped # user downloads one ZIP and runs RAVEN on any OS without fetching anything. # Attached automatically to each published release; also runnable on demand # against an existing tag. @@ -37,7 +37,7 @@ jobs: with: python-version: '3.12' - - name: Populate software/ with every platform's binaries + - name: Populate src/external/ with every platform's binaries run: python .github/scripts/assemble_offline_software.py - name: Build RAVEN--full.zip diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index bef69b5b..8d4001f7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -46,7 +46,7 @@ jobs: if ~isfolder(resultsDir); mkdir(resultsDir); end import matlab.unittest.TestRunner import matlab.unittest.plugins.XMLPlugin - cd(fullfile('testing', 'function_tests')); + cd(fullfile('tests', 'function_tests')); files = string({dir('*.m').name}); files(files == "RavenTestCase.m") = []; files(files == "tBinaries.m") = []; % run separately by the binary-tests job (Linux + macOS) diff --git a/.gitignore b/.gitignore index 956c5b58..d102dd98 100644 --- a/.gitignore +++ b/.gitignore @@ -38,15 +38,15 @@ Temporary Items # first use (see buildGlobalKEGGModel); none of them belong in the repo. The # glob (rather than a version-pinned name) keeps this working across a # KEGG_VERSION.md bump without needing its own update. -reconstruction/kegg/keggModel.mat -reconstruction/kegg/kegg*_core.tar.gz -reconstruction/kegg/kegg*_core/ +src/reconstruction/kegg/keggModel.mat +src/reconstruction/kegg/kegg*_core.tar.gz +src/reconstruction/kegg/kegg*_core/ #software -software/scip/ -software/blast+/ -software/diamond/ -software/hmmer/ -software/WoLFPSORT/ +src/external/scip/ +src/external/blast+/ +src/external/diamond/ +src/external/hmmer/ +src/external/WoLFPSORT/ !.keep #doc diff --git a/README.md b/README.md index fe1385cf..52147e85 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ - + [![Current release](https://img.shields.io/github/release/CompMetEng/RAVEN/all.svg)](https://github.com/CompMetEng/RAVEN/releases/) [![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3ACompMetEng%2FRAVEN&label=GitHub%20Discussions)](https://github.com/CompMetEng/RAVEN/discussions) diff --git a/_config.yml b/_config.yml index 0add0be6..13d66dce 100644 --- a/_config.yml +++ b/_config.yml @@ -1,4 +1,4 @@ theme: jekyll-theme-minimal -logo: RAVEN.png +logo: img/RAVEN.png show_downloads: true -keep_files: ["doc/"] +keep_files: ["docs/html/"] diff --git a/checkRaven.m b/checkRaven.m index e65111b8..3b471652 100755 --- a/checkRaven.m +++ b/checkRaven.m @@ -166,7 +166,7 @@ fprintf(myStr(' > Checking libSBML version',40)) model = []; try - evalc('model = importModel(fullfile(ravenDir,''tutorial'',''empty.xml''));'); + evalc('model = importModel(fullfile(ravenDir,''tutorials'',''data'',''empty.xml''));'); try libSBMLver=OutputSBML_RAVEN; % Only works in libSBML 5.17.0+ fprintf([libSBMLver.libSBML_version_string '\n']); @@ -193,7 +193,7 @@ end reportCheck(' > Export SBML format', @() exportModel(model, fullfile(tmpDir,'model.xml'))); -reportCheck(' > Import YAML format', @() readYAMLmodel(fullfile(ravenDir,'tutorial','empty.yml'))); +reportCheck(' > Import YAML format', @() readYAMLmodel(fullfile(ravenDir,'tutorials','data','empty.yml'))); reportCheck(' > Export YAML format', @() writeYAMLmodel(model, fullfile(tmpDir,'model.yml'))); reportCheck(' > Export Excel format', @() exportToExcelFormat(model, fullfile(tmpDir,'model.xlsx'))); @@ -300,7 +300,7 @@ function testBinary(ravenDir, tool, binName, versionArg) else binEnd = ''; end -cmd = ['"' fullfile(ravenDir,'software',tool,[binName binEnd]) '" ' versionArg]; +cmd = ['"' fullfile(ravenDir,'src','external',tool,[binName binEnd]) '" ' versionArg]; [status,~] = system(cmd); if status ~= 0 error('%s did not execute (exit status %d)', binName, status); @@ -339,7 +339,7 @@ function testBinary(ravenDir, tool, binName, versionArg) status = 0; % No need to run on Windows return; end -binDir = fullfile(ravenDir,'software'); +binDir = 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diff --git a/conversion/COBRA_structure_fields.csv b/src/conversion/COBRA_structure_fields.csv similarity index 100% rename from conversion/COBRA_structure_fields.csv rename to src/conversion/COBRA_structure_fields.csv diff --git a/conversion/addIdentifierPrefix.m b/src/conversion/addIdentifierPrefix.m similarity index 100% rename from conversion/addIdentifierPrefix.m rename to src/conversion/addIdentifierPrefix.m diff --git a/conversion/cobraNamespaces.csv b/src/conversion/cobraNamespaces.csv similarity index 100% rename from conversion/cobraNamespaces.csv rename to src/conversion/cobraNamespaces.csv diff --git a/conversion/orderRavenFields.csv b/src/conversion/orderRavenFields.csv similarity index 100% rename from conversion/orderRavenFields.csv rename to src/conversion/orderRavenFields.csv diff --git a/conversion/ravenCobraWrapper.m b/src/conversion/ravenCobraWrapper.m similarity index 98% rename from conversion/ravenCobraWrapper.m rename to src/conversion/ravenCobraWrapper.m index 652ad187..f82048df 100755 --- a/conversion/ravenCobraWrapper.m +++ b/src/conversion/ravenCobraWrapper.m @@ -45,7 +45,7 @@ ravenPath=findRAVENroot(); % Load COBRA field information -fid = fopen(fullfile(ravenPath,'conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv +fid = fopen(fullfile(ravenPath,'src','conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv fieldFile = textscan(fid,repmat('%s',1,15),'Delimiter','\t','HeaderLines',1); dbFields = ~cellfun(@isempty,fieldFile{5}); % Only keep fields with database annotations that should be translated to xxxMiriams dbFields = dbFields & ~contains(fieldFile{1},{'metInChIString','metKEGGID','metPubChemID','rxnECNumbers'}); @@ -55,7 +55,7 @@ fclose(fid); % Load conversion between additional COBRA fields and namespaces: -fid = fopen(fullfile(ravenPath,'conversion','cobraNamespaces.csv')); +fid = fopen(fullfile(ravenPath,'src','conversion','cobraNamespaces.csv')); fieldFile = textscan(fid,'%s %s','Delimiter',',','HeaderLines',0); COBRAfields = [COBRAfields; fieldFile{1}]; COBRAnamespace = [COBRAnamespace; fieldFile{2}]; diff --git a/conversion/removeIdentifierPrefix.m b/src/conversion/removeIdentifierPrefix.m similarity index 100% rename from conversion/removeIdentifierPrefix.m rename to src/conversion/removeIdentifierPrefix.m diff --git a/conversion/standardizeModelFieldOrder.m b/src/conversion/standardizeModelFieldOrder.m similarity index 85% rename from conversion/standardizeModelFieldOrder.m rename to src/conversion/standardizeModelFieldOrder.m index c0b63639..acc29029 100755 --- a/conversion/standardizeModelFieldOrder.m +++ b/src/conversion/standardizeModelFieldOrder.m @@ -29,12 +29,12 @@ ravenPath=findRAVENroot(); if ~isfield(model,'rules') % Check if model is RAVEN - fid = fopen(fullfile(ravenPath,'conversion','orderRavenFields.csv')); + fid = fopen(fullfile(ravenPath,'src','conversion','orderRavenFields.csv')); fields = textscan(fid,'%s','Delimiter',',','HeaderLines',0); fields = fields{1}; fclose(fid); else % If model is COBRA - fid = fopen(fullfile(ravenPath,'conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv + fid = fopen(fullfile(ravenPath,'src','conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv fields = textscan(fid,repmat('%s',1,15),'Delimiter','\t','HeaderLines',1); fields = fields{1}; fclose(fid); diff --git a/curation/curateModelFromTables.m b/src/curation/curateModelFromTables.m similarity index 100% rename from curation/curateModelFromTables.m rename to src/curation/curateModelFromTables.m diff --git a/curation/downloadGenomeData.m b/src/curation/downloadGenomeData.m similarity index 100% rename from curation/downloadGenomeData.m rename to src/curation/downloadGenomeData.m diff --git a/curation/getGeneData.m b/src/curation/getGeneData.m similarity index 100% rename from curation/getGeneData.m rename to src/curation/getGeneData.m diff --git a/curation/processProteinFastaFile.m b/src/curation/processProteinFastaFile.m similarity index 100% rename from curation/processProteinFastaFile.m rename to src/curation/processProteinFastaFile.m diff --git a/curation/renameModelGenes.m b/src/curation/renameModelGenes.m similarity index 100% rename from curation/renameModelGenes.m rename to src/curation/renameModelGenes.m diff --git a/deprecated/canConsume.m b/src/deprecated/canConsume.m similarity index 100% rename from deprecated/canConsume.m rename to src/deprecated/canConsume.m diff --git a/deprecated/canProduce.m b/src/deprecated/canProduce.m similarity index 100% rename from deprecated/canProduce.m rename to src/deprecated/canProduce.m diff --git a/deprecated/consumeSomething.m b/src/deprecated/consumeSomething.m similarity index 100% rename from deprecated/consumeSomething.m rename to src/deprecated/consumeSomething.m diff --git a/deprecated/makeSomething.m b/src/deprecated/makeSomething.m similarity index 100% rename from deprecated/makeSomething.m rename to src/deprecated/makeSomething.m diff --git a/software/GLPKmex/COPYING b/src/external/GLPKmex/COPYING similarity index 100% rename from software/GLPKmex/COPYING rename to src/external/GLPKmex/COPYING diff --git a/software/GLPKmex/README.md b/src/external/GLPKmex/README.md similarity index 100% rename from software/GLPKmex/README.md rename to src/external/GLPKmex/README.md diff --git a/software/GLPKmex/glpk.m b/src/external/GLPKmex/glpk.m similarity index 100% rename from software/GLPKmex/glpk.m rename to src/external/GLPKmex/glpk.m diff --git a/software/GLPKmex/glpkcc.mexa64 b/src/external/GLPKmex/glpkcc.mexa64 similarity index 100% rename from software/GLPKmex/glpkcc.mexa64 rename to src/external/GLPKmex/glpkcc.mexa64 diff --git a/software/GLPKmex/glpkcc.mexmaca64 b/src/external/GLPKmex/glpkcc.mexmaca64 similarity index 100% rename from software/GLPKmex/glpkcc.mexmaca64 rename to src/external/GLPKmex/glpkcc.mexmaca64 diff --git a/software/GLPKmex/glpkcc.mexmaci64 b/src/external/GLPKmex/glpkcc.mexmaci64 similarity index 100% rename from software/GLPKmex/glpkcc.mexmaci64 rename to src/external/GLPKmex/glpkcc.mexmaci64 diff --git a/software/GLPKmex/glpkcc.mexw64 b/src/external/GLPKmex/glpkcc.mexw64 similarity index 100% rename from software/GLPKmex/glpkcc.mexw64 rename to src/external/GLPKmex/glpkcc.mexw64 diff --git a/software/blast+/.keep b/src/external/blast+/.keep similarity index 100% rename from software/blast+/.keep rename to src/external/blast+/.keep diff --git a/software/diamond/.keep b/src/external/diamond/.keep similarity index 100% rename from software/diamond/.keep rename to src/external/diamond/.keep diff --git a/software/hmmer/.keep b/src/external/hmmer/.keep similarity index 100% rename from software/hmmer/.keep rename to src/external/hmmer/.keep diff --git a/software/libSBML/CheckAndConvert.m b/src/external/libSBML/CheckAndConvert.m similarity index 100% rename from software/libSBML/CheckAndConvert.m rename to src/external/libSBML/CheckAndConvert.m diff --git a/software/libSBML/ConvertFormulaToMathML.m b/src/external/libSBML/ConvertFormulaToMathML.m similarity index 100% rename from software/libSBML/ConvertFormulaToMathML.m rename to src/external/libSBML/ConvertFormulaToMathML.m diff --git a/software/libSBML/OutputSBML_RAVEN.m b/src/external/libSBML/OutputSBML_RAVEN.m similarity index 100% rename from software/libSBML/OutputSBML_RAVEN.m rename to src/external/libSBML/OutputSBML_RAVEN.m diff --git a/software/libSBML/OutputSBML_RAVEN.mexa64 b/src/external/libSBML/OutputSBML_RAVEN.mexa64 old mode 100644 new mode 100755 similarity index 100% rename from software/libSBML/OutputSBML_RAVEN.mexa64 rename to src/external/libSBML/OutputSBML_RAVEN.mexa64 diff --git a/software/libSBML/OutputSBML_RAVEN.mexmaca64 b/src/external/libSBML/OutputSBML_RAVEN.mexmaca64 old mode 100644 new mode 100755 similarity index 100% rename from software/libSBML/OutputSBML_RAVEN.mexmaca64 rename to src/external/libSBML/OutputSBML_RAVEN.mexmaca64 diff --git a/software/libSBML/OutputSBML_RAVEN.mexmaci64 b/src/external/libSBML/OutputSBML_RAVEN.mexmaci64 old mode 100644 new mode 100755 similarity index 100% rename from software/libSBML/OutputSBML_RAVEN.mexmaci64 rename to src/external/libSBML/OutputSBML_RAVEN.mexmaci64 diff --git a/software/libSBML/OutputSBML_RAVEN.mexw64 b/src/external/libSBML/OutputSBML_RAVEN.mexw64 similarity index 100% rename from software/libSBML/OutputSBML_RAVEN.mexw64 rename to src/external/libSBML/OutputSBML_RAVEN.mexw64 diff --git a/software/libSBML/README.md b/src/external/libSBML/README.md similarity index 100% rename from software/libSBML/README.md rename to src/external/libSBML/README.md diff --git a/software/libSBML/TranslateSBML_RAVEN.m b/src/external/libSBML/TranslateSBML_RAVEN.m similarity index 100% rename from software/libSBML/TranslateSBML_RAVEN.m rename to src/external/libSBML/TranslateSBML_RAVEN.m diff --git a/software/libSBML/TranslateSBML_RAVEN.mexa64 b/src/external/libSBML/TranslateSBML_RAVEN.mexa64 old mode 100644 new mode 100755 similarity index 100% rename from software/libSBML/TranslateSBML_RAVEN.mexa64 rename to src/external/libSBML/TranslateSBML_RAVEN.mexa64 diff --git a/software/libSBML/TranslateSBML_RAVEN.mexmaca64 b/src/external/libSBML/TranslateSBML_RAVEN.mexmaca64 old mode 100644 new mode 100755 similarity index 100% rename from software/libSBML/TranslateSBML_RAVEN.mexmaca64 rename to src/external/libSBML/TranslateSBML_RAVEN.mexmaca64 diff --git a/software/libSBML/TranslateSBML_RAVEN.mexmaci64 b/src/external/libSBML/TranslateSBML_RAVEN.mexmaci64 old mode 100644 new mode 100755 similarity index 100% rename from software/libSBML/TranslateSBML_RAVEN.mexmaci64 rename to src/external/libSBML/TranslateSBML_RAVEN.mexmaci64 diff --git a/software/libSBML/TranslateSBML_RAVEN.mexw64 b/src/external/libSBML/TranslateSBML_RAVEN.mexw64 similarity index 100% rename from software/libSBML/TranslateSBML_RAVEN.mexw64 rename to src/external/libSBML/TranslateSBML_RAVEN.mexw64 diff --git a/software/libSBML/VERSION.txt b/src/external/libSBML/VERSION.txt similarity index 100% rename from software/libSBML/VERSION.txt rename to src/external/libSBML/VERSION.txt diff --git a/software/libSBML/addLevelVersion.m b/src/external/libSBML/addLevelVersion.m similarity index 100% rename from software/libSBML/addLevelVersion.m rename to src/external/libSBML/addLevelVersion.m diff --git a/software/libSBML/applyUserValidation.m b/src/external/libSBML/applyUserValidation.m similarity index 100% rename from software/libSBML/applyUserValidation.m rename to src/external/libSBML/applyUserValidation.m diff --git a/software/libSBML/getDefaultValues.m b/src/external/libSBML/getDefaultValues.m similarity index 100% rename from software/libSBML/getDefaultValues.m rename to src/external/libSBML/getDefaultValues.m diff --git a/software/libSBML/getStructure.m b/src/external/libSBML/getStructure.m similarity index 100% rename from software/libSBML/getStructure.m rename to src/external/libSBML/getStructure.m diff --git a/software/libSBML/getStructureEnum.m b/src/external/libSBML/getStructureEnum.m similarity index 100% rename from software/libSBML/getStructureEnum.m rename to src/external/libSBML/getStructureEnum.m diff --git a/software/libSBML/getStructureFieldnames.m b/src/external/libSBML/getStructureFieldnames.m similarity index 100% rename from software/libSBML/getStructureFieldnames.m rename to src/external/libSBML/getStructureFieldnames.m diff --git a/software/libSBML/getValueType.m b/src/external/libSBML/getValueType.m similarity index 100% rename from software/libSBML/getValueType.m rename to src/external/libSBML/getValueType.m diff --git a/software/libSBML/isSBML_Model.m b/src/external/libSBML/isSBML_Model.m similarity index 100% rename from software/libSBML/isSBML_Model.m rename to src/external/libSBML/isSBML_Model.m diff --git a/software/libSBML/isoctave.m b/src/external/libSBML/isoctave.m similarity index 100% rename from software/libSBML/isoctave.m rename to src/external/libSBML/isoctave.m diff --git a/software/m2html/@template/char.m b/src/external/m2html/@template/char.m similarity index 100% rename from software/m2html/@template/char.m rename to src/external/m2html/@template/char.m diff --git a/software/m2html/@template/display.m b/src/external/m2html/@template/display.m similarity index 100% rename from software/m2html/@template/display.m rename to src/external/m2html/@template/display.m diff --git a/software/m2html/@template/get.m b/src/external/m2html/@template/get.m similarity index 100% rename from software/m2html/@template/get.m rename to src/external/m2html/@template/get.m diff --git a/software/m2html/@template/parse.m b/src/external/m2html/@template/parse.m similarity index 100% rename from software/m2html/@template/parse.m rename to src/external/m2html/@template/parse.m diff --git a/software/m2html/@template/private/finish.m b/src/external/m2html/@template/private/finish.m similarity index 100% rename from software/m2html/@template/private/finish.m rename to src/external/m2html/@template/private/finish.m diff --git a/software/m2html/@template/private/loadtpl.m b/src/external/m2html/@template/private/loadtpl.m similarity index 100% rename from software/m2html/@template/private/loadtpl.m rename to src/external/m2html/@template/private/loadtpl.m diff --git a/software/m2html/@template/private/subst.m b/src/external/m2html/@template/private/subst.m similarity index 100% rename from software/m2html/@template/private/subst.m rename to src/external/m2html/@template/private/subst.m diff --git a/software/m2html/@template/set.m b/src/external/m2html/@template/set.m similarity index 100% rename from software/m2html/@template/set.m rename to src/external/m2html/@template/set.m diff --git a/software/m2html/@template/template.m b/src/external/m2html/@template/template.m similarity index 100% rename from software/m2html/@template/template.m rename to src/external/m2html/@template/template.m diff --git a/software/m2html/Changelog b/src/external/m2html/Changelog similarity index 100% rename from software/m2html/Changelog rename to src/external/m2html/Changelog diff --git a/software/m2html/Contents.m b/src/external/m2html/Contents.m similarity index 100% rename from software/m2html/Contents.m rename to src/external/m2html/Contents.m diff --git a/software/m2html/GPL b/src/external/m2html/GPL similarity index 100% rename from software/m2html/GPL rename to src/external/m2html/GPL diff --git a/software/m2html/INSTALL b/src/external/m2html/INSTALL similarity index 100% rename from software/m2html/INSTALL rename to src/external/m2html/INSTALL diff --git a/software/m2html/LICENSE b/src/external/m2html/LICENSE similarity index 100% rename from software/m2html/LICENSE rename to src/external/m2html/LICENSE diff --git a/software/m2html/README b/src/external/m2html/README similarity index 100% rename from software/m2html/README rename to src/external/m2html/README diff --git a/software/m2html/TODO b/src/external/m2html/TODO similarity index 100% rename from software/m2html/TODO rename to src/external/m2html/TODO diff --git a/software/m2html/m2html.m b/src/external/m2html/m2html.m similarity index 100% rename from software/m2html/m2html.m rename to src/external/m2html/m2html.m diff --git a/software/m2html/mdot.m b/src/external/m2html/mdot.m similarity index 100% rename from software/m2html/mdot.m rename to src/external/m2html/mdot.m diff --git a/software/m2html/private/doxyread.m b/src/external/m2html/private/doxyread.m similarity index 100% rename from software/m2html/private/doxyread.m rename to src/external/m2html/private/doxyread.m diff --git a/software/m2html/private/doxysearch.m b/src/external/m2html/private/doxysearch.m similarity index 100% rename from software/m2html/private/doxysearch.m rename to src/external/m2html/private/doxysearch.m diff --git a/software/m2html/private/doxywrite.m b/src/external/m2html/private/doxywrite.m similarity index 100% rename from software/m2html/private/doxywrite.m rename to src/external/m2html/private/doxywrite.m diff --git a/software/m2html/private/m2htmltoolbarimages.mat b/src/external/m2html/private/m2htmltoolbarimages.mat similarity index 100% rename from software/m2html/private/m2htmltoolbarimages.mat rename to src/external/m2html/private/m2htmltoolbarimages.mat diff --git a/software/m2html/private/mexexts.m b/src/external/m2html/private/mexexts.m similarity index 100% rename from software/m2html/private/mexexts.m rename to src/external/m2html/private/mexexts.m diff --git a/software/m2html/private/mfileparse.m b/src/external/m2html/private/mfileparse.m similarity index 100% rename from software/m2html/private/mfileparse.m rename to src/external/m2html/private/mfileparse.m diff --git a/software/m2html/private/openfile.m b/src/external/m2html/private/openfile.m similarity index 100% rename from software/m2html/private/openfile.m rename to src/external/m2html/private/openfile.m diff --git a/software/m2html/private/searchindex.m b/src/external/m2html/private/searchindex.m similarity index 100% rename from software/m2html/private/searchindex.m rename to src/external/m2html/private/searchindex.m diff --git a/software/m2html/private/splitcode.m b/src/external/m2html/private/splitcode.m similarity index 100% rename from software/m2html/private/splitcode.m rename to src/external/m2html/private/splitcode.m diff --git a/software/m2html/private/strtok.m b/src/external/m2html/private/strtok.m similarity index 100% rename from software/m2html/private/strtok.m rename to src/external/m2html/private/strtok.m diff --git a/software/m2html/templates/blue/Thumbs.db b/src/external/m2html/templates/blue/Thumbs.db similarity index 100% rename from software/m2html/templates/blue/Thumbs.db rename to src/external/m2html/templates/blue/Thumbs.db diff --git a/software/m2html/templates/blue/alpha.png b/src/external/m2html/templates/blue/alpha.png similarity index 100% rename from software/m2html/templates/blue/alpha.png rename to src/external/m2html/templates/blue/alpha.png diff --git a/software/m2html/templates/blue/c++.png b/src/external/m2html/templates/blue/c++.png similarity index 100% rename from software/m2html/templates/blue/c++.png rename to src/external/m2html/templates/blue/c++.png diff --git a/software/m2html/templates/blue/c.png b/src/external/m2html/templates/blue/c.png similarity index 100% rename from software/m2html/templates/blue/c.png rename to src/external/m2html/templates/blue/c.png diff --git a/software/m2html/templates/blue/demoicon.gif b/src/external/m2html/templates/blue/demoicon.gif similarity index 100% rename from software/m2html/templates/blue/demoicon.gif rename to src/external/m2html/templates/blue/demoicon.gif diff --git a/software/m2html/templates/blue/down.png b/src/external/m2html/templates/blue/down.png similarity index 100% rename from software/m2html/templates/blue/down.png rename to src/external/m2html/templates/blue/down.png diff --git a/software/m2html/templates/blue/doxysearch.php b/src/external/m2html/templates/blue/doxysearch.php similarity index 100% rename from software/m2html/templates/blue/doxysearch.php rename to src/external/m2html/templates/blue/doxysearch.php diff --git a/software/m2html/templates/blue/fortran.png b/src/external/m2html/templates/blue/fortran.png similarity index 100% rename from software/m2html/templates/blue/fortran.png rename to src/external/m2html/templates/blue/fortran.png diff --git a/software/m2html/templates/blue/graph.tpl b/src/external/m2html/templates/blue/graph.tpl similarity index 100% rename from software/m2html/templates/blue/graph.tpl rename to src/external/m2html/templates/blue/graph.tpl diff --git a/software/m2html/templates/blue/hp.png b/src/external/m2html/templates/blue/hp.png similarity index 100% rename from software/m2html/templates/blue/hp.png rename to src/external/m2html/templates/blue/hp.png diff --git a/software/m2html/templates/blue/left.png b/src/external/m2html/templates/blue/left.png similarity index 100% rename from software/m2html/templates/blue/left.png rename to src/external/m2html/templates/blue/left.png diff --git a/software/m2html/templates/blue/linux.png b/src/external/m2html/templates/blue/linux.png similarity index 100% rename from software/m2html/templates/blue/linux.png rename to src/external/m2html/templates/blue/linux.png diff --git a/software/m2html/templates/blue/m2html.css b/src/external/m2html/templates/blue/m2html.css similarity index 100% rename from software/m2html/templates/blue/m2html.css rename to src/external/m2html/templates/blue/m2html.css diff --git a/software/m2html/templates/blue/master.tpl b/src/external/m2html/templates/blue/master.tpl similarity index 100% rename from software/m2html/templates/blue/master.tpl rename to src/external/m2html/templates/blue/master.tpl diff --git a/software/m2html/templates/blue/matlabicon.gif b/src/external/m2html/templates/blue/matlabicon.gif similarity index 100% rename from software/m2html/templates/blue/matlabicon.gif rename to src/external/m2html/templates/blue/matlabicon.gif diff --git a/software/m2html/templates/blue/mdir.tpl b/src/external/m2html/templates/blue/mdir.tpl similarity index 100% rename from software/m2html/templates/blue/mdir.tpl rename to src/external/m2html/templates/blue/mdir.tpl diff --git a/software/m2html/templates/blue/mex.png b/src/external/m2html/templates/blue/mex.png similarity index 100% rename from software/m2html/templates/blue/mex.png rename to src/external/m2html/templates/blue/mex.png diff --git a/software/m2html/templates/blue/mfile.tpl b/src/external/m2html/templates/blue/mfile.tpl similarity index 100% rename from software/m2html/templates/blue/mfile.tpl rename to src/external/m2html/templates/blue/mfile.tpl diff --git a/software/m2html/templates/blue/pcode.png b/src/external/m2html/templates/blue/pcode.png similarity index 100% rename from software/m2html/templates/blue/pcode.png rename to src/external/m2html/templates/blue/pcode.png diff --git a/software/m2html/templates/blue/right.png b/src/external/m2html/templates/blue/right.png similarity index 100% rename from software/m2html/templates/blue/right.png rename to src/external/m2html/templates/blue/right.png diff --git a/software/m2html/templates/blue/search.tpl b/src/external/m2html/templates/blue/search.tpl similarity index 100% rename from software/m2html/templates/blue/search.tpl rename to src/external/m2html/templates/blue/search.tpl diff --git a/software/m2html/templates/blue/sgi.png b/src/external/m2html/templates/blue/sgi.png similarity index 100% rename from software/m2html/templates/blue/sgi.png rename to src/external/m2html/templates/blue/sgi.png diff --git a/software/m2html/templates/blue/simulinkicon.gif b/src/external/m2html/templates/blue/simulinkicon.gif similarity index 100% rename from software/m2html/templates/blue/simulinkicon.gif rename to src/external/m2html/templates/blue/simulinkicon.gif diff --git a/software/m2html/templates/blue/solaris.png b/src/external/m2html/templates/blue/solaris.png similarity index 100% rename from software/m2html/templates/blue/solaris.png rename to src/external/m2html/templates/blue/solaris.png diff --git a/software/m2html/templates/blue/todo.tpl b/src/external/m2html/templates/blue/todo.tpl similarity index 100% rename from software/m2html/templates/blue/todo.tpl rename to src/external/m2html/templates/blue/todo.tpl diff --git a/software/m2html/templates/blue/up.png b/src/external/m2html/templates/blue/up.png similarity index 100% rename from software/m2html/templates/blue/up.png rename to src/external/m2html/templates/blue/up.png diff --git a/software/m2html/templates/blue/windows.png b/src/external/m2html/templates/blue/windows.png similarity index 100% rename from software/m2html/templates/blue/windows.png rename to src/external/m2html/templates/blue/windows.png diff --git a/software/scip/.keep b/src/external/scip/.keep similarity index 100% rename from software/scip/.keep rename to src/external/scip/.keep diff --git a/software/versions.txt b/src/external/versions.txt similarity index 100% rename from software/versions.txt rename to src/external/versions.txt diff --git a/gapfilling/canExchange.m b/src/gapfilling/canExchange.m similarity index 100% rename from gapfilling/canExchange.m rename to src/gapfilling/canExchange.m diff --git a/gapfilling/checkProduction.m b/src/gapfilling/checkProduction.m similarity index 100% rename from gapfilling/checkProduction.m rename to src/gapfilling/checkProduction.m diff --git a/gapfilling/fillGaps.m b/src/gapfilling/fillGaps.m similarity index 100% rename from gapfilling/fillGaps.m rename to src/gapfilling/fillGaps.m diff --git a/gapfilling/findLeakMetabolite.m b/src/gapfilling/findLeakMetabolite.m similarity index 100% rename from gapfilling/findLeakMetabolite.m rename to src/gapfilling/findLeakMetabolite.m diff --git a/gapfilling/fitTasks.m b/src/gapfilling/fitTasks.m similarity index 100% rename from gapfilling/fitTasks.m rename to src/gapfilling/fitTasks.m diff --git a/gapfilling/ftINITFillGaps.m b/src/gapfilling/ftINITFillGaps.m similarity index 100% rename from gapfilling/ftINITFillGaps.m rename to src/gapfilling/ftINITFillGaps.m diff --git a/gapfilling/gapFillFastCore.m b/src/gapfilling/gapFillFastCore.m similarity index 100% rename from gapfilling/gapFillFastCore.m rename to src/gapfilling/gapFillFastCore.m diff --git a/gapfilling/gapFillFastLP.m b/src/gapfilling/gapFillFastLP.m similarity index 100% rename from gapfilling/gapFillFastLP.m rename to src/gapfilling/gapFillFastLP.m diff --git a/gapfilling/gapFillMILP.m b/src/gapfilling/gapFillMILP.m similarity index 100% rename from gapfilling/gapFillMILP.m rename to src/gapfilling/gapFillMILP.m diff --git a/gapfilling/gapFillSwiftCore.m b/src/gapfilling/gapFillSwiftCore.m similarity index 100% rename from gapfilling/gapFillSwiftCore.m rename to src/gapfilling/gapFillSwiftCore.m diff --git a/gapfilling/gapFillTopological.m b/src/gapfilling/gapFillTopological.m similarity index 100% rename from gapfilling/gapFillTopological.m rename to src/gapfilling/gapFillTopological.m diff --git a/gapfilling/gapReport.m b/src/gapfilling/gapReport.m similarity index 100% rename from gapfilling/gapReport.m rename to src/gapfilling/gapReport.m diff --git a/installation/addRavenToUserPath.m b/src/installation/addRavenToUserPath.m similarity index 100% rename from installation/addRavenToUserPath.m rename to src/installation/addRavenToUserPath.m diff --git a/installation/checkFunctionUniqueness.m b/src/installation/checkFunctionUniqueness.m similarity index 100% rename from installation/checkFunctionUniqueness.m rename to src/installation/checkFunctionUniqueness.m diff --git a/installation/downloadRavenBinaries.m b/src/installation/downloadRavenBinaries.m similarity index 92% rename from installation/downloadRavenBinaries.m rename to src/installation/downloadRavenBinaries.m index 16c8ebf9..0aea8760 100644 --- a/installation/downloadRavenBinaries.m +++ b/src/installation/downloadRavenBinaries.m @@ -44,13 +44,13 @@ function downloadRavenBinaries(tools) case 'blast+' tag = 'blast-2.17.0'; asset = ['blast-2.17.0-' plat '.zip']; - destDir = fullfile(ravenDir,'software','blast+'); + destDir = fullfile(ravenDir,'src','external','blast+'); sentinel = fullfile(destDir,'blastp'); % bare name on every OS (.exe on Windows) execs = {'blastp','makeblastdb'}; case 'diamond' tag = 'diamond-2.1.17'; asset = ['diamond-2.1.17-' plat '.zip']; - destDir = fullfile(ravenDir,'software','diamond'); + destDir = fullfile(ravenDir,'src','external','diamond'); sentinel = fullfile(destDir,'diamond'); execs = {'diamond'}; case 'hmmer' @@ -61,7 +61,7 @@ function downloadRavenBinaries(tools) tag = 'hmmer-3.4.0'; asset = ['hmmer-3.4.0-' plat '.zip']; end - destDir = fullfile(ravenDir,'software','hmmer'); + destDir = fullfile(ravenDir,'src','external','hmmer'); sentinel = fullfile(destDir,'hmmsearch'); execs = {'hmmsearch'}; otherwise @@ -78,7 +78,7 @@ function downloadRavenBinaries(tools) continue; % already provisioned end - zipPath = fetchRavenDataAsset(fullfile(ravenDir,'software'),tag,asset); + zipPath = fetchRavenDataAsset(fullfile(ravenDir,'src','external'),tag,asset); unzip(zipPath,destDir); delete(zipPath); diff --git a/installation/fetchRavenDataAsset.m b/src/installation/fetchRavenDataAsset.m similarity index 100% rename from installation/fetchRavenDataAsset.m rename to src/installation/fetchRavenDataAsset.m diff --git a/installation/findRAVENroot.m b/src/installation/findRAVENroot.m similarity index 87% rename from installation/findRAVENroot.m rename to src/installation/findRAVENroot.m index e828bf79..02334031 100755 --- a/installation/findRAVENroot.m +++ b/src/installation/findRAVENroot.m @@ -1,7 +1,7 @@ function [ravenPath, prevDir] = findRAVENroot() % findRAVENroot % Finds the root of the RAVEN directory by searching for the path to -% RAVEN.png. Can also record the current directory, in case a function will +% version.txt. Can also record the current directory, in case a function will % use the ravenPath to navigate to a precise folder, and it should return to % the previous directory afterwards. See e.g. optimizeProb calling glpk. % @@ -28,7 +28,7 @@ ravenPath = ''; if ispref('RAVEN','ravenPath') prefPath = getpref('RAVEN','ravenPath'); - if isfile(fullfile(prefPath,'RAVEN.png')) + if isfile(fullfile(prefPath,'version.txt')) ravenPath = prefPath; end end @@ -37,14 +37,14 @@ ravenPath = ST(strcmp({ST.name},'findRAVENroot')).file; rootFound = 0; while rootFound == 0 - isRoot = isfile(fullfile(ravenPath,'RAVEN.png')); + isRoot = isfile(fullfile(ravenPath,'version.txt')); if isRoot rootFound = 1; else ravenPathOld = ravenPath; ravenPath = fileparts(ravenPath); if strcmp(ravenPathOld,ravenPath) - error('Cannot find the RAVEN root directory. Make sure you have not removed the RAVEN.png file from your RAVEN installation.') + error('Cannot find the RAVEN root directory. Make sure you have not removed the version.txt file from your RAVEN installation.') end end end diff --git a/installation/removeRavenFromPath.m b/src/installation/removeRavenFromPath.m similarity index 100% rename from installation/removeRavenFromPath.m rename to src/installation/removeRavenFromPath.m diff --git a/installation/updateDocumentation.m b/src/installation/updateDocumentation.m similarity index 64% rename from installation/updateDocumentation.m rename to src/installation/updateDocumentation.m index 1975dde5..97892506 100755 --- a/installation/updateDocumentation.m +++ b/src/installation/updateDocumentation.m @@ -1,47 +1,47 @@ function updateDocumentation() % updateDocumentation -% Regenerates the HTML documentation in RAVEN's doc directory from the -% function help texts. The doc directory is deleted and rebuilt, so +% Regenerates the HTML documentation in RAVEN's docs/html directory from the +% function help texts. The docs/html directory is deleted and rebuilt, so % anything hand-edited there is lost. % % The Documentation workflow runs this on every push to a release branch -% and commits the result, so doc stays in step with the sources without +% and commits the result, so docs/html stays in step with the sources without % anyone running it by hand. Run it locally only to preview. % % Usage: updateDocumentation() %Get the RAVEN path ravenDir=findRAVENroot(); +srcDir=fullfile(ravenDir,'src'); %Make sure that RAVEN-provided m2html is used -path(fullfile(ravenDir,'software','m2html'),path); +path(fullfile(ravenDir,'src','external','m2html'),path); %Get a non-redundant list of RAVEN subdirectories containing MATLAB %functions. Absolute paths are not compatible with M2HTML, so convert them %to the relative paths instead. -ravenDirs=dir(fullfile(ravenDir,'**/*.m')); +ravenDirs=dir(fullfile(srcDir,'**/*.m')); ravenDirs=unique({ravenDirs.folder})'; %Get rid of MATLAB functions from external software -ravenDirs(startsWith(ravenDirs,strcat(ravenDir,filesep,'software')))=[]; -ravenDirs(startsWith(ravenDirs,strcat(ravenDir,filesep,'legacy',filesep,'software')))=[]; +ravenDirs(startsWith(ravenDirs,strcat(srcDir,filesep,'external')))=[]; %Skip deprecated wrappers: they are on the path so existing scripts keep %working, but documenting them would advertise functions that are on their %way out. Each one names its replacement when called. -ravenDirs(startsWith(ravenDirs,strcat(ravenDir,filesep,'deprecated')))=[]; +ravenDirs(startsWith(ravenDirs,strcat(srcDir,filesep,'deprecated')))=[]; %Remove keggModel.mat if it exists -if exist(fullfile(ravenDir,'reconstruction','kegg','keggModel.mat'), 'file') == 2 - delete(fullfile(ravenDir,'reconstruction','kegg','keggModel.mat')); +if exist(fullfile(ravenDir,'src','reconstruction','kegg','keggModel.mat'), 'file') == 2 + delete(fullfile(ravenDir,'src','reconstruction','kegg','keggModel.mat')); end -%Remove the existing "doc" directory from RAVEN -docDir=fullfile(ravenDir,'doc'); +%Remove the existing "docs/html" directory from RAVEN +docDir=fullfile(ravenDir,'docs','html'); if isfolder(docDir) rmdir(docDir,'s'); end %Make relative path -relStart = numel(ravenDir)+2; +relStart = numel(srcDir)+2; for i=1:numel(ravenDirs) ravenDirs{i,1} = ravenDirs{i,1}(relStart:end); end @@ -58,11 +58,11 @@ function updateDocumentation() end end -%Save the current working directory and go to RAVEN root directory +%Save the current working directory and go to RAVEN source directory originalDir=pwd; -cd(ravenDir); +cd(srcDir); %Generate HTML documentation files for RAVEN MATLAB functions -m2html('mFiles',ravenDirs,'htmldir','doc'); +m2html('mFiles',ravenDirs,'htmldir',docDir); %Go back to the original working directory cd(originalDir); diff --git a/io/checkFileExistence.m b/src/io/checkFileExistence.m similarity index 100% rename from io/checkFileExistence.m rename to src/io/checkFileExistence.m diff --git a/io/cleanSheet.m b/src/io/cleanSheet.m similarity index 100% rename from io/cleanSheet.m rename to src/io/cleanSheet.m diff --git a/io/exportForGit.m b/src/io/exportForGit.m similarity index 100% rename from io/exportForGit.m rename to src/io/exportForGit.m diff --git a/io/exportModel.m b/src/io/exportModel.m similarity index 100% rename from io/exportModel.m rename to src/io/exportModel.m diff --git a/io/exportToExcelFormat.m b/src/io/exportToExcelFormat.m similarity index 100% rename from io/exportToExcelFormat.m rename to src/io/exportToExcelFormat.m diff --git a/io/importModel.m b/src/io/importModel.m similarity index 100% rename from io/importModel.m rename to src/io/importModel.m diff --git a/io/parseYAML.m b/src/io/parseYAML.m similarity index 100% rename from io/parseYAML.m rename to src/io/parseYAML.m diff --git a/io/readFasta.m b/src/io/readFasta.m similarity index 100% rename from io/readFasta.m rename to src/io/readFasta.m diff --git a/io/readYAMLmodel.m b/src/io/readYAMLmodel.m similarity index 100% rename from io/readYAMLmodel.m rename to src/io/readYAMLmodel.m diff --git a/io/writeExcel.m b/src/io/writeExcel.m similarity index 100% rename from io/writeExcel.m rename to src/io/writeExcel.m diff --git a/io/writeFasta.m b/src/io/writeFasta.m similarity index 100% rename from io/writeFasta.m rename to src/io/writeFasta.m diff --git a/io/writeYAMLmodel.m b/src/io/writeYAMLmodel.m similarity index 100% rename from io/writeYAMLmodel.m rename to src/io/writeYAMLmodel.m diff --git a/localization/assignCompartments.m b/src/localization/assignCompartments.m similarity index 100% rename from localization/assignCompartments.m rename to src/localization/assignCompartments.m diff --git a/localization/defaultCompartmentMap.m b/src/localization/defaultCompartmentMap.m similarity index 100% rename from localization/defaultCompartmentMap.m rename to src/localization/defaultCompartmentMap.m diff --git a/localization/getUniProtScores.m b/src/localization/getUniProtScores.m similarity index 100% rename from localization/getUniProtScores.m rename to src/localization/getUniProtScores.m diff --git a/localization/parseScores.m b/src/localization/parseScores.m similarity index 100% rename from localization/parseScores.m rename to src/localization/parseScores.m diff --git a/localization/predictLocalization.m b/src/localization/predictLocalization.m similarity index 100% rename from localization/predictLocalization.m rename to src/localization/predictLocalization.m diff --git a/manipulation/addExchangeRxns.m b/src/manipulation/addExchangeRxns.m similarity index 100% rename from manipulation/addExchangeRxns.m rename to src/manipulation/addExchangeRxns.m diff --git a/manipulation/addGenesRaven.m b/src/manipulation/addGenesRaven.m similarity index 100% rename from manipulation/addGenesRaven.m rename to src/manipulation/addGenesRaven.m diff --git a/manipulation/addMets.m b/src/manipulation/addMets.m similarity index 100% rename from manipulation/addMets.m rename to src/manipulation/addMets.m diff --git a/manipulation/addRxns.m b/src/manipulation/addRxns.m similarity index 100% rename from manipulation/addRxns.m rename to src/manipulation/addRxns.m diff --git a/manipulation/addRxnsGenesMets.m b/src/manipulation/addRxnsGenesMets.m similarity index 100% rename from manipulation/addRxnsGenesMets.m rename to src/manipulation/addRxnsGenesMets.m diff --git a/manipulation/addTransport.m b/src/manipulation/addTransport.m similarity index 100% rename from manipulation/addTransport.m rename to src/manipulation/addTransport.m diff --git a/manipulation/changeGrRules.m b/src/manipulation/changeGrRules.m similarity index 100% rename from manipulation/changeGrRules.m rename to src/manipulation/changeGrRules.m diff --git a/manipulation/changeRxns.m b/src/manipulation/changeRxns.m similarity index 100% rename from manipulation/changeRxns.m rename to src/manipulation/changeRxns.m diff --git a/manipulation/closeModel.m b/src/manipulation/closeModel.m similarity index 100% rename from manipulation/closeModel.m rename to src/manipulation/closeModel.m diff --git a/manipulation/contractModel.m b/src/manipulation/contractModel.m similarity index 100% rename from manipulation/contractModel.m rename to src/manipulation/contractModel.m diff --git a/manipulation/convertToIrrev.m b/src/manipulation/convertToIrrev.m similarity index 100% rename from manipulation/convertToIrrev.m rename to src/manipulation/convertToIrrev.m diff --git a/manipulation/copyToComps.m b/src/manipulation/copyToComps.m similarity index 100% rename from manipulation/copyToComps.m rename to src/manipulation/copyToComps.m diff --git a/manipulation/deleteUnusedGenes.m b/src/manipulation/deleteUnusedGenes.m similarity index 100% rename from manipulation/deleteUnusedGenes.m rename to src/manipulation/deleteUnusedGenes.m diff --git a/manipulation/expandModel.m b/src/manipulation/expandModel.m similarity index 100% rename from manipulation/expandModel.m rename to src/manipulation/expandModel.m diff --git a/manipulation/findDuplicateRxns.m b/src/manipulation/findDuplicateRxns.m similarity index 100% rename from manipulation/findDuplicateRxns.m rename to src/manipulation/findDuplicateRxns.m diff --git a/manipulation/findPotentialErrors.m b/src/manipulation/findPotentialErrors.m similarity index 100% rename from manipulation/findPotentialErrors.m rename to src/manipulation/findPotentialErrors.m diff --git a/manipulation/generateNewIds.m b/src/manipulation/generateNewIds.m similarity index 100% rename from manipulation/generateNewIds.m rename to src/manipulation/generateNewIds.m diff --git a/manipulation/mergeCompartments.m b/src/manipulation/mergeCompartments.m similarity index 100% rename from manipulation/mergeCompartments.m rename to src/manipulation/mergeCompartments.m diff --git a/manipulation/mergeModels.m b/src/manipulation/mergeModels.m similarity index 100% rename from manipulation/mergeModels.m rename to src/manipulation/mergeModels.m diff --git a/manipulation/permuteModel.m b/src/manipulation/permuteModel.m similarity index 100% rename from manipulation/permuteModel.m rename to src/manipulation/permuteModel.m diff --git a/manipulation/removeBadRxns.m b/src/manipulation/removeBadRxns.m similarity index 100% rename from manipulation/removeBadRxns.m rename to src/manipulation/removeBadRxns.m diff --git a/manipulation/removeGenes.m b/src/manipulation/removeGenes.m similarity index 100% rename from manipulation/removeGenes.m rename to src/manipulation/removeGenes.m diff --git a/manipulation/removeLowScoreGenes.m b/src/manipulation/removeLowScoreGenes.m similarity index 100% rename from manipulation/removeLowScoreGenes.m rename to src/manipulation/removeLowScoreGenes.m diff --git a/manipulation/removeMets.m b/src/manipulation/removeMets.m similarity index 100% rename from manipulation/removeMets.m rename to src/manipulation/removeMets.m diff --git a/manipulation/removeReactions.m b/src/manipulation/removeReactions.m similarity index 100% rename from manipulation/removeReactions.m rename to src/manipulation/removeReactions.m diff --git a/manipulation/replaceMets.m b/src/manipulation/replaceMets.m similarity index 100% rename from manipulation/replaceMets.m rename to src/manipulation/replaceMets.m diff --git a/manipulation/reverseRxns.m b/src/manipulation/reverseRxns.m similarity index 100% rename from manipulation/reverseRxns.m rename to src/manipulation/reverseRxns.m diff --git a/manipulation/setExchangeBounds.m b/src/manipulation/setExchangeBounds.m similarity index 100% rename from manipulation/setExchangeBounds.m rename to src/manipulation/setExchangeBounds.m diff --git a/manipulation/setParam.m b/src/manipulation/setParam.m similarity index 100% rename from manipulation/setParam.m rename to src/manipulation/setParam.m diff --git a/manipulation/simplifyModel.m b/src/manipulation/simplifyModel.m similarity index 100% rename from manipulation/simplifyModel.m rename to src/manipulation/simplifyModel.m diff --git a/manipulation/sortIdentifiers.m b/src/manipulation/sortIdentifiers.m similarity index 100% rename from manipulation/sortIdentifiers.m rename to src/manipulation/sortIdentifiers.m diff --git a/manipulation/sortModel.m b/src/manipulation/sortModel.m similarity index 100% rename from manipulation/sortModel.m rename to src/manipulation/sortModel.m diff --git a/manipulation/standardizeGrRules.m b/src/manipulation/standardizeGrRules.m similarity index 100% rename from manipulation/standardizeGrRules.m rename to src/manipulation/standardizeGrRules.m diff --git a/queries/buildEquation.m b/src/queries/buildEquation.m similarity index 100% rename from queries/buildEquation.m rename to src/queries/buildEquation.m diff --git a/queries/checkModelStruct.m b/src/queries/checkModelStruct.m similarity index 100% rename from queries/checkModelStruct.m rename to src/queries/checkModelStruct.m diff --git a/queries/constructEquations.m b/src/queries/constructEquations.m similarity index 100% rename from queries/constructEquations.m rename to src/queries/constructEquations.m diff --git a/queries/constructS.m b/src/queries/constructS.m similarity index 100% rename from queries/constructS.m rename to src/queries/constructS.m diff --git a/queries/getAllRxnsFromGenes.m b/src/queries/getAllRxnsFromGenes.m similarity index 100% rename from queries/getAllRxnsFromGenes.m rename to src/queries/getAllRxnsFromGenes.m diff --git a/queries/getElementalBalance.m b/src/queries/getElementalBalance.m similarity index 100% rename from queries/getElementalBalance.m rename to src/queries/getElementalBalance.m diff --git a/queries/getExchangeRxns.m b/src/queries/getExchangeRxns.m similarity index 100% rename from queries/getExchangeRxns.m rename to src/queries/getExchangeRxns.m diff --git a/queries/getGenesFromGrRules.m b/src/queries/getGenesFromGrRules.m similarity index 100% rename from queries/getGenesFromGrRules.m rename to src/queries/getGenesFromGrRules.m diff --git a/queries/getIndexes.m b/src/queries/getIndexes.m similarity index 100% rename from queries/getIndexes.m rename to src/queries/getIndexes.m diff --git a/queries/getRxnsInComp.m b/src/queries/getRxnsInComp.m similarity index 100% rename from queries/getRxnsInComp.m rename to src/queries/getRxnsInComp.m diff --git a/queries/getTransportRxns.m b/src/queries/getTransportRxns.m similarity index 100% rename from queries/getTransportRxns.m rename to src/queries/getTransportRxns.m diff --git a/queries/modelSummary.m b/src/queries/modelSummary.m similarity index 100% rename from queries/modelSummary.m rename to src/queries/modelSummary.m diff --git a/queries/parseFormulas.m b/src/queries/parseFormulas.m similarity index 100% rename from queries/parseFormulas.m rename to src/queries/parseFormulas.m diff --git a/queries/parseRxnEqu.m b/src/queries/parseRxnEqu.m similarity index 100% rename from queries/parseRxnEqu.m rename to src/queries/parseRxnEqu.m diff --git a/queries/printFluxes.m b/src/queries/printFluxes.m similarity index 100% rename from queries/printFluxes.m rename to src/queries/printFluxes.m diff --git a/queries/printModelStats.m b/src/queries/printModelStats.m similarity index 100% rename from queries/printModelStats.m rename to src/queries/printModelStats.m diff --git a/reconstruction/guessComposition.m b/src/reconstruction/guessComposition.m similarity index 100% rename from reconstruction/guessComposition.m rename to src/reconstruction/guessComposition.m diff --git a/reconstruction/homology/getBlast.m b/src/reconstruction/homology/getBlast.m similarity index 87% rename from reconstruction/homology/getBlast.m rename to src/reconstruction/homology/getBlast.m index a85e00e4..e74775da 100755 --- a/reconstruction/homology/getBlast.m +++ b/src/reconstruction/homology/getBlast.m @@ -109,7 +109,7 @@ end %Fetch the BLAST+ binaries on demand if they are not already present -if ~exist(fullfile(ravenPath,'software','blast+',['blastp' binEnd]),'file') +if ~exist(fullfile(ravenPath,'src','external','blast+',['blastp' binEnd]),'file') downloadRavenBinaries({'blast+'}); end @@ -121,7 +121,7 @@ %Create a database for the new organism and blast each of the refFastaFiles %against it -[status, message]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' fastaFile{1} '" -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']); +[status, message]=system(['"' fullfile(ravenPath,'src','external','blast+',['makeblastdb' binEnd]) '" -in "' fastaFile{1} '" -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']); if developMode blastReport.dbHashes.phr{numel(blastReport.dbHashes.phr)+1}=filemd5(fullfile(tmpDB, 'tmpDB.phr')); blastReport.dbHashes.pot{numel(blastReport.dbHashes.pot)+1}=filemd5(fullfile(tmpDB, 'tmpDB.pot')); @@ -136,7 +136,7 @@ if ~hideVerbose fprintf(['BLASTing "' modelIDs{i} '" against "' organismID{1} '"..\n']); end - [status, message]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' refFastaFiles{i} '" -out "' outFile '_' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']); + [status, message]=system(['"' fullfile(ravenPath,'src','external','blast+',['blastp' binEnd]) '" -query "' refFastaFiles{i} '" -out "' outFile '_' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']); if developMode blastReport.blastTxtOutput{numel(blastReport.blastTxtOutput)+1}=importdata([outFile '_' num2str(i)]); end @@ -152,11 +152,11 @@ if ~hideVerbose fprintf(['BLASTing "' organismID{1} '" against "' modelIDs{i} '"..\n']); end - [status, message]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' refFastaFiles{i} '" -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']); + [status, message]=system(['"' fullfile(ravenPath,'src','external','blast+',['makeblastdb' binEnd]) '" -in "' refFastaFiles{i} '" -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']); if status~=0 error('makeblastdb did not run successfully, error:\n%s',strip(message)) end - [status, message]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' fastaFile{1} '" -out "' outFile '_r' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']); + [status, message]=system(['"' fullfile(ravenPath,'src','external','blast+',['blastp' binEnd]) '" -query "' fastaFile{1} '" -out "' outFile '_r' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']); if developMode blastReport.dbHashes.phr{numel(blastReport.dbHashes.phr)+1}=filemd5(fullfile(tmpDB, 'tmpDB.phr')); blastReport.dbHashes.pot{numel(blastReport.dbHashes.pot)+1}=filemd5(fullfile(tmpDB, 'tmpDB.pot')); diff --git a/reconstruction/homology/getDiamond.m b/src/reconstruction/homology/getDiamond.m similarity index 85% rename from reconstruction/homology/getDiamond.m rename to src/reconstruction/homology/getDiamond.m index bea379d5..84f93fbe 100755 --- a/reconstruction/homology/getDiamond.m +++ b/src/reconstruction/homology/getDiamond.m @@ -98,7 +98,7 @@ end %Fetch the DIAMOND binary on demand if it is not already present -if ~exist(fullfile(ravenPath,'software','diamond',['diamond' binEnd]),'file') +if ~exist(fullfile(ravenPath,'src','external','diamond',['diamond' binEnd]),'file') downloadRavenBinaries({'diamond'}); end @@ -110,7 +110,7 @@ %Create a database for the new organism and blast each of the refFastaFiles %against it -[status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fastaFile{1} '" --db "' fullfile(tmpDB) '"']); +[status, message]=system(['"' fullfile(ravenPath,'src','external','diamond',['diamond' binEnd]) '" makedb --in "' fastaFile{1} '" --db "' fullfile(tmpDB) '"']); if developMode diamondReport.dbHashes{numel(diamondReport.dbHashes)+1} = char(regexp(message,'[a-f0-9]{32}','match')); end @@ -122,7 +122,7 @@ if ~hideVerbose fprintf(['Running DIAMOND blastp with "' modelIDs{i} '" against "' organismID{1} '"..\n']); end - [status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' refFastaFiles{i} '" --out "' outFile '_' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]); + [status, message]=system(['"' fullfile(ravenPath,'src','external','diamond',['diamond' binEnd]) '" blastp --query "' refFastaFiles{i} '" --out "' outFile '_' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]); if developMode diamondReport.diamondTxtOutput{numel(diamondReport.diamondTxtOutput)+1}=importdata([outFile '_' num2str(i)]); end @@ -138,11 +138,11 @@ if ~hideVerbose fprintf(['Running DIAMOND blastp with "' organismID{1} '" against "' modelIDs{i} '"..\n']); end - [status, message1]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' refFastaFiles{i} '" --db "' fullfile(tmpDB) '"']); + [status, message1]=system(['"' fullfile(ravenPath,'src','external','diamond',['diamond' binEnd]) '" makedb --in "' refFastaFiles{i} '" --db "' fullfile(tmpDB) '"']); if status~=0 error('DIAMOND makedb did not run successfully, error:\n%s',strip(message1)) end - [status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fastaFile{1} '" --out "' outFile '_r' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores]); + [status, message]=system(['"' fullfile(ravenPath,'src','external','diamond',['diamond' binEnd]) '" blastp --query "' fastaFile{1} '" --out "' outFile '_r' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores]); if developMode diamondReport.dbHashes{numel(diamondReport.dbHashes)+1} = char(regexp(message1,'[a-f0-9]{32}','match')); diamondReport.diamondTxtOutput{numel(diamondReport.diamondTxtOutput)+1}=importdata([outFile '_r' num2str(i)]); diff --git a/reconstruction/homology/getModelFromHomology.m b/src/reconstruction/homology/getModelFromHomology.m similarity index 100% rename from reconstruction/homology/getModelFromHomology.m rename to src/reconstruction/homology/getModelFromHomology.m diff --git a/reconstruction/homology/makeFakeBlastStructure.m b/src/reconstruction/homology/makeFakeBlastStructure.m similarity index 100% rename from reconstruction/homology/makeFakeBlastStructure.m rename to src/reconstruction/homology/makeFakeBlastStructure.m diff --git a/reconstruction/kegg/KEGG_VERSION.md b/src/reconstruction/kegg/KEGG_VERSION.md similarity index 100% rename from reconstruction/kegg/KEGG_VERSION.md rename to src/reconstruction/kegg/KEGG_VERSION.md diff --git a/reconstruction/kegg/buildGlobalGPR.m b/src/reconstruction/kegg/buildGlobalGPR.m similarity index 100% rename from reconstruction/kegg/buildGlobalGPR.m rename to src/reconstruction/kegg/buildGlobalGPR.m diff --git a/reconstruction/kegg/buildGlobalKEGGModel.m b/src/reconstruction/kegg/buildGlobalKEGGModel.m similarity index 97% rename from reconstruction/kegg/buildGlobalKEGGModel.m rename to src/reconstruction/kegg/buildGlobalKEGGModel.m index da6b0a65..e25dd916 100644 --- a/reconstruction/kegg/buildGlobalKEGGModel.m +++ b/src/reconstruction/kegg/buildGlobalKEGGModel.m @@ -26,7 +26,7 @@ % reaction ids carrying the corresponding rxn_flags quality flag. kver=keggDataVersion(); -keggDir=fullfile(ravenPath,'reconstruction','kegg'); +keggDir=fullfile(ravenPath,'src','reconstruction','kegg'); archive=fetchRavenDataAsset(keggDir,kver,[kver '_core.tar.gz']); coreDir=fullfile(keggDir,[kver '_core']); diff --git a/reconstruction/kegg/getKEGGModelForOrganism.m b/src/reconstruction/kegg/getKEGGModelForOrganism.m similarity index 98% rename from reconstruction/kegg/getKEGGModelForOrganism.m rename to src/reconstruction/kegg/getKEGGModelForOrganism.m index 6aa08f9e..8f6dfa5e 100755 --- a/reconstruction/kegg/getKEGGModelForOrganism.m +++ b/src/reconstruction/kegg/getKEGGModelForOrganism.m @@ -295,7 +295,7 @@ %First remove all reactions without genes if keepSpontaneous==true fprintf('Removing non-spontaneous reactions without GPR rules... '); - load(fullfile(ravenPath,'reconstruction','kegg','keggModel.mat'),'isSpontaneous'); + load(fullfile(ravenPath,'src','reconstruction','kegg','keggModel.mat'),'isSpontaneous'); I=~any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous); spontRxnsWithGenes=model.rxns(any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous)); else @@ -368,12 +368,12 @@ binEnd=''; end %Fetch the HMMER binary on demand if it is not already present -if ~exist(fullfile(ravenPath,'software','hmmer',['hmmsearch' binEnd]),'file') +if ~exist(fullfile(ravenPath,'src','external','hmmer',['hmmsearch' binEnd]),'file') downloadRavenBinaries({'hmmer'}); end tblFile=[tempname '.tblout']; fprintf('Querying the user-specified FASTA file against the KEGG Orthology specific HMMs... '); -[status, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmsearch' binEnd]) '" --cpu "' num2str(cores) '" --tblout "' tblFile '" "' libraryFile '" "' fastaFile '"']); +[status, output]=system(['"' fullfile(ravenPath,'src','external','hmmer',['hmmsearch' binEnd]) '" --cpu "' num2str(cores) '" --tblout "' tblFile '" "' libraryFile '" "' fastaFile '"']); if status~=0 EM=['Error when querying the concatenated HMM library:\n' output]; error('RAVEN:badInput', '%s', EM); diff --git a/reconstruction/kegg/getModelFromKEGG.m b/src/reconstruction/kegg/getModelFromKEGG.m similarity index 97% rename from reconstruction/kegg/getModelFromKEGG.m rename to src/reconstruction/kegg/getModelFromKEGG.m index ca8a3780..f61ba301 100755 --- a/reconstruction/kegg/getModelFromKEGG.m +++ b/src/reconstruction/kegg/getModelFromKEGG.m @@ -49,7 +49,7 @@ keepIncomplete=p.keepIncomplete; keepGeneral=p.keepGeneral; -modelFile=fullfile(ravenPath,'reconstruction','kegg','keggModel.mat'); +modelFile=fullfile(ravenPath,'src','reconstruction','kegg','keggModel.mat'); if isfile(modelFile) fprintf(['Importing the global KEGG model from ' strrep(modelFile,'\','/') '... ']); load(modelFile,'model','KOModel','isSpontaneous','isUndefinedStoich','isIncomplete','isGeneral'); diff --git a/reconstruction/kegg/getPhylDist.m b/src/reconstruction/kegg/getPhylDist.m similarity index 94% rename from reconstruction/kegg/getPhylDist.m rename to src/reconstruction/kegg/getPhylDist.m index 1a8c7244..f4bbbc43 100755 --- a/reconstruction/kegg/getPhylDist.m +++ b/src/reconstruction/kegg/getPhylDist.m @@ -27,7 +27,7 @@ onlyInKingdom=p.onlyInKingdom; ravenPath=findRAVENroot(); -distFile=fullfile(ravenPath,'reconstruction','kegg','keggPhylDist.mat'); +distFile=fullfile(ravenPath,'src','reconstruction','kegg','keggPhylDist.mat'); if ~exist(distFile,'file') error('getPhylDist:noData', ... ['keggPhylDist.mat not found at ' strrep(distFile,'\','/') '.\n' ... diff --git a/reconstruction/kegg/keggDataVersion.m b/src/reconstruction/kegg/keggDataVersion.m similarity index 89% rename from reconstruction/kegg/keggDataVersion.m rename to src/reconstruction/kegg/keggDataVersion.m index f8a8e9d0..7fec3802 100644 --- a/reconstruction/kegg/keggDataVersion.m +++ b/src/reconstruction/kegg/keggDataVersion.m @@ -13,7 +13,7 @@ % the raven-data release tag, e.g. 'kegg118'. ravenPath=findRAVENroot(); -versionFile=fullfile(ravenPath,'reconstruction','kegg','KEGG_VERSION.md'); +versionFile=fullfile(ravenPath,'src','reconstruction','kegg','KEGG_VERSION.md'); fid=fopen(versionFile,'r'); if fid==-1 error('keggDataVersion:fileNotFound','Cannot read %s.',strrep(versionFile,'\','/')) diff --git a/reconstruction/kegg/keggPhylDist.mat b/src/reconstruction/kegg/keggPhylDist.mat similarity index 100% rename from reconstruction/kegg/keggPhylDist.mat rename to src/reconstruction/kegg/keggPhylDist.mat diff --git a/reconstruction/kegg/readKEGGTable.m b/src/reconstruction/kegg/readKEGGTable.m similarity index 100% rename from reconstruction/kegg/readKEGGTable.m rename to src/reconstruction/kegg/readKEGGTable.m diff --git a/solver/checkSolution.m b/src/solver/checkSolution.m similarity index 100% rename from solver/checkSolution.m rename to src/solver/checkSolution.m diff --git a/solver/getMinNrFluxes.m b/src/solver/getMinNrFluxes.m similarity index 100% rename from solver/getMinNrFluxes.m rename to src/solver/getMinNrFluxes.m diff --git a/solver/optimizeProb.m b/src/solver/optimizeProb.m similarity index 99% rename from solver/optimizeProb.m rename to src/solver/optimizeProb.m index 047a39a0..de278ad1 100755 --- a/solver/optimizeProb.m +++ b/src/solver/optimizeProb.m @@ -224,7 +224,7 @@ % Ensure that RAVEN glpk binary is used, return to original % directory afterwards [ravenDir,currDir]=findRAVENroot(); - cd(fullfile(ravenDir,'software','GLPKmex')) + cd(fullfile(ravenDir,'src','external','GLPKmex')) [xopt, fmin, errnum, extra] = glpk(prob.c, prob.A, prob.b, prob.lb, prob.ub, prob.csense, prob.vartype, prob.osense, solverparams); cd(currDir) diff --git a/solver/setRavenSolver.m b/src/solver/setRavenSolver.m similarity index 81% rename from solver/setRavenSolver.m rename to src/solver/setRavenSolver.m index 9288c8df..0adf3663 100755 --- a/solver/setRavenSolver.m +++ b/src/solver/setRavenSolver.m @@ -43,15 +43,15 @@ function setRavenSolver(solver) end else ravenDir = findRAVENroot(); - if ~exist(fullfile(ravenDir,'software','scip','scip.mexw64'),'file') + if ~exist(fullfile(ravenDir,'src','external','scip','scip.mexw64'),'file') try disp('Downloading and installing RAVEN-provided SCIP MEX binary...') - websave(fullfile(ravenDir,'software','scip_mex_win.zip'),'https://github.com/SysBioChalmers/RAVEN/releases/download/v2.8.6/scip_mex_win.zip'); % Should be updated to release with SCIP functionality + websave(fullfile(ravenDir,'src','external','scip_mex_win.zip'),'https://github.com/SysBioChalmers/RAVEN/releases/download/v2.8.6/scip_mex_win.zip'); % Should be updated to release with SCIP functionality catch error('Unable to download SCIP MEX binary from the RAVEN GitHub page.') end - unzip(fullfile(ravenDir,'software','scip_mex_win.zip'),fullfile(ravenDir,'software','scip')); - delete(fullfile(ravenDir,'software','scip_mex_win.zip')); + unzip(fullfile(ravenDir,'src','external','scip_mex_win.zip'),fullfile(ravenDir,'src','external','scip')); + delete(fullfile(ravenDir,'src','external','scip_mex_win.zip')); end try scip; % The pre-compiled MEX file might fail diff --git a/solver/solveLP.m b/src/solver/solveLP.m similarity index 100% rename from solver/solveLP.m rename to src/solver/solveLP.m diff --git a/solver/splitProbForConditioning.m b/src/solver/splitProbForConditioning.m similarity index 100% rename from solver/splitProbForConditioning.m rename to src/solver/splitProbForConditioning.m diff --git a/tasks/checkTasks.m b/src/tasks/checkTasks.m similarity index 100% rename from tasks/checkTasks.m rename to src/tasks/checkTasks.m diff --git a/tasks/parseTaskList.m b/src/tasks/parseTaskList.m similarity index 100% rename from tasks/parseTaskList.m rename to src/tasks/parseTaskList.m diff --git a/utils/convertCharArray.m b/src/utils/convertCharArray.m similarity index 100% rename from utils/convertCharArray.m rename to src/utils/convertCharArray.m diff --git a/utils/deprecationWarning.m b/src/utils/deprecationWarning.m similarity index 100% rename from utils/deprecationWarning.m rename to src/utils/deprecationWarning.m diff --git a/utils/grRuleToDNF.m b/src/utils/grRuleToDNF.m similarity index 100% rename from utils/grRuleToDNF.m rename to src/utils/grRuleToDNF.m diff --git a/utils/grRuleToString.m b/src/utils/grRuleToString.m similarity index 100% rename from utils/grRuleToString.m rename to src/utils/grRuleToString.m diff --git a/utils/isDnfGrRule.m b/src/utils/isDnfGrRule.m similarity index 100% rename from utils/isDnfGrRule.m rename to src/utils/isDnfGrRule.m diff --git a/utils/legacyMethodNotice.m b/src/utils/legacyMethodNotice.m similarity index 100% rename from utils/legacyMethodNotice.m rename to src/utils/legacyMethodNotice.m diff --git a/utils/parallelWorkersRAVEN.m b/src/utils/parallelWorkersRAVEN.m similarity index 100% rename from utils/parallelWorkersRAVEN.m rename to src/utils/parallelWorkersRAVEN.m diff --git a/utils/parseGrRule.m b/src/utils/parseGrRule.m similarity index 100% rename from utils/parseGrRule.m rename to src/utils/parseGrRule.m diff --git a/utils/parseRAVENargs.m b/src/utils/parseRAVENargs.m similarity index 100% rename from utils/parseRAVENargs.m rename to src/utils/parseRAVENargs.m diff --git a/utils/printOrange.m b/src/utils/printOrange.m similarity index 100% rename from utils/printOrange.m rename to src/utils/printOrange.m diff --git a/utils/progressReport.m b/src/utils/progressReport.m similarity index 100% rename from utils/progressReport.m rename to src/utils/progressReport.m diff --git a/utils/ravenList.m b/src/utils/ravenList.m similarity index 100% rename from utils/ravenList.m rename to src/utils/ravenList.m diff --git a/utils/ravenModelFields.m b/src/utils/ravenModelFields.m similarity index 100% rename from utils/ravenModelFields.m rename to src/utils/ravenModelFields.m diff --git a/utils/runRAVENtests.m b/src/utils/runRAVENtests.m similarity index 93% rename from utils/runRAVENtests.m rename to src/utils/runRAVENtests.m index 4539d939..6801e027 100644 --- a/utils/runRAVENtests.m +++ b/src/utils/runRAVENtests.m @@ -15,7 +15,7 @@ ravenPath = findRAVENroot; curwd = pwd; -cd(fullfile(ravenPath,'testing','function_tests')); +cd(fullfile(ravenPath,'tests','function_tests')); % Collect the concrete test classes only. RavenTestCase is an abstract base % class that the test classes subclass, and runtests cannot build a suite diff --git a/utils/setRavenProgress.m b/src/utils/setRavenProgress.m similarity index 100% rename from utils/setRavenProgress.m rename to src/utils/setRavenProgress.m diff --git a/testing/function_tests/README.md b/tests/function_tests/README.md similarity index 91% rename from testing/function_tests/README.md rename to tests/function_tests/README.md index 67df9ed8..7f15dbff 100644 --- a/testing/function_tests/README.md +++ b/tests/function_tests/README.md @@ -6,8 +6,8 @@ test class per source folder (`tQueries`, `tManipulation`, `tSolver`, …). ## Running ```matlab -results = runtests('testing/function_tests'); % whole suite -results = runtests('testing/function_tests/tIO.m'); % one folder +results = runtests('tests/function_tests'); % whole suite +results = runtests('tests/function_tests/tIO.m'); % one folder ``` A working solver is required for the simulation-based tests; GLPK ships with diff --git a/testing/function_tests/RavenTestCase.m b/tests/function_tests/RavenTestCase.m similarity index 98% rename from testing/function_tests/RavenTestCase.m rename to tests/function_tests/RavenTestCase.m index 57a17d88..f6af4ee7 100644 --- a/testing/function_tests/RavenTestCase.m +++ b/tests/function_tests/RavenTestCase.m @@ -25,7 +25,7 @@ methods (TestClassSetup) function setupRaven(testCase) testCase.ravenRoot = findRAVENroot(); - loaded = load(fullfile(testCase.ravenRoot,'testing','function_tests', ... + loaded = load(fullfile(testCase.ravenRoot,'tests','function_tests', ... 'test_data','ecoli_textbook.mat'),'model'); testCase.modelTemplate = loaded.model; try diff --git a/testing/function_tests/private/getExprForRxnScore.m b/tests/function_tests/private/getExprForRxnScore.m similarity index 100% rename from testing/function_tests/private/getExprForRxnScore.m rename to tests/function_tests/private/getExprForRxnScore.m diff --git a/testing/function_tests/tAnalysis.m b/tests/function_tests/tAnalysis.m similarity index 100% rename from testing/function_tests/tAnalysis.m rename to tests/function_tests/tAnalysis.m diff --git a/testing/function_tests/tAnnotation.m b/tests/function_tests/tAnnotation.m similarity index 100% rename from testing/function_tests/tAnnotation.m rename to tests/function_tests/tAnnotation.m diff --git a/testing/function_tests/tAssignCompartments.m b/tests/function_tests/tAssignCompartments.m similarity index 100% rename from testing/function_tests/tAssignCompartments.m rename to tests/function_tests/tAssignCompartments.m diff --git a/testing/function_tests/tBinaries.m b/tests/function_tests/tBinaries.m similarity index 95% rename from testing/function_tests/tBinaries.m rename to tests/function_tests/tBinaries.m index 2630b0df..23e5f29f 100644 --- a/testing/function_tests/tBinaries.m +++ b/tests/function_tests/tBinaries.m @@ -28,7 +28,7 @@ function hmmer(testCase) methods (Access = private) function p = binPath(~, tool, name) if ispc; ext = '.exe'; elseif ismac; ext = '.mac'; else; ext = ''; end - p = fullfile(findRAVENroot(),'software',tool,[name ext]); + p = fullfile(findRAVENroot(),'src','external',tool,[name ext]); end function fetchAndRun(testCase, tool, name, versionArg) diff --git a/testing/function_tests/tBiomass.m b/tests/function_tests/tBiomass.m similarity index 100% rename from testing/function_tests/tBiomass.m rename to tests/function_tests/tBiomass.m diff --git a/testing/function_tests/tComparison.m b/tests/function_tests/tComparison.m similarity index 100% rename from testing/function_tests/tComparison.m rename to tests/function_tests/tComparison.m diff --git a/testing/function_tests/tConditions.m b/tests/function_tests/tConditions.m similarity index 100% rename from testing/function_tests/tConditions.m rename to tests/function_tests/tConditions.m diff --git a/testing/function_tests/tConversion.m b/tests/function_tests/tConversion.m similarity index 100% rename from testing/function_tests/tConversion.m rename to tests/function_tests/tConversion.m diff --git a/testing/function_tests/tCuration.m b/tests/function_tests/tCuration.m similarity index 100% rename from testing/function_tests/tCuration.m rename to tests/function_tests/tCuration.m diff --git a/testing/function_tests/tGapfilling.m b/tests/function_tests/tGapfilling.m similarity index 100% rename from testing/function_tests/tGapfilling.m rename to tests/function_tests/tGapfilling.m diff --git a/testing/function_tests/tGenomeData.m b/tests/function_tests/tGenomeData.m similarity index 98% rename from testing/function_tests/tGenomeData.m rename to tests/function_tests/tGenomeData.m index 7ea61779..06855ece 100644 --- a/testing/function_tests/tGenomeData.m +++ b/tests/function_tests/tGenomeData.m @@ -9,7 +9,7 @@ methods (Access = protected) function d = fixtureDir(testCase) - d = fullfile(testCase.ravenRoot,'testing','function_tests', ... + d = fullfile(testCase.ravenRoot,'tests','function_tests', ... 'test_data','genomeData'); end end diff --git a/testing/function_tests/tINIT.m b/tests/function_tests/tINIT.m similarity index 100% rename from testing/function_tests/tINIT.m rename to tests/function_tests/tINIT.m diff --git a/testing/function_tests/tINITtestInfo/01.svg b/tests/function_tests/tINITtestInfo/01.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/01.svg rename to tests/function_tests/tINITtestInfo/01.svg diff --git a/testing/function_tests/tINITtestInfo/02.svg b/tests/function_tests/tINITtestInfo/02.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/02.svg rename to tests/function_tests/tINITtestInfo/02.svg diff --git a/testing/function_tests/tINITtestInfo/03.svg b/tests/function_tests/tINITtestInfo/03.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/03.svg rename to tests/function_tests/tINITtestInfo/03.svg diff --git a/testing/function_tests/tINITtestInfo/04.svg b/tests/function_tests/tINITtestInfo/04.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/04.svg rename to tests/function_tests/tINITtestInfo/04.svg diff --git a/testing/function_tests/tINITtestInfo/05.svg b/tests/function_tests/tINITtestInfo/05.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/05.svg rename to tests/function_tests/tINITtestInfo/05.svg diff --git a/testing/function_tests/tINITtestInfo/06.svg b/tests/function_tests/tINITtestInfo/06.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/06.svg rename to tests/function_tests/tINITtestInfo/06.svg diff --git a/testing/function_tests/tINITtestInfo/07.svg b/tests/function_tests/tINITtestInfo/07.svg similarity index 100% rename from testing/function_tests/tINITtestInfo/07.svg rename to tests/function_tests/tINITtestInfo/07.svg diff --git a/testing/function_tests/tINITtestInfo/README.md b/tests/function_tests/tINITtestInfo/README.md similarity index 100% rename from testing/function_tests/tINITtestInfo/README.md rename to tests/function_tests/tINITtestInfo/README.md diff --git a/testing/function_tests/tIO.m b/tests/function_tests/tIO.m similarity index 96% rename from testing/function_tests/tIO.m rename to tests/function_tests/tIO.m index 53712c11..f26ace24 100644 --- a/testing/function_tests/tIO.m +++ b/tests/function_tests/tIO.m @@ -9,7 +9,7 @@ function exportForGitWritesDependencies(testCase) % Exercises the toolbox-version lookup in exportForGit via the % dependencies.txt it writes - f = fullfile(testCase.ravenRoot,'tutorial','empty.xml'); + f = fullfile(testCase.ravenRoot,'tutorials','data','empty.xml'); evalc('model = importModel(f);'); outDir = tempname; mkdir(outDir); c = onCleanup(@() rmdir(outDir,'s')); @@ -33,7 +33,7 @@ function importModelHandlesSpeciesAndReactionEdgeCases(testCase) % (and disagree with each other); a multi-reaction objective; % a reaction with more than one SUBSYSTEM note; and species % whose charge is genuinely (not just by default) zero. - f = fullfile(testCase.ravenRoot,'testing','function_tests','test_data', ... + f = fullfile(testCase.ravenRoot,'tests','function_tests','test_data', ... 'importModelEdgeCases.xml'); evalc('m = importModel(f);'); @@ -60,20 +60,20 @@ function importModelStripsRegexSpecialCompartmentName(testCase) % A compartment name containing regex metacharacters ("Golgi % (cis)") must still be recognized and stripped from the % metabolite name suffix, not corrupt the matching pattern. - f = fullfile(testCase.ravenRoot,'testing','function_tests','test_data', ... + f = fullfile(testCase.ravenRoot,'tests','function_tests','test_data', ... 'importModelSpecialCompName.xml'); evalc('m = importModel(f);'); testCase.verifyEqual(m.metNames{1}, 'metabolite one'); end function importModelReadsSBML(testCase) - f = fullfile(testCase.ravenRoot,'tutorial','empty.xml'); + f = fullfile(testCase.ravenRoot,'tutorials','data','empty.xml'); evalc('m = importModel(f);'); testCase.verifyTrue(isfield(m, 'rxns')); end function readYAMLmodelReadsYml(testCase) - f = fullfile(testCase.ravenRoot,'tutorial','empty.yml'); + f = fullfile(testCase.ravenRoot,'tutorials','data','empty.yml'); evalc('m = readYAMLmodel(f);'); testCase.verifyTrue(isfield(m, 'rxns')); end @@ -284,7 +284,7 @@ function exportForGitWritesRepo(testCase) end function checkFileExistenceFindsFile(testCase) - f = fullfile(testCase.ravenRoot,'testing','function_tests', ... + f = fullfile(testCase.ravenRoot,'tests','function_tests', ... 'test_data','ecoli_textbook.mat'); out = checkFileExistence(f, 1, false, true); testCase.verifyNotEmpty(out); @@ -296,7 +296,7 @@ function checkFileExistenceAcceptsForwardSlashes(testCase) % built by another tool is likely to use them. Treating such a path % as relative appends the working directory and turns % "C:/data/model.mat" into "C:\somewhere\C:\data\model.mat". - f = fullfile(testCase.ravenRoot,'testing','function_tests', ... + f = fullfile(testCase.ravenRoot,'tests','function_tests', ... 'test_data','ecoli_textbook.mat'); out = checkFileExistence(strrep(f,'\','/'), 1, false, true); testCase.verifyNotEmpty(out); diff --git a/testing/function_tests/tInstallation.m b/tests/function_tests/tInstallation.m similarity index 96% rename from testing/function_tests/tInstallation.m rename to tests/function_tests/tInstallation.m index 8026f44a..611fb5ee 100644 --- a/testing/function_tests/tInstallation.m +++ b/tests/function_tests/tInstallation.m @@ -11,7 +11,7 @@ function findRAVENrootReturnsInstallFolder(testCase) p = findRAVENroot(); testCase.verifyTrue(isfolder(p)); - testCase.verifyTrue(exist(fullfile(p,'installation','findRAVENroot.m'),'file')==2); + testCase.verifyTrue(exist(fullfile(p,'src','installation','findRAVENroot.m'),'file')==2); end function findRAVENrootSurvivesClearAndRepeatCalls(testCase) diff --git a/testing/function_tests/tLocalization.m b/tests/function_tests/tLocalization.m similarity index 100% rename from testing/function_tests/tLocalization.m rename to tests/function_tests/tLocalization.m diff --git a/testing/function_tests/tManipulation.m b/tests/function_tests/tManipulation.m similarity index 99% rename from testing/function_tests/tManipulation.m rename to tests/function_tests/tManipulation.m index 6dae3b3b..6b07eda4 100644 --- a/testing/function_tests/tManipulation.m +++ b/tests/function_tests/tManipulation.m @@ -138,7 +138,7 @@ function addRxnsInvalidStringEqnTypeErrors(testCase) end function addRxnsGenesMetsCopiesFromSource(testCase) - sbmlFile = fullfile(testCase.ravenRoot,'tutorial','empty.xml'); + sbmlFile = fullfile(testCase.ravenRoot,'tutorials','data','empty.xml'); testCase.assumeDependency(exist(sbmlFile,'file')==2, 'tutorial/empty.xml'); evalc('src = importModel(sbmlFile, [], true);'); evalc('m2 = addRxnsGenesMets(testCase.model, src, ''r1'', true);'); diff --git a/testing/function_tests/tNamedArgs.m b/tests/function_tests/tNamedArgs.m similarity index 100% rename from testing/function_tests/tNamedArgs.m rename to tests/function_tests/tNamedArgs.m diff --git a/testing/function_tests/tParseRAVENargs.m b/tests/function_tests/tParseRAVENargs.m similarity index 100% rename from testing/function_tests/tParseRAVENargs.m rename to tests/function_tests/tParseRAVENargs.m diff --git a/testing/function_tests/tQueries.m b/tests/function_tests/tQueries.m similarity index 100% rename from testing/function_tests/tQueries.m rename to tests/function_tests/tQueries.m diff --git a/testing/function_tests/tReconstruction.m b/tests/function_tests/tReconstruction.m similarity index 93% rename from testing/function_tests/tReconstruction.m rename to tests/function_tests/tReconstruction.m index 96e3b277..71a07e5e 100644 --- a/testing/function_tests/tReconstruction.m +++ b/tests/function_tests/tReconstruction.m @@ -92,8 +92,8 @@ function getModelFromHomologyRejectsUnknownComplexPolicy(testCase) end function getBlastRunsWhenAvailable(testCase) - fa1 = fullfile(testCase.ravenRoot,'testing','function_tests','test_data','human_galactosidases.fa'); - fa2 = fullfile(testCase.ravenRoot,'testing','function_tests','test_data','yeast_galactosidases.fa'); + fa1 = fullfile(testCase.ravenRoot,'tests','function_tests','test_data','human_galactosidases.fa'); + fa2 = fullfile(testCase.ravenRoot,'tests','function_tests','test_data','yeast_galactosidases.fa'); testCase.assumeDependency(exist(fa1,'file')==2, 'test FASTA files'); ok = true; try, evalc('bs = getBlast(''human'', fa1, {''yeast''}, {fa2});'); catch, ok = false; end @@ -102,8 +102,8 @@ function getBlastRunsWhenAvailable(testCase) end function getDiamondRunsWhenAvailable(testCase) - fa1 = fullfile(testCase.ravenRoot,'testing','function_tests','test_data','human_galactosidases.fa'); - fa2 = fullfile(testCase.ravenRoot,'testing','function_tests','test_data','yeast_galactosidases.fa'); + fa1 = fullfile(testCase.ravenRoot,'tests','function_tests','test_data','human_galactosidases.fa'); + fa2 = fullfile(testCase.ravenRoot,'tests','function_tests','test_data','yeast_galactosidases.fa'); testCase.assumeDependency(exist(fa1,'file')==2, 'test FASTA files'); ok = true; try, evalc('bs = getDiamond(''human'', fa1, {''yeast''}, {fa2});'); catch, ok = false; end @@ -116,7 +116,7 @@ function getKEGGModelForOrganismNeedsData(testCase) end function getModelFromKEGGNeedsData(testCase) - matFile = fullfile(testCase.ravenRoot, 'reconstruction', 'kegg', 'keggModel.mat'); + matFile = fullfile(testCase.ravenRoot,'src','reconstruction', 'kegg', 'keggModel.mat'); testCase.assumeFalse(exist(matFile, 'file') == 2, ... 'keggModel.mat is present; skipping the build-from-artefacts path.'); testCase.assumeFail('Downloads and assembles the full KEGG artefact set from raven-data; not run automatically.'); @@ -138,7 +138,7 @@ function buildGlobalGPRJoinsGenesThroughSharedKO(testCase) end function getPhylDistNeedsData(testCase) - distFile = fullfile(testCase.ravenRoot, 'reconstruction', 'kegg', 'keggPhylDist.mat'); + distFile = fullfile(testCase.ravenRoot,'src','reconstruction', 'kegg', 'keggPhylDist.mat'); testCase.assumeFalse(exist(distFile, 'file') == 2, ... 'keggPhylDist.mat is present; skipping error-path test.'); testCase.verifyError(@() getPhylDist(), 'getPhylDist:noData'); diff --git a/testing/function_tests/tSampling.m b/tests/function_tests/tSampling.m similarity index 100% rename from testing/function_tests/tSampling.m rename to tests/function_tests/tSampling.m diff --git a/testing/function_tests/tSolver.m b/tests/function_tests/tSolver.m similarity index 100% rename from testing/function_tests/tSolver.m rename to tests/function_tests/tSolver.m diff --git a/testing/function_tests/tSyntax.m b/tests/function_tests/tSyntax.m similarity index 96% rename from testing/function_tests/tSyntax.m rename to tests/function_tests/tSyntax.m index 69c2ebf7..66904f78 100644 --- a/testing/function_tests/tSyntax.m +++ b/tests/function_tests/tSyntax.m @@ -16,7 +16,7 @@ function allSourceFilesParse(testCase) % software/ is vendored third-party code (GLPKmex, libSBML). It is % not ours to fix, so a syntax complaint there is not a RAVEN bug. - paths = paths(~contains(paths, [filesep 'software' filesep])); + paths = paths(~contains(paths, [filesep 'external' filesep])); testCase.assertNotEmpty(paths, 'Found no .m files to check.'); diff --git a/testing/function_tests/tTasks.m b/tests/function_tests/tTasks.m similarity index 95% rename from testing/function_tests/tTasks.m rename to tests/function_tests/tTasks.m index 10360c80..3b858ecf 100644 --- a/testing/function_tests/tTasks.m +++ b/tests/function_tests/tTasks.m @@ -18,7 +18,7 @@ function checkTasksFailsWithoutKeyReaction(testCase) end function parseTaskListReturnsStruct(testCase) - taskFile = fullfile(testCase.ravenRoot,'testing','function_tests', ... + taskFile = fullfile(testCase.ravenRoot,'tests','function_tests', ... 'test_data','test_tasks.txt'); testCase.assumeDependency(exist(taskFile,'file')==2, 'test_tasks.txt'); ts = parseTaskList(taskFile); @@ -29,7 +29,7 @@ function parseTaskListReturnsStruct(testCase) function parseTaskListMatchesExpected(testCase) % The text and Excel task definitions must parse to identical % structs with exactly the expected fields and values. - dataDir = fullfile(testCase.ravenRoot,'testing','function_tests','test_data'); + dataDir = fullfile(testCase.ravenRoot,'tests','function_tests','test_data'); txtFile = fullfile(dataDir,'test_tasks.txt'); xlsFile = fullfile(dataDir,'test_tasks.xls'); testCase.assumeDependency(exist(txtFile,'file')==2, 'test_tasks.txt'); diff --git a/testing/function_tests/tUtils.m b/tests/function_tests/tUtils.m similarity index 100% rename from testing/function_tests/tUtils.m rename to tests/function_tests/tUtils.m diff --git a/testing/function_tests/test_data/ecoli_textbook.mat b/tests/function_tests/test_data/ecoli_textbook.mat similarity index 100% rename from testing/function_tests/test_data/ecoli_textbook.mat rename to tests/function_tests/test_data/ecoli_textbook.mat diff --git a/testing/function_tests/test_data/genomeData/euk.gff b/tests/function_tests/test_data/genomeData/euk.gff similarity index 100% rename from testing/function_tests/test_data/genomeData/euk.gff rename to tests/function_tests/test_data/genomeData/euk.gff diff --git a/testing/function_tests/test_data/genomeData/euk_protein.faa b/tests/function_tests/test_data/genomeData/euk_protein.faa similarity index 100% rename from testing/function_tests/test_data/genomeData/euk_protein.faa rename to tests/function_tests/test_data/genomeData/euk_protein.faa diff --git a/testing/function_tests/test_data/genomeData/prok.gff b/tests/function_tests/test_data/genomeData/prok.gff similarity index 100% rename from testing/function_tests/test_data/genomeData/prok.gff rename to tests/function_tests/test_data/genomeData/prok.gff diff --git a/testing/function_tests/test_data/human_galactosidases.fa b/tests/function_tests/test_data/human_galactosidases.fa similarity index 100% rename from testing/function_tests/test_data/human_galactosidases.fa rename to tests/function_tests/test_data/human_galactosidases.fa diff --git a/testing/function_tests/test_data/importModelEdgeCases.xml b/tests/function_tests/test_data/importModelEdgeCases.xml similarity index 100% rename from testing/function_tests/test_data/importModelEdgeCases.xml rename to tests/function_tests/test_data/importModelEdgeCases.xml diff --git a/testing/function_tests/test_data/importModelSpecialCompName.xml b/tests/function_tests/test_data/importModelSpecialCompName.xml similarity index 100% rename from testing/function_tests/test_data/importModelSpecialCompName.xml rename to tests/function_tests/test_data/importModelSpecialCompName.xml diff --git a/testing/function_tests/test_data/test_tasks.txt b/tests/function_tests/test_data/test_tasks.txt similarity index 100% rename from testing/function_tests/test_data/test_tasks.txt rename to tests/function_tests/test_data/test_tasks.txt diff --git a/testing/function_tests/test_data/test_tasks.xls b/tests/function_tests/test_data/test_tasks.xls similarity index 100% rename from testing/function_tests/test_data/test_tasks.xls rename to tests/function_tests/test_data/test_tasks.xls diff --git a/testing/function_tests/test_data/yeast_galactosidases.fa b/tests/function_tests/test_data/yeast_galactosidases.fa similarity index 100% rename from testing/function_tests/test_data/yeast_galactosidases.fa rename to tests/function_tests/test_data/yeast_galactosidases.fa diff --git a/tutorial/biomassConditions_template.tsv b/tutorials/data/cell_analysis/biomassConditions_template.tsv similarity index 100% rename from tutorial/biomassConditions_template.tsv rename to tutorials/data/cell_analysis/biomassConditions_template.tsv diff --git a/tutorial/empty.mat b/tutorials/data/empty.mat similarity index 100% rename from tutorial/empty.mat rename to tutorials/data/empty.mat diff --git a/tutorial/empty.xml b/tutorials/data/empty.xml similarity index 100% rename from tutorial/empty.xml rename to tutorials/data/empty.xml diff --git a/tutorial/empty.yml b/tutorials/data/empty.yml similarity index 100% rename from tutorial/empty.yml rename to tutorials/data/empty.yml diff --git a/tutorial/iAL1006 v1.00.xml b/tutorials/data/models/iAL1006 v1.00.xml similarity index 100% rename from tutorial/iAL1006 v1.00.xml rename to tutorials/data/models/iAL1006 v1.00.xml diff --git a/tutorial/small.yml b/tutorials/data/models/small.yml similarity index 100% rename from tutorial/small.yml rename to tutorials/data/models/small.yml diff --git a/tutorial/smallYeast.yml b/tutorials/data/models/smallYeast.yml similarity index 100% rename from tutorial/smallYeast.yml rename to tutorials/data/models/smallYeast.yml diff --git a/tutorial/smallYeastBad.yml b/tutorials/data/models/smallYeastBad.yml similarity index 100% rename from tutorial/smallYeastBad.yml rename to tutorials/data/models/smallYeastBad.yml diff --git a/tutorial/expression.txt b/tutorials/data/omics/expression.txt similarity index 100% rename from tutorial/expression.txt rename to tutorials/data/omics/expression.txt diff --git a/tutorial/sce.fa b/tutorials/data/sequences/sce.fa similarity index 100% rename from tutorial/sce.fa rename to tutorials/data/sequences/sce.fa diff --git a/tutorial/tutorial1.m b/tutorials/tutorial1.m similarity index 99% rename from tutorial/tutorial1.m rename to tutorials/tutorial1.m index abcc7db7..5fcdce00 100755 --- a/tutorial/tutorial1.m +++ b/tutorials/tutorial1.m @@ -4,7 +4,7 @@ % perform an optimization through flux balance analysis (FBA). The % resulting fluxes are visualized and exported to a PDF file. % For a more detailed description of the individual functions, see -% [raven_directory]/doc/index.html. +% [raven_directory]/docs/html/index.html. % A GEM for the filamentous fungus Penicillium chrysogenum is used in % this tutorial. The model is provided as the SBML file % "iAL1006 v1.00.xml". diff --git a/tutorial/tutorial2.m b/tutorials/tutorial2.m similarity index 100% rename from tutorial/tutorial2.m rename to tutorials/tutorial2.m diff --git a/tutorial/tutorial2_solutions.m b/tutorials/tutorial2_solutions.m similarity index 100% rename from tutorial/tutorial2_solutions.m rename to tutorials/tutorial2_solutions.m diff --git a/tutorial/tutorial3.m b/tutorials/tutorial3.m similarity index 100% rename from tutorial/tutorial3.m rename to tutorials/tutorial3.m diff --git a/tutorial/tutorial3_solutions.m b/tutorials/tutorial3_solutions.m similarity index 100% rename from tutorial/tutorial3_solutions.m rename to tutorials/tutorial3_solutions.m diff --git a/tutorial/tutorial4.m b/tutorials/tutorial4.m similarity index 100% rename from tutorial/tutorial4.m rename to tutorials/tutorial4.m diff --git a/tutorial/tutorial4_solutions.m b/tutorials/tutorial4_solutions.m similarity index 100% rename from tutorial/tutorial4_solutions.m rename to tutorials/tutorial4_solutions.m diff --git a/tutorial/tutorial5.m b/tutorials/tutorial5.m similarity index 100% rename from tutorial/tutorial5.m rename to tutorials/tutorial5.m diff --git a/tutorial/tutorial7.m b/tutorials/tutorial7.m similarity index 100% rename from tutorial/tutorial7.m rename to tutorials/tutorial7.m