Clean project structure for v3

.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

.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
-``<raven>/software/<tool>/`` using RAVEN's suffix scheme — bare name = Linux,
+``<raven>/src/external/<tool>/`` 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():

.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]"

.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-<tag>-full.zip

.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)

.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
 

README.md

@@ -1,4 +1,4 @@
-<img src="./RAVEN.png" width="200px">
+<img src="img/RAVEN.png" width="200px">
 
 [![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)

_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/"]

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 = fullfile(ravenDir,'src','external');
 
 % blast+/diamond/hmmer may be present from an on-demand download
 % (downloadRavenBinaries already chmods those) or from the offline bundle;