Release 3.0.0b2

.github/CONTRIBUTING.md

@@ -5,9 +5,9 @@ Anybody is welcome to contribute to the development of the RAVEN Toolbox, but pl
 Each function should start with a commented section describing the function and explaining the parameters. Existing functions can clarify what style should be used.
 
 ### Bugfixes, New Features and Functions
-* For any development, whether bug fixes, introducing new functions or new/updated features for existing functions: make a separate branch from `devel` and name the branch for instance after the function/feature you are fixing/developing. If you work on a fix, start the branch name with `fix/`, if you work on a feature, start the branch name with `feat/`. Examples: `fix/format_reactions` or `feat/new_algorithms`.
+* For any development, whether bug fixes, introducing new functions or new/updated features for existing functions: make a separate branch from `develop` and name the branch for instance after the function/feature you are fixing/developing. If you work on a fix, start the branch name with `fix/`, if you work on a feature, start the branch name with `feat/`. Examples: `fix/format_reactions` or `feat/new_algorithms`.
 * Make commits to this branch while developing. Aim for backward compatibility, and try to avoid very new MATLAB functions when possible, to accommodate users with older MATLAB versions.
-* When you are happy with your new function/feature, make a pull request to the `devel` branch. Also, see [Pull request](#pull-request) below.
+* When you are happy with your new function/feature, make a pull request to the `develop` branch. Also, see [Pull request](#pull-request) below.
 
 ### Semantic Commits
 Use semantic commit messages to make it easier to show what you are aiming to do:
@@ -28,26 +28,26 @@ A more detailed explanation or comments can be left in the commit description.
 
 ### External Software Update
 * 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`
+* Create a separate branch from the `develop` 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.
-* Do some testing to ensure that the new binaries are working correctly. Upon successful tests, create a Pull Request to the `devel` branch.
+* 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 `develop` branch.
 
 ### Pull Requests
-* No changes should be directly committed to the `main` or `devel` branches. Commits are made to side branches, after which pull requests are made for merging with `main` or `devel`.
+* No changes should be directly committed to the `main` or `develop` branches. Commits are made to side branches, after which pull requests are made for merging with `main` or `develop`.
 * The person making the pull request and the one accepting the merge _cannot_ be the same person.
 * Typically, wait a few days before merging, to allow for other developers to inspect the pull request.
 * A merge with the mainbranch invokes a new release (see [versioning](#versioning)).
 
 ### Versioning
-RAVEN Toolbox follows [semantic versioning](https://semver.org/). After each successful Pull Request (PR) to `main`, the `version.txt` file should be updated in a separate PR. When this PR is merged, a new [release](https://github.com/SysBioChalmers/RAVEN/releases) should be specified, with a list detailing the most significant changes since the previous release.
+RAVEN Toolbox follows [semantic versioning](https://semver.org/). After each successful Pull Request (PR) to `main`, the `version.txt` file should be updated in a separate PR. When this PR is merged, a new [release](https://github.com/CompMetEng/RAVEN/releases) should be specified, with a list detailing the most significant changes since the previous release.
 
-Ensure that the documentation is also updated (in `devel`) before creating a PR to `main`. It can be updated by running `updateDocumentation()`.
+Ensure that the documentation is also updated (in `develop`) before creating a PR to `main`. It can be updated by running `updateDocumentation()`.
 
 ### Categorize Releases
 * PRs pushed into `main` should be patch releases by default.
-* Developers who push PRs to `devel` may propose target release categories (e.g. minor or patch) that can be commented on and discussed by reviewers and other developers.
+* Developers who push PRs to `develop` may propose target release categories (e.g. minor or patch) that can be commented on and discussed by reviewers and other developers.
 * As a result of the above step, minor releases hopefully can be determined.
 * To help the process of categorizing releases, some conditions are suggested qualification for minor releases:
     * with database updates (e.g. KEGG)

.github/issue_template.md

@@ -26,4 +26,4 @@ etc. etc.
 
 **I hereby confirm that I have:**
 <!-- Note: replace [ ] with [X] to check the box -->
-- [ ] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?q=is%3Aissue) or is already [discussed](https://github.com/SysBioChalmers/RAVEN/discussions).
+- [ ] Checked that a similar issue does not [already exist](https://github.com/CompMetEng/RAVEN/issues?q=is%3Aissue) or is already [discussed](https://github.com/CompMetEng/RAVEN/discussions).

.github/pull_request_template.md

@@ -11,4 +11,4 @@
 <!-- Chose ONE of the following two options
 and replace [ ] with [X] to check the box.-->
 - [ ] This PR has `develop` as target branch, and will be resolved with a *squash-merge*.
-- [ ] This PR has `main` as target branch, and will be resolved as descriped [here](https://github.com/SysBioChalmers/RAVEN/wiki/Development-policy#make-a-new-release).
+- [ ] This PR has `main` as target branch, and will be resolved as described [here](https://github.com/CompMetEng/RAVEN/blob/develop/.github/CONTRIBUTING.md#versioning).

.github/scripts/assemble_offline_software.py

@@ -1,14 +1,14 @@
 #!/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,
+Downloads the per-platform binary ZIPs from toolbox-assets and lays them out under
+``<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).
 
 Run from the RAVEN root, or pass ``--raven <dir>``. Requires network access to
-https://github.com/SysBioChalmers/raven-data .
+https://github.com/CompMetEng/toolbox-assets .
 """
 from __future__ import annotations
 
@@ -18,11 +18,11 @@
 import zipfile
 from pathlib import Path
 
-RAVEN_DATA = "https://github.com/SysBioChalmers/raven-data/releases/download"
-# raven-data platform key -> RAVEN binary suffix.
+TOOLBOX_ASSETS = "https://github.com/CompMetEng/toolbox-assets/releases/download"
+# toolbox-assets platform key -> RAVEN binary suffix.
 PLATFORMS = {"linux-x86_64": "", "macos-arm64": ".mac", "windows-x86_64": ".exe"}
 
-# (software subdir, raven-data bundle, {platform|"_": version}, {bare executable names})
+# (software subdir, toolbox-assets bundle, {platform|"_": version}, {bare executable names})
 CLI_TOOLS = [
     ("blast+",  "blast",   {"_": "2.17.0"},                          {"blastp", "makeblastdb"}),
     ("diamond", "diamond", {"_": "2.1.17"},                          {"diamond"}),
@@ -31,7 +31,7 @@
 
 
 def _fetch(url: str) -> bytes:
-    with urllib.request.urlopen(url, timeout=120) as resp:  # noqa: S310 (pinned raven-data URLs)
+    with urllib.request.urlopen(url, timeout=120) as resp:  # noqa: S310 (pinned toolbox-assets URLs)
         return resp.read()
 
 
@@ -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():
@@ -60,7 +60,7 @@ def assemble(raven: Path) -> None:
             # macOS ships bare names; rename them to <name>.mac. Linux keeps bare names,
             # Windows already carries .exe — so only the macOS members need renaming.
             rename = {e: e + ".mac" for e in exes} if suffix == ".mac" else {}
-            _extract(_fetch(f"{RAVEN_DATA}/{bundle}-{version}/{asset}"), dest, rename)
+            _extract(_fetch(f"{TOOLBOX_ASSETS}/{bundle}-{version}/{asset}"), dest, rename)
 
 
 def main(argv: list[str] | None = None) -> None:

.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.
 #
@@ -18,7 +18,7 @@ name: Documentation
 
 on:
   push:
-    branches: [develop3, develop, main]
+    branches: [develop, main]
     paths:
       - '**.m'
       - '.github/workflows/documentation.yml'
@@ -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)
@@ -72,7 +72,7 @@ jobs:
 
   binary-tests:
     name: Binary download (${{ matrix.os }})
-    # Validate the on-demand fetch of the external binaries from raven-data on
+    # Validate the on-demand fetch of the external binaries from toolbox-assets on
     # Linux and macOS. Running the downloaded binaries also confirms the macOS
     # Gatekeeper quarantine is cleared so they can execute.
     strategy:

.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