Release 3.0.0b2

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
-      - run: pip install --upgrade pip
+      - run: python -m pip install --upgrade pip
       # Pinned so the lint result is reproducible (unpinned ruff silently
       # adds rules over time). Keep in sync with the ``dev`` extra in pyproject.
       - run: pip install ruff==0.15.15
@@ -38,7 +38,7 @@ jobs:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
-      - run: pip install --upgrade pip
+      - run: python -m pip install --upgrade pip
       # Installs runtime deps + the dev extra (mypy). Third-party stubs are
       # absent for cobra/optlang/scipy; ignore_missing_imports handles that.
       - run: pip install -e ".[dev]"
@@ -54,7 +54,7 @@ jobs:
         # Full Python range on Linux; a single Python on macOS/Windows to catch
         # OS-specific issues (paths, subprocess, file I/O) at low runner cost.
         os: [ubuntu-latest]
-        python: ["3.11", "3.12", "3.13"]
+        python: ["3.11", "3.12", "3.13", "3.14", "3.15"]
         include:
           - { os: macos-latest, python: "3.12" }
           - { os: windows-latest, python: "3.12" }
@@ -65,7 +65,12 @@ jobs:
           python-version: ${{ matrix.python }}
           cache: pip
           cache-dependency-path: pyproject.toml
-      - run: pip install --upgrade pip
+      - run: python -m pip install --upgrade pip
+      # swiglpk (a cobra/optlang dependency) publishes no Python 3.15 wheel, so pip
+      # builds it from source, which needs the GLPK headers and SWIG.
+      - name: Install GLPK build dependencies
+        if: matrix.python == '3.15'
+        run: sudo apt-get update && sudo apt-get install -y libglpk-dev swig
       # ``-e .[dev,excel]`` so every optional extra is exercised.
       # Gurobi is not installable on free runners; the relevant tests
       # skip themselves when ``optlang.gurobi_interface`` cannot import.
@@ -84,21 +89,21 @@ jobs:
     timeout-minutes: 20
     steps:
       - uses: actions/checkout@v5
-      # RAVEN is GPL and this package is MIT, so its files are never vendored
+      # RAVEN is a separate repository, so its files are never vendored
       # here -- the cross-language checks read them from a checkout instead.
-      # develop3 is the branch raven-docs documents and raven-toolbox tracks.
+      # develop is the RAVEN branch raven-docs documents and raven-toolbox tracks.
       - name: Check out MATLAB RAVEN
         uses: actions/checkout@v5
         with:
-          repository: SysBioChalmers/RAVEN
-          ref: develop3
+          repository: CompMetEng/RAVEN
+          ref: develop
           path: .raven
       - uses: actions/setup-python@v6
         with:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
-      - run: pip install --upgrade pip
+      - run: python -m pip install --upgrade pip
       # gurobipy ships a size-limited licence (2000 variables / 2000
       # constraints). That is useless at genome scale but ample for the small
       # fixtures here, and it gives the cross-solver check a second solver to
@@ -114,19 +119,3 @@ jobs:
           RAVEN_ROOT: ${{ github.workspace }}/.raven
           PYTHONUNBUFFERED: "1"
 
-  docs:
-    name: docs
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v5
-      - uses: actions/setup-python@v6
-        with:
-          python-version: "3.12"
-          cache: pip
-          cache-dependency-path: pyproject.toml
-      - run: pip install --upgrade pip
-      # The package (with autodoc's import-time extras) plus the docs toolchain.
-      - run: pip install -e ".[excel]" -r docs/requirements.txt
-      # ``-W --keep-going`` keeps the docs build warning-clean; mirrors the
-      # ReadTheDocs build (docs/conf.py + .readthedocs.yaml).
-      - run: sphinx-build -b html -W --keep-going docs docs/_build/html

.github/workflows/parity-nightly.yml

@@ -33,16 +33,12 @@ jobs:
     name: genome-scale parity
     # Forks do not have the secrets, and a scheduled run there would fail every
     # night for no reason.
-    if: github.repository == 'SysBioChalmers/raven-toolbox'
+    if: github.repository == 'CompMetEng/raven-toolbox'
     runs-on: ubuntu-latest
-    # Measured against the classic INIT MILP this job used to check (now
-    # ftINIT's run_ftinit, bounded to time_limit=600s -- see
-    # tests/parity/test_genome_scale.py): that extraction took ~68 minutes on
-    # a fast workstation, of which only ~2 were parsing and copying, and
-    # time_limit did not bound the call -- a 60-second limit still ran for
-    # well over 15 minutes -- so the real stop was pytest-timeout below. This
-    # budget is comfortably larger than ftINIT's bound so a runaway is still
-    # reported as a test failure instead of a killed job.
+    # The extraction is run_ftinit bounded to time_limit=600s (see
+    # tests/parity/test_genome_scale.py). This budget is comfortably larger
+    # than that bound, so a runaway is reported as a test failure by
+    # pytest-timeout below instead of a killed job.
     timeout-minutes: 150
 
     steps:
@@ -51,8 +47,8 @@ jobs:
       - name: Check out MATLAB RAVEN
         uses: actions/checkout@v5
         with:
-          repository: SysBioChalmers/RAVEN
-          ref: develop3
+          repository: CompMetEng/RAVEN
+          ref: develop
           path: .raven
 
       - uses: actions/setup-python@v6
@@ -61,7 +57,7 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
 
-      - run: pip install --upgrade pip
+      - run: python -m pip install --upgrade pip
       - run: pip install -e ".[dev]" gurobipy
 
       # Fail here, loudly, rather than let the tests skip and the job go green

.github/workflows/release.yml

@@ -31,7 +31,7 @@ jobs:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
-      - run: pip install --upgrade pip
+      - run: python -m pip install --upgrade pip
       - run: pip install build
       - run: python -m build
 
@@ -115,7 +115,7 @@ jobs:
     # Trusted Publishing: PyPI verifies this workflow's OIDC identity, so no
     # long-lived token is stored in the repo. Requires a one-time publisher on
     # PyPI for raven-toolbox with:
-    #   owner: SysBioChalmers   repo: raven-toolbox
+    #   owner: CompMetEng       repo: raven-toolbox
     #   workflow: release.yml   environment: pypi
     environment: pypi
     permissions: