Merge branch 'onnx' into vnnlib

Author: pobonomo

.github/actions/lint/action.yml

@@ -0,0 +1,13 @@
+name: lint
+description: Run Ruff format check and lint
+runs:
+  using: composite
+  steps:
+    - name: Ruff format check
+      uses: astral-sh/ruff-action@v3
+      with:
+        args: format --check .
+    - name: Ruff lint
+      uses: astral-sh/ruff-action@v3
+      with:
+        args: check .

.github/actions/setup-python-and-install/action.yml

@@ -0,0 +1,23 @@
+name: setup-python-and-install
+description: Set up Python and optionally install packages
+inputs:
+  python-version:
+    description: Python version to set up
+    required: true
+  packages:
+    description: Space-separated pip packages to install
+    required: false
+    default: ""
+runs:
+  using: composite
+  steps:
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ inputs.python-version }}
+    - name: Install packages
+      if: ${{ inputs.packages != '' }}
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install ${{ inputs.packages }}

.github/actions/write-license/action.yml

@@ -0,0 +1,20 @@
+name: write-license
+description: Write LICENSE secret into a gurobi.lic file and output its path
+inputs:
+  license:
+    description: The contents of the license file
+    required: true
+outputs:
+  grb_license_file:
+    description: Path to the written license file
+    value: ${{ steps.write.outputs.grb_license_file }}
+runs:
+  using: composite
+  steps:
+    - id: write
+      shell: bash
+      env:
+        LICENSE: ${{ inputs.license }}
+      run: |
+        echo "$LICENSE" > "$PWD/gurobi.lic"
+        echo "grb_license_file=$PWD/gurobi.lic" >> "$GITHUB_OUTPUT"

.github/hooks/license_embedded.py

@@ -1,33 +1,97 @@
 import json
 import sys
+from datetime import datetime
 from pathlib import Path
 
 expected_license = Path("copyright.txt").read_text().rstrip()
 
 
+def _allowed_first_line(line: str, base_first_line: str) -> bool:
+    """
+    Allow first line to either be:
+      - a single current year (YYYY), or
+      - a range START-YYYY where START is in [2023, YYYY] and YYYY is the current year.
+
+    The rest of the text (before and after the year section) must match the base template.
+    """
+    import re
+
+    m = re.search(r"\b(\d{4})\b", base_first_line)
+    if not m:
+        # If no year in base, require exact match
+        return line == base_first_line
+
+    pre = base_first_line[: m.start()]
+    post = base_first_line[m.end() :]
+
+    if not (line.startswith(pre) and line.endswith(post)):
+        return False
+
+    middle = line[len(pre) : len(line) - len(post)]
+    current_year = datetime.utcnow().year
+
+    # Accept single current year
+    if re.fullmatch(r"\d{4}", middle):
+        return int(middle) == current_year
+
+    # Accept range START-CURRENT_YEAR
+    m2 = re.fullmatch(r"(\d{4})-(\d{4})", middle)
+    if not m2:
+        return False
+
+    start, end = int(m2.group(1)), int(m2.group(2))
+    if end != current_year:
+        return False
+    if start < 2023 or start > end:
+        return False
+    return True
+
+
+def license_header_matches(text: str) -> bool:
+    base_lines = expected_license.splitlines()
+    lines = text.splitlines()
+    if len(lines) < len(base_lines):
+        return False
+
+    # Compare first line with flexible year
+    if not _allowed_first_line(lines[0], base_lines[0]):
+        return False
+
+    # Compare remaining lines exactly
+    for i in range(1, len(base_lines)):
+        if lines[i] != base_lines[i]:
+            return False
+
+    return True
+
+
 def python_check(content: str, cur_file: str) -> str:
-    if not content.startswith(expected_license):
-        return f"'{cur_file}' did not start with copyright.txt content"
-    else:
-        return ""
+    if not license_header_matches(content):
+        y = datetime.utcnow().year
+        return (
+            f"'{cur_file}' did not start with copyright.txt content. "
+            f"First line must use either '{y}' or 'START-{y}' with START>=2023."
+        )
+    return ""
 
 
 def notebook_check(content: str, cur_file: str) -> str:
     j = json.loads(content)
-    code = 0
     try:
-        if not j["metadata"]["license"]["full_text"] == expected_license:
-            code = 1
+        full_text = j["metadata"]["license"]["full_text"]
     except KeyError:
-        code = 1
-
-    if code == 1:
         return (
             f"'{cur_file}' does not have the copyright.txt content as metadata. "
             f"This should go into metadata.license.full_text"
         )
-    else:
-        return ""
+
+    if not isinstance(full_text, str) or not license_header_matches(full_text):
+        y = datetime.utcnow().year
+        return (
+            f"'{cur_file}' license metadata does not match expected text. "
+            f"First line must use either '{y}' or 'START-{y}' with START>=2023."
+        )
+    return ""
 
 
 def check_file(cur_file: str) -> str:

.github/scripts/upload_anaconda.sh

@@ -1,11 +1,8 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
-set -e
+set -euo pipefail
 set -x
 
-export PATH=$CONDA/bin:$PATH
-conda create -n upload -y python=3.10
-source activate upload
-conda install -y anaconda-client
-
-anaconda -t $ANACONDA_STAGING_TOKEN upload --force -u gurobi-machinelearning-wheels-staging dist/artifact/*
+# Install anaconda-client via pip and upload artifacts without requiring conda
+python -m pip install --upgrade anaconda-client
+anaconda -t "$ANACONDA_STAGING_TOKEN" upload --force -u gurobi-machinelearning-wheels-staging dist/*

.github/workflows/PR_license.yml

@@ -3,8 +3,7 @@
 # label added. Any changes to the PR in need of a retriggering of the workflow require the removal and re-adding of the
 # "safe to test" label.
 #
-# Since a subset of tests was already run in the nolicense workflow, this workflow runs skips the following tests:
-# - Lint with flake8.
+# Since a subset of checks already ran in the nolicense workflow, this workflow skips linting here.
 
 name: build and test PR, license required
 
@@ -15,47 +14,74 @@ on:
 permissions:
   contents: read
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build_pr_license:
+  tests:
     runs-on: ubuntu-latest
     if: contains(github.event.pull_request.labels.*.name, 'safe to test')
+    timeout-minutes: 45
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        gurobi-version: ["gurobi10", "gurobi11","gurobi12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        gurobi-version: ["gurobi11","gurobi12","gurobi13"]
         exclude:
-          - python-version: "3.12"
-            gurobi-version: "gurobi10"
+          - python-version: "3.13"
+            gurobi-version: "gurobi11"
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+      - name: Setup Python
+        uses: ./.github/actions/setup-python-and-install
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v3
+      - id: write-license
+        name: Write license
+        uses: ./.github/actions/write-license
+        with:
+          license: ${{ secrets.LICENSE }}
+      - name: Test with tox (uv)
+        env:
+          GRB_LICENSE_FILE: ${{ steps.write-license.outputs.grb_license_file }}
+          GUROBI_VERSION: ${{ matrix.gurobi-version }}
+        run: |
+          uvx tox
+
+  examples:
+    runs-on: ubuntu-latest
+    if: contains(github.event.pull_request.labels.*.name, 'safe to test')
+    needs: tests
+    timeout-minutes: 45
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+        gurobi-version: ["gurobi11","gurobi12","gurobi13"]
     steps:
-    - uses: actions/checkout@v5
-      with:
-        ref: ${{ github.event.pull_request.head.sha }}
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest tox tox-gh-actions
-    - shell: bash
-      id: write-license
-      env:
-        LICENSE: ${{ secrets.LICENSE   }}
-      run: |
-        echo "$LICENSE" > $PWD/gurobi.lic
-        echo "grb_license_file=$PWD/gurobi.lic" >> $GITHUB_OUTPUT
-    - name: Test with tox
-      run: |
-        tox
-      env:
-        GRB_LICENSE_FILE: ${{ steps.write-license.outputs.grb_license_file }}
-        GUROBI_VERSION: ${{ matrix.gurobi-version }}
-    - name: Run examples with Gurobi 11
-      if: ${{ (matrix.gurobi-version == 'gurobi11') && (matrix.python-version == '3.12') }}
-      env:
-        GRB_LICENSE_FILE: ${{ steps.write-license.outputs.grb_license_file }}
-        GUROBI_VERSION: ${{ matrix.gurobi-version }}
-      run: |
-        python_version_no_dot=$(echo "${{ matrix.python-version }}" | tr -d '.')
-        tox -e py${python_version_no_dot}-examples-${{matrix.gurobi-version}}
+      - uses: actions/checkout@v5
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+      - name: Setup Python
+        uses: ./.github/actions/setup-python-and-install
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v3
+      - id: write-license
+        name: Write license
+        uses: ./.github/actions/write-license
+        with:
+          license: ${{ secrets.LICENSE }}
+      - name: Run examples (uv)
+        env:
+          GRB_LICENSE_FILE: ${{ steps.write-license.outputs.grb_license_file }}
+          GUROBI_VERSION: ${{ matrix.gurobi-version }}
+        run: |
+          python_version_no_dot=$(echo "${{ matrix.python-version }}" | tr -d '.')
+          uvx tox -e py${python_version_no_dot}-examples-${{ matrix.gurobi-version }}

.github/workflows/PR_nolicense.yml

@@ -13,32 +13,41 @@ on:
 permissions:
   contents: read
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build_pr_nolicense:
+  lint:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v5
+      - name: Lint
+        uses: ./.github/actions/lint
+
+  test:
+    needs: lint
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        gurobi-version: ["gurobi11","gurobi12"]
-
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        gurobi-version: ["gurobi11","gurobi12","gurobi13"]
+        exclude:
+          - python-version: "3.13"
+            gurobi-version: "gurobi11"
     steps:
-    - uses: actions/checkout@v5
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox tox-gh-actions
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox, excluding the examples target
-      run: |
-        tox
-      env:
-        GUROBI_VERSION: ${{ matrix.gurobi-version }}
+      - uses: actions/checkout@v5
+      - name: Setup Python
+        uses: ./.github/actions/setup-python-and-install
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v3
+      - name: Test with tox (uv), excluding the examples target
+        env:
+          GUROBI_VERSION: ${{ matrix.gurobi-version }}
+        run: |
+          uvx tox