Pure python rewrite

.github/workflows/ci.yaml

@@ -2,14 +2,9 @@ name: CI
 
 on:
   push:
-    tags: ["*"]
-    branches:
-      - master
-      - main
-  pull_request:
-    branches:
-      - master
-      - main
+    branches: [main]
+    tags: [v*]
+  pull_request: {}
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -24,48 +19,33 @@ jobs:
       - name: Run pre-commit linting
         run: pipx run pre-commit run --all-files
 
-  check-manifest:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      # this test ensures that the sdist contains all necessary files
-      # if it fails, you need to either update MANIFEST.in,
-      # or add an explicit "ignore" rule to pyproject.toml
-      - name: Run check-manifest
-        run: pipx run check-manifest
-
   test:
     runs-on: ${{ matrix.platform }}
-    defaults:
-      run:
-        shell: bash -el {0} # needed when using setup-miniconda
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
-        platform: [ubuntu-latest, windows-latest]
+        platform: [ubuntu-latest, windows-latest, macos-latest]
         include:
           - python-version: "3.9"
             platform: ubuntu-latest
-          - python-version: "3.9"
-            platform: macos-13
+          - python-version: "3.13"
+            platform: ubuntu-latest
+        exclude:
+          # getting segfaults on _get_coefficients...
+          # probably related to the recursion limit
           - python-version: "3.10"
             platform: macos-latest
-          - python-version: "3.11"
-            platform: macos-latest
 
     steps:
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
         with:
+          version: "0.5.10"
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
           python-version: ${{ matrix.python-version }}
-          miniforge-version: latest
-          use-mamba: true
-          channels: conda-forge,gurobi,defaults
-          channel-priority: true
-
-      - name: install build deps
-        run: mamba install scip=9.1.0 gurobi gcovr
 
       - name: add gurobi license
         shell: bash
@@ -76,46 +56,46 @@ jobs:
           echo "$LICENSE" > $PWD/gurobi.lic
           echo "grb_license_file=$PWD/gurobi.lic" >> $GITHUB_OUTPUT
 
-      - name: install package
-        run: |
-          python -m pip install -U pip
-          python -m pip install -e .[dev]
-          python setup.py build_ext --inplace  # required for C coverage
-        env:
-          CYTHON_TRACE: 1 # enable coverage of cython code
-          CFLAGS: "-coverage" # enable coverage of C code
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install the project
+        run: uv sync --extra test
 
       - name: run tests
-        run: |
-          pytest --color yes -v --cov ilpy --cov-report=xml
-          gcovr --xml coverage_cpp.xml  # generate C coverage report
+        run: uv run pytest --color yes -v --cov ilpy --cov-report=xml
         env:
           GRB_LICENSE_FILE: ${{ steps.write-license.outputs.grb_license_file }}
 
       - name: upload coverage
         uses: codecov/codecov-action@v5
-        with:
-          files: ./coverage.xml,./coverage_cpp.xml
 
-  # we only deploy the sdist to PyPI, the wheel is still complicated
-  deploy-sdist:
+  # test-motile:
+  #   uses: pyapp-kit/workflows/.github/workflows/test-dependents.yml@v2
+  #   with:
+  #     dependency-repo: funkelab/motile
+  #     dependency-extras: "test"
+  #     python-version: "3.11"
+
+  deploy:
+    needs: test
     if: startsWith(github.ref, 'refs/tags')
-    needs: [test, check-manifest]
-    name: Build sdist, Publish to PyPI on tagged versions
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: write
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
-      - name: Build an sdist
-        run: |
-          python -m pip install build
-          python -m build --sdist
-      - name: Publish to PyPI
+          fetch-depth: 0
+
+      - name: 👷 Build
+        run: pipx run build
+
+      - name: 🚢 Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+
       - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
+          files: "./dist/*"

.github/workflows/publish-docs.yaml

@@ -21,17 +21,13 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/setup-python@v2
         with:
-          python-version: "3.11"
-          miniforge-version: latest
-          use-mamba: true
-          channels: conda-forge,gurobi,defaults
-          channel-priority: true
+          python-version: "3.12"
 
       - name: Install package and dependencies
         run: |
-          mamba install scip gurobi
+          python -m pip install --upgrade pip
           python -m pip install -e .[docs]
 
       - name: Build documentation

.github2/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* ilpy version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.github2/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

.github2/dependabot.yml

@@ -0,0 +1,10 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

.github2/workflows/ci.yml

@@ -0,0 +1,76 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    uses: pyapp-kit/workflows/.github/workflows/test-pyrepo.yml@v2
+    with:
+      os: ${{ matrix.platform }}
+      python-version: ${{ matrix.python-version }}
+      coverage-upload: artifact
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+  upload_coverage:
+    if: always()
+    needs: [test]
+    uses: pyapp-kit/workflows/.github/workflows/upload-coverage.yml@v2
+    secrets:
+      codecov_token: ${{ secrets.CODECOV_TOKEN }}
+
+  deploy:
+    name: Deploy
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

.pre-commit-config.yaml

@@ -1,24 +1,35 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
 ci:
   autoupdate_schedule: monthly
   autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
   autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
 
 repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.28.4
+    hooks:
+      - id: typos
+        args: [--force-exclude] # omitting --write-changes
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.8.3
     hooks:
       - id: ruff
-        args: [--fix]
+        args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
-  - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.0
-    hooks:
-      - id: cython-lint
-      - id: double-quote-cython-strings
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.13.0
     hooks:
       - id: mypy
-        files: "^ilpy/"
+        files: "^src/"
+        additional_dependencies:
+          - gurobipy

CONTRIBUTING.md

@@ -4,14 +4,7 @@ ilpy welcomes contributions
 
 ## Local development
 
-ilpy links against SCIP, so you must have SCIP installed in your environment.
-(You can install via conda)
-
-```bash
-conda install scip
-```
-
-Then clone the repo and install in editable mode.
+Clone the repo and install in editable mode.
 
 ```bash
 git clone <your-fork>

docs/conf.py

@@ -7,7 +7,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "ilpy"
-copyright = "2023, Jan Funke, Talley Lambert"
+copyright = "2023, Jan Funke, Talley Lambert"  # noqa
 author = "Jan Funke, Talley Lambert"
 
 # -- General configuration ---------------------------------------------------