Merge tag 'v0.18.4' into sympy-or

MilesCranmer · Jun 3, 2024 · 0f47a59 · 0f47a59
2 parents 5c0a49a + 6dfed1b
commit 0f47a59
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diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,4 @@
+[run]
+omit =
+    */test/*
+source = pysr
diff --git a/.deepsource.toml b/.deepsource.toml
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,16 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+
+  - package-ecosystem: "github-actions"
+    # Workflow files stored in the default location of `.github/workflows`. (You don't need to specify `/.github/workflows` for `directory`. You can use `directory: "/"`.)
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "daily"
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -24,19 +24,31 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
+    env:
+      COVERAGE_PROCESS_START: "${{ github.workspace }}/.coveragerc"
     defaults:
       run:
         shell: bash
     strategy:
       matrix:
-        julia-version: ['1.9']
-        python-version: ['3.10']
+        julia-version: ['1']
+        python-version: ['3.12']
         os: [ubuntu-latest]
+        test-id: [main]
+        include:
+          - julia-version: '1.6'
+            python-version: '3.8'
+            os: ubuntu-latest
+            test-id: include
+          - julia-version: '1'
+            python-version: '3.12'
+            os: ubuntu-latest
+            test-id: include
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: "Set up Julia"
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
       - name: "Cache Julia"
@@ -45,47 +57,63 @@ jobs:
           cache-name: ${{ matrix.os }}-test-${{ matrix.julia-version }}-${{ matrix.python-version }}
           cache-packages: false
       - name: "Set up Python"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
-      - name: "Install Coverage tool"
-        run: pip install coverage coveralls
+            pip install .
+            python -c 'import pysr'
+      - name: "Assert Julia version"
+        if: ${{ matrix.julia-version != '1'}}
+        run: python3 -c "from pysr import jl; assert jl.VERSION.major == jl.seval('v\"${{ matrix.julia-version }}\"').major; assert jl.VERSION.minor == jl.seval('v\"${{ matrix.julia-version }}\"').minor"
+      - name: "Install test dependencies"
+        run: pip install coverage coveralls pytest nbval
+      - name: "Set up coverage for subprocesses"
+        run: echo 'import coverage; coverage.process_startup()' > "${{ github.workspace }}/sitecustomize.py"
       - name: "Run tests"
-        run: |
-            coverage run --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test main
-            coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test cli
+        run: coverage run -m pysr test main,cli,startup
       - name: "Install JAX"
         run: pip install jax jaxlib # (optional import)
+        if: ${{ matrix.test-id == 'main' }}
       - name: "Run JAX tests"
-        run: coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test jax
+        run: coverage run --append -m pysr test jax
+        if: ${{ matrix.test-id == 'main' }}
       - name: "Install Torch"
         run: pip install torch # (optional import)
+        if: ${{ matrix.test-id == 'main' }}
       - name: "Run Torch tests"
-        run: coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test torch
-      - name: "Run custom env tests"
-        run: coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test env
+        run: coverage run --append -m pysr test torch
+        if: ${{ matrix.test-id == 'main' }}
       - name: "Coveralls"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: test-${{ matrix.test-name }}
+          COVERALLS_FLAG_NAME: test-${{ matrix.julia-version }}-${{ matrix.python-version }}
           COVERALLS_PARALLEL: true
         run: coveralls --service=github
 
-  incremental_install:
-    runs-on: ubuntu-latest
+  dev_install:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.12']
+        julia-version: ['1']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.8'
+            julia-version: '1.6'
     steps:
-      - uses: actions/checkout@v2
-      - name: "Build incremental install"
-        run: docker build -t pysr -f pysr/test/incremental_install_simulator.dockerfile .
-      - name: "Test incremental install"
-        run: docker run --rm pysr /bin/bash -l -c 'python3 -m pysr.test main && python3 -m pysr.test env'
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: "Install PySR"
+        run: |
+            python -m pip install --upgrade pip
+            pip install .
+      - name: "Run development test"
+        run: PYSR_TEST_JULIA_VERSION=${{ matrix.julia-version }} PYSR_TEST_PYTHON_VERSION=${{ matrix.python-version }} python -m pysr test dev
 
   conda_test:
     runs-on: ${{ matrix.os }}
@@ -94,20 +122,20 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.12']
         os: ['ubuntu-latest']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: "Cache conda"
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         env:
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
       - name: "Set up Conda"
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest
@@ -123,9 +151,9 @@ jobs:
       - name: "Install PySR"
         run: |
             python3 -m pip install .
-            python3 -m pysr install
+            python3 -c 'import pysr'
       - name: "Run tests"
-        run: cd /tmp && python -m pysr.test main
+        run: cd /tmp && python -m pysr test main
 
   coveralls:
     name: Indicate completion to coveralls.io
@@ -152,20 +180,29 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version:
+          - '3.12'
+          - '3.8'
+        os: ['ubuntu-latest']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: "Set up Python"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
       - name: "Install PySR and all dependencies"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            pip install mypy jax jaxlib torch
-            python setup.py install
+            pip install .
+            pip install mypy
+      - name: "Install additional dependencies"
+        run: python -m pip install jax jaxlib torch
+        if: ${{ matrix.python-version != '3.8' }}
       - name: "Run mypy"
-        run: mypy --install-types --non-interactive pysr
+        run: python -m mypy --install-types --non-interactive pysr
+        if: ${{ matrix.python-version != '3.8' }}
+      - name: "Run compatible mypy"
+        run: python -m mypy --ignore-missing-imports pysr
+        if: ${{ matrix.python-version == '3.8' }}
diff --git a/.github/workflows/CI_Windows.yml b/.github/workflows/CI_Windows.yml
@@ -29,14 +29,14 @@ jobs:
         shell: bash
     strategy:
       matrix:
-        julia-version: ['1.9']
-        python-version: ['3.10']
+        julia-version: ['1']
+        python-version: ['3.12']
         os: [windows-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: "Set up Julia"
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
       - name: "Cache Julia"
@@ -45,23 +45,20 @@ jobs:
           cache-name: ${{ matrix.os }}-test-${{ matrix.julia-version }}-${{ matrix.python-version }}
           cache-packages: false
       - name: "Set up Python"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
+            pip install pytest nbval
+            pip install .
+            python -c 'import pysr'
       - name: "Run tests"
         run: |
-            python -m pysr.test main
-            python -m pysr.test cli
+            python -m pysr test main,cli,startup
       - name: "Install Torch"
         run: pip install torch # (optional import)
       - name: "Run Torch tests"
-        run: python -m pysr.test torch
-      - name: "Run custom env tests"
-        run: python -m pysr.test env
+        run: python -m pysr test torch
diff --git a/.github/workflows/CI_conda_forge.yml b/.github/workflows/CI_conda_forge.yml
@@ -20,13 +20,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        os: ['ubuntu-latest', 'macos-latest']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        os: ['ubuntu-latest']
         use-mamba: [true, false]
+        include:
+          - python-version: 3.9
+            os: 'windows-latest'
+            use-mamba: true
+          - python-version: 3.12
+            os: 'windows-latest'
+            use-mamba: true
+          - python-version: 3.9
+            os: 'macos-latest'
+            use-mamba: true
+          - python-version: 3.12
+            os: 'macos-latest'
+            use-mamba: true
 
     steps:
       - name: "Set up Conda"
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest
@@ -40,4 +53,6 @@ jobs:
         run: conda activate pysr-test && conda install pysr
         if: ${{ !matrix.use-mamba }}
       - name: "Run tests"
-        run: python -m pysr.test main
+        run: |
+          pip install pytest nbval
+          python -m pysr test main,startup
diff --git a/.github/workflows/CI_docker.yml b/.github/workflows/CI_docker.yml
@@ -33,8 +33,8 @@ jobs:
         arch: ['linux/amd64']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build docker
         run: docker build --platform=${{ matrix.arch }} -t pysr .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test cli && python3 -m pysr.test env'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'pip install pytest nbval && python3 -m pysr test main,cli,startup'
diff --git a/.github/workflows/CI_docker_large_nightly.yml b/.github/workflows/CI_docker_large_nightly.yml
@@ -18,19 +18,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.6', '1.9']
-        python-version: ['3.10']
+        julia-version: ['1.6', '1']
+        python-version: ['3.8', '3.12']
         os: [ubuntu-latest]
         arch: ['linux/amd64', 'linux/arm64']
 
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v2
         with:
           platforms: all
       - name: Build docker
-        run: docker build --platform=${{ matrix.arch }} -t pysr --build-arg JLVERSION=${{ matrix.julia-version }} .
+        run: docker build --platform=${{ matrix.arch }} -t pysr --build-arg JLVERSION=${{ matrix.julia-version }} --build-arg PYVERSION=${{ matrix.python-version }} .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test cli && python3 -m pysr.test env'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'pip install pytest nbval && python3 -m pysr test main,cli,startup'
diff --git a/.github/workflows/CI_large_nightly.yml b/.github/workflows/CI_large_nightly.yml
@@ -23,30 +23,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.6', '1.8', '1.9']
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        julia-version: ['1.6', '1.8', '1.10']
+        python-version: ['3.8', '3.10', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: "Set up Julia"
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
       - name: "Set up Python"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
+            pip install pytest nbval
+            pip install .
+            python -c 'import pysr'
+      - name: "Assert Julia version"
+        if: ${{ matrix.julia-version != '1'}}
+        run: python3 -c "from pysr import jl; assert jl.VERSION.major == jl.seval('v\"${{ matrix.julia-version }}\"').major; assert jl.VERSION.minor == jl.seval('v\"${{ matrix.julia-version }}\"').minor"
       - name: "Run tests"
-        run: |
-            python -m pysr.test main
-            python -m pysr.test cli
-      - name: "Run new env test"
-        run: python -m pysr.test env
-        if: ${{ !(matrix.os == 'windows-latest' && matrix.python-version == '3.7') }}
+        run: python -m pysr test main,cli,startup