Merge branch 'main' into ias15

jobovy · Sep 12, 2024 · eaaf25d · eaaf25d
2 parents fd83246 + 7c5ad82
commit eaaf25d
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.10.0.dev0
+current_version = 1.10.1.dev0
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize =
 	{major}.{minor}.{patch}.{release}{dev}

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -226,13 +226,15 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       run: |
          sudo apt-get install libgsl-dev
-    - name: Install the GSL
+    - name: Install the GSL and OpenMP
       if: matrix.os == 'macos-12'
       run: |
-         brew install gsl
-         echo "CFLAGS=-I$(brew --prefix)/include" >> $GITHUB_ENV
-         echo "LDFLAGS=-L$(brew --prefix)/lib" >> $GITHUB_ENV
-         echo "LD_LIBRARY_PATH=$(brew --prefix)/lib" >> $GITHUB_ENV
+         brew install gsl libomp
+         brew info libomp
+         echo "CFLAGS=-I$(brew --prefix)/include -I/usr/local/opt/libomp/include" >> $GITHUB_ENV
+         echo "CPPFLAGS=-I$(brew --prefix)/include -I/usr/local/opt/libomp/include" >> $GITHUB_ENV
+         echo "LDFLAGS=-L$(brew --prefix)/lib -L/usr/local/opt/libomp/lib" >> $GITHUB_ENV
+         echo "LD_LIBRARY_PATH=$(brew --prefix)/lib:/usr/local/opt/libomp/lib" >> $GITHUB_ENV
     - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
@@ -242,9 +244,6 @@ jobs:
          pip install --upgrade --upgrade-strategy eager numpy scipy matplotlib numexpr setuptools cython pytest tqdm
     - name: Install pynbody
       if: ${{ matrix.REQUIRES_PYNBODY }}
-      env:
-        CC: gcc-11
-        CXX: g++-11
       run: |
          pip install --upgrade --upgrade-strategy eager h5py pandas pytz
          pip install --upgrade --upgrade-strategy eager wheel

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -23,7 +23,7 @@ on:
 
 jobs:
   build_wheels:
-    name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
+    name: Build wheel for ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
     runs-on: ${{ matrix.buildplat[0] }}
     strategy:
       # Ensure that a wheel builder finishes even if another fails
@@ -35,7 +35,12 @@ jobs:
         - [macos-12, macosx, x86_64]
         - [macos-14, macosx, arm64]
         - [windows-2019, win, amd64]
-        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+        python:
+        - ["cp38","3.8"]
+        - ["cp39","3.9"]
+        - ["cp310","3.10"]
+        - ["cp311","3.11"]
+        - ["cp312","3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Install GSL (Windows / Mac OS x86_64)
@@ -48,7 +53,7 @@ jobs:
               - conda-forge
           create-args: gsl
           cache-environment: true
-          cache-environment-key: ${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}-${{ hashFiles('.github/workflows/wheels.yml') }}
+          cache-environment-key: gsl-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}-${{ hashFiles('.github/workflows/wheels.yml') }}
       - name: Set GSL environment variables (Windows)
         if: matrix.buildplat[1] == 'win'
         shell: bash -l {0}
@@ -66,20 +71,106 @@ jobs:
           echo "REPAIR_LIBRARY_PATH=$CONDA_PREFIX/lib" >> $GITHUB_ENV # https://github.com/pypa/cibuildwheel/issues/816#issuecomment-916197079
           echo "$CONDA_PREFIX/bin" >> $GITHUB_PATH # necessary when we don't activate the environment
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.17
+        uses: pypa/cibuildwheel@v2.20
         env:
-          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
+          CIBW_BUILD: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
           CIBW_BUILD_VERBOSITY: 1
           CIBW_BEFORE_BUILD_LINUX: yum -y install gsl-devel
           CIBW_ARCHS_MACOS: ${{ matrix.buildplat[2] }}
-          CIBW_CONFIG_SETTINGS_MACOS: "--build-option=--no-openmp"
+          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=10.13"
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
             DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-listdeps {wheel} &&
             DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel -v --require-archs {delocate_archs} -w {dest_dir} {wheel}
       - uses: actions/upload-artifact@v4
         with:
-          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
+          name: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
           path: ./wheelhouse/*.whl
+  test_wheels:
+    name: Test Python ${{ matrix.python[1] }} wheels on ${{ matrix.buildplat[2] }} ${{ matrix.buildplat[0] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    needs: build_wheels
+    strategy:
+        # Ensure that tests finish even if another fails
+        fail-fast: false
+        matrix:
+          buildplat:
+            - [ubuntu-22.04, manylinux, x86_64]
+            - [macos-12, macosx, x86_64]
+            - [macos-14, macosx, arm64]
+            - [windows-2019, win, amd64]
+          python:
+            - ["cp38","3.8"]
+            - ["cp39","3.9"]
+            - ["cp310","3.10"]
+            - ["cp311","3.11"]
+            - ["cp312","3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - run: mkdir wheelhouse
+      - uses: actions/download-artifact@v4
+        with:
+          name: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
+          path: wheelhouse/
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python[1] }}
+      - name: Install GSL (Windows)
+        uses: mamba-org/setup-micromamba@v1
+        if: matrix.buildplat[1] == 'win'
+        with:
+          environment-name: gsl
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: gsl
+          cache-environment: true
+          cache-environment-key: gsl-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}-${{ hashFiles('.github/workflows/wheels.yml') }}
+      - name: Set GSL environment variables (Windows)
+        if: matrix.buildplat[1] == 'win'
+        shell: bash -l {0}
+        run: |
+          micromamba activate gsl
+          echo "LIBPATH=$CONDA_PREFIX\\Library\\lib" >> $GITHUB_ENV
+          echo "$CONDA_PREFIX\\Library\\bin" >> $GITHUB_PATH # necessary when we don't activate the environment
+      - name: Install wheel
+        shell: bash
+        run: python -m pip install `ls -d "$(pwd)"/wheelhouse/*.whl`
+      - name: Test built wheel in non-conda environment
+        shell: bash
+        working-directory: ${{ runner.temp }}
+        run: |
+          pip install astropy pytest
+          pytest -v $GITHUB_WORKSPACE/tests/test_orbit.py -k "test_energy_jacobi_conservation and NFW"
+      # Test that built wheels also work in a conda environment, setup environment, install wheel, and run test
+      - name: Setup test conda environment (Linux / Mac OS)
+        if: matrix.buildplat[1] != 'win'
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-wheel-conda
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: python=${{ matrix.python[1] }} numpy scipy matplotlib astropy pytest
+          cache-environment: true
+          cache-environment-key: test-wheel-conda-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}-${{ hashFiles('.github/workflows/wheels.yml') }}
+      - name: Setup test conda environment (Windows)
+        if: matrix.buildplat[1] == 'win'
+        shell: bash -l {0}
+        run: |
+          micromamba create -n test-wheel-conda -c conda-forge python=${{ matrix.python[1] }} numpy scipy matplotlib astropy pytest gsl
+          micromamba activate test-wheel-conda
+          echo "LIBPATH=$CONDA_PREFIX\\Library\\lib" >> $GITHUB_ENV
+      - name: Install built wheel in conda environment
+        shell: bash -l {0}
+        run: |
+          micromamba activate test-wheel-conda
+          python -m pip install `ls -d "$(pwd)"/wheelhouse/*.whl`
+      - name: Test built wheel in conda environment
+        shell: bash -l {0}
+        working-directory: ${{ runner.temp }}
+        run: |
+          micromamba activate test-wheel-conda
+          pytest -v $GITHUB_WORKSPACE/tests/test_orbit.py -k "test_energy_jacobi_conservation and NFW"
   build_sdist:
     name: Build source directory for release
     if: github.event_name == 'release' && github.event.action == 'created'
@@ -106,7 +197,7 @@ jobs:
 # Deploy wheels and sdist to PyPI (upon release creation)
   deploy_pypi:
     name: Deploy to PyPI
-    needs: [build_wheels, build_sdist]
+    needs: [build_wheels, test_wheels, build_sdist]
     runs-on: ubuntu-latest
     permissions:
       id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
@@ -127,7 +218,7 @@ jobs:
 # Deploy wheels and sdist to AWS S3 (main)
   deploy_s3:
     name: Deploy to AWS S3
-    needs: build_wheels
+    needs: [build_wheels, test_wheels]
     runs-on: ubuntu-latest
     if: github.event_name != 'release' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
     steps:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
   - id: check-executables-have-shebangs
   - id: check-yaml
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.2
+  rev: v3.17.0
   hooks:
   - id: pyupgrade
     args: [--py38-plus]
@@ -30,12 +30,12 @@ repos:
   - id: isort
     name: isort (python)
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.6"
+  rev: "v2.3.0"
   hooks:
     - id: codespell
-      args: ["-L", "thisE,thise,mye,tE,te,hist,ro,sav,ccompiler,aas",
+      args: ["-L", "thisE,thise,mye,tE,te,hist,ro,sav,ccompiler,aas,floatIn,dOmin",
       "-x","doc/source/_static/try-galpy.js"]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.3
+  rev: v0.6.3
   hooks:
     - id: ruff-format
diff --git a/CITATION.cff b/CITATION.cff
@@ -5,7 +5,7 @@ authors:
   given-names: "Jo"
   orcid: "https://orcid.org/0000-0001-6855-442X"
 title: "galpy"
-version: 1.10.0.dev0
+version: 1.10.1.dev0
 url: "https://github.com/jobovy/galpy"
 preferred-citation:
   type: article

diff --git a/HISTORY.txt b/HISTORY.txt
@@ -1,5 +1,15 @@
-v1.10.1 (expected around 2024-07-01)
-===================
+v1.10.1 (Expected around 2024-11-01)
+====================
+
+- Propagate general plotting keywords in Potential.plot/plotPotentials.
+
+v1.10.0 (2024-07-07)
+====================
+
+- Increased support for using OpenMP with clang and, in particular, added OpenMP support
+  in the released Mac wheels.
+
+- Removed explicit support for using Intel compilers.
 
 - Switch to using Ruff as the code formatter.
 
@@ -12,7 +22,7 @@ v1.9.2 (2024-03-04)
   treated as a spherical potential). Kuzmin-like potentials are obtained by
   replacing the spherical radius r with \sqrt(R^2 + (a + |z|^2)), while
   Miyamoto-Nagai-like potentials are obtained by replacing the spherical
-  radius with \sqrt(R^2 + (a + \\sqrt(z^2 + b^2))^2). The standard KuzminDiskPotential
+  radius with \sqrt(R^2 + (a + \sqrt(z^2 + b^2))^2). The standard KuzminDiskPotential
   and MiyamotoNagaiPotential are obtained by applying this procedure to a point-mass
   potential and the Kuzmin/Miyamoto-Nagai-like potentials generalize this to any
   spherical potential.

diff --git a/__intelcompiler.py b/__intelcompiler.py
diff --git a/doc/source/actionAngle.rst b/doc/source/actionAngle.rst
@@ -54,8 +54,8 @@ Reverse transformations are discussed in
 We start by discussing the forward and reverse transformations for the two
 specific potentials: the isochrone and the harmonic potentals.
 
-**UPDATED IN v1.8.2** Action-angle coordinates for the isochrone/harmonic potentials
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Action-angle coordinates for the isochrone/harmonic potentials
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
 The harmonic and isochrone potentials are the only potentials for which all of
 the actions, frequencies, and angles can be calculated analytically and for
@@ -197,8 +197,8 @@ We can also reverse this using ``actionAngleHarmonicInverse``
 
 .. _aafwd:
 
-**UPDATED IN v1.8.2** Forward action-angle transformations (**x**, **v**) --> (**J**, **O**, **a**)
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Forward action-angle transformations (**x**, **v**) --> (**J**, **O**, **a**)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
 Action-angle coordinates for spherical potentials
 --------------------------------------------------
@@ -861,8 +861,8 @@ which gives
 
 .. _aareverse:
 
-**UPDATED IN v1.8.2** Reverse action-angle transformations (**J**, **a**) --> (**x**, **v**, **O**)
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Reverse action-angle transformations (**J**, **a**) --> (**x**, **v**, **O**)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
 Reverse action-angle transformations for one-dimensional potentials
 ------------------------------------------------------------------

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -116,7 +116,7 @@ def linkcode_resolve(domain, info):
 # built documents.
 #
 # The short X.Y version.
-version = "1.10.0.dev0"
+version = "1.10.1.dev0"
 # The full version, including alpha/beta/rc tags.
 release = version
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"