diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 1379485e74..06bf52a7e5 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -74,6 +74,7 @@ jobs: source .venv-${{ matrix.python-version }}/bin/activate python -m pip install --upgrade pip pip install -r devtools/dev-requirements.txt + pip install matplotlib==3.9.2 - name: Benchmark with pytest-benchmark (PR) if: env.has_changes == 'true' diff --git a/.github/workflows/cache_dependencies.yml b/.github/workflows/cache_dependencies.yml index 661cec4df1..dd648d78f4 100644 --- a/.github/workflows/cache_dependencies.yml +++ b/.github/workflows/cache_dependencies.yml @@ -41,7 +41,7 @@ jobs: source .venv-${{ matrix.python-version }}/bin/activate python -m pip install --upgrade pip pip install -r devtools/dev-requirements.txt - pip install matplotlib==3.7.2 + pip install matplotlib==3.9.2 - name: Cache Python environment id: cache-env diff --git a/.github/workflows/jax_tests.yml b/.github/workflows/jax_tests.yml index 8e6c0da5a8..9749dc42a8 100644 --- a/.github/workflows/jax_tests.yml +++ b/.github/workflows/jax_tests.yml @@ -35,7 +35,6 @@ jobs: sed -i '1i\jax[cpu] == ${{ matrix.jax-version }}' ./requirements.txt cat ./requirements.txt pip install -r ./devtools/dev-requirements.txt - pip install matplotlib==3.7.2 - name: Verify dependencies run: | python --version diff --git a/.github/workflows/notebook_tests.yml b/.github/workflows/notebook_tests.yml index 1ceccb8ac1..78cd39f905 100644 --- a/.github/workflows/notebook_tests.yml +++ b/.github/workflows/notebook_tests.yml @@ -67,7 +67,7 @@ jobs: source .venv-${{ matrix.python-version }}/bin/activate python -m pip install --upgrade pip pip install -r devtools/dev-requirements.txt - pip install matplotlib==3.7.2 + pip install matplotlib==3.9.2 - name: Test notebooks with pytest and nbmake if: env.has_changes == 'true' diff --git a/.github/workflows/regression_tests.yml b/.github/workflows/regression_tests.yml index ed13617be4..540fc2ab48 100644 --- a/.github/workflows/regression_tests.yml +++ b/.github/workflows/regression_tests.yml @@ -66,7 +66,7 @@ jobs: source .venv-${{ matrix.python-version }}/bin/activate python -m pip install --upgrade pip pip install -r devtools/dev-requirements.txt - pip install matplotlib==3.7.2 + pip install matplotlib==3.9.2 - name: Set Swap Space if: env.has_changes == 'true' diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 54075f0892..1ce8b55c7a 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -72,7 +72,7 @@ jobs: source .venv-${{ matrix.combos.python_version }}/bin/activate python -m pip install --upgrade pip pip install -r devtools/dev-requirements.txt - pip install matplotlib==3.7.2 + pip install matplotlib==3.9.2 - name: Set Swap Space if: env.has_changes == 'true' diff --git a/.github/workflows/weekly_tests.yml b/.github/workflows/weekly_tests.yml index 2fb309bd8a..b1ac1e5614 100644 --- a/.github/workflows/weekly_tests.yml +++ b/.github/workflows/weekly_tests.yml @@ -26,6 +26,7 @@ jobs: run: | python -m pip install --upgrade pip pip install -r devtools/dev-requirements.txt + pip install matplotlib==3.9.2 - name: Set Swap Space uses: pierotofy/set-swap-space@master with: diff --git a/desc/basis.py b/desc/basis.py index 6dc88c5e66..0f01555cec 100644 --- a/desc/basis.py +++ b/desc/basis.py @@ -1440,7 +1440,9 @@ def zernike_radial_coeffs(l, m, exact=True): # hence they are all integers. So, we can use exact arithmetic with integer # division instead of floating point division. # [1]https://en.wikipedia.org/wiki/Zernike_polynomials#Other_representations - coeffs[ii, s] = ((-1) ** ((ll - s) // 2) * factorial((ll + s) // 2)) // ( + coeffs[ii, s] = ( + int((-1) ** ((ll - s) // 2)) * factorial((ll + s) // 2) + ) // ( factorial((ll - s) // 2) * factorial((s + mm) // 2) * factorial((s - mm) // 2) diff --git a/desc/magnetic_fields/_core.py b/desc/magnetic_fields/_core.py index 5782e0bbbe..e2d38adaa3 100644 --- a/desc/magnetic_fields/_core.py +++ b/desc/magnetic_fields/_core.py @@ -1818,10 +1818,10 @@ def from_mgrid(cls, mgrid_file, extcur=None, method="cubic", extrap=False): ir = int(mgrid["ir"][()]) # number of grid points in the R coordinate jz = int(mgrid["jz"][()]) # number of grid points in the Z coordinate kp = int(mgrid["kp"][()]) # number of grid points in the phi coordinate - Rmin = mgrid["rmin"][()] # Minimum R coordinate (m) - Rmax = mgrid["rmax"][()] # Maximum R coordinate (m) - Zmin = mgrid["zmin"][()] # Minimum Z coordinate (m) - Zmax = mgrid["zmax"][()] # Maximum Z coordinate (m) + Rmin = mgrid["rmin"][()].filled() # Minimum R coordinate (m) + Rmax = mgrid["rmax"][()].filled() # Maximum R coordinate (m) + Zmin = mgrid["zmin"][()].filled() # Minimum Z coordinate (m) + Zmax = mgrid["zmax"][()].filled() # Maximum Z coordinate (m) nfp = int(mgrid["nfp"][()]) # Number of field periods Rgrid = np.linspace(Rmin, Rmax, ir) Zgrid = np.linspace(Zmin, Zmax, jz) @@ -1833,9 +1833,15 @@ def from_mgrid(cls, mgrid_file, extcur=None, method="cubic", extrap=False): bz = np.zeros([kp, jz, ir, nextcur]) for i in range(nextcur): coil_id = "%03d" % (i + 1,) - br[:, :, :, i] += mgrid["br_" + coil_id][()] # B_R radial magnetic field - bp[:, :, :, i] += mgrid["bp_" + coil_id][()] # B_phi toroidal field (T) - bz[:, :, :, i] += mgrid["bz_" + coil_id][()] # B_Z vertical magnetic field + br[:, :, :, i] += mgrid["br_" + coil_id][ + () + ].filled() # B_R radial magnetic field + bp[:, :, :, i] += mgrid["bp_" + coil_id][ + () + ].filled() # B_phi toroidal field (T) + bz[:, :, :, i] += mgrid["bz_" + coil_id][ + () + ].filled() # B_Z vertical magnetic field # shift axes to correct order br = np.moveaxis(br, (0, 1, 2), (1, 2, 0)) @@ -1851,13 +1857,13 @@ def from_mgrid(cls, mgrid_file, extcur=None, method="cubic", extrap=False): coil_id = "%03d" % (i + 1,) ar[:, :, :, i] += mgrid["ar_" + coil_id][ () - ] # A_R radial mag. vec. potential + ].filled() # A_R radial mag. vec. potential ap[:, :, :, i] += mgrid["ap_" + coil_id][ () - ] # A_phi toroidal mag. vec. potential + ].filled() # A_phi toroidal mag. vec. potential az[:, :, :, i] += mgrid["az_" + coil_id][ () - ] # A_Z vertical mag. vec. potential + ].filled() # A_Z vertical mag. vec. potential # shift axes to correct order ar = np.moveaxis(ar, (0, 1, 2), (1, 2, 0)) diff --git a/devtools/dev-requirements_conda.yml b/devtools/dev-requirements_conda.yml index 0659821b3b..f57ab3f0de 100644 --- a/devtools/dev-requirements_conda.yml +++ b/devtools/dev-requirements_conda.yml @@ -7,7 +7,7 @@ dependencies: - matplotlib >= 3.5.0, < 4.0.0 - mpmath >= 1.0.0, < 2.0 - netcdf4 >= 1.5.4, < 2.0 - - numpy >= 1.20.0, < 2.0 + - numpy >= 1.20.0 - psutil - scipy >= 1.7.0, < 2.0 - termcolor diff --git a/requirements.txt b/requirements.txt index 0b64731d96..663c766026 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,12 +6,12 @@ interpax >= 0.3.3 matplotlib >= 3.5.0, < 4.0.0 mpmath >= 1.0.0, < 2.0 netcdf4 >= 1.5.4, < 2.0 -numpy >= 1.20.0, < 2.0.0 +numpy >= 1.20.0 nvgpu orthax plotly >= 5.16, < 6.0 psutil pylatexenc >= 2.0, < 3.0 scikit-image -scipy >= 1.7.0, < 2.0.0 +scipy >= 1.7.0 termcolor diff --git a/requirements_conda.yml b/requirements_conda.yml index 451066ceef..68ff95e72c 100644 --- a/requirements_conda.yml +++ b/requirements_conda.yml @@ -7,7 +7,7 @@ dependencies: - matplotlib >= 3.5.0, < 4.0.0 - mpmath >= 1.0.0, < 2.0 - netcdf4 >= 1.5.4, < 2.0 - - numpy >= 1.20.0, < 2.0 + - 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faa395ef87..10f1b90c12 100644 Binary files a/tests/baseline/test_trapped_fraction_Kim.png and b/tests/baseline/test_trapped_fraction_Kim.png differ diff --git a/tests/test_stability_funs.py b/tests/test_stability_funs.py index 72b4819b38..72bee4fea4 100644 --- a/tests/test_stability_funs.py +++ b/tests/test_stability_funs.py @@ -64,7 +64,8 @@ def get_vmec_data(path, quantity): """ f = Dataset(path) - rho = np.sqrt(f.variables["phi"] / np.array(f.variables["phi"])[-1]) + phi = np.array(f.variables["phi"]) + rho = np.sqrt(phi / phi[-1]) q = np.array(f.variables[quantity]) f.close() return rho, q