Merge branch 'topic/default/prepare-0.8.0' into 'branch/default'

Prepare 0.8.0rc0 See merge request fluiddyn/fluidsim!367
fluiddyn · Jan 30, 2024 · 51e02ae · 51e02ae
2 parents 46b7e6c + 26515e6
commit 51e02ae
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -73,7 +73,8 @@ pixi-test:
  - pixi info
  # - rm -rf ../transonic
  # - hg clone https://foss.heptapod.net/fluiddyn/transonic ../transonic
- - pixi run install-editable
+ - pixi run install-dependencies
+ - pixi run pip install -e . -v --no-build-isolation --no-deps -C compile-args=-j2
  - pixi run pytest -v lib
  - pixi run fluidsim-test -v
  # currently broken because of fluidfft conda issues
@@ -195,7 +196,7 @@ pages:
  - python -m venv .venv
  - . .venv/bin/activate
  - pip install fluidfft --no-deps
- - pdm install -G doc -G fft -G test --no-self
+ - pdm sync -G doc -G fft -G test --no-self
  - pip install . --config-settings=setup-args=-Dtransonic-backend=python --no-deps
  - pdm run xvfb-run --auto-servernum sphinx-build -W -b html -d doc/_build/doctrees doc doc/_build/html
  - mkdir -p public/$CI_COMMIT_REF_NAME

diff --git a/CHANGES.md b/CHANGES.md
@@ -6,6 +6,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+See also the [unreleased changes].
+
 % Type of changes
 
 % ---------------
@@ -22,11 +24,13 @@ and this project adheres to
 
 % Security Security in case of vulnerabilities.
 
-% Unreleased_
-
-% -----------
+## [0.8.0] (2024-01-28)
 
-% towncrier release notes start
+- Build and upload wheels on PyPI with Github Actions.
+- Much better CI in foss.heptapod.net and Github Actions.
+- Use the [Meson build system](https://mesonbuild.com) via
+ [meson-python](https://github.com/mesonbuild/meson-python).
+- Development: use PDM, Nox and Pixi.
 
 ## [0.7.4] (2023-10-05)
 
@@ -318,3 +322,5 @@ Merge with geofluidsim (Ashwin Vishnu Mohanan repository)
 [0.7.2]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.1...0.7.2
 [0.7.3]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.2...0.7.3
 [0.7.4]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.3...0.7.4
+[0.8.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.4...0.8.0
+[unreleased changes]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.8.0...branch%2Fdefault
diff --git a/Makefile b/Makefile
@@ -5,10 +5,15 @@ MPI_NUM_PROCS ?= 2
 
 .PHONY: black black_check clean clean_pyc clean_so cleantransonic coverage_short develop dist lint _report_coverage shortlog tests _tests_coverage tests_mpi
 
-develop:
- pdm sync --clean --no-self
+develop: sync
  pdm run pip install -e . -v --no-build-isolation --no-deps
 
+sync:
+ pdm sync --clean --no-self
+
+lock:
+ pdm lock -G :all
+
 dist:
  pip install build
  cd lib && python -m build

diff --git a/bench/profiling/simul_profile2d_vmprof.py b/bench/profiling/simul_profile2d_vmprof.py
@@ -5,7 +5,6 @@
 
 """
 
-
 from simul_profile2d import sim
 
 sim.time_stepping.start()
diff --git a/bench/spectraldns/bench_2d.py b/bench/spectraldns/bench_2d.py
@@ -19,6 +19,7 @@
  mpirun -np 2 fluidsim-bench 1152 -d 2 -s ns2d -it 10
 
 """
+
 import time
 import numpy as np
 from spectralDNS import config, get_solver, solve
@@ -68,7 +69,7 @@ def update(context):
  "T": 1e-11, # Should run 10 iterations
  "write_result": 100,
  "L": [L, L],
- "M": [10, 10] # Mesh size is pow(2, M[i]) in direction i
+ "M": [10, 10], # Mesh size is pow(2, M[i]) in direction i
  # 2**9 == 512
  },
  "doublyperiodic",

diff --git a/bench/spectraldns/bench_3d.py b/bench/spectraldns/bench_3d.py
@@ -16,6 +16,7 @@
  mpirun -np 2 fluidsim-bench 128 -d 3 -s ns3d -it 10
 
 """
+
 import time
 import numpy as np
 from numpy import zeros, sum, float64, sin, cos, prod, asscalar

diff --git a/bench/spectraldns/profile_2d.py b/bench/spectraldns/profile_2d.py
@@ -16,6 +16,7 @@
 
 
 """
+
 import time
 import numpy as np
 
@@ -71,7 +72,7 @@ def update(context):
  "T": 11 * dt, # Should run 10 iterations
  "write_result": 100,
  "L": [L, L],
- "M": [10, 10] # Mesh size is pow(2, M[i]) in direction i
+ "M": [10, 10], # Mesh size is pow(2, M[i]) in direction i
  # 2**9 == 512
  },
  "doublyperiodic",

diff --git a/bench/spectraldns/profile_3d.py b/bench/spectraldns/profile_3d.py
@@ -13,6 +13,7 @@
  fluidsim-bench 128 -d 3 -s ns3d -it 10
 
 """
+
 import time
 import numpy as np
 from numpy import zeros, sum, float64, sin, cos, prod, asscalar

diff --git a/doc/examples/simul_ns2dbouss_initfields_in_script.py b/doc/examples/simul_ns2dbouss_initfields_in_script.py
@@ -3,6 +3,7 @@
 The field initialization is done in the script.
 
 """
+
 import os
 
 import numpy as np

diff --git a/doc/examples/simul_ns2dstrat_forcing_const_energy_rate.py b/doc/examples/simul_ns2dstrat_forcing_const_energy_rate.py
@@ -1,6 +1,7 @@
 """Script for a short simulation with the solver ns2d.strat
 
 """
+
 import numpy as np
 
 from fluiddyn.util import mpi

diff --git a/doc/examples/simul_ns2dstrat_forcing_in_script.py b/doc/examples/simul_ns2dstrat_forcing_in_script.py
@@ -3,6 +3,7 @@
 Note how is used the user-defined forcing maker...
 
 """
+
 from math import pi
 import os
 

diff --git a/doc/examples/simul_ns2dstrat_initfields_in_script.py b/doc/examples/simul_ns2dstrat_initfields_in_script.py
@@ -3,6 +3,7 @@
 The field initialization is done in the script.
 
 """
+
 import os
 import numpy as np
 

diff --git a/doc/examples/simul_ns3dbouss_initfields_in_script.py b/doc/examples/simul_ns3dbouss_initfields_in_script.py
@@ -7,6 +7,7 @@
  mpirun -np 4 python simul_ns3dbouss_initfields_in_script.py
 
 """
+
 import os
 
 import numpy as np

diff --git a/doc/examples/simul_ns3dstrat_waves.py b/doc/examples/simul_ns3dstrat_waves.py
@@ -6,6 +6,7 @@
  mpirun -np 4 python simul_ns3dstrat_waves.py
 
 """
+
 import os
 from math import pi
 

diff --git a/doc/examples/time_stepping/3d/run_profile.py b/doc/examples/time_stepping/3d/run_profile.py
@@ -14,6 +14,7 @@
 ```
 
 """
+
 from pathlib import Path
 import sys
 

diff --git a/doc/release_process.md b/doc/release_process.md
@@ -1,40 +1,22 @@
 # Release process
 
-- [ ] Extended tests in doc/examples (`make tests` and `make tests_mpi`)
+- [ ] Extended tests in doc/examples (<https://foss.heptapod.net/fluiddyn/fluidsim/-/pipeline_schedules>)
 
 - [ ] Check builds of the "official" articles in <https://foss.heptapod.net/fluiddyn/fluiddyn_papers>
 
-- [ ] Topic for the release candidate
+- [ ] Topic/MR for the release candidate
 
- - [ ] Change version in `lib/fluidsim_core/_version.py` (`0.6.1rc0`)
+ - [ ] Change versions in `pyproject.toml` AND `lib/pyproject.toml` (`0.6.1rc0`)
 
- - [ ] Update changelog in `CHANGES.rst`
+ - [ ] Update changelog in `CHANGES.md`
 
  - Take into account `doc/newsfragments` + remove the fragments
 
  - Visit <https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.6.0...branch%2Fdefault>
 
  - Study `hg log -G -r "tag(0.6.0):tip"`
 
-- [ ] Tag `0.6.1rc0` in the repo
-
-- [ ] Push `fluidsim-core` release candidates to PyPI
-
- ```bash
- cd lib
- rm -rf dist
- python -m build
- twine upload dist/*
- ```
-
-- [ ] Push `fluidsim` release candidates to PyPI (no wheel!)
-
- ```bash
- cd ..
- rm -rf dist
- python -m build -s
- twine upload dist/*
- ```
+- [ ] Once merged, update, tag and push with `nox -s add-tag-for-release`.
 
 - [ ] PR on <https://github.com/conda-forge/fluidsim-core-feedstock> (rc channel)
 
@@ -66,18 +48,16 @@
  Create new environment with
 
  ```bash
- conda create -n env_fluidsim_rc \
+ mamba create -n env_fluidsim_rc \
  -c conda-forge/label/fluidsim-core_rc -c conda-forge/label/fluidsim_rc \
  fluidsim "fluidfft[build=mpi*]" "h5py[build=mpi*]"
  ```
 
 - [ ] Communicate to the community...
 
-- [ ] Topic for the release of the stable version (delete "rc0" in `lib/fluidsim_core/_version.py`)
-
-- [ ] Tag `0.6.1` in the repo
+- [ ] Topic/MR for the release of the stable version (delete "rc0" in the `pyproject.toml` files)
 
-- [ ] Push to PyPI (no wheel for fluidsim!)
+- [ ] New tag with `nox -s add-tag-for-release`
 
 - [ ] PR on <https://github.com/conda-forge/fluidsim-core-feedstock>
 

diff --git a/fluidsim/base/forcing/kolmogorov.py b/fluidsim/base/forcing/kolmogorov.py
@@ -10,6 +10,7 @@
  :private-members:
 
 """
+
 from warnings import warn
 
 import numpy as np

diff --git a/fluidsim/base/output/base.py b/fluidsim/base/output/base.py
@@ -492,9 +492,9 @@ def _compute_mean_values(self, tmin, tmax):
  lengths = self.spectra.compute_length_scales(data=data_spectra)
  result.update(lengths)
 
- result[
- "I_dissipation"
- ] = self.spect_energy_budg.compute_isotropy_dissipation(tmin)
+ result["I_dissipation"] = (
+ self.spect_energy_budg.compute_isotropy_dissipation(tmin)
+ )
 
  return result
 

diff --git a/fluidsim/base/output/cross_corr3d.py b/fluidsim/base/output/cross_corr3d.py
@@ -11,7 +11,6 @@
 
 """
 
-
 import itertools
 
 import numpy as np

diff --git a/fluidsim/base/output/horiz_means.py b/fluidsim/base/output/horiz_means.py
@@ -10,6 +10,7 @@
  :undoc-members:
 
 """
+
 import numpy as np
 import h5py
 import matplotlib.pyplot as plt

diff --git a/fluidsim/base/output/spatiotemporal_spectra.py b/fluidsim/base/output/spatiotemporal_spectra.py
@@ -1164,9 +1164,7 @@ def plot_kzkhomega(
  omega_disp = ikh / np.sqrt(ikh**2 + dkz_over_dkh**2 * xaxis**2)
  ax.plot(xaxis, omega_disp, "k-", linewidth=2)
  elif equation.startswith(r"$k_z"):
- omega_disp = xaxis / np.sqrt(
- xaxis**2 + dkz_over_dkh**2 * ikz**2
- )
+ omega_disp = xaxis / np.sqrt(xaxis**2 + dkz_over_dkh**2 * ikz**2)
  ax.plot(xaxis, omega_disp, "k-", linewidth=2)
  else:
  raise ValueError("wrong equation for dispersion relation")
@@ -1375,9 +1373,7 @@ def plot_temporal_spectra(
  aspect_ratio = self.sim.oper.Lx / self.sim.oper.Ly
 
  def modes(nx, nz):
- return np.sqrt(
- nx**2 / (nx**2 + aspect_ratio**2 * nz**2)
- )
+ return np.sqrt(nx**2 / (nx**2 + aspect_ratio**2 * nz**2))
 
  nxs = np.arange(1, 11)
  modes_nz1 = modes(nxs, 1)

diff --git a/fluidsim/base/output/spectra.py b/fluidsim/base/output/spectra.py
@@ -17,7 +17,6 @@
 
 """
 
-
 import os
 
 import numpy as np

diff --git a/fluidsim/base/output/spectra3d.py b/fluidsim/base/output/spectra3d.py
@@ -23,7 +23,6 @@
 
 """
 
-
 import os
 from textwrap import dedent
 from math import sqrt, tau

diff --git a/fluidsim/base/output/time_signals_fft.py b/fluidsim/base/output/time_signals_fft.py
@@ -108,12 +108,12 @@ def _init_save(self, sim):
  for ishell, kh_s in enumerate(self.kh_shell):
  angle = -np.pi / 2
  for ikps in range(self.nb_k_per_shell):
- kx_array_ik_approx[
- ishell * self.nb_shells + ikps
- ] = kh_s * np.cos(angle)
- ky_array_ik_approx[
- ishell * self.nb_shells + ikps
- ] = kh_s * np.sin(angle)
+ kx_array_ik_approx[ishell * self.nb_shells + ikps] = (
+ kh_s * np.cos(angle)
+ )
+ ky_array_ik_approx[ishell * self.nb_shells + ikps] = (
+ kh_s * np.sin(angle)
+ )
  angle += delta_angle
 
  self.ik0_array_ik = np.empty([self.nb_k_tot], dtype=np.int32)
@@ -161,9 +161,7 @@ def _init_save(self, sim):
  self.ky_array_ik[ik] = ky_1k
 
  if mpi.rank == 0:
- self.kh_array_ik = np.sqrt(
- self.kx_array_ik**2 + self.ky_array_ik**2
- )
+ self.kh_array_ik = np.sqrt(self.kx_array_ik**2 + self.ky_array_ik**2)
 
  self.omega_array_ik = self.output.omega_from_wavenumber(
  self.kh_array_ik

diff --git a/fluidsim/base/params.py b/fluidsim/base/params.py
@@ -10,6 +10,7 @@
 
 
 """
+
 from fluidsim_core.params import Parameters
 from fluidsim.base.solvers.info_base import InfoSolverBase
 

diff --git a/fluidsim/base/preprocess/base.py b/fluidsim/base/preprocess/base.py
@@ -8,6 +8,7 @@
  :private-members:
 
 """
+
 from fluidsim_core.params import iter_complete_params
 
 

diff --git a/fluidsim/base/preprocess/pseudo_spect.py b/fluidsim/base/preprocess/pseudo_spect.py
@@ -348,9 +348,7 @@ def calcul_viscosity(
  nu = length_scale**order / time_scale
  v.append(nu)
  if verbose:
- kolmo_len.append(
- (nu**3 / epsilon) ** (1.0 / (3 * order - 2))
- )
+ kolmo_len.append((nu**3 / epsilon) ** (1.0 / (3 * order - 2)))
  else:
  v.append(0.0)
 

diff --git a/fluidsim/base/solvers/base.py b/fluidsim/base/solvers/base.py
@@ -12,6 +12,7 @@
  :private-members:
 
 """
+
 from time import time
 import atexit
 from pathlib import Path

diff --git a/fluidsim/base/solvers/info_base.py b/fluidsim/base/solvers/info_base.py
@@ -6,6 +6,7 @@
  :private-members:
 
 """
+
 from copy import deepcopy
 
 from fluidsim_core.info import InfoSolverCore, create_info_simul # noqa