Merge branch 'topic/default/maintain' into 'branch/default'

Maintain: format and doc

See merge request fluiddyn/transonic!139

.github/workflows/ci-windows.yml

@@ -16,9 +16,9 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - uses: prefix-dev/setup-pixi@v0.4.1
+    - uses: prefix-dev/setup-pixi@v0.8.1
       with:
-        pixi-version: v0.11.1
+        pixi-version: v0.23.0
         cache: false
     - name: Tests
       run: |

CHANGES.md

@@ -24,15 +24,14 @@ See also the
 
 ## [0.6.0] (2024-01-16)
 
-- Support for
-  [Meson build](https://transonic.readthedocs.io/en/latest/packaging.html) through
-  `transonic --meson` and multi-backends
+- Support for [Meson build](https://transonic.readthedocs.io/en/latest/packaging.html)
+  through `transonic --meson` and multi-backends
 - Support for Python 3.12
 
 ## [0.5.3] (2023-08-21)
 
-- [!110](https://foss.heptapod.net/fluiddyn/transonic/-/merge_requests/110) Quick
-  fix autopep8 bug + fix CI (py3.9)
+- [!110](https://foss.heptapod.net/fluiddyn/transonic/-/merge_requests/110) Quick fix
+  autopep8 bug + fix CI (py3.9)
 
 ## [0.5.2] (2022-01-04)
 
@@ -62,8 +61,8 @@ See also the
 
 ## 0.4.9 (2021-07-02)
 
-- Avoid new Gast and Beniget versions by pinning to the previous versions (0.4.0
-  and 0.3.0). No Python 3.10 support!
+- Avoid new Gast and Beniget versions by pinning to the previous versions (0.4.0 and
+  0.3.0). No Python 3.10 support!
 
 ## 0.4.8 (2021-05-03)
 
@@ -99,8 +98,7 @@ See also the
 
 ## 0.4.1 (2019-10-08)
 
-- Cython backend: less bugs, better support for fused types, nonecheck, cdivision,
-  ...
+- Cython backend: less bugs, better support for fused types, nonecheck, cdivision, ...
 - Fix default parameters for Pythran
 
 ## 0.4.0 (2019-09-22)
@@ -137,10 +135,9 @@ See also the
 
 - Support source in multiple files
   ([#14](https://foss.heptapod.net/fluiddyn/transonic/issues/14) and #21)
-- Fix issues #8 (Recursion for boosted method), #17 (Bad formating for Pythran
-  error), #18 (Improve logging jit), #19 (Change default arguments of jit
-  decorator) and #20 (No Pythran signature generated for boosted functions without
-  arguments)!
+- Fix issues #8 (Recursion for boosted method), #17 (Bad formating for Pythran error),
+  #18 (Improve logging jit), #19 (Change default arguments of jit decorator) and #20 (No
+  Pythran signature generated for boosted functions without arguments)!
 
 ## 0.2.3 (2019-06-11)
 
@@ -202,8 +199,8 @@ See also the
 
 ## 0.1.5 (2018-12-12)
 
-- {code}`jit` for simple methods (without assignation to attributes and call of
-  other methods)
+- {code}`jit` for simple methods (without assignation to attributes and call of other
+  methods)
 - {code}`Union` for annotations
 - {code}`include` decorator
 
@@ -242,8 +239,8 @@ See also the
 
 ## 0.0.9 (2018-11-20)
 
-- {code}`TRANSONIC_COMPILE_AT_IMPORT` mode for ahead-of-time and just-in-time
-  compilation (works also in IPython)
+- {code}`TRANSONIC_COMPILE_AT_IMPORT` mode for ahead-of-time and just-in-time compilation
+  (works also in IPython)
 - By default, the fluidpythran commandline uses Pythran
 
 ## 0.0.8 (2018-11-16)

CONTRIBUTING.md

@@ -1,39 +1,38 @@
 # How to contribute to Transonic
 
-Thank you for considering contributing to Transonic. Transonic is a
-community-driven project. It's people like you that make Transonic useful and
-successful. There are many ways to contribute, from writing tutorials or
-examples, improvements to the documentation, submitting bug reports and feature
-requests, or even writing code which can be incorporated into Transonic for
-everyone to use. (Paragraph shamelessly taken and adapted from the MetPy
-project!)
+Thank you for considering contributing to Transonic. Transonic is a community-driven
+project. It's people like you that make Transonic useful and successful. There are many
+ways to contribute, from writing tutorials or examples, improvements to the
+documentation, submitting bug reports and feature requests, or even writing code which
+can be incorporated into Transonic for everyone to use. (Paragraph shamelessly taken and
+adapted from the MetPy project!)
 
 ## Reporting Issues
 
 When opening an issue to report a problem
-(<https://foss.heptapod.net/fluiddyn/transonic/issues>), please try to provide
-a minimal code example that reproduces the issue along with details of the
-system you are using. You can copy-paste the output of the command `fluidinfo
--v` provided by the Python package
-[fluiddyn](https://pypi.org/project/fluiddyn/) ([Github
-gists](https://gist.github.com/) are good for that!).
+(<https://foss.heptapod.net/fluiddyn/transonic/issues>), please try to provide a minimal
+code example that reproduces the issue along with details of the system you are using.
+You can copy-paste the output of the command `fluidinfo -v` provided by the Python
+package [fluiddyn](https://pypi.org/project/fluiddyn/)
+([Github gists](https://gist.github.com/) are good for that!).
 
 ## Development process
 
-Transonic is part of the wider project FluidDyn. For FluidDyn, we use the
-revision control software Mercurial and our main repositories are hosted here:
+Transonic is part of the wider project FluidDyn. For FluidDyn, we use the revision
+control software Mercurial and our main repositories are hosted here:
 <https://foss.heptapod.net/fluiddyn>.
 
-Please read our documentation on [developer
-essentials](https://fluiddyn.readthedocs.io/en/latest/advice_developers.html),
-and especially on [setting up
-Mercurial](https://fluiddyn.readthedocs.io/en/latest/mercurial_heptapod.html).
+Please read our documentation on
+[developer essentials](https://fluiddyn.readthedocs.io/en/latest/advice_developers.html),
+and especially on
+[setting up Mercurial](https://fluiddyn.readthedocs.io/en/latest/mercurial_heptapod.html).
 
 ## Setup a development environment and use it
 
-We use [PDM](https://pdm-project.org) so the first step is to [install this
-tool](https://pdm-project.org/latest/#installation). Then, in the root
-directory of the repository, you can create and activate a local virtual environment with:
+We use [PDM](https://pdm-project.org) so the first step is to
+[install this tool](https://pdm-project.org/latest/#installation). Then, in the root
+directory of the repository, you can create and activate a local virtual environment
+with:
 
 ```sh
 pdm install

README.md

@@ -13,13 +13,17 @@
 
 **Documentation**: <https://transonic.readthedocs.io>
 
+<!-- start short description -->
+
 Transonic is a pure Python package (requiring Python >= 3.9) to easily accelerate modern
 Python-Numpy code with different accelerators (currently [Cython], [Pythran], [Numba] and
 [JAX], but potentially later [Cupy], [PyTorch], [Weld], [Pyccel], etc...).
 
 **The accelerators are not hard dependencies of Transonic:** Python codes using Transonic
 run fine without any accelerators installed (of course without speedup)!
 
+<!-- end short description -->
+
 > [!WARNING] Transonic is still in an active development stage (see our
 > [roadmap](https://transonic.readthedocs.io/en/latest/roadmap.html)). Remarks and
 > suggestions are very welcome.

ROADMAP.md

@@ -2,44 +2,44 @@
 
 ## Cython backend (beta version)
 
-Less bugs and more Cython features... Note that unfortunately we are [limited
-by Cython bugs](backends/cython.md)!
+Less bugs and more Cython features... Note that unfortunately we are
+[limited by Cython bugs](backends/cython.md)!
 
-- [done] Header also for Pythran (`.pythran`)
+- (done) Header also for Pythran (`.pythran`)
 
-- [done] Refactore backends "for method"
+- (done) Refactore backends "for method"
 
-- [done] Recompile if header changed
+- (done) Recompile if header changed
 
-- [done] test_run.py: also check signature files
+- (done) test_run.py: also check signature files
 
-- [done] Fused types rather than more than one signature for
+- (done) Fused types rather than more than one signature for
 
-  - [done] boost functions
-  - [done] boost methods
-  - [done] blocks
-  - [done] jit functions
-  - [done] jit methods
+  - (done) boost functions
+  - (done) boost methods
+  - (done) blocks
+  - (done) jit functions
+  - (done) jit methods
 
-- [done] BackendJITCython
+- (done) BackendJITCython
 
-- [done] Check/fix
+- (done) Check/fix
 
-  - [done] boost methods
-  - [done] blocks
-  - [done] jit functions
-  - [done] jit methods
+  - (done) boost methods
+  - (done) blocks
+  - (done) jit functions
+  - (done) jit methods
 
-- [done] Cython decorators (boundscheck, wraparound, cdivision, nonecheck)
+- (done) Cython decorators (boundscheck, wraparound, cdivision, nonecheck)
 
-- [done] void type
+- (done) void type
 
-- [done] Correct use of fused types (only 1 set of annotations supported)
+- (done) Correct use of fused types (only 1 set of annotations supported)
 
 - Special function definitions
 
-  - [done] inline
-  - [done] return type
+  - (done) inline
+  - (done) return type
   - nogil
 
 - better fused types
@@ -66,8 +66,9 @@ by Cython bugs](backends/cython.md)!
 
 It would allow one to use `numba.jitclass` and Cython extension type.
 
-A interesting goal would be to rewrite [pygbm](https://github.com/ogrisel/pygbm) (written in Numba) with Transonic. Note
-that the Cython translation is [here](https://github.com/scikit-learn/scikit-learn/tree/master/sklearn/ensemble/_hist_gradient_boosting)
+A interesting goal would be to rewrite [pygbm](https://github.com/ogrisel/pygbm) (written
+in Numba) with Transonic. Note that the Cython translation is
+[here](https://github.com/scikit-learn/scikit-learn/tree/master/sklearn/ensemble/_hist_gradient_boosting)
 in scikit-learn. Good Rosetta stone!
 
 ## Backends as Transonic extensions
@@ -84,9 +85,8 @@ Which API?
 
 ## Parallelism
 
-We can already use OpenMP with Transonic-Pythran. But OpenMP pragmas are not
-understood by the other backends. Numba and Cython use different notations
-(with `prange`):
+We can already use OpenMP with Transonic-Pythran. But OpenMP pragmas are not understood
+by the other backends. Numba and Cython use different notations (with `prange`):
 
 - <https://cython.readthedocs.io/en/latest/src/userguide/parallelism.html>
 - <https://numba.pydata.org/numba-doc/dev/user/parallel.html>

THANKS.md

@@ -2,17 +2,17 @@
 
 The main contributors are:
 
-- [Pierre Augier](http://www.legi.grenoble-inp.fr/people/Pierre.Augier/)
-  (LEGI, CNRS, UGA)
+- [Pierre Augier](http://www.legi.grenoble-inp.fr/people/Pierre.Augier/) (LEGI, CNRS,
+  UGA)
 - [Ashwin Vishnu](https://github.com/ashwinvis) (KTH, Stockholm)
 - [Pierre Blanc-fatin](https://github.com/PierreBlancfat) (UGA)
 
-with ideas from [Serge Sans Paille](https://github.com/serge-sans-paille/)
-and [Wolf Vollprecht](https://twitter.com/wuoulf).
+with ideas from [Serge Sans Paille](https://github.com/serge-sans-paille/) and
+[Wolf Vollprecht](https://twitter.com/wuoulf).
 
-Of course Transonic could not exist without Serge, a benefactor to humankind
-who brings efficiency for numerical computing to snake tamers. Trugarez for his
-great work on Pythran and Beniget!
+Of course Transonic could not exist without Serge, a benefactor to humankind who brings
+efficiency for numerical computing to snake tamers. Trugarez for his great work on
+Pythran and Beniget!
 
-A very special thanks to [Laura Mendoza](https://github.com/lasofivec) who
-replaced Pierre Augier to give our presentation at [Pyconfr 2019](https://www.pycon.fr/2019/).
+A very special thanks to [Laura Mendoza](https://github.com/lasofivec) who replaced
+Pierre Augier to give our presentation at [Pyconfr 2019](https://www.pycon.fr/2019/).

_transonic_testing/src/_transonic_testing/for_test_exterior_import_jit.py

@@ -1,7 +1,7 @@
 import gast
 import numpy as np
-from .for_test_exterior_import_jit_2 import func_import_2
 
+from .for_test_exterior_import_jit_2 import func_import_2
 
 const = 1
 foo = 1

_transonic_testing/src/_transonic_testing/for_test_exterior_import_jit_2.py

@@ -1,7 +1,6 @@
 import gast
 import numpy as np
 
-
 const = 1
 foo = 1
 

_transonic_testing/src/_transonic_testing/for_test_init.py

@@ -1,7 +1,6 @@
 import numpy as np
 
-from transonic import Transonic, boost, Array, Union, const
-
+from transonic import Array, Transonic, Union, boost, const
 
 # transonic def func(int, float)
 

_transonic_testing/src/_transonic_testing/for_test_justintime.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from transonic import jit, boost
+from transonic import boost, jit
 from transonic.mpi import Path
 
 
@@ -71,9 +71,10 @@ def check(self):
         assert self.myfunc(1) == 3
 
 
+from numpy import pi
+
 # FIXME support multilevel imported jitted function call in a jitted function
 from .for_test_exterior_import_jit import foo, func_import, func_import2
-from numpy import pi
 
 const = 1
 

data_tests/test_packaging/base.py

@@ -1,4 +1,5 @@
 """A pure Python module containing a few functions"""
+
 import numpy as np
 
 

doc/Makefile

@@ -174,3 +174,6 @@ notebook:
 
 autobuild:
 	@sphinx-autobuild --watch ../src --re-ignore '_build\/.*' "$(SOURCEDIR)" "$(BUILDDIR)/html"
+
+format:
+	mdformat *.md */*.md

doc/backends.md

@@ -1,30 +1,27 @@
 # Supported backends
 
-Transonic can use different tools to accelerate the code. We use the name
-**backend**.
+Transonic can use different tools to accelerate the code. We use the name **backend**.
 
-The default backend is Pythran and currently, there are 3 other backends
-("cython", "numba" or "python"). The "python" backend is mainly used for
-internal testing.
+The default backend is Pythran and currently, there are 3 other backends ("cython",
+"numba" or "python"). The "python" backend is mainly used for internal testing.
 
 There are different methods to choose which backend is used:
 
-- An environment variable {code}`TRANSONIC_BACKEND` (which has to be "pythran",
-  "cython", "numba" or "python") should be used to change the backend globally
-  for one process.
+- An environment variable {code}`TRANSONIC_BACKEND` (which has to be "pythran", "cython",
+  "numba" or "python") should be used to change the backend globally for one process.
 - The `transonic` command-line has an option `-b` (`--backend`).
 - The functions {func}`transonic.backends.make_backend_files` and
-  {func}`transonic.dist.init_transonic_extensions` have an optional argument
-  `backend`. Note that these functions should be imported from the
-  {mod}`transonic.dist` package.
+  {func}`transonic.dist.init_transonic_extensions` have an optional argument `backend`.
+  Note that these functions should be imported from the {mod}`transonic.dist` package.
 - There are two functions {func}`transonic.config.set_backend` and
-  {func}`transonic.backends.set_backend_for_this_module`. Note that these
-  functions can be imported from the {mod}`transonic` package.
+  {func}`transonic.backends.set_backend_for_this_module`. Note that these functions can
+  be imported from the {mod}`transonic` package.
 - The `boost` and `jit` decorators have an optional argument `backend`.
 
 ```{toctree}
-:maxdepth: 2
-
+---
+maxdepth: 2
+---
 examples/bench_row_sum/txt
 backends/pythran
 backends/cython