Update numpy to 1.26 #34816

mkoeppe · 2022-12-01T22:54:32Z

https://github.com/numpy/numpy/releases

1.26.0.b1 is out, with Python 3.12 support and Cython 3 compatibility.

Depends on Drop support for Python 3.8 #35404

CC: @antonio-rojas @kiwifb @tornaria

Component: packages: standard

Issue created by migration from https://trac.sagemath.org/ticket/34816

mkoeppe · 2022-12-01T23:07:28Z

Branch: u/mkoeppe/update_numpy_to_1_24

mkoeppe · 2022-12-02T00:02:14Z

comment:2

There are a bunch of new FutureWarnings:

    FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.  (This may have returned Python scalars in past versions.

    FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.  (This may have returned Python scalars in past versions.

and also:

sage -t --random-seed=208794765845619979520719224489586219359 src/sage/plot/histogram.py
**********************************************************************
File "src/sage/plot/histogram.py", line 94, in sage.plot.histogram.Histogram.get_minmax_data
Failed example:
    h.get_minmax_data()
Exception raised:
    Traceback (most recent call last):
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.plot.histogram.Histogram.get_minmax_data[9]>", line 1, in <module>
        h.get_minmax_data()
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/plot/histogram.py", line 116, in get_minmax_data
        ydata, xdata = numpy.histogram(self.datalist, **opt)
      File "<__array_function__ internals>", line 198, in histogram
    TypeError: histogram() got an unexpected keyword argument 'normed'

sage -t --random-seed=208794765845619979520719224489586219359 src/sage/plot/plot_field.py
**********************************************************************
File "src/sage/plot/plot_field.py", line 51, in sage.plot.plot_field.PlotField.__init__
Failed example:
    r.yvec_array
Expected:
    masked_array(data=[0.0, 0.70710678118..., 0.70710678118...,
                       0.89442719...],
                 mask=[False, False, False, False],
           fill_value=1e+20)
Got:
    masked_array(data=[0.        , 0.70710678, 0.70710678, 0.89442719],
                 mask=False,
           fill_value=1e+20)

sage -t --random-seed=208794765845619979520719224489586219359 src/sage/misc/persist.pyx
**********************************************************************
File "src/sage/misc/persist.pyx", line 159, in sage.misc.persist.load
Failed example:
    hello
Expected:
    <fortran object>
Got:
    <fortran function hello>

sage -t --random-seed=208794765845619979520719224489586219359 src/sage/plot/complex_plot.pyx
**********************************************************************
File "src/sage/plot/complex_plot.pyx", line 1025, in sage.plot.complex_plot.?
Failed example:
    complex_plot(f, (0, 1), (0, 1), plot_points=300,
                 contoured=True, contour_type='linear', contour_base=1)
Expected:
    Graphics object consisting of 1 graphics primitive
Got:
    doctest:warning
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/bin/sage-runtests", line 154, in <module>
        err = DC.run()
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/control.py", line 1384, in run
        self.run_doctests()
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/control.py", line 1059, in run_doctests
        self.dispatcher.dispatch()
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 2021, in dispatch
        self.parallel_dispatch()
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 1916, in parallel_dispatch
        w.start()  # This might take some time
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 2190, in start
        super().start()
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/process.py", line 121, in start
        self._popen = self._Popen(self)
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 224, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 281, in _Popen
        return Popen(process_obj)
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_fork.py", line 19, in __init__
        self._launch(process_obj)
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_fork.py", line 71, in _launch
        code = process_obj._bootstrap(parent_sentinel=child_r)
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
        self.run()
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 2162, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 2492, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 2544, in _run
        result = runner.run(test)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 866, in run
        return self._run(test, compileflags, out)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.plot.complex_plot.?[14]>", line 1, in <module>
        complex_plot(f, (Integer(0), Integer(1)), (Integer(0), Integer(1)), plot_points=Integer(300),
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/repl/rich_output/display_manager.py", line 827, in displayhook
        plain_text, rich_output = self._rich_output_formatter(obj, dict())
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/repl/rich_output/display_manager.py", line 645, in _rich_output_formatter
        rich_output = self._call_rich_repr(obj, rich_repr_kwds)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/repl/rich_output/display_manager.py", line 605, in _call_rich_repr
        return obj._rich_repr_(self)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/plot/graphics.py", line 1001, in _rich_repr_
        return display_manager.graphics_from_save(
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/repl/rich_output/display_manager.py", line 733, in graphics_from_save
        save_function(filename, **kwds)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/misc/decorators.py", line 410, in wrapper
        return func(*args, **kwds)
      File "/Users/mkoeppe/s/sage/sage-rebasing/src/sage/plot/graphics.py", line 3358, in save
        figure.savefig(filename, **opts)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/figure.py", line 3046, in savefig
        self.canvas.print_figure(fname, **kwargs)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2295, in print_figure
        self.figure.draw(renderer)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/artist.py", line 73, in draw_wrapper
        result = draw(artist, renderer, *args, **kwargs)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
        return draw(artist, renderer)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/figure.py", line 2837, in draw
        mimage._draw_list_compositing_images(
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
        a.draw(renderer)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
        return draw(artist, renderer)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 3091, in draw
        mimage._draw_list_compositing_images(
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
        a.draw(renderer)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
        return draw(artist, renderer)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/image.py", line 646, in draw
        im, l, b, trans = self.make_image(
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/image.py", line 956, in make_image
        return self._make_image(self._A, bbox, transformed_bbox, clip,
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/image.py", line 564, in _make_image
        output = self.to_rgba(output, bytes=True, norm=False)
      File "/Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/cm.py", line 440, in to_rgba
        xx = (xx * 255).astype(np.uint8)
      File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/warnings.py", line 109, in _showwarnmsg
        sw(msg.message, msg.category, msg.filename, msg.lineno,
    :
    RuntimeWarning: invalid value encountered in cast

New commits:

`77b9aab`	`build/pkgs/numpy: Update to 1.24.0rc1`

mkoeppe · 2022-12-02T00:02:14Z

Commit: 77b9aab

sagetrac-git · 2022-12-13T01:33:23Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`9e95fc3`	`build/pkgs/numpy: Update to 1.24.0rc1`
`f8d8b51`	`build/pkgs/numpy: Update to 1.24.0rc2`

sagetrac-git · 2022-12-13T01:33:23Z

Changed commit from 77b9aab to f8d8b51

sagetrac-git · 2022-12-21T01:49:09Z

Branch pushed to git repo; I updated commit sha1. New commits:

`23e777e`	`build/pkgs/numpy: Update to 1.24.0`

sagetrac-git · 2022-12-21T01:49:09Z

Changed commit from f8d8b51 to 23e777e

tornaria · 2023-01-05T01:36:06Z

comment:8

The following seems to fix everything for me (numpy 1.24.1 from system)

diff --git a/src/sage/misc/persist.pyx b/src/sage/misc/persist.pyx
index 3ac5f1cc2b0..cb1f327c199 100644
--- a/src/sage/misc/persist.pyx
+++ b/src/sage/misc/persist.pyx
@@ -157,7 +157,7 @@ def load(*filename, compress=True, verbose=True, **kwargs):
         ....:     _ = f.write(code)
         sage: load(t)
         sage: hello
-        <fortran object>
+        <fortran ...>
     """
     import sage.repl.load
     if len(filename) != 1:
diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
index 6f0aeab87ae..b77c69b2f77 100644
--- a/src/sage/plot/complex_plot.pyx
+++ b/src/sage/plot/complex_plot.pyx
@@ -461,6 +461,8 @@ def complex_to_rgb(z_values, contoured=False, tiled=False,
             rgb[i, j, 2] = b
 
     sig_off()
+    nan_indices = np.isnan(rgb).any(-1)     # Mask for undefined points
+    rgb[nan_indices] = 1                    # Make nan_indices white
     return rgb
 
 
diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
index 3bc2b76b58e..388c2d1391d 100644
--- a/src/sage/plot/histogram.py
+++ b/src/sage/plot/histogram.py
@@ -87,13 +87,8 @@ class Histogram(GraphicPrimitive):
 
         TESTS::
 
-            sage: h = histogram([10,3,5], normed=True)[0]
-            doctest:warning...:
-            DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead.
-            See https://trac.sagemath.org/25260 for details.
+            sage: h = histogram([10,3,5], density=True)[0]
             sage: h.get_minmax_data()
-            doctest:warning ...
-            ...VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy.
             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
         """
         import numpy
diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 798671aab42..cad6a47ca8b 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -405,7 +405,7 @@ class SageMagics(Magics):
             ....: C END FILE FIB1.F
             ....: ''')
             sage: fib
-            <fortran object>
+            <fortran ...>
             sage: from numpy import array
             sage: a = array(range(10), dtype=float)
             sage: fib(a, 10)

mkoeppe · 2023-02-12T04:48:36Z

Removed branch from the issue description because it is replaced by PR #35081

Taken from #34816. This is necessary when system numpy is 1.24, and a prerequiste to update numpy in sagemath. It's probably safer at this time to merge this and leave the update for next release. Testing: void-linux/void-packages#42048 Depends on #35015 URL: #34994 Reported by: Gonzalo Tornaría Reviewer(s): Matthias Köppe, Volker Braun

### 📚 Description In preparation for important package upgrades, we remove support for Python v3.8. (Almost) all occurrences of "Python 3.8" are removed from the codebase. There are still some comments left that essentially say that in newer versions things can be simplified, but I didn't touch those and leave them for follow-up PRs. This will help with: - PRs that require Python 3.9 or above, such as sagemath#34973 and sagemath#35188. - Upgrades of Python packages that have dropped support for Python 3.8 because they follow NEP 29 and have already released a new major version that drops support according to the NEP 29 schedule. - NetworkX 3.2 (expected 2023-??; version 3.1 was released 2023-04, see sagemath#35671) - sagemath#34816 - sagemath#35703 - See also sagemath#32074. Test run: https://github.com/tobiasdiez/sage/actions/runs/4586981626     ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [x] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: sagemath#35404 Reported by: Tobias Diez Reviewer(s): Dima Pasechnik, Matthias Köppe

…-buster` and `fedora-29`    ### 📚 Description   Prerequisite of: - sagemath#34816 - sagemath#35703 - sagemath#35801 See also: - sagemath#32074 Instead of fully dropping `debian-buster` (LTS until 2024-06) in the CI, we replace it by `debian-buster-gcc_spkg` to verify that users on this platform have the recourse of installing a newer GCC. We also remove `linuxmint-19.3-gcc_8-python3.8` and change `fedora-30-python3.8` to `fedora-30` (which builds python from spkg), to prevent a merge conflict with sagemath#35404 We also add `debian-trixie` (= current testing).   ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: sagemath#35810 Reported by: Matthias Köppe Reviewer(s): Dima Pasechnik

### 📚 Description In preparation for important package upgrades, we remove support for Python v3.8. (Almost) all occurrences of "Python 3.8" are removed from the codebase. There are still some comments left that essentially say that in newer versions things can be simplified, but I didn't touch those and leave them for follow-up PRs. This will help with: - PRs that require Python 3.9 or above, such as sagemath#34973 and sagemath#35188. - Upgrades of Python packages that have dropped support for Python 3.8 because they follow NEP 29 and have already released a new major version that drops support according to the NEP 29 schedule. - NetworkX 3.2 (expected 2023-??; version 3.1 was released 2023-04, see sagemath#35671) - sagemath#34816 - sagemath#35703 - See also sagemath#32074. Test run: https://github.com/tobiasdiez/sage/actions/runs/4586981626     ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [x] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: sagemath#35404 Reported by: Tobias Diez Reviewer(s): Dima Pasechnik, Matthias Köppe

…-buster` and `fedora-29`    ### 📚 Description   Prerequisite of: - sagemath#34816 - sagemath#35703 - sagemath#35801 See also: - sagemath#32074 Instead of fully dropping `debian-buster` (LTS until 2024-06) in the CI, we replace it by `debian-buster-gcc_spkg` to verify that users on this platform have the recourse of installing a newer GCC. We also remove `linuxmint-19.3-gcc_8-python3.8` and change `fedora-30-python3.8` to `fedora-30` (which builds python from spkg), to prevent a merge conflict with sagemath#35404 We also add `debian-trixie` (= current testing).   ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: sagemath#35810 Reported by: Matthias Köppe Reviewer(s): Dima Pasechnik

NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility. 1.26.0 was released 2023-09-16. As NumPy has changed its build system from setuptools-pinned-to-an- ancient-version to meson_python, we get rid of our ancient version of `setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the same (current) version. - [x] Check portability run: https://github.com/mkoeppe/sage/actions/runs/5959239800 - [ ] Check SAGE_FAT_BINARY   Resolves sagemath#34816  ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies - Depends on sagemath#36112 (for the `meson_python` upgrades, merged here) - Depends on sagemath#35404 (merged here as part of above) - Depends on sagemath#35810 (merged here as part of above) - Depends on sagemath#36110 (merged here) - Depends on sagemath#36263 (merged here) - Depends on sagemath#36238 (merged here) - Depends on sagemath#36255 (merged here)   URL: sagemath#36123 Reported by: Matthias Köppe Reviewer(s):

NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility. 1.26.0 was released 2023-09-16. As NumPy has changed its build system from setuptools-pinned-to-an- ancient-version to meson_python, we get rid of our ancient version of `setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the same (current) version. - [x] Check portability run: https://github.com/mkoeppe/sage/actions/runs/5959239800 - [ ] Check SAGE_FAT_BINARY   Resolves #34816  ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies - Depends on #36112 (for the `meson_python` upgrades, merged here) - Depends on #35404 (merged here as part of above) - Depends on #35810 (merged here as part of above) - Depends on #36110 (merged here) - Depends on #36263 (merged here) - Depends on #36238 (merged here) - Depends on #36255 (merged here)   URL: #36123 Reported by: Matthias Köppe Reviewer(s):

### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies  - Depends on sagemath#34816 - Depends on sagemath#36279 -  URL: sagemath#36320 Reported by: Matthias Köppe Reviewer(s): John H. Palmieri, Matthias Köppe

mkoeppe added this to the sage-9.8 milestone Dec 1, 2022

mkoeppe added c: packages: standard labels Dec 1, 2022

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mkoeppe modified the milestones: sage-9.8, sage-9.9 Dec 31, 2022

tornaria mentioned this issue Feb 6, 2023

fix doctests to support numpy 1.24 #34994

Merged

mkoeppe changed the title ~~Update numpy to 1.24~~ Update numpy to 1.24.x Feb 12, 2023

mkoeppe modified the milestones: sage-10.0, sage-10.1 Apr 30, 2023

mkoeppe removed this from the sage-10.1 milestone Aug 7, 2023

mkoeppe added p: critical / 2 and removed p: major / 3 labels Aug 21, 2023

mkoeppe changed the title ~~Update numpy to 1.24.x~~ Update numpy to 1.26 Aug 21, 2023

mkoeppe added this to the sage-10.2 milestone Aug 21, 2023

vbraun closed this as completed in #36123 Oct 8, 2023

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Update numpy to 1.26 #34816

Update numpy to 1.26 #34816

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Update numpy to 1.26 #34816

Update numpy to 1.26 #34816

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mkoeppe commented Dec 1, 2022 • edited Loading

mkoeppe commented Dec 1, 2022

mkoeppe commented Dec 2, 2022

mkoeppe commented Dec 2, 2022

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tornaria commented Jan 5, 2023

mkoeppe commented Feb 12, 2023

mkoeppe commented Dec 1, 2022 •

edited

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