Open OnDraganov opened 1 month ago
It seems like you're using a Mac with an Intel chip, not the Apple M-series chips. There isn't a binary build of chalc available for this platform. While I get around to fixing that, could you try the following: run brew install automake autoconf libtool
before trying to install chalc
again?
Edit: I've pushed v3.1.2 with binaries for x86_64 on MacOS, so try using that instead. The phimaker dependency has also been updated to 0.1.3 to fix the issue you had with the phimaker dependency.
I don't know which fix did the it, but I ran the automake
installation and then installed chalc
via pip
and it was successful.
There is now a problem when importing due to numpy >=2.0.0
shenanigans--I will try with pre-2.0.0 numpy
, and let you know.
Could you post the error message here? chalc >= 2.0.0
will not work with pre-2.0.0 numpy
due to ABI compatibility issues.
Sure, I copy it below. Despite the warning it imports, but it might crash when used I guess.
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/usr/local/lib/python3.10/site-packages/ipykernel/__main__.py", line 4, in <module>
app.launch_new_instance()
File "/usr/local/lib/python3.10/site-packages/traitlets/config/application.py", line 978, in launch_instance
app.start()
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelapp.py", line 712, in start
self.io_loop.start()
File "/usr/local/lib/python3.10/site-packages/tornado/platform/asyncio.py", line 215, in start
self.asyncio_loop.run_forever()
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/base_events.py", line 603, in run_forever
self._run_once()
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/base_events.py", line 1909, in _run_once
handle._run()
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/events.py", line 80, in _run
self._context.run(self._callback, *self._args)
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 510, in dispatch_queue
await self.process_one()
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 499, in process_one
await dispatch(*args)
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 406, in dispatch_shell
await result
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 730, in execute_request
reply_content = await reply_content
File "/usr/local/lib/python3.10/site-packages/ipykernel/ipkernel.py", line 383, in do_execute
res = shell.run_cell(
File "/usr/local/lib/python3.10/site-packages/ipykernel/zmqshell.py", line 528, in run_cell
return super().run_cell(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2885, in run_cell
result = self._run_cell(
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2940, in _run_cell
return runner(coro)
File "/usr/local/lib/python3.10/site-packages/IPython/core/async_helpers.py", line 129, in _pseudo_sync_runner
coro.send(None)
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3139, in run_cell_async
has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3318, in run_ast_nodes
if await self.run_code(code, result, async_=asy):
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3378, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "/var/folders/nj/7fxzyf4x4859skpz67mhqf4h0000gn/T/ipykernel_74474/2291322110.py", line 1, in <module>
import chalc
File "/usr/local/lib/python3.10/site-packages/chalc/__init__.py", line 20, in <module>
from . import plotting
File "/usr/local/lib/python3.10/site-packages/chalc/plotting.py", line 10, in <module>
import seaborn as sns
File "/usr/local/lib/python3.10/site-packages/seaborn/__init__.py", line 2, in <module>
from .rcmod import * # noqa: F401,F403
File "/usr/local/lib/python3.10/site-packages/seaborn/rcmod.py", line 5, in <module>
from . import palettes
File "/usr/local/lib/python3.10/site-packages/seaborn/palettes.py", line 9, in <module>
from .utils import desaturate, get_color_cycle
File "/usr/local/lib/python3.10/site-packages/seaborn/utils.py", line 11, in <module>
import pandas as pd
File "/usr/local/lib/python3.10/site-packages/pandas/__init__.py", line 26, in <module>
from pandas.compat import (
File "/usr/local/lib/python3.10/site-packages/pandas/compat/__init__.py", line 27, in <module>
from pandas.compat.pyarrow import (
File "/usr/local/lib/python3.10/site-packages/pandas/compat/pyarrow.py", line 8, in <module>
import pyarrow as pa
File "/usr/local/lib/python3.10/site-packages/pyarrow/__init__.py", line 65, in <module>
import pyarrow.lib as _lib
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
AttributeError: _ARRAY_API not found
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/usr/local/lib/python3.10/site-packages/ipykernel/__main__.py", line 4, in <module>
app.launch_new_instance()
File "/usr/local/lib/python3.10/site-packages/traitlets/config/application.py", line 978, in launch_instance
app.start()
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelapp.py", line 712, in start
self.io_loop.start()
File "/usr/local/lib/python3.10/site-packages/tornado/platform/asyncio.py", line 215, in start
self.asyncio_loop.run_forever()
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/base_events.py", line 603, in run_forever
self._run_once()
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/base_events.py", line 1909, in _run_once
handle._run()
File "/usr/local/Cellar/python@3.10/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/events.py", line 80, in _run
self._context.run(self._callback, *self._args)
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 510, in dispatch_queue
await self.process_one()
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 499, in process_one
await dispatch(*args)
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 406, in dispatch_shell
await result
File "/usr/local/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 730, in execute_request
reply_content = await reply_content
File "/usr/local/lib/python3.10/site-packages/ipykernel/ipkernel.py", line 383, in do_execute
res = shell.run_cell(
File "/usr/local/lib/python3.10/site-packages/ipykernel/zmqshell.py", line 528, in run_cell
return super().run_cell(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2885, in run_cell
result = self._run_cell(
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2940, in _run_cell
return runner(coro)
File "/usr/local/lib/python3.10/site-packages/IPython/core/async_helpers.py", line 129, in _pseudo_sync_runner
coro.send(None)
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3139, in run_cell_async
has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3318, in run_ast_nodes
if await self.run_code(code, result, async_=asy):
File "/usr/local/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3378, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "/var/folders/nj/7fxzyf4x4859skpz67mhqf4h0000gn/T/ipykernel_74474/2291322110.py", line 1, in <module>
import chalc
File "/usr/local/lib/python3.10/site-packages/chalc/__init__.py", line 20, in <module>
from . import plotting
File "/usr/local/lib/python3.10/site-packages/chalc/plotting.py", line 10, in <module>
import seaborn as sns
File "/usr/local/lib/python3.10/site-packages/seaborn/__init__.py", line 2, in <module>
from .rcmod import * # noqa: F401,F403
File "/usr/local/lib/python3.10/site-packages/seaborn/rcmod.py", line 5, in <module>
from . import palettes
File "/usr/local/lib/python3.10/site-packages/seaborn/palettes.py", line 9, in <module>
from .utils import desaturate, get_color_cycle
File "/usr/local/lib/python3.10/site-packages/seaborn/utils.py", line 11, in <module>
import pandas as pd
File "/usr/local/lib/python3.10/site-packages/pandas/__init__.py", line 49, in <module>
from pandas.core.api import (
File "/usr/local/lib/python3.10/site-packages/pandas/core/api.py", line 9, in <module>
from pandas.core.dtypes.dtypes import (
File "/usr/local/lib/python3.10/site-packages/pandas/core/dtypes/dtypes.py", line 24, in <module>
from pandas._libs import (
File "/usr/local/lib/python3.10/site-packages/pyarrow/__init__.py", line 65, in <module>
import pyarrow.lib as _lib
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
AttributeError: _ARRAY_API not found
@OnDraganov should be fixed in v3.1.3, the issue was an incompatible version of pandas.
Unfortunately, I am still getting the error on import. Currently chalc
version 3.1.3
and pandas
version 2.2.2
Could you post the new error log?
Sorry for a delay—it is the same exact error, that is why I did not post it again.
Would you mind posting the result of 'pip list' here? I suspect that there is some numpy 2 incompatible package polluting the dependency chain.
Ah, that might very well be. I will try a fresh venv
, only install chalc
, and try.
My pip list is as follows:
Package Version
----------------------------- -----------
alabaster 0.7.13
anndata 0.8.0
appnope 0.1.3
ase 3.23.0
asttokens 2.0.8
attrs 22.1.0
Babel 2.13.1
backcall 0.2.0
beautifulsoup4 4.11.1
biopython 1.81
bleach 5.0.1
build 1.2.1
CacheControl 0.14.0
certifi 2022.9.24
cffi 1.17.0
chalc 3.1.3
charset-normalizer 2.1.1
chromatic_tda 1.1.3
cleo 2.1.0
click 8.1.3
click-default-group 1.2.2
cloup 0.13.1
colour 0.1.5
commonmark 0.9.1
contourpy 1.0.5
cramjam 2.6.2
crashtest 0.4.1
customtkinter 5.0.1
cycler 0.11.0
Cython 0.29.32
darkdetect 0.7.1
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
Deprecated 1.2.13
distlib 0.3.8
docutils 0.20.1
dulwich 0.21.7
entrypoints 0.4
et-xmlfile 1.1.0
ete3 3.1.3
exceptiongroup 1.1.2
executing 1.1.0
fanstatic 1.3
fastjsonschema 2.20.0
fastparquet 2023.4.0
filelock 3.15.4
fonttools 4.37.3
fsspec 2023.4.0
future 0.18.2
giotto-ph 0.2.2
glcontext 2.3.7
gudhi 3.10.0
h5py 3.11.0
hopcroftkarp 1.2.5
hupper 1.12.1
idna 3.4
igraph 0.10.4
imagesize 1.4.1
importlib-metadata 6.8.0
iniconfig 2.0.0
installer 0.7.0
ipykernel 6.16.0
ipython 8.5.0
isosurfaces 0.1.0
jaraco.classes 3.3.0
jedi 0.18.1
Jinja2 3.1.2
joblib 1.2.0
js 1.0
jsonschema 4.16.0
jupyter_client 7.3.5
jupyter-core 4.11.1
jupyterlab-pygments 0.2.2
keyring 24.2.0
kiwisolver 1.4.4
kmapper 2.0.1
lazy_loader 0.1rc2
legacy-api-wrap 1.4
leidenalg 0.9.1
Levenshtein 0.21.1
littleutils 0.2.2
llvmlite 0.43.0
lxml 4.9.3
ManimPango 0.4.3
mapbox-earcut 1.0.1
MarkupSafe 2.1.1
matplotlib 3.8.4
matplotlib-inline 0.1.6
miniball 1.2.0
mistune 2.0.4
moderngl 5.7.3
moderngl-window 2.4.2
more-itertools 10.0.0
msgpack 1.0.8
multipledispatch 0.6.0
mypy 1.5.0
mypy-extensions 1.0.0
natsort 8.2.0
nbclient 0.7.0
nbconvert 7.2.1
nbformat 5.7.0
nbscript 0.1.0
nest-asyncio 1.5.5
networkx 3.0
numba 0.60.0
numpy 2.0.1
openpyxl 3.0.10
ordereddict 1.1
outdated 0.2.1
packaging 24.1
pandas 2.2.2
pandas-flavor 0.3.0
pandocfilters 1.5.0
parmap 1.6.0
parso 0.8.3
PasteDeploy 3.1.0
patsy 0.5.3
persim 0.3.5
pexpect 4.8.0
phat 1.5.0
phimaker 0.1.3
phylotreelib 1.22.1
pickleshare 0.7.5
Pillow 9.2.0
pingouin 0.5.3
pip 24.2
pkginfo 1.11.1
plaster 1.1.2
plaster-pastedeploy 1.0.1
platformdirs 4.2.2
plotly 5.10.0
pluggy 1.5.0
poetry 1.8.3
poetry-core 1.9.0
poetry-plugin-export 1.8.0
POT 0.8.2
prompt-toolkit 3.0.31
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
py3Dmol 2.1.0
pyarrow 12.0.0
pybind11 2.11.1
pycairo 1.23.0
pycparser 2.21
pydub 0.25.1
pyglet 2.0.1
Pygments 2.17.2
pynndescent 0.5.7
pyobjc-core 9.0
pyobjc-framework-Cocoa 9.0
pyparsing 3.0.9
pyproject_hooks 1.0.0
PyQt5 5.15.9
PyQt5-Qt5 5.15.2
PyQt5-sip 12.12.2
pyramid 2.0.1
pyrr 0.10.3
pyrsistent 0.18.1
pytest 8.2.0
python-dateutil 2.8.2
python-whois 0.8.0
pytz 2022.4
pytz-deprecation-shim 0.1.0.post0
pyzmq 24.0.1
qc-procrustes 0.0.0.post0
rapidfuzz 3.2.0
readme-renderer 40.0
requests 2.28.1
requests-toolbelt 1.0.0
rfc3986 2.0.0
rich 12.6.0
ripser 0.6.4
rpy2 3.5.4
scanpy 1.10.0
scikit-learn 1.5.1
scikit-tda 1.0.0
scipy 1.14.0
screeninfo 0.8.1
seaborn 0.13.2
seaborn-extensions 0.1.1
sequencelib 2.18.5
session-info 1.0.0
setuptools 69.2.0
setuptools-scm 7.0.5
shellingham 1.5.4
six 1.16.0
skia-pathops 0.7.4
snowballstemmer 2.2.0
soupsieve 2.3.2.post1
Sphinx 7.2.6
sphinxcontrib-applehelp 1.0.7
sphinxcontrib-devhelp 1.0.5
sphinxcontrib-htmlhelp 2.0.4
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.6
sphinxcontrib-serializinghtml 1.1.9
srt 3.5.2
stack-data 0.5.1
statsmodels 0.13.2
stdlib-list 0.8.0
svgelements 1.8.4
tabulate 0.8.10
tadasets 0.0.4
tenacity 8.1.0
texttable 1.6.7
threadpoolctl 3.1.0
tinycss2 1.1.1
tk 0.1.0
tomli 2.0.1
tomlkit 0.13.0
torch 1.12.1
torch-topological 0.1.5
tornado 6.2
tqdm 4.64.1
traitlets 5.4.0
translationstring 1.4
treedist 1.0.1
trove-classifiers 2024.7.2
twine 4.0.2
typing_extensions 4.11.0
tzdata 2024.1
tzlocal 4.2
ujson 5.9.0
umap-learn 0.5.6
urllib3 1.26.12
venusian 3.1.0
virtualenv 20.26.3
watchdog 2.1.9
wcwidth 0.2.5
webencodings 0.5.1
WebOb 1.8.7
wheel 0.43.0
wrapt 1.15.0
xarray 2022.10.0
xattr 1.1.0
zipp 3.16.2
zope.deprecation 5.0
zope.interface 6.4.post2
With a fresh venv
it does not throw the error. So possibly it might just be a warning that can be ignored? The pip list for the virtual environment is as follows:
Package Version
------------------- -----------
chalc 3.1.3
contourpy 1.2.1
cycler 0.12.1
fonttools 4.53.1
h5py 3.11.0
hupper 1.12.1
kiwisolver 1.4.5
matplotlib 3.8.4
numpy 2.0.1
packaging 24.1
pandas 2.2.2
PasteDeploy 3.1.0
phimaker 0.1.3
pillow 10.4.0
pip 24.0
plaster 1.1.2
plaster-pastedeploy 1.0.1
pyparsing 3.1.2
pyramid 2.0.1
python-dateutil 2.9.0.post0
pytz 2024.1
seaborn 0.13.2
setuptools 69.2.0
six 1.16.0
translationstring 1.4
tzdata 2024.1
venusian 3.1.0
WebOb 1.8.8
zope.deprecation 5.0
zope.interface 7.0.1
pip install chalc
, version3.1.1
fails when building wheel on mac for me. I include log file with the error. It ends withCMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
. I used python 3.10 on macOS Sonoma 14.5 with Intel processor. The error also occurs in a fresh virtual environment.