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Pre-requirements dependency on Numpy 1.18.5 breaks scipy
In testing #13, I ran into a bug when I tried to import Imviz:
>>> from jdaviz import Imviz
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\jdaviz\__init__.py", line 11, in <module>
from jdaviz.configs.specviz import Specviz, SpecViz # noqa
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\jdaviz\configs\__init__.py", line 1, in <module>
from .cubeviz import * # noqa
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\jdaviz\configs\cubeviz\__init__.py", line 1, in <module>
from .plugins import * # noqa
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\jdaviz\configs\cubeviz\plugins\__init__.py", line 1, in <module>
from .viewers import * # noqa
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\jdaviz\configs\cubeviz\plugins\viewers.py", line 2, in <module>
from glue_jupyter.bqplot.image import BqplotImageView
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\glue_jupyter\bqplot\image\__init__.py", line 1, in <module>
from .layer_artist import * # noqa
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\glue_jupyter\bqplot\image\layer_artist.py", line 1, in <module>
import skimage.measure
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\skimage\measure\__init__.py", line 6, in <module>
from ._polygon import approximate_polygon, subdivide_polygon
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\skimage\measure\_polygon.py", line 2, in <module>
from scipy import signal
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\scipy\signal\__init__.py", line 310, in <module>
from ._peak_finding import *
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\scipy\signal\_peak_finding.py", line 8, in <module>
from scipy.stats import scoreatpercentile
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\scipy\stats\__init__.py", line 441, in <module> from .stats import *
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\scipy\stats\stats.py", line 43, in <module>
from . import distributions
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\scipy\stats\distributions.py", line 11, in <module>
from . import _discrete_distns
File "E:\STScI\gitRepos\aas239-jwebbinar\envvalidate\lib\site-packages\scipy\stats\_discrete_distns.py", line 19, in <module>
from .biasedurn import (_PyFishersNCHypergeometric,
File "biasedurn.pyx", line 1, in init scipy.stats.biasedurn
ModuleNotFoundError: No module named 'numpy.random.bit_generator'
Pey Lian was able to trace it down to our pre-requirement on numpy:
https://github.com/spacetelescope/aas239-jwebbinar/blob/main/00_Installation/pre-requirements.txt#L2
specifically:
https://numpy.org/doc/stable/release/1.19.0-notes.html#numpy-random-bit-generator-moved-to-numpy-random-bit-generator
This above pinning on numpy==1.18.5 seems incompatible with our scipy requirement:
https://github.com/spacetelescope/aas239-jwebbinar/blob/main/00_Installation/requirements.txt#L1
Even though scipy 1.7.3 claims support for numpy>=1.16.5, this seems to be breaking... This was fixed when Pey Lian suggested I upgrade numpy. Is there a reason why we have numpy pinned to 1.18.5 @mustaric @eteq @orifox?
BUG: Windows installation error
I was tasked to check if our environments are still working here. As of writing, the installation works on my macOS (Validation notebook runs successfully and my Specviz Demo notebook runs without hiccup), but I ran into an issue on the Windows side. Figured I'd report it in case anyone in the future is looking, but obviously don't have the bandwidth to diagnose:
Running on Windows 11 22000.434 with Python 3.9.7 (tags/v3.9.7:1016ef3, Aug 30 2021, 20:19:38) [MSC v.1929 64 bit (AMD64)] on win32
pre-requirements.txt install worked ok. Failed on pip install -r requirements_windows.txt:
ERROR: Could not find a version that satisfies the requirement pyregion>=2.0 (from aplpy) (from versions: 0.1rc0, 1.0, 1.0.1, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.2, 2.0, 2.1.1b1, 2.1.1)
ERROR: No matching distribution found for pyregion>=2.0
Specifically:
Collecting pyregion==2.0
Using cached pyregion-2.0.tar.gz (1.1 MB)
ERROR: Command errored out with exit status 1:
command: 'E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\Scripts\python.exe' -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\Duy\\AppData\\Local\\Temp\\pip-install-k8tmmcch\\pyregion_5b22fa19ab4044ebb857b95af1d76652\\setup.py'"'"'; __file__='"'"'C:\\Users\\Duy\\AppData\\Local\\Temp\\pip-install-k8tmmcch\\pyregion_5b22fa19ab4044ebb857b95af1d76652\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4'
cwd: C:\Users\Duy\AppData\Local\Temp\pip-install-k8tmmcch\pyregion_5b22fa19ab4044ebb857b95af1d76652\
Complete output (40 lines):
running egg_info
creating C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4\pyregion.egg-info
writing C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4\pyregion.egg-info\PKG-INFO
writing dependency_links to C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4\pyregion.egg-info\dependency_links.txt
writing requirements to C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4\pyregion.egg-info\requires.txt
writing top-level names to C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4\pyregion.egg-info\top_level.txt
writing manifest file 'C:\Users\Duy\AppData\Local\Temp\pip-pip-egg-info-f8x99qr4\pyregion.egg-info\SOURCES.txt'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\Duy\AppData\Local\Temp\pip-install-k8tmmcch\pyregion_5b22fa19ab4044ebb857b95af1d76652\setup.py", line 116, in <module>
setup(
File "E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\lib\site-packages\setuptools\__init__.py", line 153, in setup
return distutils.core.setup(**attrs)
File "C:\Program Files\Python\Python309\lib\distutils\core.py", line 148, in setup
dist.run_commands()
File "C:\Program Files\Python\Python309\lib\distutils\dist.py", line 966, in run_commands
self.run_command(cmd)
File "C:\Program Files\Python\Python309\lib\distutils\dist.py", line 985, in run_command
cmd_obj.run()
File "E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\lib\site-packages\setuptools\command\egg_info.py", line 299, in run
self.find_sources()
File "E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\lib\site-packages\setuptools\command\egg_info.py", line 306, in find_sources
mm.run()
File "E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\lib\site-packages\setuptools\command\egg_info.py", line 541, in run
self.add_defaults()
File "E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\lib\site-packages\setuptools\command\egg_info.py", line 578, in add_defaults
sdist.add_defaults(self)
File "C:\Program Files\Python\Python309\lib\distutils\command\sdist.py", line 228, in add_defaults
self._add_defaults_ext()
File "C:\Program Files\Python\Python309\lib\distutils\command\sdist.py", line 311, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
File "C:\Program Files\Python\Python309\lib\distutils\cmd.py", line 299, in get_finalized_command
cmd_obj.ensure_finalized()
File "C:\Program Files\Python\Python309\lib\distutils\cmd.py", line 107, in ensure_finalized
self.finalize_options()
File "E:\STScI\gitRepos\aas239-jwebbinar\envbuildtest2022\lib\site-packages\astropy_helpers\commands\build_ext.py", line 260, in finalize_options
src_path = os.path.relpath(
File "C:\Program Files\Python\Python309\lib\ntpath.py", line 703, in relpath
raise ValueError("path is on mount %r, start on mount %r" % (
ValueError: path is on mount 'E:', start on mount 'C:'
----------------------------------------
Looks like it has to do with my environment being on a different drive. 🤷
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