help needed with installation error - Requested phat has different version about scikit-tda HOT 12 OPEN

pip recently began validating metadata (I think this came with release 20.3, when the dependency resolver was added). This error indicates a mismatch between the claimed version and metadata in the phat package. You might need to file an issue with that package, I’m not familiar with it but I hope this info is helpful.

from scikit-tda.

An issue has been filed here: xoltar/phat#4.

I think the best solution for now is to downgrade to an earlier version of pip for now.

from scikit-tda.

Thanks for your reply. I have downgraded pip to 20.2.3, and the download was partially successful. I received the error that the phat wheel could not be built, and cechmate and phat have incompatible versions. It also warned me that updating may lead to error in the future. The error report is at the end and the errors are marked with new section headings.

Questions:

1. Should I be concerned? Can I still run things properly despite the error reports?
2. This is unrelated: are there plans to make a conda package?

installation log

pip install scikit-tda
Collecting scikit-tda
Using cached scikit_tda-0.1.0-py3-none-any.whl (2.9 kB)
Requirement already satisfied: matplotlib in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (3.3.4)
Collecting pybind11
Downloading pybind11-2.6.2-py2.py3-none-any.whl (191 kB)
|████████████████████████████████| 191 kB 912 kB/s
Requirement already satisfied: pillow in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (8.1.0)
Requirement already satisfied: scikit-learn in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (0.23.2)
Collecting cechmate
Using cached cechmate-0.1.0-py3-none-any.whl (23 kB)
Requirement already satisfied: numpy in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (1.19.2)
Requirement already satisfied: scipy in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (1.6.0)
Requirement already satisfied: Cython in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (0.29.21)
Collecting phat
Using cached phat-1.5.0a.tar.gz (4.7 MB)
Collecting kmapper
Downloading kmapper-1.4.1-py3-none-any.whl (95 kB)
|████████████████████████████████| 95 kB 1.3 MB/s
Collecting ripser
Downloading ripser-0.6.0.tar.gz (71 kB)
|████████████████████████████████| 71 kB 1.6 MB/s
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting tadasets
Downloading tadasets-0.0.4-py3-none-any.whl (7.1 kB)
Collecting persim
Downloading persim-0.2.0-py3-none-any.whl (31 kB)
Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/lib/python3.7/site-packages (from matplotlib->scikit-tda) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in ./opt/anaconda3/lib/python3.7/site-packages (from matplotlib->scikit-tda) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in ./opt/anaconda3/lib/python3.7/site-packages (from matplotlib->scikit-tda) (2.8.1)
Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/lib/python3.7/site-packages (from matplotlib->scikit-tda) (1.3.1)
Requirement already satisfied: joblib>=0.11 in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-learn->scikit-tda) (1.0.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-learn->scikit-tda) (2.1.0)
Requirement already satisfied: Jinja2 in ./opt/anaconda3/lib/python3.7/site-packages (from kmapper->scikit-tda) (2.11.3)
Collecting deprecated
Downloading Deprecated-1.2.11-py2.py3-none-any.whl (9.1 kB)
Collecting hopcroftkarp
Downloading hopcroftkarp-1.2.5.tar.gz (16 kB)
Requirement already satisfied: six in ./opt/anaconda3/lib/python3.7/site-packages (from cycler>=0.10->matplotlib->scikit-tda) (1.15.0)
Requirement already satisfied: MarkupSafe>=0.23 in ./opt/anaconda3/lib/python3.7/site-packages (from Jinja2->kmapper->scikit-tda) (1.1.1)
Requirement already satisfied: wrapt<2,>=1.10 in ./opt/anaconda3/lib/python3.7/site-packages (from deprecated->persim->scikit-tda) (1.12.1)
Building wheels for collected packages: phat, ripser, hopcroftkarp
Building wheel for phat (setup.py) ... error

error 1

ERROR: Command errored out with exit status 1:
command: /Users/alexsiu/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9_/k8j6nbmd1fvg_znf04dzdfhh0000gn/T/pip-install-15qmjsge/phat/setup.py'"'"'; file='"'"'/private/var/folders/9_/k8j6nbmd1fvg_znf04dzdfhh0000gn/T/pip-install-15qmjsge/phat/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/9_/k8j6nbmd1fvg_znf04dzdfhh0000gn/T/pip-wheel-v16mr3r2
cwd: /private/var/folders/9_/k8j6nbmd1fvg_znf04dzdfhh0000gn/T/pip-install-15qmjsge/phat/
Complete output (40 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
copying python/phat.py -> build/lib.macosx-10.9-x86_64-3.7
running build_ext
Traceback (most recent call last):
File "", line 1, in
File "/private/var/folders/9_/k8j6nbmd1fvg_znf04dzdfhh0000gn/T/pip-install-15qmjsge/phat/setup.py", line 66, in
py_modules = ['phat'],
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/site-packages/setuptools/init.py", line 153, in setup
return distutils.core.setup(**attrs)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 299, in run
self.run_command('build')
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/site-packages/setuptools/command/build_ext.py", line 79, in run
_build_ext.run(self)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
build_ext.build_ext.run(self)
File "/Users/alexsiu/opt/anaconda3/lib/python3.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/private/var/folders/9/k8j6nbmd1fvg_znf04dzdfhh0000gn/T/pip-install-15qmjsge/phat/setup.py", line 40, in build_extensions
import pybind11
ModuleNotFoundError: No module named 'pybind11'
----------------------------------------
ERROR: Failed building wheel for phat
Running setup.py clean for phat
Building wheel for ripser (PEP 517) ... done
Created wheel for ripser: filename=ripser-0.6.0-cp37-cp37m-macosx_10_9_x86_64.whl size=75770 sha256=127863a6628273a6aae6e11d5e49ed747ff9b7e36aa685e9d1f79cb8002fed98
Stored in directory: /Users/alexsiu/Library/Caches/pip/wheels/e8/b2/61/e9e1faaee99a8c232366e211456483ed0215c171f5b3db2f6f
Building wheel for hopcroftkarp (setup.py) ... done
Created wheel for hopcroftkarp: filename=hopcroftkarp-1.2.5-py2.py3-none-any.whl size=18091 sha256=d5c0a64293e1fbbcd3dd06894a37f8ff64841a4686aaa3a9133a754bee46d3cc
Stored in directory: /Users/alexsiu/Library/Caches/pip/wheels/d2/9f/a8/67f1b86e47cd17338d3d07939f4660378e65b758c4594f96e3
Successfully built ripser hopcroftkarp
Failed to build phat
Installing collected packages: pybind11, phat, deprecated, hopcroftkarp, persim, cechmate, kmapper, ripser, tadasets, scikit-tda
Running setup.py install for phat ... done

error 2

DEPRECATION: phat was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. pip 21.0 will remove support for this functionality. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at pypa/pip#8368.
ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.

We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.

cechmate 0.1.0 requires phat==1.5.0a0, but you'll have phat 1.5.0 which is incompatible.
Successfully installed cechmate-0.1.0 deprecated-1.2.11 hopcroftkarp-1.2.5 kmapper-1.4.1 persim-0.2.0 phat-1.5.0 pybind11-2.6.2 ripser-0.6.0 scikit-tda-0.1.0 tadasets-0.0.4
WARNING: You are using pip version 20.2.3; however, version 21.0.1 is available.
You should consider upgrading via the '/Users/alexsiu/opt/anaconda3/bin/python -m pip install --upgrade pip' command.

from scikit-tda.

Has anyone found a solution to the issue @a-cys posted above on the 23rd?

from scikit-tda.

Bumping this issue since I'm running into the same problems

from scikit-tda.

from scikit-tda.

It’s not the most ideal solution, but we’ve removed cechmate from the scikit-TDA package and deployed a new version. This should unblock everyone who doesn’t need cechmate, which we believe is most of our users.

currently we’re considering sun setting cechmate all together, so if anyone does have interest in keeping it alive, please let us know!

from scikit-tda.

Thanks for addressing the issue with cechmate, which I understand I will likely not need to use your tea package. Is the phat package required? I ask because my attempt to install cechmate failed, at least in part, because it requires phat.

Thanks again. David Wilt

from scikit-tda.

from scikit-tda.

from scikit-tda.

from scikit-tda.

from scikit-tda.