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PyBaMM version 21.08 does not install

See original GitHub issue

PyBaMM version 21.08
Python version 3.9.5

Describe the bug I’m trying to pip install the latest version of PyBaMM which is 21.08 but I get several errors and warnings. I’m using the Miniconda installation of Python. I did not have a problem installing the last version PyBaMM on my computer. So there is something wrong with the installation process for version 21.08.

To Reproduce Steps to reproduce the behaviour:

pip install pybamm
See errors and warnings shown below.

Collecting pybamm
  Using cached pybamm-21.8.tar.gz (889 kB)
    ERROR: Command errored out with exit status 1:
     command: /opt/miniconda3/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4q/qh3l23cd6jzdclcq6l_bvzm0kyy0fc/T/pip-install-qx2hel0f/pybamm_e6b5ed7ff70c4a8eb7d01b9468cb7681/setup.py'"'"'; __file__='"'"'/private/var/folders/4q/qh3l23cd6jzdclcq6l_bvzm0kyy0fc/T/pip-install-qx2hel0f/pybamm_e6b5ed7ff70c4a8eb7d01b9468cb7681/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 /private/var/folders/4q/qh3l23cd6jzdclcq6l_bvzm0kyy0fc/T/pip-pip-egg-info-8ujq764a
         cwd: /private/var/folders/4q/qh3l23cd6jzdclcq6l_bvzm0kyy0fc/T/pip-install-qx2hel0f/pybamm_e6b5ed7ff70c4a8eb7d01b9468cb7681/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/4q/qh3l23cd6jzdclcq6l_bvzm0kyy0fc/T/pip-install-qx2hel0f/pybamm_e6b5ed7ff70c4a8eb7d01b9468cb7681/setup.py", line 18, in <module>
        import CMakeBuild
    ModuleNotFoundError: No module named 'CMakeBuild'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/61/0a/f9732746658d728e22282d4b6d2ebd3e50128e6c5d00662fd668e870ccbe/pybamm-21.8.tar.gz#sha256=51af2c85110c948df176f974afe980bb4d34744a3bd03ca0cd29ba965d9d8b64 (from https://pypi.org/simple/pybamm/) (requires-python:>=3.6,<3.10). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Using cached pybamm-0.4.0.post1-cp39-cp39-macosx_10_9_x86_64.whl (1.4 MB)
Collecting casadi>=3.5.0
  Using cached casadi-3.5.5.post2-cp39-none-macosx_10_13_x86_64.macosx_10_13_intel.whl (21.2 MB)
Requirement already satisfied: scipy>=1.3 in /opt/miniconda3/lib/python3.9/site-packages (from pybamm) (1.7.1)
Requirement already satisfied: pandas>=0.24 in /opt/miniconda3/lib/python3.9/site-packages (from pybamm) (1.3.2)
Collecting jupyter
  Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Collecting pybtex
  Using cached pybtex-0.24.0-py2.py3-none-any.whl (561 kB)
Collecting autograd>=1.2
  Using cached autograd-1.3-py3-none-any.whl
Collecting anytree>=2.4.3
  Using cached anytree-2.8.0-py2.py3-none-any.whl (41 kB)
Collecting scikit-fem>=0.2.0
  Using cached scikit_fem-3.2.0-py3-none-any.whl (116 kB)
Requirement already satisfied: numpy>=1.16 in /opt/miniconda3/lib/python3.9/site-packages (from pybamm) (1.20.3)
Collecting jax==0.2.5
  Using cached jax-0.2.5-py3-none-any.whl
Requirement already satisfied: matplotlib>=2.0 in /opt/miniconda3/lib/python3.9/site-packages (from pybamm) (3.4.2)
Collecting pybamm
  Using cached pybamm-0.4.0-cp39-cp39-macosx_10_9_x86_64.whl (1.4 MB)
  Using cached pybamm-0.2.4.post3-py3-none-any.whl (520 kB)
Requirement already satisfied: six>=1.9.0 in /opt/miniconda3/lib/python3.9/site-packages (from anytree>=2.4.3->pybamm) (1.16.0)
Collecting future>=0.15.2
  Using cached future-0.18.2-py3-none-any.whl
Requirement already satisfied: kiwisolver>=1.0.1 in /opt/miniconda3/lib/python3.9/site-packages (from matplotlib>=2.0->pybamm) (1.3.1)
Requirement already satisfied: pillow>=6.2.0 in /opt/miniconda3/lib/python3.9/site-packages (from matplotlib>=2.0->pybamm) (8.3.1)
Requirement already satisfied: cycler>=0.10 in /opt/miniconda3/lib/python3.9/site-packages (from matplotlib>=2.0->pybamm) (0.10.0)
Requirement already satisfied: pyparsing>=2.2.1 in /opt/miniconda3/lib/python3.9/site-packages (from matplotlib>=2.0->pybamm) (2.4.7)
Requirement already satisfied: python-dateutil>=2.7 in /opt/miniconda3/lib/python3.9/site-packages (from matplotlib>=2.0->pybamm) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in /opt/miniconda3/lib/python3.9/site-packages (from pandas>=0.24->pybamm) (2021.1)
Collecting meshio>=4.0.4
  Using cached meshio-5.0.0-py3-none-any.whl (163 kB)
Collecting jupyter-console
  Using cached jupyter_console-6.4.0-py3-none-any.whl (22 kB)
Collecting ipykernel
  Using cached ipykernel-6.4.1-py3-none-any.whl (124 kB)
Collecting nbconvert
  Using cached nbconvert-6.1.0-py3-none-any.whl (551 kB)
Collecting qtconsole
  Using cached qtconsole-5.1.1-py3-none-any.whl (119 kB)
Collecting ipywidgets
  Using cached ipywidgets-7.6.4-py2.py3-none-any.whl (121 kB)
Collecting notebook
  Using cached notebook-6.4.3-py3-none-any.whl (9.9 MB)
Requirement already satisfied: appnope in /opt/miniconda3/lib/python3.9/site-packages (from ipykernel->jupyter->pybamm) (0.1.2)
Requirement already satisfied: ipython-genutils in /opt/miniconda3/lib/python3.9/site-packages (from ipykernel->jupyter->pybamm) (0.2.0)
Requirement already satisfied: tornado<7.0,>=4.2 in /opt/miniconda3/lib/python3.9/site-packages (from ipykernel->jupyter->pybamm) (6.1)
Collecting jupyter-client<8.0
  Using cached jupyter_client-7.0.2-py3-none-any.whl (122 kB)
Requirement already satisfied: traitlets<6.0,>=4.1.0 in /opt/miniconda3/lib/python3.9/site-packages (from ipykernel->jupyter->pybamm) (5.0.5)
Collecting debugpy<2.0,>=1.0.0
  Using cached debugpy-1.4.3-cp39-cp39-macosx_10_15_x86_64.whl (1.7 MB)
Requirement already satisfied: matplotlib-inline<0.2.0,>=0.1.0 in /opt/miniconda3/lib/python3.9/site-packages (from ipykernel->jupyter->pybamm) (0.1.2)
Requirement already satisfied: ipython<8.0,>=7.23.1 in /opt/miniconda3/lib/python3.9/site-packages (from ipykernel->jupyter->pybamm) (7.26.0)
Requirement already satisfied: backcall in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (0.2.0)
Requirement already satisfied: pexpect>4.3 in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (4.8.0)
Requirement already satisfied: decorator in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (5.0.9)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (3.0.17)
Requirement already satisfied: pickleshare in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (0.7.5)
Requirement already satisfied: jedi>=0.16 in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (0.18.0)
Requirement already satisfied: setuptools>=18.5 in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (52.0.0.post20210125)
Requirement already satisfied: pygments in /opt/miniconda3/lib/python3.9/site-packages (from ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (2.10.0)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /opt/miniconda3/lib/python3.9/site-packages (from jedi>=0.16->ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (0.8.2)
Collecting jupyter-core>=4.6.0
  Using cached jupyter_core-4.7.1-py3-none-any.whl (82 kB)
Collecting entrypoints
  Using cached entrypoints-0.3-py2.py3-none-any.whl (11 kB)
Collecting pyzmq>=13
  Using cached pyzmq-22.2.1-cp39-cp39-macosx_10_15_universal2.whl (2.0 MB)
Collecting nest-asyncio>=1.5
  Using cached nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB)
Requirement already satisfied: ptyprocess>=0.5 in /opt/miniconda3/lib/python3.9/site-packages (from pexpect>4.3->ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (0.7.0)
Requirement already satisfied: wcwidth in /opt/miniconda3/lib/python3.9/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython<8.0,>=7.23.1->ipykernel->jupyter->pybamm) (0.2.5)
Collecting widgetsnbextension~=3.5.0
  Using cached widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB)
Collecting nbformat>=4.2.0
  Using cached nbformat-5.1.3-py3-none-any.whl (178 kB)
Collecting jupyterlab-widgets>=1.0.0
  Using cached jupyterlab_widgets-1.0.1-py3-none-any.whl (243 kB)
Collecting jsonschema!=2.5.0,>=2.4
  Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting attrs>=17.4.0
  Using cached attrs-21.2.0-py2.py3-none-any.whl (53 kB)
Collecting pyrsistent>=0.14.0
  Using cached pyrsistent-0.18.0-cp39-cp39-macosx_10_9_x86_64.whl (68 kB)
Collecting argon2-cffi
  Using cached argon2_cffi-21.1.0-cp35-abi3-macosx_10_14_x86_64.whl (38 kB)
Collecting terminado>=0.8.3
  Using cached terminado-0.12.1-py3-none-any.whl (15 kB)
Collecting prometheus-client
  Using cached prometheus_client-0.11.0-py2.py3-none-any.whl (56 kB)
Collecting jinja2
  Using cached Jinja2-3.0.1-py3-none-any.whl (133 kB)
Collecting Send2Trash>=1.5.0
  Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB)
Requirement already satisfied: cffi>=1.0.0 in /opt/miniconda3/lib/python3.9/site-packages (from argon2-cffi->notebook->jupyter->pybamm) (1.14.6)
Requirement already satisfied: pycparser in /opt/miniconda3/lib/python3.9/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter->pybamm) (2.20)
Collecting MarkupSafe>=2.0
  Using cached MarkupSafe-2.0.1-cp39-cp39-macosx_10_9_x86_64.whl (13 kB)
Collecting defusedxml
  Using cached defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Collecting bleach
  Using cached bleach-4.1.0-py2.py3-none-any.whl (157 kB)
Collecting jupyterlab-pygments
  Using cached jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)
Collecting testpath
  Using cached testpath-0.5.0-py3-none-any.whl (84 kB)
Collecting mistune<2,>=0.8.1
  Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting pandocfilters>=1.4.1
  Using cached pandocfilters-1.4.3-py3-none-any.whl
Collecting nbclient<0.6.0,>=0.5.0
  Using cached nbclient-0.5.4-py3-none-any.whl (66 kB)
Collecting packaging
  Using cached packaging-21.0-py3-none-any.whl (40 kB)
Collecting webencodings
  Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting qtpy
  Using cached QtPy-1.11.0-py2.py3-none-any.whl (58 kB)
Installing collected packages: pyrsistent, attrs, pyzmq, nest-asyncio, jupyter-core, jsonschema, entrypoints, webencodings, packaging, nbformat, MarkupSafe, jupyter-client, testpath, pandocfilters, nbclient, mistune, jupyterlab-pygments, jinja2, defusedxml, debugpy, bleach, terminado, Send2Trash, prometheus-client, nbconvert, ipykernel, argon2-cffi, notebook, widgetsnbextension, qtpy, jupyterlab-widgets, qtconsole, meshio, jupyter-console, ipywidgets, future, scikit-fem, jupyter, casadi, autograd, anytree, pybamm
Successfully installed MarkupSafe-2.0.1 Send2Trash-1.8.0 anytree-2.8.0 argon2-cffi-21.1.0 attrs-21.2.0 autograd-1.3 bleach-4.1.0 casadi-3.5.5.post2 debugpy-1.4.3 defusedxml-0.7.1 entrypoints-0.3 future-0.18.2 ipykernel-6.4.1 ipywidgets-7.6.4 jinja2-3.0.1 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-7.0.2 jupyter-console-6.4.0 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 jupyterlab-widgets-1.0.1 meshio-5.0.0 mistune-0.8.4 nbclient-0.5.4 nbconvert-6.1.0 nbformat-5.1.3 nest-asyncio-1.5.1 notebook-6.4.3 packaging-21.0 pandocfilters-1.4.3 prometheus-client-0.11.0 pybamm-0.2.4.post3 pyrsistent-0.18.0 pyzmq-22.2.1 qtconsole-5.1.1 qtpy-1.11.0 scikit-fem-3.2.0 terminado-0.12.1 testpath-0.5.0 webencodings-0.5.1 widgetsnbextension-3.5.1

According to pip list, the version of PyBaMM that is installed appears to be 0.2.4.post3.

Running a PyBaMM example gives the following module not found error.

Traceback (most recent call last):
  File "/Users/g72/Desktop/ORNL/MegaPack/pybamm-examples/example1.py", line 2, in <module>
    import pybamm
  File "/opt/miniconda3/lib/python3.9/site-packages/pybamm/__init__.py", line 105, in <module>
    from .expression_tree.operations.evaluate import (
  File "/opt/miniconda3/lib/python3.9/site-packages/pybamm/expression_tree/operations/evaluate.py", line 13, in <module>
    import jax
ModuleNotFoundError: No module named 'jax'

Expected behaviour Expected behavior is to install PyBaMM version 21.08 with pip.