Saint's Log

Fixing my VS Code Python Environment

I mentioned in my last post (Learning about Large Language Models) that I recently started going through Sebastian Raschka’s Build a Large Language Model from Scratch book. It had been a while since I ran python code on my laptop so I needed to do some cleanup to restore my environment. I cloned the repo and started executing the first cell in Chapter 2:

from importlib.metadata import version

print("torch version:", version("torch"))
print("tiktoken version:", version("tiktoken"))

I got this error: PackageNotFoundError: No package metadata was found for torch".

{
	"name": "PackageNotFoundError",
	"message": "No package metadata was found for torch",
	"stack": "---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
File /opt/homebrew/Cellar/python@3.11/3.11.1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/metadata/__init__.py:563, in Distribution.from_name(cls, name)
    562 try:
--> 563     return next(cls.discover(name=name))
    564 except StopIteration:

StopIteration: 

During handling of the above exception, another exception occurred:

PackageNotFoundError                      Traceback (most recent call last)
Cell In[2], line 7
      3 print(sys.version)
      5 from importlib.metadata import version
----> 7 print(\"torch version:\", version(\"torch\"))
      8 print(\"tiktoken version:\", version(\"tiktoken\"))

File /opt/homebrew/Cellar/python@3.11/3.11.1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/metadata/__init__.py:1008, in version(distribution_name)
   1001 def version(distribution_name):
   1002     \"\"\"Get the version string for the named package.
   1003 
   1004     :param distribution_name: The name of the distribution package to query.
   1005     :return: The version string for the package as defined in the package's
   1006         \"Version\" metadata key.
   1007     \"\"\"
-> 1008     return distribution(distribution_name).version

File /opt/homebrew/Cellar/python@3.11/3.11.1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/metadata/__init__.py:981, in distribution(distribution_name)
    975 def distribution(distribution_name):
    976     \"\"\"Get the ``Distribution`` instance for the named package.
    977 
    978     :param distribution_name: The name of the distribution package as a string.
    979     :return: A ``Distribution`` instance (or subclass thereof).
    980     \"\"\"
--> 981     return Distribution.from_name(distribution_name)

File /opt/homebrew/Cellar/python@3.11/3.11.1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/metadata/__init__.py:565, in Distribution.from_name(cls, name)
    563     return next(cls.discover(name=name))
    564 except StopIteration:
--> 565     raise PackageNotFoundError(name)

PackageNotFoundError: No package metadata was found for torch"
}

Here is python setup I had:

saint@MacBookPro LLMs-from-scratch % which python3
/opt/homebrew/bin/python3
saint@MacBookPro LLMs-from-scratch % python3 --version
Python 3.10.9

How is this showing version 3.10.9 but VS Code is using 3.11 from brew (per the file paths in the error messages? This is how to print the version from a python script as per Printing Python version in output – Stack Overflow

import sys
print("Python version")
print(sys.version)
print(sys.path)

Since I have brew installed, this might be what I need: the comment that “If you brew-install Python, but pip is still not in your path, you might need to re-link, like this brew unlink python && brew link python” at python – How do I install pip on macOS or OS X? – Stack Overflow.

saint@MacBookPro LLMs-from-scratch % brew unlink python
Unlinking /opt/homebrew/Cellar/python@3.11/3.11.1... 11 symlinks removed.
saint@MacBookPro LLMs-from-scratch % brew link python
Error: unknown or unsupported macOS version: :dunno

python3 --version still shows 3.10.9.

saint@MacBookPro LLMs-from-scratch % ls -l `which python3`
lrwxr-xr-x  1 saint  admin  40 Jan 27  2023 /opt/homebrew/bin/python3 -> ../Cellar/python@3.10/3.10.9/bin/python3

Is my brew too old?

saint@MacBookPro LLMs-from-scratch % brew --version
Homebrew 4.0.26
Homebrew/homebrew-core (git revision 5b93511fd6b; last commit 2023-03-19)
Homebrew/homebrew-cask (git revision dccc1df2ac; last commit 2023-03-19)

git – How do I update Homebrew? – Stack Overflow says to just run brew update. Look at this list! Scary how much of this outdated stuff is likely to be insecure.

saint@MacBookPro LLMs-from-scratch % brew update
==> Downloading https://ghcr.io/v2/homebrew/portable-ruby/portable-ruby/blobs/sha256:d9faa506c014dedc0b034a68103ba75c9a58242f4d6c67b6ca0f649c39602bcf
######################################################################################################################################################################################################################################### 100.0%
==> Pouring portable-ruby-3.3.7.arm64_big_sur.bottle.tar.gz
==> Homebrew collects anonymous analytics.
Read the analytics documentation (and how to opt-out) here:
  https://docs.brew.sh/Analytics
No analytics have been recorded yet (nor will be during this `brew` run).

==> homebrew/core is old and unneeded, untapping to save space...
Untapping homebrew/core...
Untapped 3 commands and 7398 formulae (7,130 files, 1GB).
==> homebrew/cask is old and unneeded, untapping to save space...
Untapping homebrew/cask...
Untapped 7333 casks (4,415 files, 487.2MB).
==> Downloading https://formulae.brew.sh/api/formula_tap_migrations.jws.json
Updated 4 taps (microsoft/git, homebrew/cask-versions, homebrew/core and homebrew/cask).
==> New Formulae

...<hundreds of lines omitted but included python entries below>

python-argcomplete
python-freethreading
python-gdbm@3.12
python-gdbm@3.13
python-matplotlib
python-packaging
python-setuptools
python-tk@3.12
python-tk@3.13
python@3.12
python@3.13
pyupgrade
...

==> Deleted Installed Formulae
icu4c ✘
==> Deleted Installed Casks
git-credential-manager-core ✘                                                                                            microsoft-openjdk11 ✘
Error: Unexpected method 'appcast' called on Cask adoptopenjdk16.
Follow the instructions here:
  https://github.com/Homebrew/homebrew-cask#reporting-bugs
==> Downloading https://formulae.brew.sh/api/cask_tap_migrations.jws.json
==> Outdated Formulae
aom                 fb303               fribidi             gnuplot             jasper              libheif             libtool             lua                 openblas            pstoedit            sqlite              xorgproto
arpack              fbthrift            gcc                 graphicsmagick      jbig2dec            libidn              libunistring        lz4                 openexr             pyqt@5              suite-sparse        xz
autoconf            fig2dev             gd                  harfbuzz            jpeg-turbo          libidn2             libvmaf             maven               openjdk             python@3.10         sundials            zstd
boost               fizz                gdbm                hdf5                jpeg-xl             liblqr              libx11              mpdecimal           openjpeg            python@3.11         tcl-tk
brotli              flac                gettext             highway             libaec              libomp              libxau              mpfr                openssl@1.1         python@3.9          texinfo
ca-certificates     fltk                ghostscript         hwloc               libavif             libpng              libxcb              mpg123              openssl@3           qscintilla2         wangle
cairo               fmt                 giflib              icu4c@76            libcerf             libraw              libxdmcp            netpbm              opus                qt@5                watchman
cmake               folly               git-gui             imagemagick         libde265            libsndfile          libxext             ninja               pango               readline            webp
double-conversion   fontconfig          glib                imath               libevent            libsodium           libxrender          octave              pcre2               shared-mime-info    wget
edencommon          freetype            gmp                 isl                 libffi              libtiff             little-cms2         open-mpi            pixman              snappy              x265
==> Outdated Casks
git-credential-manager                                                          microsoft-openjdk                                                               microsoft-openjdk@11

You have 113 outdated formulae and 3 outdated casks installed.
You can upgrade them with brew upgrade
or list them with brew outdated.
Error: Unexpected method 'appcast' called on Cask adoptopenjdk16.
Follow the instructions here:
  https://github.com/Homebrew/homebrew-cask#reporting-bugs
==> Migrating cask git-credential-manager-core to git-credential-manager
Error: inreplace failed
/opt/homebrew/Caskroom/git-credential-manager/.metadata/2.1.2/20230703191748.675/Casks/git-credential-manager.rb:
  expected replacement of /\A\s*cask\s+"git\-credential\-manager\-core"/ with "cask \"git-credential-manager\""

python3 --version is still 3.10.9 after this. I tried running pip but zsh sayd command not found. Unfortunately, linking or unlinking of either python or python3 fails with the errors below (despite ls -l `which python3` showing the same path as before).

saint@MacBookPro LLMs-from-scratch % brew unlink python3
Error: Unexpected method 'appcast' called on Cask adoptopenjdk16.
Follow the instructions here:
  https://github.com/Homebrew/homebrew-cask#reporting-bugs
Error: No such keg: /opt/homebrew/Cellar/python3

I decided to install python3 again.

saint@MacBookPro LLMs-from-scratch % brew install python3
==> Downloading https://formulae.brew.sh/api/formula.jws.json
==> Downloading https://formulae.brew.sh/api/cask.jws.json
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.13/manifests/3.13.1
######################################################################################################################################################################################################################################### 100.0%
==> Fetching dependencies for python@3.13: mpdecimal, ca-certificates, openssl@3, readline, sqlite and xz
==> Downloading https://ghcr.io/v2/homebrew/core/mpdecimal/manifests/4.0.0-1
######################################################################################################################################################################################################################################### 100.0%
==> Fetching mpdecimal
==> Downloading https://ghcr.io/v2/homebrew/core/mpdecimal/blobs/sha256:0f5f269bed0e6be2de3edfc4b52867e656f993e5bcff40717f26ee94dd0d2211
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-12-31
######################################################################################################################################################################################################################################### 100.0%
==> Fetching ca-certificates
...
<lots of omitted lines>
...
==> Fetching harfbuzz
==> Downloading https://ghcr.io/v2/homebrew/core/harfbuzz/blobs/sha256:2f892566c02b3c8c61aed6f7867b4405e5c814df8500ef4bc4ca91a9e40205a9
######################################################################################################################################################################################################################################### 100.0%
==> Fetching openjdk
==> Downloading https://ghcr.io/v2/homebrew/core/openjdk/blobs/sha256:1285eadf2b5998cda49e4470ee3875e855b0be199765401ad77dc38aea573f49
######################################################################################################################################################################################################################################### 100.0%
Error: can't modify frozen String: "The bottle needs the Xcode Command Line Tools to be installed at /Library/Developer/CommandLineTools.\nDevelopment tools provided by Xcode.app are not sufficient.\n\nYou can install the Xcode Command Line Tools, if desired, with:\n    xcode-select --install\n"

This was the new state of affairs is that command (failed):

saint@MacBookPro LLMs-from-scratch % python3 --version
Python 3.13.1
saint@MacBookPro LLMs-from-scratch % which python3
/opt/homebrew/bin/python3
saint@MacBookPro LLMs-from-scratch % ls -l `which python3`
lrwxr-xr-x  1 saint  admin  40 Feb  4 17:02 /opt/homebrew/bin/python3 -> ../Cellar/python@3.13/3.13.1/bin/python3
saint@MacBookPro LLMs-from-scratch % which pip
pip not found

Ah, all that agonizing and look at this – did I need to be using pip3 all this time?

saint@MacBookPro LLMs-from-scratch % which pip3
/opt/homebrew/bin/pip3
saint@MacBookPro LLMs-from-scratch % ls -l `which pip3`
lrwxr-xr-x  1 saint  admin  37 Feb  4 17:02 /opt/homebrew/bin/pip3 -> ../Cellar/python@3.13/3.13.1/bin/pip3
saint@MacBookPro LLMs-from-scratch % 

Interestingly, I still can’t install pytorch using pip3?

saint@MacBookPro LLMs-from-scratch % pip3 install pytorch

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try brew install
    xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a Python library that isn't in Homebrew,
    use a virtual environment:
    
    python3 -m venv path/to/venv
    source path/to/venv/bin/activate
    python3 -m pip install xyz
    
    If you wish to install a Python application that isn't in Homebrew,
    it may be easiest to use 'pipx install xyz', which will manage a
    virtual environment for you. You can install pipx with
    
    brew install pipx
    
    You may restore the old behavior of pip by passing
    the '--break-system-packages' flag to pip, or by adding
    'break-system-packages = true' to your pip.conf file. The latter
    will permanently disable this error.
    
    If you disable this error, we STRONGLY recommend that you additionally
    pass the '--user' flag to pip, or set 'user = true' in your pip.conf
    file. Failure to do this can result in a broken Homebrew installation.
    
    Read more about this behavior here: <https://peps.python.org/pep-0668/>

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.

I then tried installing brew as suggested above:

saint@MacBookPro LLMs-from-scratch % brew install pytorch
==> Downloading https://formulae.brew.sh/api/formula.jws.json
==> Downloading https://formulae.brew.sh/api/cask.jws.json
==> Downloading https://ghcr.io/v2/homebrew/core/pytorch/manifests/2.5.1_4
######################################################################################################################################################################################################################################### 100.0%
==> Fetching dependencies for pytorch: abseil, libuv, libyaml, gmp, isl, mpfr, lz4, zstd, make, gcc, openblas, numpy, protobuf, pybind11, sleef and libomp
==> Downloading https://ghcr.io/v2/homebrew/core/abseil/manifests/20240722.1
######################################################################################################################################################################################################################################### 100.0%
==> Fetching abseil
==> Downloading https://ghcr.io/v2/homebrew/core/abseil/blobs/sha256:be7b3373c56a0e1ee2c0c2e85ee4d17e2105ac1d9d6d63011da28d636fec7424
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libuv/manifests/1.50.0
######################################################################################################################################################################################################################################### 100.0%
==> Fetching libuv
==> Downloading https://ghcr.io/v2/homebrew/core/libuv/blobs/sha256:9a70ed97116c4960f0484159c07145df8e768b1a62be68c071070869ba4c3644
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libyaml/manifests/0.2.5
######################################################################################################################################################################################################################################### 100.0%
==> Fetching libyaml
==> Downloading https://ghcr.io/v2/homebrew/core/libyaml/blobs/sha256:0ec9bf8082245c008803b42dcae3e6a0c8cd7a67aed589d9b6482b115c0a543b
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/gmp/manifests/6.3.0
######################################################################################################################################################################################################################################### 100.0%
==> Fetching gmp
==> Downloading https://ghcr.io/v2/homebrew/core/gmp/blobs/sha256:6683d73d6677d28e1e8d1b92d6ebfbc068c1d33e19b79114a22a648a99ba5991
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/isl/manifests/0.27
######################################################################################################################################################################################################################################### 100.0%
==> Fetching isl
==> Downloading https://ghcr.io/v2/homebrew/core/isl/blobs/sha256:de143fddb0e20b6b73016ead1e625ebd429db53918200d093e4da98f1e758889
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/mpfr/manifests/4.2.1
######################################################################################################################################################################################################################################### 100.0%
==> Fetching mpfr
==> Downloading https://ghcr.io/v2/homebrew/core/mpfr/blobs/sha256:51f0ca19e897731b928742401c9c8d1d7d93c3c275aa8a66a77b9ac01d0c223c
######################################################################################################################################################################################################################################### 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/lz4/manifests/1.10.0-1
Already downloaded: /Users/saint/Library/Caches/Homebrew/downloads/8e11e90eb21a06e0f199af9d80e011e3693c77dd353b2477579d95c8471a5802--lz4-1.10.0-1.bottle_manifest.json
==> Fetching lz4
==> Downloading https://ghcr.io/v2/homebrew/core/lz4/blobs/sha256:5bd143b7b784989e549637ea4e484af85ba481e640dde69bc35f3843ae25abc6
Already downloaded: /Users/saint/Library/Caches/Homebrew/downloads/8af6cbc3dc870dba18d9a1b3f311f2d43b56a020a1e565289122cfda703ab791--lz4--1.10.0.arm64_sequoia.bottle.1.tar.gz
==> Downloading https://ghcr.io/v2/homebrew/core/zstd/manifests/1.5.6
Already downloaded: /Users/saint/Library/Caches/Homebrew/downloads/29403e0df5404d8aeca0e750ac135ec9ef44fc5eeb6df69170ed602acabf0ffb--zstd-1.5.6.bottle_manifest.json
==> Fetching zstd
==> Downloading https://ghcr.io/v2/homebrew/core/zstd/blobs/sha256:487f35700f563b07036cfd429e4e7a4e37f13e22578e688cbfee2fa9484aaf9d
Already downloaded: /Users/saint/Library/Caches/Homebrew/downloads/bcdf6b56ea7b8b23105f1518ddd0830ac5a56c333b0274959c10084ea3a31346--zstd--1.5.6.arm64_sequoia.bottle.tar.gz
==> Downloading https://ghcr.io/v2/homebrew/core/make/manifests/4.4.1-1
######################################################################################################################################################################################################################################### 100.0%
==> Fetching make
==> Downloading https://ghcr.io/v2/homebrew/core/make/blobs/sha256:f361639a5ec1a9355e12f985c511dd6631b6790452a52057032a3a07a690ca4e
######################################################################################################################################################################################################################################### 100.0%
Error: can't modify frozen String: "The bottle needs the Xcode Command Line Tools to be installed at /Library/Developer/CommandLineTools.\nDevelopment tools provided by Xcode.app are not sufficient.\n\nYou can install the Xcode Command Line Tools, if desired, with:\n    xcode-select --install\n"

saint@MacBookPro LLMs-from-scratch % xcode-select --install
xcode-select: note: install requested for command line developer tools

I installed the command line developer tools when prompted below.

Trying to run the first cell in VS Code with the updated setup now gave this error:

{
	"name": "",
	"message": "",
	"stack": "Running cells with 'Python 3.13.1' requires the ipykernel package.
Run the following command to install 'ipykernel' into the Python environment. 
Command: '/opt/homebrew/bin/python3 -m pip install ipykernel -U --user --force-reinstall'"
}

saint@MacBookPro LLMs-from-scratch % /opt/homebrew/bin/python3 -m pip install ipykernel -U --user --force-reinstall

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try brew install
    xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a Python library that isn't in Homebrew,
    use a virtual environment:
    
    python3 -m venv path/to/venv
    source path/to/venv/bin/activate
    python3 -m pip install xyz
    
    If you wish to install a Python application that isn't in Homebrew,
    it may be easiest to use 'pipx install xyz', which will manage a
    virtual environment for you. You can install pipx with
    
    brew install pipx
    
    You may restore the old behavior of pip by passing
    the '--break-system-packages' flag to pip, or by adding
    'break-system-packages = true' to your pip.conf file. The latter
    will permanently disable this error.
    
    If you disable this error, we STRONGLY recommend that you additionally
    pass the '--user' flag to pip, or set 'user = true' in your pip.conf
    file. Failure to do this can result in a broken Homebrew installation.
    
    Read more about this behavior here: <https://peps.python.org/pep-0668/>

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.

saint@MacBookPro LLMs-from-scratch % brew install ipykernel
==> Downloading https://formulae.brew.sh/api/formula.jws.json
==> Downloading https://formulae.brew.sh/api/cask.jws.json
Warning: No available formula with the name "ipykernel".
==> Searching for similarly named formulae and casks...
Error: No formulae or casks found for ipykernel.

I override the warning using the --break-system-packages flag and the VS Code notebook now runs.

saint@MacBookPro LLMs-from-scratch % python3 -m pip install ipykernel -U --user --force-reinstall --break-system-package
Collecting ipykernel
  Downloading ipykernel-6.29.5-py3-none-any.whl.metadata (6.3 kB)
Collecting appnope (from ipykernel)
  Downloading appnope-0.1.4-py2.py3-none-any.whl.metadata (908 bytes)
Collecting comm>=0.1.1 (from ipykernel)
  Downloading comm-0.2.2-py3-none-any.whl.metadata (3.7 kB)
Collecting debugpy>=1.6.5 (from ipykernel)
  Downloading debugpy-1.8.12-cp313-cp313-macosx_14_0_universal2.whl.metadata (1.3 kB)
Collecting ipython>=7.23.1 (from ipykernel)
  Downloading ipython-8.32.0-py3-none-any.whl.metadata (5.0 kB)
Collecting jupyter-client>=6.1.12 (from ipykernel)
  Downloading jupyter_client-8.6.3-py3-none-any.whl.metadata (8.3 kB)
Collecting jupyter-core!=5.0.*,>=4.12 (from ipykernel)
  Downloading jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting matplotlib-inline>=0.1 (from ipykernel)
  Downloading matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting nest-asyncio (from ipykernel)
  Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB)
Collecting packaging (from ipykernel)
  Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting psutil (from ipykernel)
  Downloading psutil-6.1.1-cp36-abi3-macosx_11_0_arm64.whl.metadata (22 kB)
Collecting pyzmq>=24 (from ipykernel)
  Downloading pyzmq-26.2.1-cp313-cp313-macosx_10_15_universal2.whl.metadata (6.2 kB)
Collecting tornado>=6.1 (from ipykernel)
  Downloading tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl.metadata (2.5 kB)
Collecting traitlets>=5.4.0 (from ipykernel)
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting decorator (from ipython>=7.23.1->ipykernel)
  Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel)
  Downloading jedi-0.19.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting pexpect>4.3 (from ipython>=7.23.1->ipykernel)
  Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting prompt_toolkit<3.1.0,>=3.0.41 (from ipython>=7.23.1->ipykernel)
  Downloading prompt_toolkit-3.0.50-py3-none-any.whl.metadata (6.6 kB)
Collecting pygments>=2.4.0 (from ipython>=7.23.1->ipykernel)
  Downloading pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB)
Collecting stack_data (from ipython>=7.23.1->ipykernel)
  Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting python-dateutil>=2.8.2 (from jupyter-client>=6.1.12->ipykernel)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting platformdirs>=2.5 (from jupyter-core!=5.0.*,>=4.12->ipykernel)
  Downloading platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
Collecting parso<0.9.0,>=0.8.4 (from jedi>=0.16->ipython>=7.23.1->ipykernel)
  Downloading parso-0.8.4-py2.py3-none-any.whl.metadata (7.7 kB)
Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython>=7.23.1->ipykernel)
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting wcwidth (from prompt_toolkit<3.1.0,>=3.0.41->ipython>=7.23.1->ipykernel)
  Downloading wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->jupyter-client>=6.1.12->ipykernel)
  Downloading six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting executing>=1.2.0 (from stack_data->ipython>=7.23.1->ipykernel)
  Downloading executing-2.2.0-py2.py3-none-any.whl.metadata (8.9 kB)
Collecting asttokens>=2.1.0 (from stack_data->ipython>=7.23.1->ipykernel)
  Downloading asttokens-3.0.0-py3-none-any.whl.metadata (4.7 kB)
Collecting pure-eval (from stack_data->ipython>=7.23.1->ipykernel)
  Downloading pure_eval-0.2.3-py3-none-any.whl.metadata (6.3 kB)
Downloading ipykernel-6.29.5-py3-none-any.whl (117 kB)
Downloading comm-0.2.2-py3-none-any.whl (7.2 kB)
Downloading debugpy-1.8.12-cp313-cp313-macosx_14_0_universal2.whl (2.5 MB)
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Downloading ipython-8.32.0-py3-none-any.whl (825 kB)
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Downloading jupyter_client-8.6.3-py3-none-any.whl (106 kB)
Downloading jupyter_core-5.7.2-py3-none-any.whl (28 kB)
Downloading matplotlib_inline-0.1.7-py3-none-any.whl (9.9 kB)
Downloading pyzmq-26.2.1-cp313-cp313-macosx_10_15_universal2.whl (1.3 MB)
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Downloading tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl (436 kB)
Downloading traitlets-5.14.3-py3-none-any.whl (85 kB)
Downloading appnope-0.1.4-py2.py3-none-any.whl (4.3 kB)
Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB)
Downloading packaging-24.2-py3-none-any.whl (65 kB)
Downloading psutil-6.1.1-cp36-abi3-macosx_11_0_arm64.whl (248 kB)
Downloading jedi-0.19.2-py2.py3-none-any.whl (1.6 MB)
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Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB)
Downloading platformdirs-4.3.6-py3-none-any.whl (18 kB)
Downloading prompt_toolkit-3.0.50-py3-none-any.whl (387 kB)
Downloading pygments-2.19.1-py3-none-any.whl (1.2 MB)
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Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Downloading stack_data-0.6.3-py3-none-any.whl (24 kB)
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Downloading executing-2.2.0-py2.py3-none-any.whl (26 kB)
Downloading parso-0.8.4-py2.py3-none-any.whl (103 kB)
Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
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Downloading pure_eval-0.2.3-py3-none-any.whl (11 kB)
Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB)
Installing collected packages: wcwidth, pure-eval, ptyprocess, traitlets, tornado, six, pyzmq, pygments, psutil, prompt_toolkit, platformdirs, pexpect, parso, packaging, nest-asyncio, executing, decorator, debugpy, asttokens, appnope, stack_data, python-dateutil, matplotlib-inline, jupyter-core, jedi, comm, jupyter-client, ipython, ipykernel
  WARNING: The script pygmentize is installed in '/Users/saint/Library/Python/3.13/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script debugpy is installed in '/Users/saint/Library/Python/3.13/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts jupyter, jupyter-migrate and jupyter-troubleshoot are installed in '/Users/saint/Library/Python/3.13/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts jupyter-kernel, jupyter-kernelspec and jupyter-run are installed in '/Users/saint/Library/Python/3.13/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts ipython and ipython3 are installed in '/Users/saint/Library/Python/3.13/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed appnope-0.1.4 asttokens-3.0.0 comm-0.2.2 debugpy-1.8.12 decorator-5.1.1 executing-2.2.0 ipykernel-6.29.5 ipython-8.32.0 jedi-0.19.2 jupyter-client-8.6.3 jupyter-core-5.7.2 matplotlib-inline-0.1.7 nest-asyncio-1.6.0 packaging-24.2 parso-0.8.4 pexpect-4.9.0 platformdirs-4.3.6 prompt_toolkit-3.0.50 psutil-6.1.1 ptyprocess-0.7.0 pure-eval-0.2.3 pygments-2.19.1 python-dateutil-2.9.0.post0 pyzmq-26.2.1 six-1.17.0 stack_data-0.6.3 tornado-6.4.2 traitlets-5.14.3 wcwidth-0.2.13

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
saint@MacBookPro LLMs-from-scratch % 

First cell now fails because the torch package cannot be found:

{
	"name": "PackageNotFoundError",
	"message": "No package metadata was found for torch",
	"stack": "---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
File /opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/metadata/__init__.py:407, in Distribution.from_name(cls, name)
    406 try:
--> 407     return next(iter(cls.discover(name=name)))
    408 except StopIteration:

StopIteration: 

During handling of the above exception, another exception occurred:

PackageNotFoundError                      Traceback (most recent call last)
Cell In[1], line 3
      1 from importlib.metadata import version
----> 3 print(\"torch version:\", version(\"torch\"))
      4 print(\"tiktoken version:\", version(\"tiktoken\"))

File /opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/metadata/__init__.py:987, in version(distribution_name)
    980 def version(distribution_name: str) -> str:
    981     \"\"\"Get the version string for the named package.
    982 
    983     :param distribution_name: The name of the distribution package to query.
    984     :return: The version string for the package as defined in the package's
    985         \"Version\" metadata key.
    986     \"\"\"
--> 987     return distribution(distribution_name).version

File /opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/metadata/__init__.py:960, in distribution(distribution_name)
    954 def distribution(distribution_name: str) -> Distribution:
    955     \"\"\"Get the ``Distribution`` instance for the named package.
    956 
    957     :param distribution_name: The name of the distribution package as a string.
    958     :return: A ``Distribution`` instance (or subclass thereof).
    959     \"\"\"
--> 960     return Distribution.from_name(distribution_name)

File /opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/metadata/__init__.py:409, in Distribution.from_name(cls, name)
    407     return next(iter(cls.discover(name=name)))
    408 except StopIteration:
--> 409     raise PackageNotFoundError(name)

PackageNotFoundError: No package metadata was found for torch"
}

These are the commands I tried to install pytorch before finding the correct one: pip3 install torch --break-system-packages.

saint@MacBookPro LLMs-from-scratch % brew install torch
==> Downloading https://formulae.brew.sh/api/formula.jws.json
==> Downloading https://formulae.brew.sh/api/cask.jws.json
Warning: No available formula with the name "torch". Did you mean tor, pytorch or orc?
==> Searching for similarly named formulae and casks...
==> Formulae
pytorch ✔                                                    torchvision                                                  tor                                                          orc

To install pytorch ✔, run:
  brew install pytorch ✔
saint@MacBookPro LLMs-from-scratch % brew install pytorch
Warning: pytorch 2.5.1_4 is already installed and up-to-date.
To reinstall 2.5.1_4, run:
  brew reinstall pytorch
saint@MacBookPro LLMs-from-scratch % pip3 install torch

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try brew install
    xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a Python library that isn't in Homebrew,
    use a virtual environment:
    
    python3 -m venv path/to/venv
    source path/to/venv/bin/activate
    python3 -m pip install xyz
    
    If you wish to install a Python application that isn't in Homebrew,
    it may be easiest to use 'pipx install xyz', which will manage a
    virtual environment for you. You can install pipx with
    
    brew install pipx
    
    You may restore the old behavior of pip by passing
    the '--break-system-packages' flag to pip, or by adding
    'break-system-packages = true' to your pip.conf file. The latter
    will permanently disable this error.
    
    If you disable this error, we STRONGLY recommend that you additionally
    pass the '--user' flag to pip, or set 'user = true' in your pip.conf
    file. Failure to do this can result in a broken Homebrew installation.
    
    Read more about this behavior here: <https://peps.python.org/pep-0668/>

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
saint@MacBookPro LLMs-from-scratch % 
saint@MacBookPro LLMs-from-scratch % pip3 install torch --break-system-packages
Collecting torch
  Downloading torch-2.6.0-cp313-none-macosx_11_0_arm64.whl.metadata (28 kB)
Collecting filelock (from torch)
  Downloading filelock-3.17.0-py3-none-any.whl.metadata (2.9 kB)
Collecting typing-extensions>=4.10.0 (from torch)
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting networkx (from torch)
  Downloading networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting jinja2 (from torch)
  Downloading jinja2-3.1.5-py3-none-any.whl.metadata (2.6 kB)
Collecting fsspec (from torch)
  Downloading fsspec-2025.2.0-py3-none-any.whl.metadata (11 kB)
Collecting setuptools (from torch)
  Downloading setuptools-75.8.0-py3-none-any.whl.metadata (6.7 kB)
Collecting sympy==1.13.1 (from torch)
  Downloading sympy-1.13.1-py3-none-any.whl.metadata (12 kB)
Collecting mpmath<1.4,>=1.1.0 (from sympy==1.13.1->torch)
  Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting MarkupSafe>=2.0 (from jinja2->torch)
  Downloading MarkupSafe-3.0.2-cp313-cp313-macosx_11_0_arm64.whl.metadata (4.0 kB)
Downloading torch-2.6.0-cp313-none-macosx_11_0_arm64.whl (66.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.5/66.5 MB 74.3 MB/s eta 0:00:00
Downloading sympy-1.13.1-py3-none-any.whl (6.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.2/6.2 MB 75.0 MB/s eta 0:00:00
Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Downloading filelock-3.17.0-py3-none-any.whl (16 kB)
Downloading fsspec-2025.2.0-py3-none-any.whl (184 kB)
Downloading jinja2-3.1.5-py3-none-any.whl (134 kB)
Downloading networkx-3.4.2-py3-none-any.whl (1.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 63.7 MB/s eta 0:00:00
Downloading setuptools-75.8.0-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 37.0 MB/s eta 0:00:00
Downloading MarkupSafe-3.0.2-cp313-cp313-macosx_11_0_arm64.whl (12 kB)
Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 27.9 MB/s eta 0:00:00
Installing collected packages: mpmath, typing-extensions, sympy, setuptools, networkx, MarkupSafe, fsspec, filelock, jinja2, torch
Successfully installed MarkupSafe-3.0.2 filelock-3.17.0 fsspec-2025.2.0 jinja2-3.1.5 mpmath-1.3.0 networkx-3.4.2 setuptools-75.8.0 sympy-1.13.1 torch-2.6.0 typing-extensions-4.12.2

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
saint@MacBookPro LLMs-from-scratch % 

The pytorch import finally works! The next error is also a PackageNotFoundError: "No package metadata was found for tiktoken" which I addressed with the same installation steps:

saint@MacBookPro LLMs-from-scratch % pip3 install tiktoken                     

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try brew install
    xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a Python library that isn't in Homebrew,
    use a virtual environment:
    
    python3 -m venv path/to/venv
    source path/to/venv/bin/activate
    python3 -m pip install xyz
    
    If you wish to install a Python application that isn't in Homebrew,
    it may be easiest to use 'pipx install xyz', which will manage a
    virtual environment for you. You can install pipx with
    
    brew install pipx
    
    You may restore the old behavior of pip by passing
    the '--break-system-packages' flag to pip, or by adding
    'break-system-packages = true' to your pip.conf file. The latter
    will permanently disable this error.
    
    If you disable this error, we STRONGLY recommend that you additionally
    pass the '--user' flag to pip, or set 'user = true' in your pip.conf
    file. Failure to do this can result in a broken Homebrew installation.
    
    Read more about this behavior here: <https://peps.python.org/pep-0668/>

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
saint@MacBookPro LLMs-from-scratch % 
saint@MacBookPro LLMs-from-scratch % pip3 install tiktoken --break-system-packages
Collecting tiktoken
  Downloading tiktoken-0.8.0-cp313-cp313-macosx_11_0_arm64.whl.metadata (6.6 kB)
Collecting regex>=2022.1.18 (from tiktoken)
  Downloading regex-2024.11.6-cp313-cp313-macosx_11_0_arm64.whl.metadata (40 kB)
Collecting requests>=2.26.0 (from tiktoken)
  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.26.0->tiktoken)
  Downloading charset_normalizer-3.4.1-cp313-cp313-macosx_10_13_universal2.whl.metadata (35 kB)
Collecting idna<4,>=2.5 (from requests>=2.26.0->tiktoken)
  Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.26.0->tiktoken)
  Downloading urllib3-2.3.0-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests>=2.26.0->tiktoken)
  Downloading certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB)
Downloading tiktoken-0.8.0-cp313-cp313-macosx_11_0_arm64.whl (982 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 982.8/982.8 kB 24.2 MB/s eta 0:00:00
Downloading regex-2024.11.6-cp313-cp313-macosx_11_0_arm64.whl (284 kB)
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
Downloading certifi-2025.1.31-py3-none-any.whl (166 kB)
Downloading charset_normalizer-3.4.1-cp313-cp313-macosx_10_13_universal2.whl (195 kB)
Downloading idna-3.10-py3-none-any.whl (70 kB)
Downloading urllib3-2.3.0-py3-none-any.whl (128 kB)
Installing collected packages: urllib3, regex, idna, charset-normalizer, certifi, requests, tiktoken
Successfully installed certifi-2025.1.31 charset-normalizer-3.4.1 idna-3.10 regex-2024.11.6 requests-2.32.3 tiktoken-0.8.0 urllib3-2.3.0

[notice] A new release of pip is available: 24.3.1 -> 25.0
[notice] To update, run: python3.13 -m pip install --upgrade pip
saint@MacBookPro LLMs-from-scratch % 

Finally, my machine is in a state that can run the code in the Jupyter notebook! This is such a brittle environment. I need to switch to a managed environment to avoid this type of mess.