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Goal: Introduce ideas and practices to assist in managing the reproducibility of environments created using Conda and Pip.

Create an Example Environment

To help demonstrate the various concepts, lets create the following environment:

[salexan5@mblog2 ~] cd /project/arcc/salexan5/conda
[salexan5@mblog2 conda]$ module load miniconda3/24.3.0
[salexan5@mblog2 conda]$ conda create -p py_conda_pip_env python=3.12
[salexan5@mblog2 conda]$ conda activate /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ python --version
Python 3.12.4
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ which python
/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/bin/python
# Create a self contined environment i.e don't install anything into the local home folder.
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ export PYTHONUSERBASE=$CONDA_PREFIX
# Use conda to install: numpy
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ conda install numpy
# Use pip to install: nltk
# has dependencies: click, joblib, regex and tqdm
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ pip install nltk

What is Installed? conda list

The conda list command will provide details of all packages as well as conda environment libraries:

(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ conda list
...
click                     8.1.7                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
nltk                      3.8.1                    pypi_0    pypi
numpy                     2.0.1           py312h1103770_0    conda-forge
regex                     2024.7.24                pypi_0    pypi
tqdm                      4.66.4                   pypi_0    pypi
 full conda list
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ conda list
# packages in environment at /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
click                     8.1.7                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
libblas                   3.9.0           23_linux64_openblas    conda-forge
libcblas                  3.9.0           23_linux64_openblas    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 14.1.0               h77fa898_0    conda-forge
libgfortran-ng            14.1.0               h69a702a_0    conda-forge
libgfortran5              14.1.0               hc5f4f2c_0    conda-forge
libgomp                   14.1.0               h77fa898_0    conda-forge
liblapack                 3.9.0           23_linux64_openblas    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_hac2b453_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libstdcxx-ng              14.1.0               hc0a3c3a_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
ncurses                   6.5                  h59595ed_0    conda-forge
nltk                      3.8.1                    pypi_0    pypi
numpy                     2.0.1           py312h1103770_0    conda-forge
openssl                   3.3.1                h4bc722e_2    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
python                    3.12.4          h194c7f8_0_cpython    conda-forge
python_abi                3.12                    4_cp312    conda-forge
readline                  8.2                  h8228510_1    conda-forge
regex                     2024.7.24                pypi_0    pypi
setuptools                71.0.4             pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tqdm                      4.66.4                   pypi_0    pypi
tzdata                    2024a                h0c530f3_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge

What is Installed? pip list -v

The pip list command will only list the explicitly python packages.

Look at the Installer column to identify what was installed via conda install, pip install, by default.

(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ pip list -v
Package    Version   Location                                                                                  Installer
---------- --------- ----------------------------------------------------------------------------------------- ---------
click      8.1.7     /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages pip
joblib     1.4.2     /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages pip
nltk       3.8.1     /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages pip
numpy      2.0.1     /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages conda
pip        24.0      /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages
regex      2024.7.24 /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages pip
setuptools 71.0.4    /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages
tqdm       4.66.4    /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages pip
wheel      0.43.0    /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages

Check under the python related lib folder.

 List what's in: /project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages/
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ ls /project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages/
click                     joblib                  numpy                     pkg_resources              setuptools                         wheel
click-8.1.7.dist-info     joblib-1.4.2.dist-info  numpy-2.0.1.dist-info     README.txt                 setuptools-71.0.4-py3.12.egg-info  wheel-0.43.0.dist-info
_distutils_hack           nltk                    pip                       regex                      tqdm
distutils-precedence.pth  nltk-3.8.1.dist-info    pip-24.0-py3.12.egg-info  regex-2024.7.24.dist-info  tqdm-4.66.4.dist-info

What is Installed? conda env export

The output of the conda env export command you can use to recreate.

Identify what was install via conda install vs pip install:

(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ conda env export > env.yml
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ cat env.yml
name: /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env
...
dependencies:
...
  - numpy=2.0.1=py312h1103770_0
...
  - python=3.12.4=h194c7f8_0_cpython
...
  - pip:
      - click==8.1.7
      - joblib==1.4.2
      - nltk==3.8.1
      - regex==2024.7.24
      - tqdm==4.66.4
prefix: /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env
 full output:
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ conda env export > env.yml
(/cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env) [salexan5@mblog2 conda]$ cat env.yml
name: /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - bzip2=1.0.8=h4bc722e_7
  - ca-certificates=2024.7.4=hbcca054_0
  - ld_impl_linux-64=2.40=hf3520f5_7
  - libblas=3.9.0=23_linux64_openblas
  - libcblas=3.9.0=23_linux64_openblas
  - libexpat=2.6.2=h59595ed_0
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=14.1.0=h77fa898_0
  - libgfortran-ng=14.1.0=h69a702a_0
  - libgfortran5=14.1.0=hc5f4f2c_0
  - libgomp=14.1.0=h77fa898_0
  - liblapack=3.9.0=23_linux64_openblas
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.27=pthreads_hac2b453_1
  - libsqlite=3.46.0=hde9e2c9_0
  - libstdcxx-ng=14.1.0=hc0a3c3a_0
  - libuuid=2.38.1=h0b41bf4_0
  - libxcrypt=4.4.36=hd590300_1
  - libzlib=1.3.1=h4ab18f5_1
  - ncurses=6.5=h59595ed_0
  - numpy=2.0.1=py312h1103770_0
  - openssl=3.3.1=h4bc722e_2
  - pip=24.0=pyhd8ed1ab_0
  - python=3.12.4=h194c7f8_0_cpython
  - python_abi=3.12=4_cp312
  - readline=8.2=h8228510_1
  - setuptools=71.0.4=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - tzdata=2024a=h0c530f3_0
  - wheel=0.43.0=pyhd8ed1ab_1
  - xz=5.2.6=h166bdaf_0
  - pip:
      - click==8.1.7
      - joblib==1.4.2
      - nltk==3.8.1
      - regex==2024.7.24
      - tqdm==4.66.4
prefix: /cluster/medbow/project/arcc/salexan5/conda/py_conda_pip_env

Extend Conda Environment to Jupyter Kernel

 

Python, Conda and Pip: Suggested Best Practices

 

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