Installation instructions need to be more specific

I created a new environment in conda with python 3.10 and followed the instructions: pip install snakemake snakedeploy This installs cookiecutter as a dependency, but then I had to install click manually pip install click which installs click-8.1.7 required for cookiecutter 2.6.0 Then I deployed the workflow with --tag 1.3.0 and tried to run snakemake with the default config file. I got this error:

snakemake \
  --use-singularity \
  --singularity-args "-B /scratch:/scratch \
    -B /g/kosinski:/g/kosinski \  
  --nv " \
  --jobs 200 \
  --restart-times 5 \
  --profile slurm_noSidecar \
  --rerun-incomplete \
  --rerun-triggers mtime \
  --latency-wait 30 \
  -n

...

Traceback (most recent call last):
  File "/home/dmolodenskiy/.conda/envs/sm310/bin/snakemake", line 8, in <module>
    sys.exit(main())
  File "/home/dmolodenskiy/.conda/envs/sm310/lib/python3.10/site-packages/snakemake/__init__.py", line 2736, in main
    parser = get_argument_parser()
  File "/home/dmolodenskiy/.conda/envs/sm310/lib/python3.10/site-packages/snakemake/__init__.py", line 1607, in get_argument_parser
    lp_solvers = pulp.list_solvers(onlyAvailable=True)
AttributeError: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'?

this is result of my pip freeze command:

pip freeze
appdirs==1.4.4
arrow==1.3.0
attrs==23.2.0
binaryornot==0.4.4
certifi==2024.6.2
cffi==1.16.0
charset-normalizer==3.3.2
click==8.1.7
ConfigArgParse==1.7
connection_pool==0.0.3
cookiecutter==2.6.0
cryptography==42.0.8
datrie==0.8.2
Deprecated==1.2.14
docutils==0.21.2
dpath==2.2.0
fastjsonschema==2.20.0
gitdb==4.0.11
GitPython==3.1.43
humanfriendly==10.0
idna==3.7
Jinja2==3.1.4
jsonschema==4.22.0
jsonschema-specifications==2023.12.1
jupyter_core==5.7.2
markdown-it-py==3.0.0
MarkupSafe==2.1.5
mdurl==0.1.2
nbformat==5.10.4
numpy==2.0.0
packaging==24.1
pandas==2.2.2
plac==1.4.3
platformdirs==4.2.2
psutil==6.0.0
PuLP==2.8.0
pycparser==2.22
PyGithub==2.3.0
Pygments==2.17.2
PyJWT==2.8.0
PyNaCl==1.5.0
python-dateutil==2.9.0.post0
python-slugify==8.0.4
pytz==2024.1
PyYAML==6.0.1
referencing==0.35.1
requests==2.32.3
reretry==0.11.8
rich==13.7.1
rpds-py==0.18.1
six==1.16.0
smart-open==7.0.4
smmap==5.0.1
snakedeploy==0.10.0
snakemake==7.32.4
stopit==1.1.2
tabulate==0.9.0
text-unidecode==1.3
throttler==1.2.2
toposort==1.10
traitlets==5.14.3
types-python-dateutil==2.8.19.20240106
typing_extensions==4.12.2
tzdata==2024.1
urllib3==2.2.2
wrapt==1.16.0
yte==1.5.4

KosinskiLab / AlphaPulldownSnakemake

Installation instructions need to be more specific #18