Example 1 requirments not suitably defined #5
Description
Installing the requirements defined for example 1 in its requirements.txt file can lead to the creation of an environment which is unable to execute the example.
on python 3.8 the environment can be solved as in the attached details.
-> % uv pip install -r requirements.txt
Resolved 73 packages in 2.42s
Built datrie==0.8.3
Built snakemake==7.32.4
Built stopit==1.1.2
Built connection-pool==0.0.3
Prepared 57 packages in 30.33s
Installed 73 packages in 105ms
+ aiohappyeyeballs==2.4.4
+ aiohttp==3.10.11
+ aiosignal==1.3.1
+ appdirs==1.4.4
+ argparse-dataclass==2.0.0
+ async-timeout==5.0.1
+ attrs==25.3.0
+ casaconfig==1.3.1
+ casadata==2025.8.7
+ casatools==6.6.5.31
+ certifi==2025.8.3
+ charset-normalizer==3.4.3
+ configargparse==1.7.1
+ connection-pool==0.0.3
+ datasets==3.1.0
+ datrie==0.8.3
+ dill==0.3.8
+ docutils==0.20.1
+ dpath==2.2.0
+ fastjsonschema==2.21.2
+ filelock==3.16.1
+ frozenlist==1.5.0
+ fsspec==2024.9.0
+ gitdb==4.0.12
+ gitpython==3.1.45
+ hf-xet==1.1.10
+ huggingface-hub==0.34.5
+ humanfriendly==10.0
+ idna==3.10
+ importlib-resources==6.4.5
+ jinja2==3.1.6
+ jsonschema==4.23.0
+ jsonschema-specifications==2023.12.1
+ jupyter-core==5.8.1
+ markupsafe==2.1.5
+ multidict==6.1.0
+ multiprocess==0.70.16
+ nbformat==5.10.4
+ numpy==1.24.4
+ packaging==25.0
+ pandas==2.0.3
+ pillow==10.4.0
+ pkgutil-resolve-name==1.3.10
+ platformdirs==4.3.6
+ propcache==0.2.0
+ psutil==7.0.0
+ pulp==3.1.1
+ pyarrow==17.0.0
+ python-dateutil==2.9.0.post0
+ pytz==2025.2
+ pyyaml==6.0.2
+ referencing==0.35.1
+ requests==2.32.4
+ reretry==0.11.8
+ rpds-py==0.20.1
+ six==1.17.0
+ smart-open==7.3.1
+ smmap==5.0.2
+ snakemake==7.32.4
+ stopit==1.1.2
+ tabulate==0.9.0
+ throttler==1.2.2
+ toposort==1.10
+ tqdm==4.67.1
+ traitlets==5.14.3
+ typing-extensions==4.13.2
+ tzdata==2025.2
+ urllib3==2.2.3
+ wrapt==1.17.3
+ xxhash==3.5.0
+ yarl==1.15.2
+ yte==1.9.0
+ zipp==3.20.2This environment leads to the following execution error
-> % snakemake -c 1 all
Traceback (most recent call last):
File "/home/matthew/src/mpol-example/01-generate-mock-baselines/.venv/bin/snakemake", line 10, in <module>
sys.exit(main())
File "/home/matthew/src/mpol-example/01-generate-mock-baselines/.venv/lib/python3.8/site-packages/snakemake/__init__.py", line 2736, in main
parser = get_argument_parser()
File "/home/matthew/src/mpol-example/01-generate-mock-baselines/.venv/lib/python3.8/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'
which appears to be tied to pulp versioning. Indeed requiring pulp<2.8.0 does solve this issue however it is up to the user to make this determination and manually download pulp.
It could be more helpful if pulp is already pinned with this version requirement if the user is intended to run snakemake to produce mock visibility data.