Problem with install/dependencies of snakemake

[Fred-07]

After standard installation method from the "Snakemake tutorial", Snakemake can not be executed.
Running the basic worflow (https://snakemake.readthedocs.io/en/stable/tutorial/basics.html) reports:

Building DAG of jobs...
Traceback (most recent call last):
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/snakemake/__init__.py", line 733, in snakemake
    success = workflow.execute(
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/snakemake/workflow.py", line 1037, in execute
    logger.run_info("\n".join(dag.stats()))
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/snakemake/dag.py", line 2415, in stats
    yield tabulate(rows, headers="keys")
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/tabulate/__init__.py", line 2048, in tabulate
    list_of_lists, headers = _normalize_tabular_data(
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/tabulate/__init__.py", line 1471, in _normalize_tabular_data
    rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/tabulate/__init__.py", line 1471, in <lambda>
    rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/tabulate/__init__.py", line 107, in _is_separating_line
    (len(row) >= 1 and row[0] == SEPARATING_LINE)
  File "/data/progs/Mamba/packages_dirs/snakemake-mini/lib/python3.10/site-packages/snakemake/rules.py", line 1222, in __eq__
    return self.name == other.name and self.output == other.output
AttributeError: 'str' object has no attribute 'name'

I tried on 2 different machines.
I tried with an older version of snakemake (7.8.5) and with Python 3.10 and 3.9

It would be useful to have a Conda environment file (from conda export) included with each snakemake release. It would help to identify problematic versions of dependencies if any.

[DrYak]

I don't know if this is going to help:

• I did update one mamba installation of Snakemake yesterday to 7.15.1 and it works.
• I update another mamba installation of Snakemake today and it breaks as above.
  So the source lies in the differences between the two.

If I update --dry-run the still working one, this are the dependencies package update that have change in between the time frame:

 - azure-core            1.25.1  pyhd8ed1ab_0  conda-forge                 
  + azure-core            1.26.0  pyhd8ed1ab_0  conda-forge/noarch      87kB
  - boto3                1.24.86  pyhd8ed1ab_0  conda-forge                 
  + boto3                1.24.89  pyhd8ed1ab_0  conda-forge/noarch      74kB
  - botocore             1.27.86  pyhd8ed1ab_0  conda-forge                 
  + botocore             1.27.89  pyhd8ed1ab_0  conda-forge/noarch       6MB
  - gitpython             3.1.27  pyhd8ed1ab_0  conda-forge                 
  + gitpython             3.1.28  pyhd8ed1ab_0  conda-forge/noarch     127kB
  - google-api-core       2.10.1  pyhd8ed1ab_0  conda-forge                 
  + google-api-core       2.10.2  pyhd8ed1ab_0  conda-forge/noarch      73kB
  - importlib_resources    5.9.0  pyhd8ed1ab_0  conda-forge                 
  + importlib_resources   5.10.0  pyhd8ed1ab_0  conda-forge/noarch      30kB
  - tabulate              0.8.10  pyhd8ed1ab_0  conda-forge                 
  + tabulate               0.9.0  pyhd8ed1ab_1  conda-forge/noarch      36kB
  - typing-extensions      4.3.0  hd8ed1ab_0    conda-forge                 
  + typing-extensions      4.4.0  hd8ed1ab_0    conda-forge/noarch       9kB
  - typing_extensions      4.3.0  pyha770c72_0  conda-forge                 
  + typing_extensions      4.4.0  pyha770c72_0  conda-forge/noarch      30kB

Could it be the shift from tabulet 0.8 to 0.9?
(It's in the backtrace above).

[DrYak]

YES, CONFIRMED : it is an incompatibility of dependencies.

Downgrading tabluate fixes the problem:

mamba install 'tabulate=0.8.10'

[DrYak]

PR with fix

[Fred-07]

Thanks for solving this issue so quickly!

[DrYak]

Johaness even released a new 7.15.2 that's compatible with this latest tabulate. Yay!
🎊