Make SPRAS installable #126
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P.S. I only added Tony in the |
agitter
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Sep 22, 2023
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I reviewed https://packaging.python.org/en/latest/specifications/declaring-project-metadata/#declaring-project-metadata and made suggestions for the metadata. We should let @annaritz comment as well.
Do we want to comment on installing with pip either in the main readme or in the contributing guide for developers?
Everything else looks good to me.
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This commit adds the ability to install spras as a python module using pip, which is something we'll need for running in remote environments such as on the OSPool. The installation "instructions" used by pip during building are laid out in `pyproject.toml`. While I chose to use setup-tools as a builder backend in this first pass, other builder backends with more robust build features are available and may eventually be switched to (eg flit, poetry). Several additional files had to be modified to adhere to python packaging guidelines, the most notable of which was changing `src` to spras, and referencing the new spras directory instead of src. Several lines of omicsintegrator2.py were also modified becasue they were dealing with an absolute path, which made the workflow un-runnable outside of the repo. I verified that all tests and the entirety of the snakefile still run both in the conda environment from the repo root (which is how the tool is currently used) and in a separate directory with spras installed where the input data, snakefile, and config file have been brought along. For testing, install spras using `pip install .` in the repo root. If the extra development packages are needed, spras can be installed with the command `pip install .[dev]`. Spras can also be installed via `pip install -e .` to make the installation editable. That is, when installed via this command, you can continue to edit spras in the repo and have those changes reflected anywhere you run spras on the machine. Note that several package versions had to be modified (they're noted in pyproject.toml) to get past a few versioning issues between conda and pypi. To the extent of my knowledge and testing, these changes didn't affect the way spras runs. Famous last words?
In general, this was just implementing @agitter's suggested changes. One of the questions that was raised was why I unpinned the version of docutils. I had to double check, but it looks like pinning the version caused a compatibility issue, specifically with the pip- installed package `sphinx-rtd-theme`. Rather than unpinning Docutils or bumping it down by a version, I bumped `sphinx-rtd-theme` up two versions (in both `environment.yaml` and the `pyproject.toml`) to satisfy the dependency conflict. The change appears not to have caused issues, but I'm also not aware of how the doc-building mechanism works, so I'm not sure how to give it a more robust test.
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agitter
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Oct 13, 2023
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I tested the installation locally
$ conda create -n spras-new python=3.8
$ conda activate spras-new
$ python -m pip install -e .[dev] .
This failed with
...
Collecting semver>=2.8.1 (from spython==0.2->spras==0.0.1)
Obtaining dependency information for semver>=2.8.1 from https://files.pythonhosted.org/packages/9a/77/0cc7a8a3bc7e53d07e8f47f147b92b0960e902b8254859f4aee5c4d7866b/semver-3.0.2-py3-none-any.whl.metadata
Downloading semver-3.0.2-py3-none-any.whl.metadata (5.0 kB)
INFO: pip is looking at multiple versions of spras[dev] to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install spras 0.0.1 (from \spras) and spras[dev]==0.0.1 because these package versions have conflicting dependencies.
The conflict is caused by:
The user requested spras 0.0.1 (from \spras)
spras[dev] 0.0.1 depends on spras 0.0.1 (from \spras)
To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
It looks like the command tries to install the dev and non-dev versions. Using
$ python -m pip install -e .[dev]
succeeded. If you agree that is the correct command, can you please update the documentation accordingly?
I checked the machine learning figures and Cytoscape session produced by the default Snakemake workflow, and everything still looks good.
agitter
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Oct 13, 2023
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This commit adds the ability to install spras as a python module using pip, which is something we'll need for running in remote environments such as on the OSPool. The installation "instructions" used by pip during building are laid out in
pyproject.toml. While I chose to use setup-tools as a builder backend in this first pass, other builder backends with more robust build features are available and may eventually be switched to (eg flit, poetry).Several additional files had to be modified to adhere to python packaging guidelines, the most notable of which was changing
srcto spras, and referencing the new spras directory instead of src. Several lines of omicsintegrator2.py were also modified becasue they were dealing with an absolute path, which made the workflow un-runnable outside of the repo. I verified that all tests and the entirety of the snakefile still run both in the conda environment from the repo root (which is how the tool is currently used) and in a separate directory with spras installed where the input data, snakefile, and config file have been brought along.For testing, install spras using
pip install .in the repo root. If the extra development packages are needed, spras can be installed with the commandpip install .[dev]. Spras can also be installed viapip install -e .to make the installation editable. That is, when installed via this command, you can continue to edit spras in the repo and have those changes reflected anywhere you run spras on the machine.Note that several package versions had to be modified (they're noted in pyproject.toml) to get past a few versioning issues between conda and pypi. To the extent of my knowledge and testing, these changes didn't affect the way spras runs. Famous last words?
If this passes tests and is merged, it closes #86.