CI failures due to pip install errors

[lbianchi-lbl]

• https://github.com/watertap-org/parameter-sweep/actions/runs/11936898790/job/33271628726?pr=17
• Only affects dev installation
• Cannot be reproduced locally
• My best guess at this time is that this has something to do with setuptools_scm being unable to set the version correctly (see the log below, where it appears as 0.0+g49757ff ), possibly because of the "pseudo-commit" created by GitHub at the https://github.com/{owner}/{repo}/refs/pull/{pull}/merge URL endpoint

Ignoring Sphinx: markers 'python_version < "3.9"' don't match your environment
Obtaining file:///home/runner/work/parameter-sweep/parameter-sweep
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Checking if build backend supports build_editable: started
  Checking if build backend supports build_editable: finished with status 'done'
  Getting requirements to build editable: started
  Getting requirements to build editable: finished with status 'done'
  Preparing editable metadata (pyproject.toml): started
  Preparing editable metadata (pyproject.toml): finished with status 'done'
Collecting watertap@ git+https://github.com/watertap-org/watertap@main (from -r requirements-dev.txt (line 11))
  Cloning https://github.com/watertap-org/watertap (to revision main) to /tmp/pip-install-_gbr2ta9/watertap_eeeb01f2b668419f983a6642406cbc73
  Running command git clone --filter=blob:none --quiet https://github.com/watertap-org/watertap /tmp/pip-install-_gbr2ta9/watertap_eeeb01f2b668419f983a6642406cbc73
  Resolved https://github.com/watertap-org/watertap to commit ccfc64d0143a4c437a7c82a036c4284c72704a23
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting black==24.3.0 (from -r requirements-dev.txt (line 1))
  Downloading black-24.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (75 kB)
Collecting pytest-cov (from -r requirements-dev.txt (line 2))
  Downloading pytest_cov-6.0.0-py3-none-any.whl.metadata (27 kB)
Collecting coverage (from -r requirements-dev.txt (line 3))
  Downloading coverage-7.6.7-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Collecting Sphinx==7.3.7 (from -r requirements-dev.txt (line 6))
  Downloading sphinx-7.3.7-py3-none-any.whl.metadata (6.0 kB)
Collecting sphinx-autoapi==3.0.0 (from -r requirements-dev.txt (line 7))
  Downloading sphinx_autoapi-3.0.0-py2.py3-none-any.whl.metadata (4.8 kB)
Collecting sphinx-rtd-theme==2.0.0 (from -r requirements-dev.txt (line 8))
  Downloading sphinx_rtd_theme-2.0.0-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting click>=8.0.0 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting mypy-extensions>=0.4.3 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Downloading mypy_extensions-1.0.0-py3-none-any.whl.metadata (1.1 kB)
Collecting packaging>=22.0 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pathspec>=0.9.0 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Downloading pathspec-0.12.1-py3-none-any.whl.metadata (21 kB)
Collecting platformdirs>=2 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Downloading platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
Collecting tomli>=1.1.0 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Using cached tomli-2.1.0-py3-none-any.whl.metadata (10.0 kB)
Collecting typing-extensions>=4.0.1 (from black==24.3.0->-r requirements-dev.txt (line 1))
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting sphinxcontrib-applehelp (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-devhelp (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-jsmath (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.9 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinxcontrib-qthelp (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting Jinja2>=3.0 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting Pygments>=2.14 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB)
Collecting docutils<0.22,>=0.18.1 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB)
Collecting snowballstemmer>=2.0 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl.metadata (6.5 kB)
Collecting babel>=2.9 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading babel-2.16.0-py3-none-any.whl.metadata (1.5 kB)
Collecting alabaster~=0.7.14 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB)
Collecting imagesize>=1.3 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading imagesize-1.4.1-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting requests>=2.25.0 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting anyascii (from sphinx-autoapi==3.0.0->-r requirements-dev.txt (line 7))
  Downloading anyascii-0.3.2-py3-none-any.whl.metadata (1.5 kB)
Collecting PyYAML (from sphinx-autoapi==3.0.0->-r requirements-dev.txt (line 7))
  Downloading PyYAML-6.0.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting astroid>=2.7 (from sphinx-autoapi==3.0.0->-r requirements-dev.txt (line 7))
  Downloading astroid-3.3.5-py3-none-any.whl.metadata (4.5 kB)
Collecting docutils<0.22,>=0.18.1 (from Sphinx==7.3.7->-r requirements-dev.txt (line 6))
  Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB)
Collecting sphinxcontrib-jquery<5,>=4 (from sphinx-rtd-theme==2.0.0->-r requirements-dev.txt (line 8))
  Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl.metadata (2.6 kB)
Collecting pytest>=4.6 (from pytest-cov->-r requirements-dev.txt (line 2))
  Downloading pytest-8.3.3-py3-none-any.whl.metadata (7.5 kB)
Collecting pyomo>=6.7.3 (from parameter-sweep==0.0+g49757ff)
  Downloading Pyomo-6.8.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.0 kB)
Collecting numpy (from parameter-sweep==0.0+g49757ff)
  Downloading numpy-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting h5py (from parameter-sweep==0.0+g49757ff)
  Downloading h5py-3.12.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting idaes-pse (from parameter-sweep==0.0+g49757ff)
  Downloading idaes_pse-2.6.0-py3-none-any.whl.metadata (8.4 kB)
Collecting idaes-pse@ git+https://github.com/watertap-org/idaes-pse@2.7.0.dev0.watertap.24.11.19 (from watertap@ git+https://github.com/watertap-org/watertap@main->-r requirements-dev.txt (line 11))
  Cloning https://github.com/watertap-org/idaes-pse (to revision 2.7.0.dev0.watertap.24.11.19) to /tmp/pip-install-_gbr2ta9/idaes-pse_7871649ddd5e4bad80beb9633bbb864e
  Running command git clone --filter=blob:none --quiet https://github.com/watertap-org/idaes-pse /tmp/pip-install-_gbr2ta9/idaes-pse_7871649ddd5e4bad80beb9633bbb864e
  Resolved https://github.com/watertap-org/idaes-pse to commit c4336bae9231543cb4768465e36f8b14c273d6e4
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
INFO: pip is looking at multiple versions of watertap to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install -r requirements-dev.txt (line 11) and parameter-sweep 0.0+g49757ff (from /home/runner/work/parameter-sweep/parameter-sweep) because these package versions have conflicting dependencies.

The conflict is caused by:
    The user requested parameter-sweep 0.0+g49757ff (from /home/runner/work/parameter-sweep/parameter-sweep)
    watertap 1.2.dev0 depends on parameter-sweep>=0.1.dev5

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip to attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

[lbianchi-lbl]

It turns out that this is a known issue (pypa/setuptools-scm#480) due to the way actions/checkout works by default, i.e. not cloning the entire Git history, which can cause setuptools-scm to fail to find the information it needs to deduce the version if the commit is not tagged directly.

If this is true, it's very likely that setuptools-scm never actually worked as intended in the jobs that started failing in #17, and the reason why we haven't experienced this until now is that there was no version incompatibility causing the error (i.e. if there was no version incompatibility, parameter-sweep would be installed as 0.0+g1234567 without otherwise causing errors).

Conversely, the jobs that did not start failing in #17 are those that don't rely on actions/checkout to clone the repository, allowing setuptools-scm to work correctly.

#19 resolves this issue by adding a fetch-depth: 0 input to actions/checkout so that the full Git history is available to setuptools-scm.