Spring cleaning for dependencies, Pt. 2: The Tree-Chopping

[lbianchi-lbl]

Resolves: #705

Motivation

• Running pip install "." from this branch in a fresh environment results in the following being installed:

  Package         Version
--------------- ----------
certifi         2022.12.7
click           8.1.3
contourpy       1.0.7
cycler          0.11.0
fonttools       4.39.0
idaes-pse       2.0.0.dev3
kiwisolver      1.4.4
matplotlib      3.7.1
numpy           1.24.2
packaging       23.0
pandas          1.5.3
Pillow          9.4.0
pip             23.0.1
ply             3.11
Pyomo           6.5.0
pyparsing       3.0.9
python-dateutil 2.8.2
pytz            2022.7.1
scipy           1.10.1
setuptools      65.6.3
six             1.16.0
wheel           0.38.4

• The current set of dependencies is most similar to the combined ui,dmf,grid,omlt targets:

pip install ".[ui,dmf,grid,omlt]"

Package                  Version
------------------------ ----------
addheader                0.3.2
anyio                    3.6.2
argon2-cffi              21.3.0
argon2-cffi-bindings     21.2.0
arrow                    1.2.3
asttokens                2.2.1
attrs                    22.2.0
backcall                 0.2.0
beautifulsoup4           4.11.2
bleach                   6.0.0
certifi                  2022.12.7
cffi                     1.15.1
charset-normalizer       3.1.0
click                    8.1.3
colorama                 0.4.6
comm                     0.1.2
contourpy                1.0.7
coramin                  0.1.1
cycler                   0.11.0
debugpy                  1.6.6
decorator                5.1.1
defusedxml               0.7.1
et-xmlfile               1.1.0
exceptiongroup           1.1.1
executing                1.2.0
fastjsonschema           2.16.3
fonttools                4.39.0
fqdn                     1.5.1
gridx-egret              0.5.3
gridx-prescient          2.2.1
idaes-pse                2.0.0.dev3
idna                     3.4
iniconfig                2.0.0
ipykernel                6.21.3
ipython                  8.11.0
ipython-genutils         0.2.0
ipywidgets               8.0.4
isoduration              20.11.0
jedi                     0.18.2
Jinja2                   3.1.2
jsonpointer              2.3
jsonschema               4.17.3
jupyter                  1.0.0
jupyter_client           8.0.3
jupyter-console          6.6.3
jupyter_core             5.2.0
jupyter-events           0.6.3
jupyter_server           2.4.0
jupyter_server_terminals 0.4.4
jupyterlab-pygments      0.2.2
jupyterlab-widgets       3.0.5
kiwisolver               1.4.4
lxml                     4.9.2
MarkupSafe               2.1.2
matplotlib               3.7.1
matplotlib-inline        0.1.6
mistune                  2.0.5
nbclassic                0.5.3
nbclient                 0.7.2
nbconvert                7.2.10
nbformat                 5.7.3
nest-asyncio             1.5.6
networkx                 3.0
notebook                 6.5.3
notebook_shim            0.2.2
numpy                    1.24.2
omlt                     1.1
openpyxl                 3.1.2
packaging                23.0
pandas                   1.5.3
pandocfilters            1.5.0
parso                    0.8.3
pexpect                  4.8.0
pickleshare              0.7.5
Pillow                   9.4.0
Pint                     0.20.1
pip                      23.0.1
platformdirs             3.1.1
pluggy                   1.0.0
ply                      3.11
prometheus-client        0.16.0
prompt-toolkit           3.0.38
psutil                   5.9.4
ptyprocess               0.7.0
pure-eval                0.2.2
pycparser                2.21
Pygments                 2.14.0
Pyomo                    6.5.0
pyparsing                3.0.9
PyPDF2                   3.0.1
pyrsistent               0.19.3
pytest                   7.2.2
python-dateutil          2.8.2
python-json-logger       2.0.7
pytz                     2022.7.1
PyYAML                   6.0
pyzmq                    25.0.1
qtconsole                5.4.1
QtPy                     2.3.0
requests                 2.28.2
rfc3339-validator        0.1.4
rfc3986-validator        0.1.1
scipy                    1.10.1
seaborn                  0.12.2
Send2Trash               1.8.0
setuptools               65.6.3
six                      1.16.0
sniffio                  1.3.0
soupsieve                2.4
stack-data               0.6.2
terminado                0.17.1
tinycss2                 1.2.1
tinydb                   4.7.1
tomli                    2.0.1
tornado                  6.2
traitlets                5.9.0
uri-template             1.2.0
urllib3                  1.26.15
wcwidth                  0.2.6
webcolors                1.12
webencodings             0.5.1
websocket-client         1.5.1
wheel                    0.38.4
widgetsnbextension       4.0.5
xlrd                     2.0.1

Changes proposed in this PR:

• Split non-core dependencies in categories selectable as extras_require targets

Caveats

• Most likely causes widespread test failures Tests are now passing
• Would still need to update the documentation Documentation has been updated (I might have missed something)

Decisions

• After some deliberation, it was decided not to exposes a catch-all extras_require target (e.g. complete, all). This follows the "explicit is better than implicit" principle and requires downstream clients to pro-actively "opt in" to the sets of optional dependencies they need

For reviewers

• Check documentation, especially installation steps
  • I've done a first pass based on what I could find, but it's entirely possible that I've missed something

Legal Acknowledgement

By contributing to this software project, I agree to the following terms and conditions for my contribution:

1. I agree my contributions are submitted under the license terms described in the LICENSE.txt file at the top level of this directory.
2. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer.

[ksbeattie]

This is waiting for #1138

[andrewlee94]

A couple of comments that I wanted to check on, but otherwise this is looking good to me.

[andrewlee94]

One thing I do not see here is instructions on how to get the optional dependencies; this is one of our user facing sets of install instructions so we probably need to cover it here (or point to the README for more details and to avoid the possibility of conflicting instrucitons).

[lbianchi-lbl]

Good point. I agree that the optional dependencies instructions should be included in the user-facing installation material. I think I'll copy what's in the README to the Sphinx docs, and we can revisit later if the repetition becomes a problem.

[lbianchi-lbl]

I've added a How-to page on optional dependencies: https://idaes-pse--1133.org.readthedocs.build/en/1133/how_to_guides/opt_dependencies.html

[andrewlee94]

Looks good to me.

[ksbeattie]

LGTM