fix - lock cython version, add missing pip deps

[JoshCu]

Fixes #651
breakout from #660

Summary

Adds required pip packages to requirements.txt
Locks cython version to fix ./compile.sh

requirements.txt

Additions

• pyarrow
• deprecated
• geopandas

Changes

• Cython==0.29.36

Testing

Before

#0 65.83 Compiler crash traceback from this point on:
#0 65.83   File "/opt/venv/lib64/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 4968, in analyse_types
#0 65.83     performance_hint(index.pos, "Index should be typed for more efficient access")
#0 65.83 TypeError: performance_hint() missing 1 required positional argument: 'env'
#0 65.83 Traceback (most recent call last):
#0 65.83   File "/t-route/src/troute-routing/setup.py", line 122, in <module>
#0 65.83 Fortran compiler type is: gnu95
#0 65.83 Compiling troute/routing/fast_reach/reach.pyx because it changed.
#0 65.83 Compiling troute/routing/fast_reach/mc_reach.pyx because it changed.
#0 65.83 Compiling troute/routing/fast_reach/diffusive.pyx because it changed.
#0 65.83 Compiling troute/routing/fast_reach/simple_da.pyx because it changed.
#0 65.83 [1/4] Cythonizing troute/routing/fast_reach/diffusive.pyx
#0 65.83 [2/4] Cythonizing troute/routing/fast_reach/mc_reach.pyx
#0 65.83     ext_modules = cythonize(ext_modules, compiler_directives={"language_level": 3})
#0 65.83   File "/opt/venv/lib64/python3.9/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
#0 65.83     cythonize_one(*args)
#0 65.83   File "/opt/venv/lib64/python3.9/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
#0 65.83     raise CompileError(None, pyx_file)
#0 65.83 Cython.Compiler.Errors.CompileError: troute/routing/fast_reach/mc_reach.pyx
------
Dockerfile.troute:20
--------------------
  18 |     RUN python -m pip install -r requirements.txt
  19 |
  20 | >>> RUN ./compiler.sh no-e
  21 |
  22 |     # increase max open files soft limit
--------------------
ERROR: failed to solve: process "/bin/sh -c ./compiler.sh no-e" did not complete successfully: exit code: 1

After

Screenshot is of a docker build step successfully running, before it would fail on that step.

Notes

Using legacy 'setup.py install' for troute.network, since package 'wheel' is not installed. this warning does appear when compiling.
Without version locks on all the pip packages, it would be a good idea to have some schedulled tests to catch any breaking updates to packages. #669 or #670 could help?

Todos

• Update ngen documentation about installing those packages

Checklist

• PR has an informative and human-readable title
• Changes are limited to a single goal (no scope creep)
• Code can be automatically merged (no conflicts)
• Code follows project standards (link if applicable)
• Passes all existing automated tests
• Any change in functionality is tested
• New functions are documented (with a description, list of inputs, and expected output)
• Placeholder code is flagged / future todos are captured in comments
• Visually tested in supported browsers and devices (see checklist below 👇)
• Project documentation has been updated (including the "Unreleased" section of the CHANGELOG)
• Reviewers requested with the Reviewers tool ➡️

[JoshCu]

As this is still open and related to this #614 I'm going to also set pyarrow <12.0 and retest

[JoshCu]

As this is still open and related to this #614 I'm going to also set pyarrow <12.0 and retest

build works as expected with both cython<3.0.4 and pyyarrow <12.0

[TrupeshKumarPatel]

Could you please double check the installation and test run without any version specification on thepyarrow? Because on my branch here build log, downloads pyarrow-14.0.0 and test ran just fine.

[JoshCu]

I think the pyarrow version is an issue specific to running t-route with ngen, #614
I'm not sure if it would be best to address the issue closest to the root (here) to stop other things that use it all needing the same patch. Or if it should be addressed in ngen as that's where it appears to break things?

[shorvath-noaa]

@JoshCu @TrupeshKumarPatel I tested these changes and they work fine on my end. Is the above conversation about locking in pyarrow version ongoing or is this PR ready for approval/merging?