Problems installing VizierDB/web-api

[ricci]

I'm having multiple problems installing the web-api using the instructions in the README; I'll document them here as I find them.

System information:

> uname -a
Linux node0.ricci-240764.testbed-pg0.utah.cloudlab.us 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
> lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 22.04.5 LTS
Release:	22.04
Codename:	jammy
> conda --version
conda 24.9.2
> which python
/users/ricci/anaconda3/bin/python
>  python --version
Python 3.12.7

(the system python is 3.10.12, but I don't think that should matter?)

[ricci]

First error: if I try to run conda env create -f environment.yaml as suggested by the first set of instructions, I get:

/users/ricci/anaconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
  action(self, namespace, argument_values, option_string)
Channels:
 - vida-nyu
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
Channels:
 - vida-nyu
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides requested tk ==8.5.18 0
  - nothing provides requested scipy ==0.19.0 np113py27_0
  - nothing provides requested requests ==2.14.2 py27_0
  - nothing provides requested readline ==6.2 2
  - nothing provides requested qt ==4.8.7 3
  - nothing provides requested numpy ==1.13.0 py27_0
  - nothing provides requested nodejs ==6.10.3 0
  - nothing provides requested mkl ==2017.0.1 0
  - nothing provides requested markupsafe ==0.23 py27_2
  - nothing provides requested jpeg ==9b 2
  - package pyqt-4.11.4-py27_2 requires qt 4.8.*, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ jpeg ==9b 2 does not exist (perhaps a typo or a missing channel);
├─ markupsafe ==0.23 py27_2 does not exist (perhaps a typo or a missing channel);
├─ mkl ==2017.0.1 0 does not exist (perhaps a typo or a missing channel);
├─ nodejs ==6.10.3 0 does not exist (perhaps a typo or a missing channel);
├─ numpy ==1.13.0 py27_0 does not exist (perhaps a typo or a missing channel);
├─ pyqt ==4.11.4 py27_2 is installable and it requires
│  └─ qt 4.8.* , which requires
│     └─ zlib >=1.2.11,<1.3.0a0 , which can be installed;
├─ qt ==4.8.7 3 does not exist (perhaps a typo or a missing channel);
├─ readline ==6.2 2 does not exist (perhaps a typo or a missing channel);
├─ requests ==2.14.2 py27_0 does not exist (perhaps a typo or a missing channel);
├─ scipy ==0.19.0 np113py27_0 does not exist (perhaps a typo or a missing channel);
├─ tk ==8.5.18 0 does not exist (perhaps a typo or a missing channel);
└─ zlib ==1.2.8 3 is not installable because it conflicts with any installable versions previously reported.

[ricci]

If I follow the alternate instructions, when I get to the pip install -r requirements.txt step, I get:

Collecting spylon>=0.3.0 (from -r requirements.txt (line 6))
  Using cached spylon-0.3.0.tar.gz (140 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [18 lines of output]
      /tmp/pip-install-c4zq4zzt/spylon_131a3ddf5cc64a0d97e0652805b9466f/versioneer.py:485: SyntaxWarning: invalid escape sequence '\s'
        LONG_VERSION_PY['git'] = '''
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-c4zq4zzt/spylon_131a3ddf5cc64a0d97e0652805b9466f/setup.py", line 32, in <module>
          version=versioneer.get_version(),
                  ^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-install-c4zq4zzt/spylon_131a3ddf5cc64a0d97e0652805b9466f/versioneer.py", line 1473, in get_version
          return get_versions()["version"]
                 ^^^^^^^^^^^^^^
        File "/tmp/pip-install-c4zq4zzt/spylon_131a3ddf5cc64a0d97e0652805b9466f/versioneer.py", line 1406, in get_versions
          cfg = get_config_from_root(root)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-install-c4zq4zzt/spylon_131a3ddf5cc64a0d97e0652805b9466f/versioneer.py", line 412, in get_config_from_root
          parser = configparser.SafeConfigParser()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?
      [end of output]

Looking further into this, it appears to me that spylon is broken on python 3.12, due to some API changes.

[ricci]

If I force an older python by creating the conda environment with conda create --name vizier python=3.11 pip, I can get through the two pip steps, but

> conda install pyqt=4.11.4=py27_4
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pyqt==4.11.4=py27_4
 
...

If I remove the version pin and do conda install pyqt, that works, but then when I try to actually try to start vizier with

cd vizier
python server.py

(so using vizier/config.yaml), there are still package problems:

>  python server.py 
Traceback (most recent call last):
  File "/users/ricci/web-api/vizier/server.py", line 20, in <module>
    from flask import Flask, jsonify, make_response, request, send_file
  File "/users/ricci/anaconda3/envs/vizier/lib/python3.11/site-packages/flask/__init__.py", line 19, in <module>
    from jinja2 import Markup, escape
ImportError: cannot import name 'Markup' from 'jinja2' (/users/ricci/anaconda3/envs/vizier/lib/python3.11/site-packages/jinja2/__init__.py)

[okennedy]

Hi Rob!

Welcome!

This repo needs to be archived >.> You can find the modern version at https://github.com/VizierDB/vizier-scala/

Installation instructions on the wiki should be working: https://github.com/VizierDB/vizier-scala/wiki