Doc issues: Installing a development environment

[woutdenolf]

https://mxcubeweb.readthedocs.io/en/latest/dev/environment.html

This is not a thing (see conda/conda#12313)

conda env create -f conda-environment.yml python=3.9

SpecNotFound: Invalid name 'python=3.9', try the format: user/package

I guess you can do this

conda create python=3.9 --name mxcubeweb
conda env update --name mxcubeweb --file conda-environment.yml

but it reverts to python 3.11 because

The following packages are incompatible
├─ nodejs 18.*|20.*  is installable with the potential options
│  ├─ nodejs [18.19.0|18.20.2|20.12.2|20.9.0] would require
│  │  └─ openssl >=3.2.1,<4.0a0 , which can be installed;
│  ├─ nodejs [18.20.3|20.12.2|...|22.5.1] would require
│  │  └─ openssl >=3.3.1,<4.0a0 , which can be installed;
│  ├─ nodejs 20.9.0 would require
│  │  └─ openssl >=3.1.4,<4.0a0 , which can be installed;
│  └─ nodejs [18.10.0|18.11.0|...|20.8.1], which can be installed;
├─ pnpm 9**  is installable with the potential options
│  ├─ pnpm [9.0.1|9.0.2|...|9.0.6] would require
│  │  └─ nodejs >=20.9.0,<21.0a0 , which can be installed (as previously explained);
│  ├─ pnpm [9.0.1|9.0.2|...|9.9.0] would require
│  │  └─ nodejs [>=18.19.0,<19.0a0 |>=18.20.2,<19.0a0 |>=20.12.2,<21.0a0 ], which can be installed (as previously explained);
│  └─ pnpm [9.4.0|9.5.0|...|9.9.0] would require
│     └─ nodejs [>=22.4.0,<23.0a0 |>=22.4.1,<23.0a0 |>=22.5.1,<23.0a0 |>=22.6.0,<23.0a0 ] with the potential options
│        ├─ nodejs [18.20.3|20.12.2|...|22.5.1], which can be installed (as previously explained);
│        └─ nodejs [22.6.0|22.7.0] would require
│           └─ openssl >=3.3.1,<4.0a0 , which can be installed;
└─ python 3.9  is not installable because it requires
   └─ openssl >=1.1.1h,<1.1.2a , which conflicts with any installable versions previously reported.

Missing package

conda install redis-server

The package authlib is not optional

Traceback (most recent call last):
  File "/home/denolf/dev/sb/mxcubeweb/mxcubeweb/__init__.py", line 123, in build_server_and_config
    mxcube.init(
  File "/home/denolf/dev/sb/mxcubeweb/mxcubeweb/app.py", line 296, in init
    _UserManagerCls = import_component(
                      ^^^^^^^^^^^^^^^^^
  File "/home/denolf/dev/sb/mxcubeweb/mxcubeweb/core/components/component_base.py", line 22, in import_component
    mod = importlib.import_module(_module)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/users/denolf/.local/wdnbashutils/virtualenvs/mxcubeweb/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/denolf/dev/sb/mxcubeweb/mxcubeweb/core/components/user/usermanager.py", line 12, in <module>
    from authlib.integrations.flask_client import OAuth
ModuleNotFoundError: No module named 'authlib'

[fabcor-maxiv]

Thanks for the report @woutdenolf.

Seems like there are 3 separate issues in this ticket: 1. issue with environment creation for a specific Python version with conda, 2. missing redis-server, and 3. missing authlib. Is that right? If yes, do you mind opening 3 separate tickets? It will be easier to discuss without creating confusion.

[marcus-oscarsson]

@woutdenolf Did you clone from GitHub or GitLab ?

[woutdenolf]

GitLab.

[woutdenolf]

do you mind opening 3 separate tickets

Ok. On gitlab or github?

[marcus-oscarsson]

do you mind opening 3 separate tickets

Ok. On gitlab or github?

:), Ok it would perhaps be a good idea if I explain how we use GitLab and GitHub, ill give you a ring later.

• So the issue you have with authlib comes from our internal ESRF GitLab repository and it have been fixed
• The conda issue is clearly a general issue we should deal with that on GitHub
• I'm a bit surprised that you have a dependency on redis-server, can you quickly check where it comes from ?

[woutdenolf]

I'm a bit surprised that you have a dependency on redis-server

It's in the docs. No idea whether it is actually used or not:
https://mxcubeweb.readthedocs.io/en/latest/dev/environment.html#running-the-application-server

[marcus-oscarsson]

Ah, thanks for spotting that !, its outdated now

[fabcor-maxiv]

See this ticket #1383 to discuss the issue with creating the conda environment for Python3.8 or Python3.9.

[woutdenolf]

I opened this issue for the conda command: #1384

[marcus-oscarsson]

Thanks