Environement setup

[Loveashik]

Hey @MomirMilutinovic, I updated my local repo and here are the observations. As the project evolves, I may run into issues updating my local environment, because previous versions may have created conflicting configurations.

1. As for now, when I try to run ./setup.sh , I get the following error:

1. Setting up conda environment

CondaValueError: prefix already exists: /home/my_user/miniconda3/envs/pubtrends_datasets


CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

Followed by this:

2. Generating test sample of GEOmetadb
Parse error near line 3: table gse already exists
  CREATE TABLE gse(   ID REAL,   title TEXT,   gse TEXT,   status TEXT,   submis
               ^--- error here
Parse error near line 34: table gsm already exists
  CREATE TABLE gsm(   ID REAL,   title TEXT,   gsm TEXT,   series_id TEXT,   gpl
               ^--- error here
Parse error near line 72: table gse_gsm already exists
  CREATE TABLE gse_gsm(gse TEXT,gsm TEXT);
               ^--- error here

2. Why the database needs to be downloaded to a path outside the repository? It is like the project modifies the file structure outside of it which could bring problems. Is it possible to move the download location inside the project, or at least provide an option to choose the installation path?
   Additionally, if I already have the database installed locally, should this step be skipped in that case?
3. Your setup.sh assumes that the user already has conda installed but in the README.md there is no info about it. Better to let .setup.sh handle full environment setup logic.
4. What do you think about switching from conda to the uv package manager, which is more modern, faster, and simpler to reproduce across environments?

[MomirMilutinovic]

Let me address your questions point by point:

1. The error with conda init occurs because the setup script assumes that the environment has not been created. I will modify the script to check if the environment is already present. Similarly, the script also assumes that the test database has not been created, which will also be fixed in the next PR.
2. The database download path was chosen based on Oleg's suggestion and because it helps reduces clutter in the project directory. Nevertheless, it is a good idea to make the database path user-specified and to skip downloading the database if it is already available. I will add an option to choose the database path and a check to see if it is already installed.
3. It seems that conda is listed a prerequisite in README.md in the main branch. Do I need to add more info about the specific version of conda that should be installed?
4. I have taken a look at uv's GitHub page and documentation, and I think that it would streamline some of the workflows. I especially like that uv run always synchronizes the environment, which is quite handy for running bash scripts and tests.