feat: Refine the constructor of Project to hide repositories

[thomass-dev]

Closes #1160

This PR intends to ease the project API by centralizing all the action in the constructor.

To note:

• Remove all actions from the CLI except "launch UI", which implicitly create the specified project.
• Rename the command skore to skore-ui.
• Release the constraints on project name.
• Remove all project management scripts and open function in favor of the project class constructor.
• Create implicitly the project when calling the constructor.
• Add project clear function to allow user to explicitly clear a project.

---

# create project

import skore
project = skore.Project("project.skore")

# work on existing project

import skore
project = skore.Project("project.skore", exist_ok=True)

# work on existing project and clear explicitly

import skore
project = skore.Project("project.skore", exist_ok=True)
project.clear()

# work on existing project, but without knowing it

import skore
project = skore.Project("project.skore")

---------------------------------------------------------------------------
FileExistsError                           Traceback (most recent call last)
[...]
FileExistsError: Project 'project.skore' already exists.

[github-actions]

Coverage Report for backend

File	Stmts	Miss	Cover	Missing
venv/lib/python3.12/site-packages/skore
__init__.py	14	0	100%
__main__.py	8	8	0%	3–19
exceptions.py	3	3	0%	4–19
venv/lib/python3.12/site-packages/skore/cli
__init__.py	5	5	0%	3–8
cli.py	16	16	0%	3–59
color_format.py	49	49	0%	3–116
venv/lib/python3.12/site-packages/skore/persistence
__init__.py	0	0	100%
venv/lib/python3.12/site-packages/skore/persistence/item
__init__.py	59	4	91%	89, 100–103
altair_chart_item.py	24	1	93%	15
cross_validation_reporter_item.py	109	12	89%	28–41, 125–126, 259, 262
item.py	24	1	96%	86
matplotlib_figure_item.py	33	1	95%	18
media_item.py	24	0	100%
numpy_array_item.py	29	1	94%	16
pandas_dataframe_item.py	31	1	94%	14
pandas_series_item.py	31	1	94%	14
pickle_item.py	33	0	100%
pillow_image_item.py	32	1	94%	16
plotly_figure_item.py	25	1	93%	15
polars_dataframe_item.py	29	1	94%	14
polars_series_item.py	24	1	93%	14
primitive_item.py	25	2	91%	13–15
sklearn_base_estimator_item.py	31	1	94%	15
skrub_table_report_item.py	10	1	86%	11
venv/lib/python3.12/site-packages/skore/persistence/repository
__init__.py	3	0	100%
item_repository.py	59	5	91%	15–16, 202–203, 226
view_repository.py	19	2	86%	9–10
venv/lib/python3.12/site-packages/skore/persistence/storage
__init__.py	4	0	100%
abstract_storage.py	22	0	100%
disk_cache_storage.py	33	1	95%	44
in_memory_storage.py	20	0	100%
venv/lib/python3.12/site-packages/skore/persistence/view
__init__.py	2	0	100%
view.py	5	0	100%
venv/lib/python3.12/site-packages/skore/project
__init__.py	2	0	100%
project.py	62	1	99%	237
venv/lib/python3.12/site-packages/skore/sklearn
__init__.py	5	0	100%
_base.py	140	4	97%	91, 94, 168–>173, 183–184
find_ml_task.py	45	1	95%	71–>87, 80–>87, 86
types.py	2	0	100%
venv/lib/python3.12/site-packages/skore/sklearn/_cross_validation
__init__.py	6	0	100%
metrics_accessor.py	163	0	100%
report.py	87	0	100%
venv/lib/python3.12/site-packages/skore/sklearn/_estimator
__init__.py	6	0	100%
metrics_accessor.py	265	4	97%	149–158, 183–>236, 191, 434–>437, 783–>786
report.py	120	0	99%	215–>221, 223–>225
utils.py	11	11	0%	1–19
venv/lib/python3.12/site-packages/skore/sklearn/_plot
__init__.py	4	0	100%
precision_recall_curve.py	121	1	98%	229–>246, 317
prediction_error.py	97	0	100%
roc_curve.py	128	0	100%
utils.py	88	0	100%
venv/lib/python3.12/site-packages/skore/sklearn/cross_validation
__init__.py	2	0	100%
cross_validation_helpers.py	47	4	90%	104–>136, 123–126
cross_validation_reporter.py	35	1	95%	187
venv/lib/python3.12/site-packages/skore/sklearn/cross_validation/plots
__init__.py	0	0	100%
compare_scores_plot.py	29	24	16%	10, 28–116
timing_plot.py	29	24	17%	10, 26–123
venv/lib/python3.12/site-packages/skore/sklearn/train_test_split
__init__.py	0	0	100%
train_test_split.py	36	2	94%	16–17
venv/lib/python3.12/site-packages/skore/sklearn/train_test_split/warning
__init__.py	8	0	100%
high_class_imbalance_too_few_examples_warning.py	17	3	78%	16–18, 80
high_class_imbalance_warning.py	18	2	88%	16–18
random_state_unset_warning.py	11	1	87%	15
shuffle_true_warning.py	9	0	91%	44–>exit
stratify_is_set_warning.py	11	1	87%	15
time_based_column_warning.py	22	1	89%	17, 69–>exit
train_test_split_warning.py	5	1	80%	21
venv/lib/python3.12/site-packages/skore/ui
__init__.py	0	0	100%
app.py	30	7	71%	48–53, 65–67
dependencies.py	4	0	100%
launch.py	26	15	39%	36–57
project_routes.py	62	0	100%
venv/lib/python3.12/site-packages/skore/utils
__init__.py	6	0	100%
_accessor.py	7	0	100%
_logger.py	21	4	84%	14–18
_patch.py	11	5	46%	19–35
_progress_bar.py	30	0	100%
_show_versions.py	31	0	100%
TOTAL	2694	236	91%

Tests	Skipped	Failures	Errors	Time
587	3 💤	0 ❌	0 🔥	2m 51s ⏱️

[github-actions]

Documentation preview @ 435847f

[glemaitre]

I'm almost happy with what I see:

• I like some simplification here.
• I don't like that we don't have the open anymore. We should be able to trigger the UI launch on the Python side. Having this in the Project constructor does not make any sense. So we will need a kind of factory. This open will have a symmetry between the CLI and Python. But it is orthogonal with the work here: It only need to create the project and attach the server info to it.

[MarieS-WiMLDS]

Thank you for these changes!! It should really make it easier for users to grasp how to create a project.

I have two additional comments:

• the first one is about the delete function, it looks like a bit a function that would delete the project now. I don't really have an idea how to solve this. A mitigation could be to have a delete_project function (function that i'd like to have anyway, but it's not a great solution to be explicit about the purpose of delete)
• I disagree with @glemaitre on the fact that the creation function should also open the UI. these are two different things, we should have a python func to launch UI indeed, but it would be dedicated to this and only this.

[glemaitre]

I disagree with @glemaitre on the fact that the creation function should also open the UI. these are two different things, we should have a python func to launch UI indeed, but it would be dedicated to this and only this.

@MarieS-WiMLDS Let's move the discussion in this #1002 since it will not impact this PR.

[glemaitre]

With the discussion that we had and use if_exist="raise"/"load", I'm find with the current PR.

[MarieS-WiMLDS]

Great simplification :) !!

[rouk1]

I know I'm late to the show but if_exists default value to raise is very awkward to me. Indeed how do one rerun an cell containing a Project() statement if you don't now that kwarg ? (note that its not discoverable by IDE probably cause we do not have stubs I suppose).

To me reloading an existing project is something more common than creating one.

[glemaitre]

I know I'm late to the show but if_exists default value to raise is very awkward to me.

Never too late and it was open to debate during the review.

One point that I took from @thomass-dev was that you could implicitly modify the DB, adding new version of items without taking care. And thus I thought that it would easier to go back to a less conservative way, with feedback.

Now, something that I'm figuring out (during my 🏃‍♂️) is that if clear would allow me to clean up for instance a specific run because I mess up, then I would be fine with if_exist="load" because I can easily go back.

[glemaitre]

Indeed how do one rerun an cell containing a Project() statement if you don't now that kwarg ?

For sure, you error message should mention this kwargs to make you do the right choice (I did not read the updated code however).

[rouk1]

Another issue that I have with this PR is that as the project parameter of the create_app factory is no longer optional the server app is no longer easily debuggable.

i.e. when you run it from the command line you can not pass a path hence it crashes when run.

uvicorn  skore.ui.app:create_app --factory --reload --reload-dir skore/src --host 0.0.0.0 --port 22140 --timeout-graceful-shutdown 0 --log-level info
INFO:     Will watch for changes in these directories: ['/Users/rouk1/dev/skore/skore/src']
INFO:     Uvicorn running on http://0.0.0.0:22140 (Press CTRL+C to quit)
INFO:     Started reloader process [19757] using StatReload
ERROR:    Error loading ASGI app factory: create_app() missing 1 required positional argument: 'project'

This how you get to debug the FastAPI app in vscode.

{
  // launch.json
  "version": "0.2.0",
  "configurations": [
    {
      "name": "Run webapp",
      "type": "debugpy",
      "request": "launch",
      "module": "uvicorn",
      "args": [
        "skore.ui.app:create_app",
        "--factory",
        "--reload",
        "--reload-dir",
        "skore/src",
        "--host",
        "0.0.0.0",
        "--port",
        "22140",
        "--timeout-graceful-shutdown",
        "0",
        "--log-level",
        "info"
      ],
      "console": "integratedTerminal",
      "jinja": true,
      "env": {
        "DEBUG": "1",
      }
    }
  ]
}

[thomass-dev]

Thanks @rouk1 for your review, i will revert the create_app changes.