Updating devtools, removing dashboard (#192)

* Move tool configurations together

* Removed unused imports, pass ruff linter

* Remove the GAMA Dashboard

* Bump black

* Bump mypy

* Replace flake8 with ruff

* Move mypy configuration to pyproject.toml

* Remove optional requirements for Dashboard

* Bump pre-commit

* Fix an issue introduced by the new eps penalty in sklearn 1.2

The default value changed from 1e-15 to "auto" that is equivalent to np.finfo(y_pred.dtype).eps.

* Explicitly add datetime format for parsing from log

* Load data as pandas dataframe

Because some pixels were inferred as categorical.
See also #193

.coveragerc

@@ -2,7 +2,6 @@
 ignore_errors = True
 omit =
     tests/*
-    gama/dashboard/*
 exclude_lines =
     pragma: no cover
     def __repr__

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.261
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 23.3.0
     hooks:
       - id: black
         language_version: python3.10
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.971
+    rev: v1.2.0
     hooks:
       - id: mypy
         files: gama/.*
-  - repo: https://github.com/pycqa/flake8
-    rev: 5.0.3
-    hooks:
-      - id: flake8
-        files: gama/.*

README.md

@@ -24,7 +24,7 @@ Using this log, insight can be obtained on the behaviour of the search procedure
 For example, it can produce a graph that shows pipeline fitness over time:
 ![graph of fitness over time](https://github.com/openml-lab/gama/blob/master/docs/source/technical_guide/images/viz.gif)
 
-For more examples and information on the visualization, see [the technical guide](https://openml-labs.github.io/gama/master/user_guide/index.html#dashboard).
+*Note: we temporarily disabled support for the GAMA Dashboard, we will add out-of-the-box visualization again later this year.* 
 
 ## Installing GAMA
 

codecov.yml

@@ -4,4 +4,3 @@ codecov:
 
 ignore:
   - "gama/utilities/cli.py"
-  - "gama/dashboard/**/*"

docs/source/advanced_guide/logging.rst

@@ -51,5 +51,3 @@ An overview the log levels:
  - `INFO`: General information about the optimization process.
  - `WARNING`: Serious errors that do not prohibit GAMA from running to completion (but results could be suboptimal).
  - `ERROR`: Errors which prevent GAMA from running to completion.
-
-As described in :ref:`dashboard-section` the files in the output directory can be used to generate visualizations about the optimization process.

docs/source/conf.py

@@ -17,13 +17,16 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 # -- Adding the module to document ----------------------------------------
+import datetime
+import gama
 import os
+import shutil
 import sys
 
 sys.path.insert(0, os.path.abspath("../.."))
 
 # -- Copying Example files over -------------------------------------------
-import shutil
+
 
 example_dir = "../../examples"
 example_doc_dir = "./user_guide/examples"
@@ -67,8 +70,6 @@
 # The master toctree document.
 master_doc = "index"
 
-import datetime
-
 # General information about the project.
 project = "gama"
 copyright = f"2018-{datetime.datetime.now().year}, Pieter Gijsbers"
@@ -79,7 +80,6 @@
 # built documents.
 #
 # The short X.Y version.
-import gama
 
 version = gama.__version__
 # The full version, including alpha/beta/rc tags.

docs/source/releases.rst

@@ -1,6 +1,11 @@
 Release Notes
 =============
 
+Version 23.0.0
+--------------
+
+We (temporarily) removed the Dashboard, it had not been maintained for a while
+
 Version 22.0.0
 --------------
 

docs/source/user_guide/index.rst

@@ -32,11 +32,6 @@ For ease of use, GAMA provides a `fit`, `predict` and `predict_proba` function a
 
 -----
 
-.. include:: dashboard.rst
-    :start-line: 1
-
------
-
 .. include:: hyperparameters.rst
     :start-line: 1