Init the refactoring

.github/workflows/build-doc.yml

@@ -76,11 +76,9 @@ jobs:
           echo "AUTODOC_NOTEBOOKS_BRANCH=${AUTODOC_NOTEBOOKS_BRANCH}" >> $GITHUB_ENV
           # check computed variables
           echo "Notebooks source: ${AUTODOC_NOTEBOOKS_REPO_URL}/tree/${AUTODOC_NOTEBOOKS_BRANCH}"
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
+      - uses: actions/checkout@v4
       - name: Setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.python-version }}
           cache: "pip"
@@ -92,9 +90,6 @@ jobs:
           python -m pip install -U pip setuptools
           pip install .
           pip install -r docs/requirements.txt
-          # ensure having keras 3 instead of keras 2.15 installed by tensorflow
-          pip uninstall -y keras
-          pip install "keras>=3"
       - name: generate documentation
         id: sphinx-build
         run: |
@@ -119,7 +114,7 @@ jobs:
           ')
           echo doc_version=${doc_version} >> $GITHUB_OUTPUT
       - name: upload as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.doc-artifact-name }}
           path: ${{ inputs.doc-path }}

.github/workflows/deploy-doc.yml

@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     if: inputs.binder-env-fullref != ''
     steps:
-      - uses: actions/checkout@v3  # checkout triggering branch to get scripts/trigger_binder.sh
+      - uses: actions/checkout@v4  # checkout triggering branch to get scripts/trigger_binder.sh
       - name: Trigger a build for default binder env ref on each BinderHub deployments in the mybinder.org federation
         run: |
           binder_env_full_ref=${{ inputs.binder-env-fullref }}
@@ -39,9 +39,9 @@ jobs:
   deploy-doc:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: ${{ inputs.doc-artifact-name }}
           path: ${{ inputs.doc-path }}
@@ -59,10 +59,10 @@ jobs:
     needs: [deploy-doc]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: gh-pages
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Generate versions.json

.github/workflows/python-publish.yml

@@ -14,8 +14,8 @@ jobs:
     outputs:
       package_version: ${{ steps.get_package_version.outputs.version }}
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.9'
     - name: Install dependencies
@@ -33,7 +33,7 @@ jobs:
         echo "version=$version"
         echo "version=$version" >> $GITHUB_OUTPUT
     - name: Upload as build artifacts
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: dist
         path: dist
@@ -59,7 +59,7 @@ jobs:
     outputs:
       tuto-tag-name: ${{ steps.push-tuto-release-tag.outputs.new_tag_name }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: replace decomon version to install in colab notebooks
         run: |
           version=${{ needs.deploy.outputs.package_version }}

.github/workflows/python-tests.yml

@@ -15,18 +15,18 @@ jobs:
   linters:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: create requirements.txt so that pip cache with setup-python works
         run: echo "pre-commit" > requirements_precommit.txt
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
           cache: pip
           cache-dependency-path: requirements_precommit.txt
       - name: install pre-commit
         run: python -m pip install pre-commit
       - name: get cached pre-commit hooks
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pre-commit
           key: pre-commit|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
@@ -36,8 +36,8 @@ jobs:
   type-checking:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.9
           cache: pip
@@ -48,7 +48,7 @@ jobs:
           python -m pip install --upgrade tox setuptools
       - name: Restore cached .tox
         id: cache-tox
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key:
@@ -70,8 +70,8 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
@@ -82,7 +82,7 @@ jobs:
           python -m pip install --upgrade tox setuptools
       - name: Restore cached .tox
         id: cache-tox
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
           key:
@@ -123,7 +123,7 @@ jobs:
           echo "coverage_exists=${coverage_exists}" >> $GITHUB_OUTPUT
       - name: Export coverage report (if existing)
         if: steps.check-coverage-report.outputs.coverage_exists == 'true'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage
           path: |

binder/environment.yml

@@ -8,7 +8,7 @@ dependencies:
       - kaggle
       - pandas
       - scipy
-      - tensorboard>=2.13
-#      - tensorflow>=2.15  # conflicting dependencies with decomon (keras 2)
+      - tensorboard>=2.16
+      - tensorflow>=2.16
       - jupyter-server-proxy
-      - ..  # decomon
+      - ..  # decomon

binder/postBuild

@@ -1,9 +1,3 @@
-# install tensorflow backend separately from decomon (dependencies conflict as tf 2.15 requires keras 2)
-pip install tensorflow>=2.15
-# use keras 3 instead of keras 2 installed by tensorflow
-pip uninstall -y keras
-pip install "keras>=3"
-
 # tensorboard launches at startup
 mv binder/tensorboardserverextension.py ${NB_PYTHON_PREFIX}/lib/python*/site-packages/
 # enable tensorboard extension

docs/generate_nb_index.py

@@ -4,7 +4,6 @@
 import os
 import re
 import urllib.parse
-from typing import List, Tuple
 
 NOTEBOOKS_LIST_PLACEHOLDER = "[[notebooks-list]]"
 NOTEBOOKS_PAGE_TEMPLATE_RELATIVE_PATH = "tutorials.template.md"
@@ -25,15 +24,15 @@
 
 def extract_notebook_title_n_description(
     notebook_filepath: str,
-) -> Tuple[str, List[str]]:
+) -> tuple[str, list[str]]:
     # load notebook
     with open(notebook_filepath, "rt", encoding="utf-8") as f:
         notebook = json.load(f)
 
     # find title + description: from first cell,  h1 title + remaining text.
     # or title from filename else
     title = ""
-    description_lines: List[str] = []
+    description_lines: list[str] = []
     cell = notebook["cells"][0]
     if cell["cell_type"] == "markdown":
         firstline = cell["source"][0].strip()
@@ -51,7 +50,7 @@ def extract_notebook_title_n_description(
     return title, description_lines
 
 
-def filter_tags_from_description(description_lines: List[str], html_tag_to_remove: str) -> List[str]:
+def filter_tags_from_description(description_lines: list[str], html_tag_to_remove: str) -> list[str]:
     description = "".join(description_lines)
     # opening/closing tags
     opening_tag = html_tag_to_remove
@@ -147,7 +146,7 @@ def get_binder_link(
     return link
 
 
-def get_repo_n_branches_for_binder_n_github_links() -> Tuple[bool, str, str, str, str, str, bool]:
+def get_repo_n_branches_for_binder_n_github_links() -> tuple[bool, str, str, str, str, str, bool]:
     # repos + branches to use for binder environment and notebooks content.
     creating_links = True
     use_nbgitpuller = False

docs/requirements.txt

@@ -1,4 +1,4 @@
 sphinx
 myst_parser
 sphinx_rtd_theme
-tensorflow>=2.15  # install a backend for keras 3 (and tensorflow is the one needed by default)
+tensorflow>=2.16  # install a backend for keras 3 (and tensorflow is the one needed by default)

docs/source/getting_started.md

@@ -8,29 +8,34 @@ within a box domain.
 
 ````python
 # Imports
+import keras
 import numpy as np
-from keras.layers import Dense
+from keras.layers import Dense, Input
 from keras.models import Sequential
 
-from decomon import get_lower_box, get_upper_box
-from decomon.models import clone
+# from decomon import get_lower_box, get_upper_box
+from decomon import clone
 
 # Toy example with a Keras model:
-model = Sequential([Dense(10, activation="relu", input_dim=2)])
+model = Sequential([Input((2,)), Dense(10, activation="relu")])
+
+# Convert into a decomon neural network
+decomon_model = clone(
+    model,
+    final_ibp=True, # keep constant bounds
+    final_affine=False  # drop affine bounds
+)
 
 # Create a fake box with the right shape
 x_min = np.zeros((1, 2))
 x_max = np.ones((1, 2))
-
-# Convert into a decomon neural network
-decomon_model = clone(model)
+x_box = np.concatenate([x_min[:, None], x_max[:, None]], axis=1)
 
 # Get lower and upper bounds
-lower_bound = get_lower_box(decomon_model, x_min, x_max)
-upper_bound = get_upper_box(decomon_model, x_min, x_max)
+lower_bound, upper_bound = decomon_model.predict_on_single_batch_np(x_box)  # more efficient than predict on very small batch
 
-print(lower_bound)
-print(upper_bound)
+print(f"lower bound: {lower_bound}")
+print(f"upper bound: {upper_bound}")
 ````
 
 Other types of domains are possible and illustrated

pyproject.toml

@@ -79,3 +79,7 @@ module = [
     "torch.*"
 ]
 ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "decomon.visualization.model_visualization"
+ignore_errors = true

src/decomon/__init__.py

@@ -8,12 +8,12 @@
 
 import keras
 
-from . import layers, models
-from .metrics.loss import get_adv_loss, get_lower_loss, get_model, get_upper_loss
-from .models.models import get_AB as get_grid_params
-from .models.models import get_AB_finetune as get_grid_slope
-from .wrapper import (
-    check_adv_box,
+from .models import clone
+
+# from .metrics.loss import get_adv_loss, get_lower_loss, get_model, get_upper_loss
+# from .models.models import get_AB as get_grid_params
+# from .models.models import get_AB_finetune as get_grid_slope
+from .wrapper import (  # check_adv_box,; refine_box,
     get_adv_box,
     get_adv_noise,
     get_lower_box,
@@ -22,9 +22,9 @@
     get_range_noise,
     get_upper_box,
     get_upper_noise,
-    refine_box,
 )
-from .wrapper_with_tuning import get_lower_box_tuning, get_upper_box_tuning
+
+# from .wrapper_with_tuning import get_lower_box_tuning, get_upper_box_tuning
 
 try:
     __version__ = version("decomon")