chore: erase traces of substratools

.github/workflows/build.yml

@@ -17,13 +17,6 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Clone substra-tools
-        uses: actions/checkout@v2
-        with:
-          repository: substra/substra-tools
-          path: substra-tools
-          ref: main
-
       - name: Clone substra
         uses: actions/checkout@v2
         with:
@@ -38,11 +31,10 @@ jobs:
           path: substrafl
           ref: main
 
-      - name: Install substra, substra-tools and substrafl
+      - name: Install substra and substrafl
         run: |
           pip install -e ./substrafl
           pip install -e ./substra
-          pip install -e ./substra-tools
 
       - name: Copy substra and substrafl api doc in the doc
         run: |

.github/workflows/test-examples-subprocess.yml

@@ -35,11 +35,6 @@ jobs:
           sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-      - name: Checkout substra-tools on main
-        uses: actions/checkout@v4
-        with:
-          repository: substra/substra-tools
-          path: substratools
 
       - name: Checkout substra on main
         uses: actions/checkout@v4
@@ -58,7 +53,6 @@ jobs:
           pip install --upgrade pip
           pip install --upgrade -e substrafl
           pip install --upgrade -e substra
-          pip install --upgrade -e substratools
 
       - name: Install examples dependencies
         run: |

README.md

@@ -37,7 +37,7 @@ To deploy the documentation locally you need to install all the necessary requir
 You also need to manually install [pandoc](https://github.com/jgm/pandoc/releases/tag/3.1.11.1).
 
 
-### Install substra, substratools and substrafl in editable mode
+### Install substra and substrafl in editable mode
 
 :warning: if you have these repositories installed in non-editable mode, it will not work.
 
@@ -48,11 +48,6 @@ git clone [email protected]:Substra/substra.git
 cd substra && pip install -e . && cd ..
 ```
 
-```sh
-git clone [email protected]:Substra/substra-tools.git
-cd substra-tools && pip install -e . && cd ..
-```
-
 ```sh
 git clone [email protected]:Substra/substrafl.git
 cd substrafl && pip install -e '.[dev]' && cd ..

docker/substra-documentation-examples/Dockerfile

@@ -4,22 +4,18 @@ WORKDIR /usr/src/app
 
 ### Dirty build to install docker client ###
 # We need to install a docker client because substra debug mode relies on Docker (DinD in a side container)
-# and we need a docker client to authenticate this docker against our container registry to download substra-tools.
 RUN apt update && apt install --yes apt-transport-https ca-certificates curl gnupg lsb-release
 RUN curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
 RUN echo "deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/debian $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
 RUN apt update && apt install --yes docker-ce-cli
 
-COPY  substra-tools/ substra-tools/
 COPY  substra/ substra/
 COPY  substrafl/ substrafl/
 
 RUN cd substrafl && python -m pip install --no-cache-dir -e .
 
 RUN cd substra && python -m pip install --no-cache-dir -e .
 
-RUN cd substra-tools && python -m pip install --no-cache-dir -e .
-
 COPY substra-documentation/Makefile substra-documentation/
 COPY substra-documentation/examples_requirements.txt substra-documentation/
 COPY substra-documentation/docs/source/examples substra-documentation/docs/source/examples/

docs/source/additional/release.rst

@@ -27,7 +27,6 @@ This is an overview of the main changes, please have a look at the changelog of
 - `substra changelog <https://github.com/Substra/substra/blob/main/CHANGELOG.md>`__
 - `substrafl changelog <https://github.com/Substra/substrafl/blob/main/CHANGELOG.md>`__
 - `frontend changelog <https://github.com/Substra/substra-frontend/blob/main/CHANGELOG.md>`__
-- `substra-tools changelog <https://github.com/Substra/substra-tools/blob/main/CHANGELOG.md>`__
 - `backend changelog <https://github.com/Substra/substra-backend/blob/main/CHANGELOG.md>`__
 - `orchestrator changelog <https://github.com/Substra/orchestrator/blob/main/CHANGELOG.md>`__
 
@@ -707,7 +706,7 @@ This means that all opener.py file should be changed from:
 
 .. code-block:: python
 
-  import substratools as tools
+  from substra import tools
 
   class TestOpener(tools.Opener):
       def get_X(self, folders):
@@ -726,7 +725,7 @@ to:
 
 .. code-block:: python
 
-  import substratools as tools
+  from substra import tools
 
   class TestOpener(tools.Opener):
       def get_data(self, folders):

docs/source/conf.py

@@ -41,20 +41,13 @@
 if os.environ.get("READTHEDOCS_VERSION_TYPE") == "tag" or current_commit in tagged_commits:
     # Index 0 means latest release
     SUBSTRA_VERSION = compat_table["releases"][0]["components"]["substra"]["version"]
-    TOOLS_VERSION = compat_table["releases"][0]["components"]["substra-tools"]["version"]
     SUBSTRAFL_VERSION = compat_table["releases"][0]["components"]["substrafl"]["version"]
 
 else:
     SUBSTRA_VERSION = "main"
-    TOOLS_VERSION = "main"
     SUBSTRAFL_VERSION = "main"
 
-print(
-    f"Versions of the components used:"
-    f"\n - substra: {SUBSTRA_VERSION}"
-    f"\n - substra-tools: {TOOLS_VERSION}"
-    f"\n - substrafl: {SUBSTRAFL_VERSION}"
-)
+print(f"Versions of the components used:" f"\n - substra: {SUBSTRA_VERSION}" f"\n - substrafl: {SUBSTRAFL_VERSION}")
 
 
 class SubSectionTitleOrder:
@@ -195,12 +188,6 @@ class Repo:
         doc_dir="docs/api",
         dest_doc_dir="substrafl_doc/api",
     ),
-    Repo(
-        pkg_name="substratools",
-        repo_name="substra-tools",
-        installation_cmd="#egg=substratools",
-        version=TOOLS_VERSION,
-    ),
 ]
 
 

docs/source/documentation/concepts.rst

@@ -9,7 +9,6 @@ Substra overview
 .. toctree::
    :maxdepth: 1
 
-   substra_tools
 
 Assets
 ------

docs/source/examples/substra_core/diabetes_example/assets/dataset/diabetes_opener.py

@@ -1,19 +1,15 @@
 import pathlib
 import numpy as np
 import pandas as pd
-import substratools as tools
+from substra import tools
 
 
 class DiabetesOpener(tools.Opener):
     def fake_data(self, n_samples=None):
         N_SAMPLES = n_samples if n_samples and n_samples <= 100 else 100
 
         features = ["age", "sex", "bmi", "bp", "s1", "s2", "s3", "s4", "s5", "s6"]
-        return pd.DataFrame(
-            data=np.random.random((N_SAMPLES, len(features))), columns=features
-        )
+        return pd.DataFrame(data=np.random.random((N_SAMPLES, len(features))), columns=features)
 
     def get_data(self, folders):
-        return pd.read_csv(
-            next(pathlib.Path(folders[0]).glob("*.csv")), dtype={"sex": "category"}
-        )
+        return pd.read_csv(next(pathlib.Path(folders[0]).glob("*.csv")), dtype={"sex": "category"})

docs/source/examples/substra_core/diabetes_example/assets/functions/aggregation/Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas numpy substratools
+RUN pip3 install pandas numpy substra
 
 # add your algorithm script to docker image
 ADD federated_analytics_functions.py .

docs/source/examples/substra_core/diabetes_example/assets/functions/federated_analytics_functions.py

@@ -5,10 +5,10 @@
 
 import numpy as np
 import pandas as pd
-import substratools as tools
+from substra import tools
 
 
-# We are using helper decorators from the substratools library to avoid rewriting boilerplate code.
+# We are using helper decorators from the substra.tools library to avoid rewriting boilerplate code.
 # The function to be registered takes an `inputs` parameter, which will be matched to the list of
 # `FunctionInputSpec` provided in the `FunctionSpec` definition.
 # In a similar way, the parameter `outputs` will be matched to the `FunctionOutputSpec`.
@@ -20,8 +20,7 @@ def local_first_order_computation(inputs, outputs, task_properties):
         "n_samples": len(df),
         "means": df.select_dtypes(include=np.number).sum().to_dict(),
         "counts": {
-            name: series.value_counts().to_dict()
-            for name, series in df.select_dtypes(include="category").items()
+            name: series.value_counts().to_dict() for name, series in df.select_dtypes(include="category").items()
         },
     }
     save_states(states, outputs["local_analytics_first_moments"])

docs/source/examples/substra_core/diabetes_example/assets/functions/local_first_order_computation/Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas numpy substratools
+RUN pip3 install pandas numpy substra
 
 # add your algorithm script to docker image
 ADD federated_analytics_functions.py .

docs/source/examples/substra_core/diabetes_example/assets/functions/local_second_order_computation/Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas numpy substratools
+RUN pip3 install pandas numpy substra
 
 # add your algorithm script to docker image
 ADD federated_analytics_functions.py .

docs/source/examples/substra_core/diabetes_example/assets/requirements.txt

@@ -1,5 +1,4 @@
 matplotlib==3.9.2
 scikit-learn==1.5.2
 pandas==2.2.2
-substra
-substratools
+substra

docs/source/examples/substra_core/titanic_example/assets/dataset/titanic_opener.py

@@ -4,18 +4,13 @@
 
 import numpy as np
 import pandas as pd
-import substratools as tools
+from substra import tools
 
 
 class TitanicOpener(tools.Opener):
     def get_data(self, folders):
         # find csv files
-        paths = [
-            os.path.join(folder, f)
-            for folder in folders
-            for f in os.listdir(folder)
-            if f.endswith(".csv")
-        ]
+        paths = [os.path.join(folder, f) for folder in folders for f in os.listdir(folder) if f.endswith(".csv")]
 
         # load data
         data = pd.concat([pd.read_csv(path) for path in paths])

docs/source/examples/substra_core/titanic_example/assets/function_random_forest/predict/Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substratools
+RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substra
 
 # add your function script to docker image
 ADD titanic_function_rf.py .

docs/source/examples/substra_core/titanic_example/assets/function_random_forest/titanic_function_rf.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 import pandas as pd
-import substratools as tools
+from substra import tools
 from sklearn.ensemble import RandomForestClassifier
 
 

docs/source/examples/substra_core/titanic_example/assets/function_random_forest/train/Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substratools
+RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substra
 
 # add your function script to docker image
 ADD titanic_function_rf.py .

docs/source/examples/substra_core/titanic_example/assets/metric/Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.12-slim
 
 # install dependencies
-RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substratools
+RUN pip3 install pandas numpy 'scikit-learn==1.5.2' substra
 
 # add your metrics script to docker image
 ADD titanic_metrics.py .

docs/source/examples/substra_core/titanic_example/assets/metric/titanic_metrics.py

@@ -1,4 +1,4 @@
-import substratools as tools
+from substra import tools
 from sklearn.metrics import accuracy_score
 import pandas as pd
 

docs/source/examples/substra_core/titanic_example/assets/requirements.txt

@@ -2,4 +2,4 @@ matplotlib==3.9.2
 scikit-learn==1.5.2
 pandas==2.2.2
 substra
-substratools
+

docs/source/examples/substrafl/get_started/torch_fedavg_assets/dataset/mnist_opener.py

@@ -1,6 +1,6 @@
 import pathlib
 import numpy as np
-import substratools as tools
+from substra import tools
 
 
 class MnistOpener(tools.Opener):

docs/source/examples/substrafl/go_further/diabetes_substrafl_assets/dataset/diabetes_substrafl_opener.py

@@ -1,7 +1,7 @@
 import pathlib
 import numpy as np
 import pandas as pd
-import substratools as tools
+from substra import tools
 
 
 class DiabetesOpener(tools.Opener):

docs/source/examples/substrafl/go_further/sklearn_fedavg_assets/dataset/iris_opener.py

@@ -1,6 +1,6 @@
 import pathlib
 import numpy as np
-import substratools as tools
+from substra import tools
 
 
 class IrisOpener(tools.Opener):

docs/source/examples/substrafl/go_further/torch_cyclic_assets/dataset/cyclic_mnist_opener.py

@@ -1,6 +1,6 @@
 import pathlib
 import numpy as np
-import substratools as tools
+from substra import tools
 
 
 class MnistOpener(tools.Opener):