Add --all-files option to precommit command to avoid skipping the test

No tests were actually done by the linter action because `pre-commit run` look only files in the index by default. When checkout a whole PR, no files are in the index so no files are checked. Previously, the job returned something like Trim Trailing Whitespace.............................(no files to check)Skipped Fix End of Files.....................................(no files to check)Skipped Check Yaml...........................................(no files to check)Skipped Check for added large files..........................(no files to check)Skipped Pretty format JSON...................................(no files to check)Skipped isort (python).......................................(no files to check)Skipped black................................................(no files to check)Skipped nbqa-isort...........................................(no files to check)Skipped nbqa-black...........................................(no files to check)Skipped nbqa-pycln...........................................(no files to check)Skipped nbstripout...........................................(no files to check)Skipped Now the checks are done (and should read as "Passed") We make a `pre-commit run --all-files` in this commit to have the job pass. We also remove the pretty-format-json hook which was tampering with the notebooks (oddly only remotely on the github runner, not locally on my laptop), and was not very useful for the repository anyway.
airbus · Nov 17, 2023 · 1ba371e · 1ba371e
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -105,7 +105,7 @@ jobs:
           path: ~/.cache/pre-commit
           key: pre-commit|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
       - name: pre-commit checks
-        run: pre-commit run --show-diff-on-failure --color=always
+        run: pre-commit run --show-diff-on-failure --color=always --all-files
 
   build-windows:
     needs: [setup]

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -56,7 +56,7 @@ jobs:
           path: ~/.cache/pre-commit
           key: pre-commit|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
       - name: pre-commit checks
-        run: pre-commit run --show-diff-on-failure --color=always
+        run: pre-commit run --show-diff-on-failure --color=always --all-files
 
   build-windows:
     needs: [setup]

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,8 +21,6 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
-    -   id: pretty-format-json
-        args: ["--autofix", "--no-sort-keys", "--indent", "4"]
 
   - repo: https://github.com/psf/black
     rev: 22.3.0 # Replace by any tag/version: https://github.com/psf/black/tags

diff --git a/docs/contribute.md b/docs/contribute.md
@@ -84,9 +84,9 @@ Here are the steps to follow:
           ```shell
           poetry env use 3.8.11
           ```
-      
-      - Preinstall gym 0.21.0 with appropriate option to avoid an error during installation 
-        (see this [issue](https://github.com/openai/gym/issues/3176) 
+
+      - Preinstall gym 0.21.0 with appropriate option to avoid an error during installation
+        (see this [issue](https://github.com/openai/gym/issues/3176)
         and this [solution](https://github.com/python-poetry/poetry/issues/3433#issuecomment-840509576)):
           ```shell
           poetry run python -m pip install "pip==22"  # starting with pip 23.1, gym 0.21.0 is not intallable anymore
@@ -132,8 +132,8 @@ as it can also be installed by conda via the conda-forge channel.
     poetry self add poetry-dynamic-versioning
     ```
 
-- Preinstall gym 0.21.0 with appropriate option to avoid an error during installation 
-  (see this [issue](https://github.com/openai/gym/issues/3176) 
+- Preinstall gym 0.21.0 with appropriate option to avoid an error during installation
+  (see this [issue](https://github.com/openai/gym/issues/3176)
   and this [solution](https://github.com/python-poetry/poetry/issues/3433#issuecomment-840509576)):
     ```shell
     poetry run python -m pip install "pip==22"  # starting with pip 23.1, gym 0.21.0 is not intallable anymore

diff --git a/docs/install.md b/docs/install.md
@@ -125,8 +125,8 @@ pip install -U scikit-decide
 
 ## Troubleshooting
 
-You may encounter an [error when installing `gym==0.21.0`](https://github.com/openai/gym/issues/3176) which happens to be a dependency of `scikit-decide[all]`. 
-This is because its installation does not respect PEP 517 which is enforced by default by last versions of pip and setuptools. 
+You may encounter an [error when installing `gym==0.21.0`](https://github.com/openai/gym/issues/3176) which happens to be a dependency of `scikit-decide[all]`.
+This is because its installation does not respect PEP 517 which is enforced by default by last versions of pip and setuptools.
 The solution is to install it beforehand:
 ```shell
 # preinstall gym==0.21.0 with legacy method (python setup.py) because its requirements list is broken
@@ -145,7 +145,7 @@ pip install -U scikit-decide[all]
 ```
 
 ::: tip Note
-Newer versions of gym or [gymnasium](https://gymnasium.farama.org/), typically greater than 0.26 are not yet possible 
-because of a conflict between [`ray[rllib]`](https://github.com/ray-project/ray/issues/34396) 
+Newer versions of gym or [gymnasium](https://gymnasium.farama.org/), typically greater than 0.26 are not yet possible
+because of a conflict between [`ray[rllib]`](https://github.com/ray-project/ray/issues/34396)
 and [`stable-baselines3`](https://github.com/DLR-RM/stable-baselines3/issues/1452).
-:::
+:::
diff --git a/examples/up_bridge.py b/examples/up_bridge.py
@@ -3,20 +3,20 @@
 # LICENSE file in the root directory of this source tree.
 
 import sys
-from skdecide.hub.domain.up import UPDomain
-from skdecide.hub.solver.up import UPSolver
-from skdecide.hub.solver.lazy_astar import LazyAstar
 
 import unified_planning
 from unified_planning.shortcuts import (
-    UserType,
     BoolType,
-    OneshotPlanner,
     Fluent,
     InstantaneousAction,
     Not,
+    OneshotPlanner,
+    UserType,
 )
 
+from skdecide.hub.domain.up import UPDomain
+from skdecide.hub.solver.lazy_astar import LazyAstar
+from skdecide.hub.solver.up import UPSolver
 from skdecide.utils import rollout
 
 # Example 1: Solving a basic example, the same as

diff --git a/skdecide/hub/domain/flight_planning/__init__.py b/skdecide/hub/domain/flight_planning/__init__.py
@@ -1,4 +1,3 @@
 # Copyright (c) AIRBUS and its affiliates.
 # This source code is licensed under the MIT license found in the
 # LICENSE file in the root directory of this source tree.
-
diff --git a/skdecide/hub/domain/flight_planning/domain.py b/skdecide/hub/domain/flight_planning/domain.py
@@ -36,6 +36,7 @@
 from skdecide.hub.space.gym import EnumSpace, ListSpace, MultiDiscreteSpace
 from skdecide.utils import match_solvers
 
+
 class WeatherDate:
     day: int
     month: int
@@ -159,7 +160,6 @@ def previous_day(self):
         return WeatherDate(day, month, year, forecast=self.forecast)
 
 
-
 class State:
     """
     Definition of a aircraft state during the flight plan
@@ -190,11 +190,12 @@ def __hash__(self):
         return hash((self.pos, int(self.mass), self.alt, int(self.time)))
 
     def __eq__(self, other):
-        return (self.pos == other.pos
-                and int(self.mass) == int(other.mass)
-                and self.alt == other.alt
-                and int(self.time) == int(other.time)
-            )
+        return (
+            self.pos == other.pos
+            and int(self.mass) == int(other.mass)
+            and self.alt == other.alt
+            and int(self.time) == int(other.time)
+        )
 
     def __ne__(self, other):
         return (
@@ -774,7 +775,7 @@ def set_network(
         half_vertical_points = nb_vertical_points // 2
 
         distp = (
-            graph_width * p0.distanceTo(p1) *0.022
+            graph_width * p0.distanceTo(p1) * 0.022
         )  # meters, around 2.2%*graphwidth of the p0 to p1 distance
 
         descent_dist = min(
@@ -785,20 +786,20 @@ def set_network(
             ),
             p0.distanceTo(p1),
         )  # meters
-        
+
         climb_dist = 220_000 * (
             max(self.ac["cruise"]["height"] - p0.height, 0)
             / self.ac["cruise"]["height"]
         )  # meters
-        
+
         total_distance = p0.distanceTo(p1)
         if total_distance < (climb_dist + descent_dist):
             climb_dist = total_distance * max(
-                (climb_dist / (climb_dist + descent_dist)) - 0.1
-            ,0)
+                (climb_dist / (climb_dist + descent_dist)) - 0.1, 0
+            )
             descent_dist = total_distance * max(
-                descent_dist / (climb_dist + descent_dist) - 0.1
-            ,0)
+                descent_dist / (climb_dist + descent_dist) - 0.1, 0
+            )
             possible_altitudes = [cruise_alt_min for k in range(nb_vertical_points)]
 
         else:
@@ -816,11 +817,15 @@ def set_network(
         if climbing_slope:
             climbing_ratio = climbing_slope
         else:
-            climbing_ratio = (possible_altitudes[0] / climb_dist if climb_dist != 0 else 0)
+            climbing_ratio = (
+                possible_altitudes[0] / climb_dist if climb_dist != 0 else 0
+            )
         if descending_slope:
             descending_ratio = descending_slope
         else:
-            descending_ratio = (possible_altitudes[0] / descent_dist if descent_dist != 0 else 0)
+            descending_ratio = (
+                possible_altitudes[0] / descent_dist if descent_dist != 0 else 0
+            )
         # Initialisation of the graph matrix
         pt = [
             [
@@ -838,33 +843,37 @@ def set_network(
 
         # set climb phase
         i_initial = 1
-        if climbing_ratio != 0 :         
+        if climbing_ratio != 0:
             dist = 0
             alt = p0.height
             while dist < climb_dist and i_initial != nb_forward_points:
 
                 local_dist = (
-                    pt[i_initial - 1][half_lateral_points][half_vertical_points].distanceTo(
-                        p1
-                    )
+                    pt[i_initial - 1][half_lateral_points][
+                        half_vertical_points
+                    ].distanceTo(p1)
                 ) / (nb_forward_points - i_initial)
                 dist += local_dist
                 alt += int(local_dist * climbing_ratio)
 
                 for k in range(nb_vertical_points):
-                    bearing = pt[i_initial - 1][half_lateral_points][k].initialBearingTo(p1)
+                    bearing = pt[i_initial - 1][half_lateral_points][
+                        k
+                    ].initialBearingTo(p1)
                     pt[i_initial][half_lateral_points][k] = pt[i_initial - 1][
                         half_lateral_points
-                    ][k].destination(local_dist, bearing, min(possible_altitudes[0], alt))
+                    ][k].destination(
+                        local_dist, bearing, min(possible_altitudes[0], alt)
+                    )
                 i_initial += 1
 
         # set last step, descent
         i_final = 1
-        if descending_ratio != 0 :
+        if descending_ratio != 0:
             dist = 0
             alt = p1.height
 
-            while dist < descent_dist and i_final != nb_forward_points-1:
+            while dist < descent_dist and i_final != nb_forward_points - 1:
                 local_dist = (
                     pt[nb_forward_points - i_final][half_lateral_points][
                         half_vertical_points
@@ -905,20 +914,18 @@ def set_network(
             pt[half_forward_points][nb_lateral_points - 1][k] = pt[half_forward_points][
                 half_lateral_points
             ][k].destination(
-                distp * half_lateral_points, bearing + 90, height=pt[half_forward_points][
-                half_lateral_points
-            ][k].height
+                distp * half_lateral_points,
+                bearing + 90,
+                height=pt[half_forward_points][half_lateral_points][k].height,
             )
             pt[half_forward_points][0][k] = pt[half_forward_points][
                 half_lateral_points
             ][k].destination(
-                distp * half_lateral_points, bearing - 90, height=pt[half_forward_points][
-                half_lateral_points
-            ][k].height
+                distp * half_lateral_points,
+                bearing - 90,
+                height=pt[half_forward_points][half_lateral_points][k].height,
             )
 
-
-
         for j in range(1, half_lateral_points + 1):
             for k in range(len(possible_altitudes)):
                 # +j (left)
@@ -1024,7 +1031,9 @@ def set_network(
                     ][half_lateral_points + j][k].destination(
                         total_distance / (half_forward_points - i + 1),
                         bearing,
-                        height=pt[half_forward_points + i][half_lateral_points][k].height,
+                        height=pt[half_forward_points + i][half_lateral_points][
+                            k
+                        ].height,
                     )
 
                     bearing = pt[half_forward_points + i - 1][half_lateral_points - j][
@@ -1042,7 +1051,9 @@ def set_network(
                     ][half_lateral_points - j][k].destination(
                         total_distance / (half_forward_points - i + 1),
                         bearing,
-                        height=pt[half_forward_points + i][half_lateral_points][k].height,
+                        height=pt[half_forward_points + i][half_lateral_points][
+                            k
+                        ].height,
                     )
                 for i in range(abs(half_forward_points - i_final), half_forward_points):
                     alt = pt[half_forward_points + i - 1][half_lateral_points][k].height

diff --git a/skdecide/hub/domain/up/__init__.py b/skdecide/hub/domain/up/__init__.py
@@ -2,4 +2,4 @@
 # This source code is licensed under the MIT license found in the
 # LICENSE file in the root directory of this source tree.
 
-from .up import UPDomain, SkUPState, SkUPAction
+from .up import SkUPAction, SkUPState, UPDomain
diff --git a/skdecide/hub/domain/up/up.py b/skdecide/hub/domain/up/up.py
@@ -3,30 +3,29 @@
 # LICENSE file in the root directory of this source tree.
 
 from typing import Dict, List, Optional, Tuple, Union
-import gym
 
+import gym
 import unified_planning as up
-from unified_planning.model.state import UPState
-
-from skdecide.core import ImplicitSpace, Space, Value
-from skdecide.domains import DeterministicPlanningDomain
-from skdecide.hub.space.gym import ListSpace, DictSpace
-from skdecide.utils import logger
-
-from unified_planning.model import Problem, UPState, InstantaneousAction, FNode
-from unified_planning.plans import ActionInstance
+from unified_planning.engines.compilers.grounder import GrounderHelper
+from unified_planning.engines.sequential_simulator import (
+    UPSequentialSimulator,
+    evaluate_quality_metric,
+)
+from unified_planning.exceptions import UPValueError
+from unified_planning.model import FNode, InstantaneousAction, Problem, UPState
 from unified_planning.model.metrics import (
     MaximizeExpressionOnFinalState,
     Oversubscription,
     TemporalOversubscription,
 )
+from unified_planning.model.state import UPState
+from unified_planning.plans import ActionInstance
 from unified_planning.shortcuts import FluentExp
-from unified_planning.engines.sequential_simulator import (
-    UPSequentialSimulator,
-    evaluate_quality_metric,
-)
-from unified_planning.engines.compilers.grounder import GrounderHelper
-from unified_planning.exceptions import UPValueError
+
+from skdecide.core import ImplicitSpace, Space, Value
+from skdecide.domains import DeterministicPlanningDomain
+from skdecide.hub.space.gym import DictSpace, ListSpace
+from skdecide.utils import logger
 
 
 class SkUPState:

diff --git a/skdecide/hub/solver/up/up.py b/skdecide/hub/solver/up/up.py
@@ -4,15 +4,15 @@
 
 from __future__ import annotations
 
+from typing import Any, Callable, Dict, List
+
 from unified_planning.engines import Engine
 from unified_planning.exceptions import UPValueError
 from unified_planning.shortcuts import FluentExp, SequentialSimulator
 
-from skdecide.hub.domain.up import UPDomain, SkUPState, SkUPAction
-from typing import Any, Callable, Dict, List
-
 from skdecide import Solver, Value
 from skdecide.builders.solver import DeterministicPolicies, Utilities
+from skdecide.hub.domain.up import SkUPAction, SkUPState, UPDomain
 
 
 # TODO: remove Markovian req?

diff --git a/tests/domains/python/test_up_bridge_domain.py b/tests/domains/python/test_up_bridge_domain.py
@@ -2,23 +2,23 @@
 # This source code is licensed under the MIT license found in the
 # LICENSE file in the root directory of this source tree.
 
-import pytest
 import sys
 
 import gym
+import pytest
 
 
 @pytest.mark.skipif(sys.version_info < (3, 10), reason="requires python3.10 or higher")
 def test_up_bridge_domain():
     noexcept = True
 
     try:
-        from skdecide.hub.domain.up import UPDomain
-        from skdecide.hub.solver.lazy_astar import LazyAstar
-
         import unified_planning
         from unified_planning.shortcuts import Fluent, InstantaneousAction, Not
 
+        from skdecide.hub.domain.up import UPDomain
+        from skdecide.hub.solver.lazy_astar import LazyAstar
+
         x = Fluent("x")
         y = Fluent("y")