adding mujoco, bug-fixed gym + little reorganizing

pyproject.toml

@@ -1,16 +1,11 @@
-[tool.mypy]
-strict = true
-allow_redefinition = true
-ignore_missing_imports = true
-
 [tool.setuptools.packages.find]
 include = ["cneuromax"]
 
 [project]
 name = "cneuromax"
 requires-python = ">=3.10" # Did not test with lower versions
 authors = [{ name = "The SIMEXP Laboratory", email = "[email protected]" }]
-description = "The Courtois Neuromod Project's centralized Machine Learning repository"
+description = "The CNeuromod project's centralized Machine Learning repository"
 version = "0.0.1"
 # The following assumes that we build on top of the NGC PyTorch Docker image.
 dependencies = [
@@ -19,8 +14,19 @@ dependencies = [
     "hydra-zen==0.12.0", # Cleaner Hydra configs
     "beartype==0.16.4", # Dynamic type checking
     "wandb==0.16.2", # Logging
-    "submitit@git+https://github.com/courtois-neuromod/submitit@b289f81004ab063b185dc97982934c266e605fad", # Local & SLURM job launcher
-    "hydra-submitit-launcher@git+https://github.com/courtois-neuromod/hydra@9e227a095345b5ea3d914efa95b74b622e7d1fdf#subdirectory=plugins/hydra_submitit_launcher/", # Launcher config
+    """
+    submitit@git+https://github.com/courtois-neuromod/submitit@\
+    b289f81004ab063b185dc97982934c266e605fad""", # Local & SLURM job launcher
+    # CNeuroMod fork that launches the `tasks_per_node` with `mpi` rather
+    # than the original `submitit` method. Used for
+    # `cneuromax/fitting/neuroevolution/`.
+    """
+    hydra-submitit-launcher@git+https://github.com/courtois-neuromod/hydra@\
+    9e227a095345b5ea3d914efa95b74b622e7d1fdf\
+    #subdirectory=plugins/hydra_submitit_launcher/""", # Launcher config
+    # CNeuroMod fork that implements the missing connecting feature to
+    # `submitit`'s `python` option. Also modifies the `local` launcher
+    # so that it queues the jobs sequentially rather than in parallel.
     # OPTIONAL for cneuromax/
     "hydra-orion-sweeper==1.6.4", # Hyperparameter optimization
     "jaxtyping==0.2.25", # Torch tensor annotations
@@ -40,7 +46,12 @@ dependencies = [
     # MANDATORY for cneuromax/fitting/neuroevolution/
     "mpi4py==3.1.5", # Inter-process communication
     "torchrl==0.2.1", # For reinforcement/imitation Learning tasks
-    "gymnasium==0.29.1", # RL/IL environments
+    """
+    gymnasium@git+https://github.com/Farama-Foundation/Gymnasium@\
+    6baf8708bfb08e37ce3027b529193169eaa230fd""", # RL/IL environments
+    # Bug fixes for Gymnasium
+    # OPTIONAL for cneuromax/fitting/neuroevolution/
+    "mujoco==3.1.1", # MuJoCo physics engine
     # MANDATORY for docs/
     "sphinx==7.2.6", # Documentation generator
     "esbonio==0.16.4", # Language server to render sphinx
@@ -85,9 +96,9 @@ ignore = [
             # Disabled to make it less verbose to log since printing is
             # disabled, see: https://docs.astral.sh/ruff/rules/print/
     "NPY002", # `numpy-legacy-random`
-              # Replace legacy np.random.{method_name} call with np.random.Generator
-              # Disabled as we use `lightning.seed_everything` to set the randomness
-              # which still uses the legacy seeding method.
+              # Replace legacy np.random.{method_name} call with
+              # np.random.Generator
+              # Disabled for legacy purposes.
     "S301", # `suspicious-pickle-usage`
             # `pickle` and modules that wrap it can be unsafe when used to
             # deserialize untrusted data, possible security issue
@@ -104,6 +115,11 @@ ignore = [
               # Disabled as we use Beartype for dynamic type checking.
 ]
 
+[tool.mypy]
+strict = true
+allow_redefinition = true
+ignore_missing_imports = true
+
 [tool.ruff.pycodestyle]
 max-doc-length = 72