to be deleted

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ['3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v3
@@ -20,15 +20,15 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[dev]
+          pip install .[all]
       - name: Black Formatting
         run: |
           black .
 
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --ignore=E203,E266,E501,W503,F403,F401 --show-source --statistics
+          flake8 . --count --select=E9,F63,F7,F82 --ignore=E203,E266,E501,W503,F403,F401,F821 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=18 --max-line-length=89 --statistics
 

.github/workflows/python-package-conda.yml

@@ -13,14 +13,15 @@ jobs:
     - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.10
+        python-version: '3.10'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda env update --file environment.yml --name base
+        python -m pip install --upgrade pip
+        pip install .[all]
     - name: Lint with flake8
       run: |
         conda install flake8
@@ -30,5 +31,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        conda install pytest
         pytest

.gitignore

@@ -182,6 +182,5 @@ wandb/
 
 scripts.py
 
-*.ipynb
 models/
-*.DS_Store
+*.DS_Store

README.md

@@ -21,9 +21,7 @@
 
 ## Installing the package
 
-The codebase requires python >= 3.10
-
-To install the latest stable version:
+The codebase requires python >= 3.10. To install the latest stable version:
 
 ```bash
 pip install torchgfn

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api"
 [tool.poetry]
 name = "torchgfn"
 packages = [{include = "gfn", from = "src"}]
-version = "1.1"
+version = "1.1.1"
 description = "A torch implementation of GFlowNets"
 authors = ["Salem Lahou <[email protected]>", "Joseph Viviano <[email protected]>", "Victor Schmidt <[email protected]>"]
 license = "MIT"
@@ -26,16 +26,17 @@ torch = ">=1.9.0"
 torchtyping = ">=0.1.4"
 
 # dev dependencies.
-black = { version = "22.3.0", optional = true }
+black = { version = "*", optional = true }
+flake8 = { version = "*", optional = true }
 gitmopy = { version = "*", optional = true }
 myst-parser = { version = "*", optional = true }
 pre-commit = { version = "*", optional = true }
 pytest = { version = "*", optional = true }
 renku-sphinx-theme = { version = "*", optional = true }
 sphinx = { version = "*", optional = true }
+sphinx_rtd_theme = { version = "*", optional = true }
 sphinx-autoapi = { version = "*", optional = true }
 sphinx-math-dollar = { version = "*", optional = true }
-sphinx_rtd_theme = { version = "*", optional = true }
 tox = { version = "*", optional = true }
 
 # scripts dependencies.
@@ -52,30 +53,32 @@ dev = [
     "pre-commit",
     "pytest",
     "renku-sphinx-theme",
-    "sphinx",
+    "sphinx_rtd_theme",
     "sphinx-autoapi",
     "sphinx-math-dollar",
-    "sphinx_rtd_theme",
-    "tox"
+    "sphinx",
+    "tox",
+    "flake8",
 ]
 
 scripts = ["tqdm", "wandb", "scikit-learn", "scipy"]
 
 all = [
+    "black",
+    "flake8",
+    "myst-parser",
     "pre-commit",
     "pytest",
     "renku-sphinx-theme",
+    "scikit-learn",
+    "scipy",
     "sphinx_rtd_theme",
     "sphinx-autoapi",
     "sphinx-math-dollar",
     "sphinx",
     "tox",
-    "black",
-    "myst-parser",
     "tqdm",
     "wandb",
-    "scikit-learn",
-    "scipy"
 ]
 
 [project.urls]

src/gfn/env.py

@@ -23,16 +23,21 @@ def __init__(
         sf: Optional[TT["state_shape", torch.float]] = None,
         device_str: Optional[str] = None,
         preprocessor: Optional[Preprocessor] = None,
+        log_reward_clip: Optional[float] = -100.0,
     ):
         """Initializes an environment.
 
         Args:
-            s0: Representation of the initial state. All individual states would be of the same shape.
-            sf (optional): Representation of the final state. Only used for a human readable representation of
-                the states or trajectories.
-            device_str (Optional[str], optional): 'cpu' or 'cuda'. Defaults to None, in which case the device is inferred from s0.
-            preprocessor (Optional[Preprocessor], optional): a Preprocessor object that converts raw states to a tensor that can be fed
-                into a neural network. Defaults to None, in which case the IdentityPreprocessor is used.
+            s0: Representation of the initial state. All individual states would be of
+                the same shape.
+            sf: Representation of the final state. Only used for a human
+                readable representation of the states or trajectories.
+            device_str: 'cpu' or 'cuda'. Defaults to None, in which case the device is
+                inferred from s0.
+            preprocessor: a Preprocessor object that converts raw states to a tensor
+                that can be fed into a neural network. Defaults to None, in which case
+                the IdentityPreprocessor is used.
+            log_reward_clip: Used to clip small rewards (in particular, log(0) rewards).
         """
         self.device = torch.device(device_str) if device_str is not None else s0.device
 
@@ -53,6 +58,7 @@ def __init__(
 
         self.preprocessor = preprocessor
         self.is_discrete = False
+        self.log_reward_clip = log_reward_clip
 
     @abstractmethod
     def make_States_class(self) -> type[States]:
@@ -184,12 +190,12 @@ def backward_step(
         return new_states
 
     def reward(self, final_states: States) -> TT["batch_shape", torch.float]:
-        """Either this or log_reward needs to be implemented."""
-        return torch.exp(self.log_reward(final_states))
+        """This (and potentially log_reward) needs to be implemented."""
+        raise NotImplementedError("reward function not implemented")
 
     def log_reward(self, final_states: States) -> TT["batch_shape", torch.float]:
-        """Either this or reward needs to be implemented."""
-        raise NotImplementedError("log_reward function not implemented")
+        """Calculates the log reward (clipping small rewards)."""
+        return torch.log(self.reward(final_states)).clip(self.log_reward_clip)
 
     @property
     def log_partition(self) -> float:
@@ -203,8 +209,9 @@ class DiscreteEnv(Env, ABC):
     """
     Base class for discrete environments, where actions are represented by a number in
     {0, ..., n_actions - 1}, the last one being the exit action.
-    `DiscreteEnv` allow specifying the validity of actions (forward and backward), via mask tensors, that
-    are directly attached to `States` objects.
+
+    `DiscreteEnv` allows for  specifying the validity of actions (forward and backward),
+    via mask tensors, that are directly attached to `States` objects.
     """
 
     def __init__(
@@ -214,16 +221,22 @@ def __init__(
         sf: Optional[TT["state_shape", torch.float]] = None,
         device_str: Optional[str] = None,
         preprocessor: Optional[Preprocessor] = None,
+        log_reward_clip: Optional[float] = -100.0,
     ):
         """Initializes a discrete environment.
 
         Args:
             n_actions: The number of actions in the environment.
-
+            s0: The initial state tensor (shared among all trajectories).
+            sf: The final state tensor (shared among all trajectories).
+            device_str: String representation of a torch.device.
+            preprocessor: An optional preprocessor for intermediate states.
+            log_reward_clip: Used to clip small rewards (in particular, log(0) rewards).
         """
         self.n_actions = n_actions
-        super().__init__(s0, sf, device_str, preprocessor)
+        super().__init__(s0, sf, device_str, preprocessor, log_reward_clip)
         self.is_discrete = True
+        self.log_reward_clip = log_reward_clip
 
     def make_Actions_class(self) -> type[Actions]:
         env = self

src/gfn/gym/box.py

@@ -20,6 +20,7 @@ def __init__(
         R2: float = 2.0,
         epsilon: float = 1e-4,
         device_str: Literal["cpu", "cuda"] = "cpu",
+        log_reward_clip: float = -100.0,
     ):
         assert 0 < delta <= 1, "delta must be in (0, 1]"
         self.delta = delta
@@ -30,7 +31,7 @@ def __init__(
         self.R1 = R1
         self.R2 = R2
 
-        super().__init__(s0=s0)
+        super().__init__(s0=s0, log_reward_clip=log_reward_clip)
 
     def make_States_class(self) -> type[States]:
         env = self
@@ -116,14 +117,15 @@ def is_action_valid(
 
         return True
 
-    def log_reward(self, final_states: States) -> TT["batch_shape", torch.float]:
+    def reward(self, final_states: States) -> TT["batch_shape", torch.float]:
+        """Reward is distance from the goal point."""
         R0, R1, R2 = (self.R0, self.R1, self.R2)
         ax = abs(final_states.tensor - 0.5)
         reward = (
             R0 + (0.25 < ax).prod(-1) * R1 + ((0.3 < ax) * (ax < 0.4)).prod(-1) * R2
         )
 
-        return reward.log()
+        return reward
 
     @property
     def log_partition(self) -> float:

src/gfn/gym/discrete_ebm.py

@@ -1,5 +1,5 @@
 from abc import ABC, abstractmethod
-from typing import ClassVar, Literal, Tuple, cast
+from typing import ClassVar, Literal, Tuple
 
 import torch
 import torch.nn as nn
@@ -48,14 +48,19 @@ def __init__(
         alpha: float = 1.0,
         device_str: Literal["cpu", "cuda"] = "cpu",
         preprocessor_name: Literal["Identity", "Enum"] = "Identity",
+        log_reward_clip: float = -100.0,
     ):
         """Discrete EBM environment.
 
         Args:
-            ndim (int, optional): dimension D of the sampling space {0, 1}^D.
-            energy (EnergyFunction): energy function of the EBM. Defaults to None. If None, the Ising model with Identity matrix is used.
-            alpha (float, optional): interaction strength the EBM. Defaults to 1.0.
-            device_str (str, optional): "cpu" or "cuda". Defaults to "cpu".
+            ndim: dimension D of the sampling space {0, 1}^D.
+            energy: energy function of the EBM. Defaults to None. If
+                None, the Ising model with Identity matrix is used.
+            alpha: interaction strength the EBM. Defaults to 1.0.
+            device_str: "cpu" or "cuda". Defaults to "cpu".
+            preprocessor_name: "KHot" or "OneHot" or "Identity".
+                Defaults to "KHot".
+            log_reward_clip: Minimum log reward allowable (namely, for log(0)).
         """
         self.ndim = ndim
 
@@ -89,6 +94,7 @@ def __init__(
             sf=sf,
             device_str=device_str,
             preprocessor=preprocessor,
+            log_reward_clip=log_reward_clip,
         )
 
     def make_States_class(self) -> type[DiscreteStates]:
@@ -133,16 +139,7 @@ def make_masks(
                 return forward_masks, backward_masks
 
             def update_masks(self) -> None:
-                # The following two lines are for typing only.
-                self.forward_masks = cast(
-                    TT["batch_shape", "n_actions", torch.bool],
-                    self.forward_masks,
-                )
-                self.backward_masks = cast(
-                    TT["batch_shape", "n_actions - 1", torch.bool],
-                    self.backward_masks,
-                )
-
+                self.set_default_typing()
                 self.forward_masks[..., : env.ndim] = self.tensor == -1
                 self.forward_masks[..., env.ndim : 2 * env.ndim] = self.tensor == -1
                 self.forward_masks[..., -1] = torch.all(self.tensor != -1, dim=-1)
@@ -183,16 +180,22 @@ def maskless_backward_step(
         # action i in [ndim, 2*ndim-1] corresponds to replacing s[i - ndim] with 1.
         # A backward action asks "what index should be set back to -1", hence the fmod
         # to enable wrapping of indices.
-        return states.tensor.scatter(
-            -1,
-            actions.tensor.fmod(self.ndim),
-            -1,
-        )
+        return states.tensor.scatter(-1, actions.tensor.fmod(self.ndim), -1)
+
+    def reward(self, final_states: DiscreteStates) -> TT["batch_shape"]:
+        """Not used during training but provided for completeness.
+
+        Note the effect of clipping will be seen in these values.
+        """
+        return torch.exp(self.log_reward(final_states))
 
     def log_reward(self, final_states: DiscreteStates) -> TT["batch_shape"]:
+        """The energy weighted by alpha is our log reward."""
         raw_states = final_states.tensor
         canonical = 2 * raw_states - 1
-        return -self.alpha * self.energy(canonical)
+        log_reward = -self.alpha * self.energy(canonical)
+
+        return log_reward.clip(self.log_reward_clip)
 
     def get_states_indices(self, states: DiscreteStates) -> TT["batch_shape"]:
         """The chosen encoding is the following: -1 -> 0, 0 -> 1, 1 -> 2, then we convert to base 3"""