Specify environment variables as sequences to ensure compatibility with huggingface

Author: georg-wolflein

CONTRIBUTING.md

@@ -141,7 +141,8 @@ At this point, you should at least define the following parts (the `task.yaml` f
      commit: abc123
      branch: main
      env:  # (optional)
-       MY_TOKEN: "${env:MY_TOKEN}"
+       - name: MY_TOKEN
+         value: "${env:MY_TOKEN}"
    ```
 4. **`arguments`**: inputs your tool expects.
 5. **`returns`**: outputs your tool produces.
@@ -155,7 +156,8 @@ For example, to set the environment variable `MY_ENV_VAR` to the value `"abc"`,
 ```yaml
 repo:
   env:
-    MY_ENV_VAR: "abc"
+    - name: MY_ENV_VAR
+      value: "abc"
 ``` 
 The main use case for environment variables is to supply **secret tokens** such as API keys. For this, you may use a special syntax (`"${env:MY_TOKEN}"`) to insert environment variables from your *local environment*, defined in the top-level `.env` file.
 
@@ -172,7 +174,8 @@ Then you can tell ToolArena that the local `HF_TOKEN` environment variable defin
 > ```yaml
 > repo:
 >   env:
->     HF_TOKEN: "${env:HF_TOKEN}"
+>     - name: HF_TOKEN
+>       value: "${env:HF_TOKEN}"
 > ``` 
 
 

tasks/cobra_extract_features/task.yaml

@@ -6,10 +6,8 @@ repo:
   commit: null # Commit hash of the repository (optional, default is the latest commit). It is recommended to use a specific commit to ensure reproducibility.
   # branch: main # Branch of the repository (optional)
   env:
-    # Here, you can specify environment variables that should be available for installing the repository or running the task.
-    # The format is key: value, where value is a string that can include variables from the local environment.
-    # You may also leave this empty if the repository does not require any tokens/secrets.
-    HF_TOKEN: "${env:HF_TOKEN}"  # Example environment variable that sets HF_TOKEN to the local environment variable HF_TOKEN.
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 papers: [lenz2025cobra] # List of papers that this task is based on. Papers are specified by their IDs in the papers.bib file.
 category: pathology # Category of the task.
 description: Perform feature extraction on an input image using COBRA. The provided tile features have 1.0 mpp (224 microns / 224 px per patch).  # Description of the task. This should be 1-3 sentences in length, explaining to the LLM what this tool should do.

tasks/cobra_heatmaps/task.yaml

@@ -6,10 +6,8 @@ repo:
   commit: null # Commit hash of the repository (optional, default is the latest commit). It is recommended to use a specific commit to ensure reproducibility.
   # branch: main # Branch of the repository (optional)
   env:
-    # Here, you can specify environment variables that should be available for installing the repository or running the task.
-    # The format is key: value, where value is a string that can include variables from the local environment.
-    # You may also leave this empty if the repository does not require any tokens/secrets.
-    HF_TOKEN: "${env:HF_TOKEN}"  # Example environment variable that sets HF_TOKEN to the local environment variable HF_TOKEN.
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 papers: [lenz2025cobra] # List of papers that this task is based on. Papers are specified by their IDs in the papers.bib file.
 category: pathology # Category of the task.
 description: Create unsupervised heatmaps using COBRA. The provided tile features have 1.0 mpp (224 microns / 224 px per patch).  # Description of the task. This should be 1-3 sentences in length, explaining to the LLM what this tool should do.

tasks/conch_extract_features/task.yaml

@@ -4,7 +4,8 @@ repo:
   url: "https://github.com/mahmoodlab/CONCH"
   commit: 171f2be
   env:
-    HF_TOKEN: "${env:HF_TOKEN}"  # required for downloading models
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 papers: [lu2024conch]
 category: pathology
 requires: cuda

tasks/eagle_extract_features/task.yaml

@@ -3,7 +3,7 @@ repo:
   name: EAGLE # Name of the repository.
   url: "https://github.com/KatherLab/EAGLE" # URL of the repository.
   branch: simple_feature_extraction # Branch of the repository (optional)
-  env: {}
+  env: []
 papers: [neidlinger2025eagle] # List of papers that this task is based on. Papers are specified by their IDs in the papers.bib file.
 category: pathology # Category of the task.
 requires: cuda # If your task requires a GPU, change this to "cuda".

tasks/medsss_generate/task.yaml

@@ -4,7 +4,8 @@ repo:
   url: "https://github.com/pixas/MedSSS"
   commit: ebbfd02
   env:
-    HF_TOKEN: "${env:HF_TOKEN}"  # required for downloading models
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 requires: cuda
 papers: [jiang2025medsss]
 category: llms

tasks/mopadi_generate_counterfactuals/task.yaml

@@ -4,7 +4,8 @@ repo:
   url: "https://github.com/KatherLab/mopadi"
   commit: 4e76820
   env:
-    HF_TOKEN: "${env:HF_TOKEN}"
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 papers: [zigutyte2024mopadi]
 category: pathology
 requires: cuda

tasks/musk_extract_features/task.yaml

@@ -4,7 +4,8 @@ repo:
   url: "https://github.com/lilab-stanford/MUSK"
   commit: e1699c2
   env:
-    HF_TOKEN: "${env:HF_TOKEN}"  # required for downloading models
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 papers: [xiang2025musk]
 category: pathology
 requires: cuda

tasks/retfound_feature_vector/task.yaml

@@ -4,7 +4,8 @@ repo:
   url: "https://github.com/rmaphoh/RETFound_MAE"
   commit: 897d71c
   env:
-    HF_TOKEN: "${env:HF_TOKEN}"  # required for downloading models
+    - name: HF_TOKEN
+      value: "${env:HF_TOKEN}"
 papers: [zhou2023retfound]
 category: misc  # imaging
 requires: cuda

tasks/textgrad_medical_qa_optimize/task.yaml

@@ -4,7 +4,8 @@ repo:
   url: "https://github.com/zou-group/textgrad"
   commit: bf5b0c5
   env:
-    OPENAI_API_KEY: "${env:OPENAI_API_KEY}"
+    - name: OPENAI_API_KEY
+      value: "${env:OPENAI_API_KEY}"
 papers: [yuksekgonul2024textgrad]
 category: llms
 description: >