gotap integration, data/parameters cleanup

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: mmaelicke

.github/workflows/docker-image.yml

@@ -47,7 +47,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v4
         with:
-          images: ghcr.io/vforwater/tbr_template_python
+          images: ghcr.io/tool-spec/tbr_template_python
 
       - name: Build and push
         uses: docker/build-push-action@v3

.gitignore

@@ -120,6 +120,10 @@ venv.bak/
 # mkdocs documentation
 /site
 
+# gotap-generated bindings (built during Docker build)
+src/parameters.py
+out/
+
 # mypy
 .mypy_cache/
 .dmypy.json

CITATION.cff

@@ -34,5 +34,5 @@ keywords:
   - docker
   - tool-spec
 license: CC-BY-4.0
-version: '0.6.1'
+version: '0.7.0'
 date-released: '2026-02-13'

Dockerfile

@@ -1,20 +1,14 @@
+# Build gotap from source, then discard Go
+FROM golang:1.25-alpine AS gotap-builder
+RUN apk add --no-cache git
+ARG GOTAP_VERSION=main
+RUN git clone --depth 1 --branch ${GOTAP_VERSION} https://github.com/tool-spec/gotap.git /gotap && \
+    cd /gotap && go build -o gotap .
+
 # Pull any base image that includes python3
 FROM python:3.12
-
-# install the toolbox runner tools
-RUN pip install "json2args[data]>=0.6.2"
-
-# if you do not need data-preloading as your tool does that on its own
-# you can use this instread of the line above to use a json2args version
-# with less dependencies
-# RUN pip install json2args>=0.6.2
-
-# Build spec binary from source
-RUN apt-get update && apt-get install -y golang-go git && \
-    git clone https://github.com/hydrocode-de/gotap.git /tmp/gotap && \
-    cd /tmp/gotap && go build -o /usr/local/bin/spec ./main.go && \
-    rm -rf /tmp/gotap && \
-    apt-get remove -y golang-go git && apt-get autoremove -y && apt-get clean
+COPY --from=gotap-builder /gotap/gotap /usr/local/bin/gotap
+RUN chmod +x /usr/local/bin/gotap
 
 # Do anything you need to install tool dependencies here
 RUN echo "Replace this line with a tool"
@@ -26,8 +20,12 @@ RUN mkdir /out
 RUN mkdir /src
 COPY ./src /src
 
+# Generate parameter bindings from tool.yml at build time (replaces json2args)
+WORKDIR /src
+RUN gotap generate --spec-file=tool.yml --target=python --output=parameters.py
+
 # copy the citation file - looks funny to make COPY not fail if the file is not there
 COPY ./CITATION.cf[f] /src/CITATION.cff
 
 WORKDIR /src
-CMD ["spec", "run", "foobar", "--input-file", "/in/input.json"]
+CMD ["gotap", "run", "foobar", "--input-file", "/in/input.json"]

docker-compose.yml

@@ -4,9 +4,7 @@ services:
       context: .
       dockerfile: Dockerfile
     volumes:
-      - ./src:/src
       - ./in:/in
       - ./out:/out
     environment:
-      - TOOL_RUN=foobar
-    command: python run.py
+      - TOOL_RUN=foobar

in/input.json

@@ -1,15 +1,15 @@
 {
-    "foobar": {
-        "parameters": {
-            "foo_int": 42,
-            "foo_float": 13.37,
-            "foo_string": "Never eat yellow snow",
-            "foo_enum": "bar",
-            "foo_array": [34, 55, 23, 43, 23]
-        },
-        "data": {
-            "foo_matrix": "/in/foo_matrix.dat",
-            "foo_csv": "/in/foo_csv.csv"
-        }
+  "foobar": {
+    "parameters": {
+      "foo_int": 42,
+      "foo_float": 13.37,
+      "foo_string": "Never eat yellow snow",
+      "foo_enum": "bar",
+      "foo_array": [34, 55, 23, 43, 23]
+    },
+    "data": {
+      "foo_matrix": "/in/foo_matrix.dat",
+      "foo_csv": "/in/foo_csv.csv"
     }
+  }
 }

src/run.py

@@ -1,13 +1,15 @@
+import logging
 import os
 from datetime import datetime as dt
 
-from json2args import get_parameter
-from json2args.data import get_data
-from json2args.logger import logger
+from parameters import get_parameters, get_data
 
-# parse parameters
-kwargs = get_parameter()
-data = get_data(as_dict=True)
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+# parse parameters (generated by gotap at container build time)
+params = get_parameters()
+data = get_data()
 
 # check if a toolname was set in env
 toolname = os.environ.get('TOOL_RUN', 'foobar').lower()
@@ -16,14 +18,11 @@
 if toolname == 'foobar':
     # RUN the tool here and create the output in /out
     logger.info('This toolbox does not include any tool. Did you run the template?\n')
-    
-    # write parameters to STDOUT.log
-    logger.info(kwargs)
-
-    for name, ds in data.items():
-        logger.info(f"\n### {name}")
-        logger.info(ds)
-    
+
+    logger.info(vars(params))
+
+    for name, path in data.items():
+        logger.info(f"\n### {name}: %s", path)
 
 # In any other case, it was not clear which tool to run
 else: