Update components (#938)

* use python package to render readme

* bump viash version

* update dependencies

Author: rcannood

_viash.yaml

@@ -1,7 +1,7 @@
 name: openproblems
 version: dev
 organization: openproblems-bio
-viash_version: 0.9.4
+viash_version: 0.9.7
 
 description: |
   Open Problems is a living, extensible, community-guided benchmarking platform.

src/project/render_readme/config.vsh.yaml

@@ -19,24 +19,17 @@ argument_groups:
         default: README.md
         required: false
 resources:
-  - type: r_script
-    path: script.R
+  - type: python_script
+    path: script.py
 test_resources:
-  - type: r_script
-    path: test.R
+  - type: python_script
+    path: test.py
 engines:
   - type: docker
-    image: openproblems/base_r:1
+    image: openproblems/base_python:1
     setup:
-      - type: r
-        cran:
-          - processx
-        github:
-          - openproblems-bio/core/packages/r/openproblems.utils
-          - openproblems-bio/core/packages/r/openproblems
-          - openproblems-bio/core/packages/r/openproblems.docs
       - type: apt
-        packages: [jq, curl]
+        packages: [jq, curl, git]
       - type: docker
         # download and install quarto-*-linux-amd64.deb from latest release
         run: |

src/project/render_readme/script.R

@@ -0,0 +1,47 @@
+from pathlib import Path
+import subprocess
+
+from openproblems.project import read_task_metadata, render_task_readme_qmd
+
+## VIASH START
+par = {
+    "input": "path/to/input",
+    "output": "path/to/input/README.md",
+}
+## VIASH END
+
+print("Read task metadata", flush=True)
+metadata = read_task_metadata(par["input"])
+
+print("Render README.qmd content", flush=True)
+qmd_content = render_task_readme_qmd(metadata)
+
+output_path = Path(par["output"])
+output_path.parent.mkdir(parents=True, exist_ok=True)
+qmd_path = output_path.with_suffix(".qmd")
+
+print("Write README.qmd to file", flush=True)
+qmd_path.write_text(qmd_content)
+
+print("Render README.qmd to README.md", flush=True)
+out = subprocess.run(
+    ["quarto", "render", str(qmd_path), "--output", "-"],
+    capture_output=True,
+    text=True,
+)
+
+if out.returncode != 0:
+    stdout = (out.stdout or "").strip()
+    stderr = (out.stderr or "").strip()
+    details = []
+    if stdout:
+        details.append(f"stdout:\n{stdout}")
+    if stderr:
+        details.append(f"stderr:\n{stderr}")
+    if not details:
+        details.append("No output captured from Quarto")
+    raise RuntimeError(
+        "Failed to render README.qmd with Quarto.\n\n" + "\n\n".join(details)
+    )
+
+output_path.write_text(out.stdout)

src/project/render_readme/script.py

@@ -0,0 +1,74 @@
+import subprocess
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+## VIASH START
+meta = {
+    "executable": "foo",
+}
+## VIASH END
+
+task_template_repo = "https://github.com/openproblems-bio/task_template.git"
+
+with TemporaryDirectory() as tmpdir:
+    tmpdir_path = Path(tmpdir)
+    task_template_path = tmpdir_path / "task_template"
+    input_path = task_template_path / "src" / "api"
+    output_path = Path(tmpdir) / "README.md"
+    qmd_path = Path(tmpdir) / "README.qmd"
+
+    clone_cmd = [
+        "git",
+        "clone",
+        "--depth",
+        "1",
+        task_template_repo,
+        str(task_template_path),
+    ]
+
+    print(">> Cloning task_template", flush=True)
+    clone_out = subprocess.run(clone_cmd, capture_output=True, text=True)
+
+    if clone_out.stdout:
+        print(clone_out.stdout)
+    if clone_out.stderr:
+        print(clone_out.stderr)
+
+    if clone_out.returncode:
+        print(f"script: '{' '.join(clone_cmd)}' exited with an error.")
+        exit(clone_out.returncode)
+
+    cmd = [
+        meta["executable"],
+        "--input",
+        str(input_path),
+        "--output",
+        str(output_path),
+    ]
+
+    print(">> Running the script as test", flush=True)
+    out = subprocess.run(cmd, capture_output=True, text=True)
+
+    if out.stdout:
+        print(out.stdout)
+    if out.stderr:
+        print(out.stderr)
+
+    if out.returncode:
+        print(f"script: '{' '.join(cmd)}' exited with an error.")
+        exit(out.returncode)
+
+    print(">> Checking whether output files exist", flush=True)
+    assert output_path.exists(), "README.md was not generated"
+    assert qmd_path.exists(), "README.qmd was not generated"
+
+    print(">> Checking file contents", flush=True)
+    output_lines = output_path.read_text().splitlines()
+    qmd_lines = qmd_path.read_text().splitlines()
+
+    assert any("## Description" in line for line in output_lines), "README.md is missing description section"
+    assert any("flowchart TB" in line for line in output_lines), "README.md is missing task graph"
+    assert any("## File format:" in line for line in output_lines), "README.md is missing file format section"
+    assert any("format: gfm" in line for line in qmd_lines), "README.qmd header is missing gfm format"
+
+print("All checks succeeded!", flush=True)

src/project/render_readme/test.R

@@ -44,8 +44,10 @@ test_resources:
 
 engines:
   - type: docker
-    image: openproblems/base_r:1.0.0
+    image: openproblems/base_r:1
     setup:
+      - type: apt
+        packages: [wget]
       - type: docker
         run: |
           export QUARTO_VERSION="1.7.32" && \