From e2e1528607f20ea0ac3281d1508eeb3faca5d501 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Sat, 29 Jun 2024 17:58:57 +0200
Subject: [PATCH] Use v2 linter for v2 problems (#71)

So far only on libpetab-python/develop

Required for https://github.com/PEtab-dev/petab_test_suite/pull/14
---
 .ci_pip_reqs.txt               |  2 +-
 .github/workflows/ci_tests.yml |  1 +
 petabtests/file.py             | 20 +++++++++++++++-----
 3 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/.ci_pip_reqs.txt b/.ci_pip_reqs.txt
index 65e9674..99b0ecf 100644
--- a/.ci_pip_reqs.txt
+++ b/.ci_pip_reqs.txt
@@ -1,4 +1,4 @@
 pytest
 flake8
-https://github.com/petab-dev/libpetab-python/archive/develop.zip
+git+https://github.com/PEtab-dev/libpetab-python@develop
 sympy>=1.12.1
diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
index ddebb60..4b2480c 100644
--- a/.github/workflows/ci_tests.yml
+++ b/.github/workflows/ci_tests.yml
@@ -28,6 +28,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         pip install -e .
+        pip uninstall -y petab
         pip install -r .ci_pip_reqs.txt
     - name: Run tests
       run: |
diff --git a/petabtests/file.py b/petabtests/file.py
index b55effe..b58ffb8 100644
--- a/petabtests/file.py
+++ b/petabtests/file.py
@@ -8,7 +8,8 @@
 import petab
 import yaml
 from petab.C import *  # noqa: F403
-
+from petab.v1.lint import lint_problem as lint_problem_v1
+from petab.v2.lint import lint_problem as lint_problem_v2
 from .C import *  # noqa: F403
 
 __all__ = [
@@ -180,13 +181,22 @@ def write_problem(
 
     # write yaml
     yaml_file = problem_yaml_name(test_id)
-    with open(os.path.join(dir_, yaml_file), 'w') as outfile:
+    yaml_path = os.path.join(dir_, yaml_file)
+    with open(yaml_path, 'w') as outfile:
         yaml.dump(config, outfile, default_flow_style=False)
 
     # validate written PEtab files
-    problem = petab.Problem.from_yaml(os.path.join(dir_, yaml_file))
-    if petab.lint_problem(problem):
-        raise RuntimeError("Invalid PEtab problem, see messages above.")
+    if format_version == 1:
+        # PEtab v1
+        problem = petab.Problem.from_yaml(yaml_path)
+        if lint_problem_v1(problem):
+            raise RuntimeError("Invalid PEtab problem, see messages above.")
+    else:
+        # v2
+        validation_result = lint_problem_v2(yaml_path)
+        if validation_result:
+            print(validation_result)
+            raise RuntimeError("Invalid PEtab problem, see messages above.")
 
 
 def write_solution(