Merge pull request #169 from hpsim/refact/signac_version

bump signac versions, see #169

CHANGELOG.rst

@@ -9,8 +9,10 @@ Changelog
 - Fix missing of groups in `obr run --list-operations` view, see https://github.com/hpsim/OBR/pull/159. 
 - Make view folders relative see https://github.com/hpsim/OBR/pull/164
 - Use cached version of git repo instead of cloning, see https://github.com/hpsim/OBR/pull/166
+- Bump signac version, see https://github.com/hpsim/OBR/pull/169
 - Validate simulation state after runSerial|ParallelSolver, see https://github.com/hpsim/OBR/pull/168
 
+
 0.2.0 (2023-09-14)
 ------------------
 - Add --json=file.json option to obr query, which writes the result of the query to a json file.

pyproject.toml

@@ -17,8 +17,8 @@ requires-python = ">=3.6"
 dependencies = [
     "click",
     "PyYAML",
-    "signac==1.8.0",
-    "signac-flow==0.23.0",
+    "signac==2.1.0",
+    "signac-flow==0.26.1",
     "GitPython==3.1.31",
     "pandas",
     "DeepDiff",

src/obr/OpenFOAM/case.py

@@ -6,7 +6,7 @@
 from typing import Union, Generator, Tuple, Any
 from pathlib import Path
 from subprocess import check_output
-from signac.contrib.job import Job
+from signac.job import Job
 from datetime import datetime
 from Owls.parser.FoamDict import FileParser
 from Owls.parser.LogFile import LogFile

src/obr/cli.py

@@ -23,12 +23,7 @@
 import json
 import logging
 
-from signac.contrib.job import Job
-from .signac_wrapper.operations import OpenFOAMProject, get_values
-from .create_tree import create_tree
-from .core.parse_yaml import read_yaml
-from .core.queries import input_to_queries, query_impl, build_filter_query, Query
-from .core.core import map_view_folder_to_job_id
+from signac.job import Job
 from pathlib import Path
 from subprocess import check_output
 from git.repo import Repo
@@ -38,6 +33,12 @@
 from typing import Union, Optional, Any
 from copy import deepcopy
 
+from .signac_wrapper.operations import OpenFOAMProject, get_values
+from .create_tree import create_tree
+from .core.parse_yaml import read_yaml
+from .core.queries import input_to_queries, query_impl, build_filter_query, Query
+from .core.core import map_view_folder_to_job_id
+
 
 def check_cli_operations(
     project: OpenFOAMProject, operations: list[str], list_operations: Optional[Any]
@@ -341,7 +342,7 @@ def init(ctx: click.Context, **kwargs):
     if kwargs.get("verbose", 0) >= 1:
         logging.info(config)
 
-    project = OpenFOAMProject.init_project(root=kwargs["folder"])
+    project = OpenFOAMProject.init_project(path=kwargs["folder"])
     create_tree(project, config, kwargs)
 
     logging.info("successfully initialised")

src/obr/core.py

@@ -0,0 +1 @@
+#!/usr/bin/env python3

src/obr/core/core.py

@@ -10,7 +10,7 @@
 from subprocess import check_output
 from typing import Union, Generator
 from datetime import datetime
-from signac.contrib.job import Job
+from signac.job import Job
 from copy import deepcopy
 
 # these are to be replaced with each other

src/obr/core/queries.py

@@ -1,10 +1,11 @@
-from dataclasses import dataclass, field
-from typing import Any, Union, Callable, Iterable
-from copy import deepcopy
 import re
 import logging
-from signac.contrib.job import Job
 import pandas as pd
+
+from dataclasses import dataclass, field
+from typing import Any, Union, Callable, Iterable
+from copy import deepcopy
+from signac.job import Job
 from typing import TYPE_CHECKING, Union
 from enum import Enum
 

src/obr/create_tree.py

@@ -21,7 +21,7 @@
 from collections.abc import MutableMapping
 from pathlib import Path
 from subprocess import check_output
-from signac.contrib.job import Job
+from signac.job import Job
 from obr.signac_wrapper.operations import OpenFOAMProject
 from copy import deepcopy
 

src/obr/signac_wrapper/operations.py

@@ -9,7 +9,7 @@
 from ..core.core import execute
 from .labels import owns_mesh, final, finished
 from obr.OpenFOAM.case import OpenFOAMCase
-from signac.contrib.job import Job
+from signac.job import Job
 from typing import Union, Literal
 from datetime import datetime
 import logging
@@ -111,7 +111,7 @@ def basic_eligible(job: Job, operation: str) -> bool:
 def parent_job_is_ready(job: Job) -> str:
     """Checks whether the parent of the given job is ready"""
     if job.sp().get("parent_id"):
-        project = OpenFOAMProject.get_project(root=job.path + "/../..")
+        project = OpenFOAMProject.get_project(path=job.path + "/../..")
         parent_job = project.open_job(id=job.sp().get("parent_id"))
         return parent_job.doc["state"].get("global", "")
     return ""

tests/test_create_tree.py

@@ -91,7 +91,7 @@ def open_job(self, statepoint):
 
 
 def test_create_tree(tmpdir, emit_test_config):
-    project = OpenFOAMProject.init_project(root=tmpdir)
+    project = OpenFOAMProject.init_project(path=tmpdir)
 
     create_tree(project, emit_test_config, {"folder": tmpdir}, skip_foam_src_check=True)
 
@@ -118,7 +118,7 @@ def test_create_tree(tmpdir, emit_test_config):
 
 
 def test_call_generate_tree(tmpdir, emit_test_config):
-    project = OpenFOAMProject.init_project(root=tmpdir)
+    project = OpenFOAMProject.init_project(path=tmpdir)
     workspace_dir = tmpdir / "workspace"
     view_dir = tmpdir / "view"
 
@@ -146,7 +146,7 @@ def test_call_generate_tree(tmpdir, emit_test_config):
 
 def test_cache_folder(tmpdir, emit_test_config):
     emit_test_config["case"]["cache_folder"] = f"{tmpdir}/tmp"
-    project = OpenFOAMProject.init_project(root=tmpdir)
+    project = OpenFOAMProject.init_project(path=tmpdir)
 
     create_tree(project, emit_test_config, {"folder": tmpdir}, skip_foam_src_check=True)
 
@@ -166,8 +166,8 @@ def test_cache_folder(tmpdir, emit_test_config):
     # after purgin and recreating the workspace, the cache folder should be used
     Path(f"{tmpdir}/tmp/test").touch()
     shutil.rmtree(workspace_dir)
-    os.remove(f"{tmpdir}/signac.rc")
-    project = OpenFOAMProject.init_project(root=tmpdir)
+    shutil.rmtree(tmpdir /".signac")
+    project = OpenFOAMProject.init_project(path=tmpdir)
     create_tree(project, emit_test_config, {"folder": tmpdir}, skip_foam_src_check=True)
     project.run(names=["fetchCase"])
 

tests/test_md5sum.py

@@ -35,7 +35,7 @@ def emit_test_config():
 
 
 def test_md5sum_calculation(tmpdir, emit_test_config):
-    project = OpenFOAMProject.init_project(root=tmpdir)
+    project = OpenFOAMProject.init_project(path=tmpdir)
 
     create_tree(project, emit_test_config, {"folder": tmpdir}, skip_foam_src_check=True)
 

tests/test_queries.py

@@ -134,7 +134,7 @@ def get_project(tmpdir):
     }
     os.chdir(tmpdir)
 
-    project = OpenFOAMProject.init_project(root=tmpdir)
+    project = OpenFOAMProject.init_project(path=tmpdir)
     create_tree(project, config, {"folder": tmpdir}, skip_foam_src_check=True)
     project.run(names=["fetchCase"])
     return project