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‎dapi/__init__.py‎

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -80,6 +80,7 @@
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from pathlib import Path
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83+
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def _get_version():
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"""Read version from pyproject.toml, falling back for older Python."""
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try:
@@ -90,13 +91,8 @@ def _get_version():
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import tomli as tomllib # Use tomli and alias it as tomllib
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try:
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<<<<<<< Updated upstream
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pyproject_path = Path(__file__).parent / "pyproject.toml"
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with open(pyproject_path, "rb") as f: # tomllib expects bytes
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=======
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pyproject_path = Path(__file__).parent.parent / "pyproject.toml"
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with open(pyproject_path, "rb") as f: # tomllib expects bytes
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>>>>>>> Stashed changes
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data = tomllib.load(f)
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return data["tool"]["poetry"]["version"]
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except (FileNotFoundError, KeyError, ImportError, tomllib.TOMLDecodeError):

‎examples/mpm/mpm-minimal.ipynb‎

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@@ -26,116 +26,16 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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<<<<<<< Updated upstream
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"Obtaining file:///Users/krishna/dev/DesignSafe/dapi\n",
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" Installing build dependencies ... \u001b[?25ldone\n",
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"\u001b[?25h Checking if build backend supports build_editable ... \u001b[?25ldone\n",
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"\u001b[?25h Getting requirements to build editable ... \u001b[?25ldone\n",
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"\u001b[?25h Preparing editable metadata (pyproject.toml) ... \u001b[?25ldone\n",
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"\u001b[?25hRequirement already satisfied: exceptiongroup<2.0.0,>=1.3.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.3.0)\n",
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"Requirement already satisfied: griffe<2.0.0,>=1.7.3 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.7.3)\n",
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"Requirement already satisfied: jsonschema<5.0.0,>=4.24.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (4.24.0)\n",
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"Requirement already satisfied: mkdocs<2.0.0,>=1.6.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.6.1)\n",
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"Requirement already satisfied: mkdocs-autorefs<2.0.0,>=1.4.2 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.4.2)\n",
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"Requirement already satisfied: mkdocs-material<10.0.0,>=9.6.14 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (9.6.14)\n",
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"Requirement already satisfied: mkdocstrings<0.30.0,>=0.29.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (0.29.1)\n",
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"Requirement already satisfied: numpy<2.1.0,>=1.21.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (2.0.2)\n",
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"Requirement already satisfied: pandas<3.0.0,>=1.3.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (2.3.0)\n",
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"Requirement already satisfied: pymysql<2.0.0,>=1.1.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.1.1)\n",
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"Requirement already satisfied: python-dotenv<2.0.0,>=1.1.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.1.0)\n",
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"Requirement already satisfied: sqlalchemy<3.0.0,>=2.0.41 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (2.0.41)\n",
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"Requirement already satisfied: tapipy<2.0.0,>=1.8.4 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (1.8.4)\n",
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"Requirement already satisfied: tomli>=1.1.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (2.2.1)\n",
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"Requirement already satisfied: tqdm<5.0.0,>=4.67.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from dapi==0.4.2) (4.67.1)\n",
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"Requirement already satisfied: typing-extensions>=4.6.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from exceptiongroup<2.0.0,>=1.3.0->dapi==0.4.2) (4.14.0)\n",
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"Requirement already satisfied: colorama>=0.4 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from griffe<2.0.0,>=1.7.3->dapi==0.4.2) (0.4.6)\n",
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"Requirement already satisfied: attrs>=22.2.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from jsonschema<5.0.0,>=4.24.0->dapi==0.4.2) (25.3.0)\n",
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"Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from jsonschema<5.0.0,>=4.24.0->dapi==0.4.2) (2025.4.1)\n",
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"Requirement already satisfied: referencing>=0.28.4 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from jsonschema<5.0.0,>=4.24.0->dapi==0.4.2) (0.36.2)\n",
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"Requirement already satisfied: rpds-py>=0.7.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from jsonschema<5.0.0,>=4.24.0->dapi==0.4.2) (0.25.1)\n",
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"Requirement already satisfied: click>=7.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (8.1.8)\n",
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"Requirement already satisfied: ghp-import>=1.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (2.1.0)\n",
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"Requirement already satisfied: importlib-metadata>=4.4 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (8.7.0)\n",
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"Requirement already satisfied: jinja2>=2.11.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (3.1.6)\n",
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"Requirement already satisfied: markdown>=3.3.6 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (3.8)\n",
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"Requirement already satisfied: markupsafe>=2.0.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (3.0.2)\n",
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"Requirement already satisfied: mergedeep>=1.3.4 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (1.3.4)\n",
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"Requirement already satisfied: mkdocs-get-deps>=0.2.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (0.2.0)\n",
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"Requirement already satisfied: packaging>=20.5 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (25.0)\n",
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"Requirement already satisfied: pathspec>=0.11.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (0.12.1)\n",
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"Requirement already satisfied: pyyaml-env-tag>=0.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (1.1)\n",
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"Requirement already satisfied: pyyaml>=5.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (6.0.2)\n",
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"Requirement already satisfied: watchdog>=2.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs<2.0.0,>=1.6.1->dapi==0.4.2) (6.0.0)\n",
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"Requirement already satisfied: babel~=2.10 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (2.17.0)\n",
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"Requirement already satisfied: backrefs~=5.7.post1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (5.8)\n",
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"Requirement already satisfied: mkdocs-material-extensions~=1.3 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (1.3.1)\n",
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"Requirement already satisfied: paginate~=0.5 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (0.5.7)\n",
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"Requirement already satisfied: pygments~=2.16 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (2.19.1)\n",
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"Requirement already satisfied: pymdown-extensions~=10.2 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (10.15)\n",
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"Requirement already satisfied: requests~=2.26 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (2.32.4)\n",
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"Requirement already satisfied: python-dateutil>=2.8.2 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from pandas<3.0.0,>=1.3.0->dapi==0.4.2) (2.9.0.post0)\n",
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"Requirement already satisfied: pytz>=2020.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from pandas<3.0.0,>=1.3.0->dapi==0.4.2) (2025.2)\n",
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"Requirement already satisfied: tzdata>=2022.7 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from pandas<3.0.0,>=1.3.0->dapi==0.4.2) (2025.2)\n",
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"Requirement already satisfied: PyJWT>=1.7.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (2.10.1)\n",
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"Requirement already satisfied: atomicwrites<2.0.0,>=1.4.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (1.4.1)\n",
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"Requirement already satisfied: certifi>=2020.11.8 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (2025.4.26)\n",
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"Requirement already satisfied: cloudpickle>=1.6.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (3.1.1)\n",
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"Requirement already satisfied: cryptography>=3.3.2 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (45.0.4)\n",
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"Requirement already satisfied: openapi_core==0.16.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (0.16.0)\n",
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"Requirement already satisfied: openapi_spec_validator<0.6.0,>=0.5.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (0.5.4)\n",
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"Requirement already satisfied: setuptools>=21.0.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (80.9.0)\n",
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"Requirement already satisfied: six<2.0,>=1.10 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (1.17.0)\n",
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"Requirement already satisfied: urllib3<2.0.0,>=1.26.5 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (1.26.20)\n",
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"Requirement already satisfied: isodate in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (0.7.2)\n",
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"Requirement already satisfied: jsonschema-spec<0.2.0,>=0.1.1 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (0.1.3)\n",
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"Requirement already satisfied: more-itertools in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (10.7.0)\n",
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"Requirement already satisfied: openapi-schema-validator<0.4.0,>=0.3.0 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (0.3.4)\n",
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"Requirement already satisfied: parse in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (1.20.2)\n",
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"Requirement already satisfied: werkzeug in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (3.1.3)\n",
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"Requirement already satisfied: cffi>=1.14 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from cryptography>=3.3.2->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (1.17.1)\n",
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"Requirement already satisfied: charset_normalizer<4,>=2 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from requests~=2.26->mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (3.4.2)\n",
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"Requirement already satisfied: idna<4,>=2.5 in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from requests~=2.26->mkdocs-material<10.0.0,>=9.6.14->dapi==0.4.2) (3.10)\n",
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"Requirement already satisfied: pycparser in /Users/krishna/dev/DesignSafe/dapi/env/lib/python3.9/site-packages (from cffi>=1.14->cryptography>=3.3.2->tapipy<2.0.0,>=1.8.4->dapi==0.4.2) (2.22)\n",
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"Building wheels for collected packages: dapi\n",
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" Building editable for dapi (pyproject.toml) ... \u001b[?25ldone\n",
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"\u001b[?25h Created wheel for dapi: filename=dapi-0.4.2-py3-none-any.whl size=4067 sha256=45bb3f8236d06942da898366513f474a9fb0ab9f06eb242733edea6f7e97331f\n",
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" Stored in directory: /private/var/folders/w8/xz590jyd7r36zmxcspgzj3z40000gn/T/pip-ephem-wheel-cache-bbokgmyb/wheels/4c/51/46/2eb544e5cdddc745a3f608890dcac74e54c3ba4a42b4993717\n",
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"Successfully built dapi\n",
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"Installing collected packages: dapi\n",
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" Attempting uninstall: dapi\n",
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" Found existing installation: dapi 0.4.2\n",
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" Uninstalling dapi-0.4.2:\n",
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" Successfully uninstalled dapi-0.4.2\n",
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"Successfully installed dapi-0.4.2\n",
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"\n",
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=======
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"\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
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"poetry 2.1.3 requires importlib-metadata<8.7,>=4.4; python_version < \"3.10\", but you have importlib-metadata 8.7.0 which is incompatible.\u001b[0m\u001b[31m\n",
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"\u001b[0m\n",
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>>>>>>> Stashed changes
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"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m24.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m25.1.1\u001b[0m\n",
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"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n"
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]
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}
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"source": [
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<<<<<<< Updated upstream
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"# Dapi installation\n",
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"#!pip uninstall dapi --yes\n",
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"\n",
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"#!pip install dapi --user --quiet\n",
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"\n",
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"!pip install git+https://github.com/DesignSafe-CI/dapi.git@dev --user --quiet\n",
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"\n",
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"# Install editable local version of dapi\n",
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"#!pip install -e ../../"
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=======
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"!pip install --upgrade --ignore-installed --no-cache-dir --user --quiet dapi"
38+
"!pip install --upgrade --ignore-installed --no-cache-dir --user --quiet --no-warn-script-location dapi"
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"### ⚠️ Please restart the kernel by choosing Kernel >> Restart kernel ⚠️"
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>>>>>>> Stashed changes
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]
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]
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},
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{
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<<<<<<< Updated upstream
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=======
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"cell_type": "markdown",
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>>>>>>> Stashed changes
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"cell_type": "code",
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"execution_count": null,
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"id": "feee3ce0",

‎examples/mpm/uniaxial_stress/results.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -25,9 +25,10 @@
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],
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"source": [
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"import pandas as pd\n",
28-
"df = pd.read_hdf('results/uniaxial-stress-2d-usf/particles09.h5', 'table')\n",
29-
"print(\"Maximum σ_yy: {}\".format(df['stress_yy'].max()))\n",
30-
"print(\"Minimum σ_xx: {}\".format(df['stress_xx'].min()))"
28+
"\n",
29+
"df = pd.read_hdf(\"results/uniaxial-stress-2d-usf/particles09.h5\", \"table\")\n",
30+
"print(\"Maximum σ_yy: {}\".format(df[\"stress_yy\"].max()))\n",
31+
"print(\"Minimum σ_xx: {}\".format(df[\"stress_xx\"].min()))"
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]
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}
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],

‎examples/mpm/uniaxial_stress/test_benchmark.py‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,14 @@
11
import os
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import pathlib
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import pandas as pd
4+
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# Get current path
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os.chdir(pathlib.Path(__file__).parent.absolute())
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# Read results as DF
7-
df = pd.read_hdf('results/uniaxial-stress-2d-usf/particles09.h5', 'table')
8+
df = pd.read_hdf("results/uniaxial-stress-2d-usf/particles09.h5", "table")
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# Maximum stress in yy and xx
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syy = -0.9999999999999999
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sxx = 0.0
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# Check results are consistent
12-
assert round(df['stress_yy'].max() - syy, 8) == 0.0
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assert round(df['stress_xx'].max() - sxx, 8) == 0.0
13+
assert round(df["stress_yy"].max() - syy, 8) == 0.0
14+
assert round(df["stress_xx"].max() - sxx, 8) == 0.0

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