opencloning 0.2.8.3__tar.gz → 0.3.0__tar.gz

{opencloning-0.2.8.3 → opencloning-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.8.3
+Version: 0.3.0
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
 Author: Manuel Lera-Ramirez
@@ -15,8 +15,9 @@ Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
 Requires-Dist: biopython (==1.84)
 Requires-Dist: fastapi
 Requires-Dist: httpx (>=0.25.0,<0.26.0)
-Requires-Dist: opencloning-linkml (==0.2.6.1a0)
+Requires-Dist: opencloning-linkml (==0.3.0a0)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
+Requires-Dist: packaging (>=25.0,<26.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: primer3-py (==2.0.3)
 Requires-Dist: pydantic (>=2.7.1,<3.0.0)
@@ -48,6 +49,12 @@ This API provides a series of entry points. The API documentation can be accesse
 
 The API functions can also be used to write python scripts to automate cloning. See the [scripting examples](examples/scripting) for more information.
 
+## Migrating between model versions and fixing model bugs
+
+* The data model changes, so the json files you created may not be compatible with the newest version of the library, which uses the latest data mode. You can easily fix this using `python -m opencloning_linkml.migrations.migrate file.json
+` see [full documentation](https://github.com/OpenCloning/OpenCloning_LinkML?tab=readme-ov-file#migration-from-previous-versions-of-the-schema).
+* Before version 0.3, there was a bug for assembly fields that included locations spanning the origin. See the details and how to fix it in the documentation of [this file](./src/opencloning/bug_fixing/README.md).
+
 ## Getting started
 
 If you want to quickly set up a local instance of the frontend and backend of the application, check [getting started in 5 minutes](https://github.com/manulera/OpenCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
@@ -61,7 +68,7 @@ You can install this as a python package:
 python -m venv .venv
 # Activate the virtual environment
 source .venv/bin/activate
-# Install the package from github (will be in pypi at some point)
+# Install the package from pypi
 pip install opencloning
 # Run the API (uvicorn should be installed in the virtual environment)
 uvicorn opencloning.main:app

{opencloning-0.2.8.3 → opencloning-0.3.0}/README.md

@@ -17,6 +17,12 @@ This API provides a series of entry points. The API documentation can be accesse
 
 The API functions can also be used to write python scripts to automate cloning. See the [scripting examples](examples/scripting) for more information.
 
+## Migrating between model versions and fixing model bugs
+
+* The data model changes, so the json files you created may not be compatible with the newest version of the library, which uses the latest data mode. You can easily fix this using `python -m opencloning_linkml.migrations.migrate file.json
+` see [full documentation](https://github.com/OpenCloning/OpenCloning_LinkML?tab=readme-ov-file#migration-from-previous-versions-of-the-schema).
+* Before version 0.3, there was a bug for assembly fields that included locations spanning the origin. See the details and how to fix it in the documentation of [this file](./src/opencloning/bug_fixing/README.md).
+
 ## Getting started
 
 If you want to quickly set up a local instance of the frontend and backend of the application, check [getting started in 5 minutes](https://github.com/manulera/OpenCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
@@ -30,7 +36,7 @@ You can install this as a python package:
 python -m venv .venv
 # Activate the virtual environment
 source .venv/bin/activate
-# Install the package from github (will be in pypi at some point)
+# Install the package from pypi
 pip install opencloning
 # Run the API (uvicorn should be installed in the virtual environment)
 uvicorn opencloning.main:app

{opencloning-0.2.8.3 → opencloning-0.3.0}/pyproject.toml

@@ -1,9 +1,14 @@
+[project]
+name = "opencloning"
+dynamic = ["version"]
+
+
 [tool.poetry]
 authors = ["Manuel Lera-Ramirez <manulera14@gmail.com>"]
 description = "Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others."
 license = "MIT"
 name = "opencloning"
-version = "v0.2.8.3"
+version = "0.3.0"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"
@@ -22,9 +27,10 @@ pydantic = "^2.7.1"
 pandas = "^2.2.3"
 openpyxl = "^3.1.5"
 pyyaml = "^6.0.2"
-opencloning-linkml = "0.2.6.1a0"
+opencloning-linkml = "0.3.0a0"
 primer3-py = "2.0.3"
 biopython = "1.84"
+packaging = "^25.0"
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.0.4"
@@ -47,9 +53,14 @@ ipython = "^8.20.0"
 ipykernel = "^6.28.0"
 
 [build-system]
-build-backend = "poetry.core.masonry.api"
-requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry_dynamic_versioning.backend"
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
 
 [tool.black]
 skip-string-normalization = true
 line-length = 119
+
+[tool.poetry-dynamic-versioning]
+enable = false
+style = "pep440"
+vcs = "git"

opencloning-0.3.0/src/opencloning/_version.py

@@ -0,0 +1,7 @@
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version(__name__.split('.')[0])
+except PackageNotFoundError:
+    # package not installed
+    __version__ = '0.0.0'

{opencloning-0.2.8.3 → opencloning-0.3.0}/src/opencloning/assembly2.py

@@ -465,6 +465,17 @@ def assemble(fragments, assembly, is_insertion=False):
         is_circular = assembly_is_circular(assembly, fragments)
 
     subfragment_representation = edge_representation2subfragment_representation(assembly, is_circular)
+
+    # Sanity check
+    for asm_edge in assembly:
+        u, v, loc_u, loc_v = asm_edge
+        f_u = fragments[u - 1] if u > 0 else fragments[-u - 1].reverse_complement()
+        f_v = fragments[v - 1] if v > 0 else fragments[-v - 1].reverse_complement()
+        seq_u = str(loc_u.extract(f_u).seq).upper()
+        seq_v = str(loc_v.extract(f_v).seq).upper()
+        if seq_u != seq_v:
+            raise ValueError('Mismatch in assembly')
+
     # We transform into Dseqrecords (for primers)
     dseqr_fragments = [f if isinstance(f, _Dseqrecord) else _Dseqrecord(f) for f in fragments]
     subfragments = get_assembly_subfragments(dseqr_fragments, subfragment_representation)

{opencloning-0.2.8.3 → opencloning-0.3.0}/src/opencloning/batch_cloning/pombe/__init__.py

@@ -9,9 +9,7 @@ from .pombe_summary import main as pombe_summary
 from .pombe_gather import main as pombe_gather
 import shutil
 import traceback
-import json
 from ...get_router import get_router
-from ...utils import api_version
 from fastapi import Request
 
 router = get_router()
@@ -75,10 +73,6 @@ async def post_batch_cloning(
         except Exception:
             raise HTTPException(status_code=400, detail='Summary failed')
 
-        # Write the version
-        with open(os.path.join(temp_dir, 'version.json'), 'w') as f:
-            f.write(json.dumps(api_version(), indent=2))
-
         # zip the temp dir and return it
         zip_filename = f'{temp_dir}_archive'
         shutil.make_archive(zip_filename, 'zip', temp_dir)