clinicedc 2.0.34__tar.gz → 2.0.35__tar.gz

clinicedc-2.0.35/PKG-INFO

@@ -0,0 +1,368 @@
+Metadata-Version: 2.4
+Name: clinicedc
+Version: 2.0.35
+Summary: A clinical trials data management framework built on Django
+Keywords: django,clinicedc,edc,clinical trials,research,data management,esource
+Author: Erik van Widenfelt, Jonathan Willitts
+Author-email: Erik van Widenfelt <ew2789@gmail.com>, Jonathan Willitts <j.willitts@ucl.ac.uk>
+License-Expression: GPL-3.0-or-later
+License-File: LICENSE
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Web Environment
+Classifier: Framework :: Django
+Classifier: Framework :: Django :: 5.2
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: argon2-cffi>=25.1.0
+Requires-Dist: arrow>=1.3.0
+Requires-Dist: beautifulsoup4>=4.13.5
+Requires-Dist: boto3>=1.39.16
+Requires-Dist: celery>=5.5.3
+Requires-Dist: cryptography>=45.0.7
+Requires-Dist: django>=5.2.4
+Requires-Dist: django-admin-rangefilter>=0.13.3
+Requires-Dist: django-audit-fields>=2.0.3
+Requires-Dist: django-crypto-fields>=1.1.2
+Requires-Dist: django-db-views>=0.1.11
+Requires-Dist: django-defender>=0.9.8
+Requires-Dist: django-environ>=0.12.0
+Requires-Dist: django-logentry-admin>=1.1.0
+Requires-Dist: django-multisite2>=2.1.0
+Requires-Dist: django-pandas>=0.6.7
+Requires-Dist: django-pylabels>=1.0.1
+Requires-Dist: django-redis>=6.0.0
+Requires-Dist: django-revision>=2.0.1
+Requires-Dist: django-sequences>=3.0
+Requires-Dist: django-simple-history>=3.10.1
+Requires-Dist: django-storages>=1.14.6
+Requires-Dist: djangorestframework>=3.16.0
+Requires-Dist: fontawesomefree>=6.6.0
+Requires-Dist: gunicorn>=23.0.0
+Requires-Dist: inflect>=7.5.0
+Requires-Dist: mempass>=0.1.2
+Requires-Dist: mysqlclient>=2.2.7
+Requires-Dist: psycopg2>=2.9.10
+Requires-Dist: pycups>=2.0.4
+Requires-Dist: pypdf>=5.9.0
+Requires-Dist: python-dateutil>=2.9.0.post0
+Requires-Dist: python-memcached>=1.62
+Requires-Dist: reportlab>=4.4.3
+Requires-Dist: sqlalchemy>=2.0.42
+Requires-Dist: sqlglot>=27.8.0
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: twilio>=9.7.0
+Maintainer: Erik van Widenfelt
+Maintainer-email: Erik van Widenfelt <ew2789@gmail.com>
+Requires-Python: >=3.12, <3.14
+Project-URL: Changelog, https://github.com/clinicedc/clinicedc/blob/main/CHANGES
+Project-URL: Documentation, https://github.com/clinicedc/clinicedc/docs
+Project-URL: Homepage, https://github.com/clinicedc/clinicedc
+Project-URL: Repository, https://github.com/clinicedc/clinicedc.git
+Description-Content-Type: text/x-rst
+
+|pypi| |actions| |uv| |ruff| |downloads| |django-packages|
+
+clinicedc -  A clinical trials data management framework built on Django
+========================================================================
+
+A data management framework built on Django for multisite randomized longitudinal clinical trials.
+
+Documentation: `clinicedc.readthedocs.io <https://clinicedc.readthedocs.io/>`_
+
+Source code: https://github.com/clinicedc/clinicedc
+
+`Here is a python module that extends Django <https://github.com/clinicedc/clinicedc>`__ to empower you to build an EDC / eSource system to handle data
+collection and management for multi-site longitudinal clinical trials.
+
+Refer to the specific open projects listed below for example EDC systems built with these modules.
+The more recent the trial the better the example.
+
+The codebase continues to evolve over many years of conducting clinical trials for mostly NIH-funded clinical trials through
+the `Harvard T Chan School of Public Health <https://aids.harvard.edu>`__, the
+`Botswana-Harvard AIDS Institute Partnership <https://aids.harvard.edu/research/bhp>`__
+in Gaborone, Botswana and the `London School of Hygiene and Tropical Medicine <https://lshtm.ac.uk>`__.
+Almost all trials were originally related to HIV/AIDS research.
+
+More recent work with the `RESPOND Africa Group <https://www.ucl.ac.uk/global-health/respond-africa>`__ formerly at the
+`Liverpool School of Tropical Medicine <https://lstm.ac.uk>`__ and now with the `University College London Institute for Global Health <https://www.ucl.ac.uk/global-health/>`__ has expanded into Diabetes (DM),
+Hypertension (HTN) and models of integrating care in Africa (https://inteafrica.org) for the
+three main chronic conditions -- HIV/DM/HTN.
+
+See also https://www.ucl.ac.uk/global-health/respond-africa
+
+The implementations we develop with this framework are mostly eSource systems rather than the traditional EDCs.
+
+The projects listed below consist of a subset of trial-specific modules that make heavy use of modules in this framework.
+
+Contacts
+--------
+
+For further information go to https://github.com/erikvw.
+
+|jet-brains| Thanks to `JetBrains <https://www.jetbrains.com>`_ for support with an opensource PyCharm IDE license.
+
+|django|
+
+Framework stack
+---------------
+============ ============ =========
+python       Django       mysql
+============ ============ =========
+python 3.12+ Django 5.2+  mysql 8+
+============ ============ =========
+
+
+How we describe the CLINICEDC projects in our protocol documents
+----------------------------------------------------------------
+
+Here is a simple example of a data management section for a study protocol document: `data_management_section`_
+
+.. _data_management_section: https://github.com/clinicedc/edc/blob/main/docs/protocol_data_management_section.rst
+
+
+Projects that use ``clinicedc``
+-------------------------------
+Recent examples of ``clinicedc`` applications using this codebase:
+
+INTECOMM Trial
+~~~~~~~~~~~~~~
+Controlling chronic diseases in Africa: Development and evaluation of an integrated community-based management model for HIV, Diabetes and Hypertension in Tanzania and Uganda
+
+https://github.com/intecomm-trial/intecomm-edc (2022-2025)
+
+EFFECT Trial
+~~~~~~~~~~~~
+Fluconazole plus flucytosine vs. fluconazole alone for cryptococcal antigen-positive patients identified through screening:
+
+A phase III randomised controlled trial
+
+https://github.com/effect-trial/effect-edc (2021- )
+
+http://www.isrctn.com/ISRCTN30579828
+
+META Trial (Phase III)
+~~~~~~~~~~~~~~~~~~~~~~
+A randomised placebo-controlled double-blind phase III trial to determine the effects of metformin versus placebo on the incidence of diabetes in HIV-infected persons with pre-diabetes in Tanzania.
+
+https://github.com/meta-trial/meta-edc (2021- )
+
+(The same codebase is used for META Phase 2 and META Phase 3)
+
+http://www.isrctn.com/ISRCTN77382043
+
+Mapitio
+~~~~~~~
+
+Retrospective HIV/Diabetes/Hypertension Cohort (Tanzania)
+
+https://github.com/mapitio/mapitio-edc (2020-2022)
+
+MOCCA Trial
+~~~~~~~~~~~
+
+Integrated care for HIV and non-communicable diseases in Africa: a pilot study to inform a large-scale trial (MOCCA and MOCCA Extension Study)
+
+https://github.com/mocca-trail/mocca-edc (2020-2022)
+
+http://www.isrctn.com/ISRCTN71437522
+
+INTE Africa Trial
+~~~~~~~~~~~~~~~~~
+Evaluating the integration of health services for chronic diseases in Africa
+
+(32 sites in Uganda and Tanzania)
+
+https://github.com/inte-africa-trial/inte-edc (2020-2022)
+
+https://inteafrica.org
+
+http://www.isrctn.com/ISRCTN43896688
+
+META Trial (Phase II)
+~~~~~~~~~~~~~~~~~~~~~
+A randomised placebo-controlled double-blind phase II trial to determine the effects of metformin versus placebo on the incidence of diabetes in HIV-infected persons with pre-diabetes in Tanzania.
+
+(3 sites in Tanzania)
+
+https://github.com/meta-trial/meta-edc (2019-2021)
+
+http://www.isrctn.com/ISRCTN76157257
+
+
+The Ambition Trial
+~~~~~~~~~~~~~~~~~~
+
+High dose AMBISOME on a fluconazole backbone for cryptococcal meningitis induction therapy in sub-Saharan Africa
+
+(7 sites in Botswana, Malawi, South Africa, Uganda, Zimbabwe)
+
+https://github.com/ambition-trial/ambition-edc (2018-2021)
+
+http://www.isrctn.com/ISRCTN72509687
+
+Start with main repo `ambition-edc`
+
+The Botswana Combination Prevention Project
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+(30 remote offline sites in Botswana)
+
+https://github.com/botswana-combination-prevention-project (2013-2018)
+
+https://clinicaltrials.gov/ct2/show/NCT01965470
+
+https://www.ncbi.nlm.nih.gov/pubmed/?term=NCT01965470
+
+https://aids.harvard.edu/tag/bcpp/
+
+Start with main repo `bcpp`
+
+
+Optional modules
+----------------
+
+=========================== ============================= ==================================
+edc-csf_                    |edc-csf|                     |pypi-edc-csf|
+edc-he_                     |edc-he|                      |pypi-edc-he|
+edc-microbiology_           |edc-microbiology|            |pypi-edc-microbiology|
+edc-microscopy_             |edc-microscopy|              |pypi-edc-microscopy|
+edc-mnsi_                   |edc-mnsi|                    |pypi-edc-mnsi|
+edc-phq9_                   |edc-phq9|                    |pypi-edc-phq9|
+edc-qol_                    |edc-qol|                     |pypi-edc-qol|
+=========================== ============================= ==================================
+
+Testing modules
+---------------
+=========================== ============================= ==================================
+clinicedc-tests_            |clinicedc-tests|             |pypi-clinicedc-tests|
+edc-test-settings_          |edc-test-settings|           |pypi-edc-test-settings|
+=========================== ============================= ==================================
+
+
+Env
+---
+
+.. code-block:: bash
+
+    uv venv
+    source .venv/bin/activate
+    uv sync --no-sources --upgrade
+
+Tests
+-----
+
+.. code-block:: bash
+
+    uv run --group test runtests.py
+
+
+Lint and format
+---------------
+
+.. code-block:: bash
+
+    uvx ruff check
+
+
+.. |pypi| image:: https://img.shields.io/pypi/v/clinicedc.svg
+    :target: https://pypi.python.org/pypi/edc
+
+.. |downloads| image:: https://pepy.tech/badge/clinicedc
+   :target: https://pepy.tech/project/clinicedc
+
+.. |django| image:: https://www.djangoproject.com/m/img/badges/djangomade124x25.gif
+   :target: http://www.djangoproject.com/
+   :alt: Made with Django
+
+
+.. _edc-csf: https://github.com/clinicedc/edc-csf
+.. _edc-dx: https://github.com/clinicedc/edc-dx
+.. _edc-dx-review: https://github.com/clinicedc/edc-dx-review
+.. _edc-he: https://github.com/clinicedc/edc-he
+.. _edc-icecap-a: https://github.com/clinicedc/edc-icecap-a
+.. _edc-mnsi: https://github.com/clinicedc/edc-mnsi
+.. _edc-microbiology: https://github.com/clinicedc/edc-microbiology
+.. _edc-microscopy: https://github.com/clinicedc/edc-microscopy
+.. _edc-phq9: https://github.com/clinicedc/edc-phq9
+.. _edc-qol: https://github.com/clinicedc/edc-qol
+.. _edc-test-settings: https://github.com/clinicedc/edc-test-settings
+.. _clinicedc-tests: https://github.com/clinicedc/clinicedc-tests
+
+.. |edc-csf| image:: https://github.com/clinicedc/edc-csf/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-csf/actions/workflows/build.yml
+.. |edc-dx| image:: https://github.com/clinicedc/edc-dx/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-dx/actions/workflows/build.yml
+.. |edc-dx-review| image:: https://github.com/clinicedc/edc-dx-review/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-dx-review/actions/workflows/build.yml
+.. |edc-he| image:: https://github.com/clinicedc/edc-he/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-he/actions/workflows/build.yml
+.. |edc-icecap-a| image:: https://github.com/clinicedc/edc-icecap-a/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-icecap-a/actions/workflows/build.yml
+.. |edc-mnsi| image:: https://github.com/clinicedc/edc-mnsi/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-mnsi/actions/workflows/build.yml
+.. |edc-microbiology| image:: https://github.com/clinicedc/edc-microbiology/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-microbiology/actions/workflows/build.yml
+.. |edc-microscopy| image:: https://github.com/clinicedc/edc-microscopy/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-microscopy/actions/workflows/build.yml
+.. |edc-phq9| image:: https://github.com/clinicedc/edc-phq9/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-phq9/actions/workflows/build.yml
+.. |edc-qol| image:: https://github.com/clinicedc/edc-qol/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-qol/actions/workflows/build.yml
+.. |edc-rx| image:: https://github.com/clinicedc/edc-rx/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-rx/actions/workflows/build.yml
+.. |edc-test-settings| image:: https://github.com/clinicedc/edc-test-settings/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/edc-test-settings/actions/workflows/build.yml
+.. |clinicedc-tests| image:: https://github.com/clinicedc/clinicedc-tests/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/clinicedc-tests/actions/workflows/build.yml
+
+.. |pypi-edc-csf| image:: https://img.shields.io/pypi/v/edc-csf.svg
+    :target: https://pypi.python.org/pypi/edc-csf
+.. |pypi-edc-dx| image:: https://img.shields.io/pypi/v/edc-dx.svg
+    :target: https://pypi.python.org/pypi/edc-dx
+.. |pypi-edc-dx-review| image:: https://img.shields.io/pypi/v/edc-dx-review.svg
+    :target: https://pypi.python.org/pypi/edc-dx-review
+.. |pypi-edc-he| image:: https://img.shields.io/pypi/v/edc-he.svg
+    :target: https://pypi.python.org/pypi/edc-he
+.. |pypi-edc-icecap-a| image:: https://img.shields.io/pypi/v/edc-he.svg
+    :target: https://pypi.python.org/pypi/edc-icecap-a
+.. |pypi-edc-mnsi| image:: https://img.shields.io/pypi/v/edc-mnsi.svg
+    :target: https://pypi.python.org/pypi/edc-mnsi
+.. |pypi-edc-microbiology| image:: https://img.shields.io/pypi/v/edc-microbiology.svg
+    :target: https://pypi.python.org/pypi/edc-microbiology
+.. |pypi-edc-microscopy| image:: https://img.shields.io/pypi/v/edc-microscopy.svg
+    :target: https://pypi.python.org/pypi/edc-microscopy
+.. |pypi-edc-phq9| image:: https://img.shields.io/pypi/v/edc-phq9.svg
+    :target: https://pypi.python.org/pypi/edc-phq9
+.. |pypi-edc-qol| image:: https://img.shields.io/pypi/v/edc-qol.svg
+    :target: https://pypi.python.org/pypi/edc-qol
+.. |pypi-edc-rx| image:: https://img.shields.io/pypi/v/edc-rx.svg
+    :target: https://pypi.python.org/pypi/edc-rx
+.. |pypi-edc-test-settings| image:: https://img.shields.io/pypi/v/edc-test-settings.svg
+    :target: https://pypi.python.org/pypi/edc-test-settings
+.. |pypi-clinicedc-tests| image:: https://img.shields.io/pypi/v/clinicedc-tests.svg
+    :target: https://pypi.python.org/pypi/clinicedc-tests
+
+.. |jet-brains| image:: https://resources.jetbrains.com/storage/products/company/brand/logos/PyCharm_icon.png
+    :target: https://jb.gg/OpenSource
+    :width: 25
+    :alt: JetBrains PyCharm
+
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :target: https://github.com/psf/black
+
+.. |django-packages| image:: https://img.shields.io/badge/Published%20on-Django%20Packages-0c3c26
+    :target: https://djangopackages.org/packages/p/clinicedc/
+
+.. |actions| image:: https://github.com/clinicedc/clinicedc/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/clinicedc/clinicedc/actions/workflows/build.yml
+
+.. |uv| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json
+  :target: https://github.com/astral-sh/uv
+
+.. |ruff| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+    :target: https://github.com/astral-sh/ruff
+    :alt: Ruff

clinicedc-2.0.35/pyproject.toml

@@ -0,0 +1,307 @@
+[build-system]
+requires = ["uv_build>=0.8.2,<0.9.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-root = "src"
+module-name = [
+    "clinicedc",
+    "edc_action_item",
+    "edc_adherence",
+    "edc_adverse_event",
+    "edc_analytics",
+    "edc_appconfig",
+    "edc_appointment",
+    "edc_auth",
+    "edc_consent",
+    "edc_constants",
+    "edc_crf",
+    "edc_dashboard",
+    "edc_data_manager",
+    "edc_device",
+    "edc_document_status",
+    "edc_dx",
+    "edc_dx_review",
+    "edc_egfr",
+    "edc_export",
+    "edc_facility",
+    "edc_fieldsets",
+    "edc_form_describer",
+    "edc_form_label",
+    "edc_form_runners",
+    "edc_form_validators",
+    "edc_glucose",
+    "edc_identifier",
+    "edc_lab",
+    "edc_lab_dashboard",
+    "edc_lab_panel",
+    "edc_lab_results",
+    "edc_label",
+    "edc_list_data",
+    "edc_listboard",
+    "edc_locator",
+    "edc_ltfu",
+    "edc_metadata",
+    "edc_model",
+    "edc_model_admin",
+    "edc_model_fields",
+    "edc_model_form",
+    "edc_model_to_dataframe",
+    "edc_navbar",
+    "edc_notification",
+    "edc_offstudy",
+    "edc_pdf_reports",
+    "edc_pdutils",
+    "edc_pharmacy",
+    "edc_prn",
+    "edc_protocol",
+    "edc_protocol_incident",
+    "edc_pylabels",
+    "edc_qareports",
+    "edc_randomization",
+    "edc_refusal",
+    "edc_registration",
+    "edc_reportable",
+    "edc_review_dashboard",
+    "edc_screening",
+    "edc_search",
+    "edc_sites",
+    "edc_subject_dashboard",
+    "edc_timepoint",
+    "edc_transfer",
+    "edc_unblinding",
+    "edc_utils",
+    "edc_view_utils",
+    "edc_visit_schedule",
+    "edc_visit_tracking",
+    "edc_vitals",
+]
+source-include = ["edc_*/templates/**", "edc_*/locale/**", "locale/**"]
+source-exclude = ["edc_*/tests/**", "edc_*/notebooks/**", "tests/**", "bin"]
+namespace = false
+
+[project]
+name = "clinicedc"
+version = "2.0.35"
+description = "A clinical trials data management framework built on Django"
+readme = {file = "README.rst", content-type = "text/x-rst"}
+keywords = ["django", "clinicedc", "edc", "clinical trials", "research", "data management", "esource"]
+authors = [
+    { name = "Erik van Widenfelt", email = "ew2789@gmail.com" },
+    { name = "Jonathan Willitts", email = "j.willitts@ucl.ac.uk" }
+]
+maintainers = [
+    { name = "Erik van Widenfelt", email = "ew2789@gmail.com" },
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Web Environment",
+    "Framework :: Django",
+    "Framework :: Django :: 5.2",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+license = "GPL-3.0-or-later"
+license-files = ["LICEN[CS]E*"]
+requires-python = '>=3.12,<3.14'
+dependencies = [
+    "argon2-cffi>=25.1.0",
+    "arrow>=1.3.0",
+    "beautifulsoup4>=4.13.5",
+    "boto3>=1.39.16",
+    "celery>=5.5.3",
+    "cryptography>=45.0.7",
+    "django>=5.2.4",
+    "django-admin-rangefilter>=0.13.3",
+    "django-audit-fields>=2.0.3",
+    "django-crypto-fields>=1.1.2",
+    "django-db-views>=0.1.11",
+    "django-defender>=0.9.8",
+    "django-environ>=0.12.0",
+    "django-logentry-admin>=1.1.0",
+    "django-multisite2>=2.1.0",
+    "django-pandas>=0.6.7",
+    "django-pylabels>=1.0.1",
+    "django-redis>=6.0.0",
+    "django-revision>=2.0.1",
+    "django-sequences>=3.0",
+    "django-simple-history>=3.10.1",
+    "django-storages>=1.14.6",
+    "djangorestframework>=3.16.0",
+    "fontawesomefree>=6.6.0",
+    "gunicorn>=23.0.0",
+    "inflect>=7.5.0",
+    "mempass>=0.1.2",
+    "mysqlclient>=2.2.7",
+    "psycopg2>=2.9.10",
+    "pycups>=2.0.4",
+    "pypdf>=5.9.0",
+    "python-dateutil>=2.9.0.post0",
+    "python-memcached>=1.62",
+    "reportlab>=4.4.3",
+    "sqlalchemy>=2.0.42",
+    "sqlglot>=27.8.0",
+    "tqdm>=4.67.1",
+    "twilio>=9.7.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/clinicedc/clinicedc"
+Documentation = "https://github.com/clinicedc/clinicedc/docs"
+Repository = "https://github.com/clinicedc/clinicedc.git"
+Changelog = "https://github.com/clinicedc/clinicedc/blob/main/CHANGES"
+
+[tool.ruff]
+line-length = 95
+indent-width = 4
+target-version = "py312"
+exclude = ["migrations", ".tox", ".venv"]
+
+[tool.ruff.lint]
+select = [
+    "A",
+    "ARG",
+    "B",
+    "C90",
+    "COM",
+    "DJ",
+    "DTZ",
+    "E",
+    "F",
+    "FA",
+    "FURB",
+    "I",
+    "INT",
+    "N",
+    "PD",
+    "PERF",
+    "PL",
+    "PLR",
+    "PTH",
+    "RET",
+    "RUF",
+    "S",
+    "SIM",
+    "T20",
+    "TRY",
+    "UP",
+    "W",
+    # "FIX",
+]
+ignore = [
+    "DJ008",
+    "DJ007",
+    "DJ006",
+    "COM812",
+    "PLC0206",
+    "TRY003", # temporarily
+    "PLR0913", # temporarily
+    "ARG001", # temporarily
+    "DJ012", # temporarily
+]
+
+[tool.ruff.lint.per-file-ignores]
+    "__init__.py" = ["F401"]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 12
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
+[tool.coverage.run]
+parallel = false
+branch = true
+source = ["src"]
+
+[tool.coverage.paths]
+source = ["src"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+omit = ["requirements.txt", "*/migrations/*"]
+exclude_lines = [
+  "pragma: no cover",
+  "if TYPE_CHECKING:",
+]
+
+[tool.rstcheck]
+ignore_directives = ["toctree"]
+
+[dependency-groups]
+docs = [
+    "furo>=2025.7.19",
+    "sphinx>=8.2.3",
+    "sphinx-design>=0.6.1",
+    "sphinx-inline-tabs>=2023.4.21",
+]
+lint = [
+    "ruff>=0.13.2",
+]
+
+test = [
+    "arrow>=1.3.0",
+    "clinicedc-tests>=0.1.5",
+    "coverage>=7.10.1",
+    "django-audit-fields>=2.0.0",
+    "django-webtest>=1.9.13",
+    "edc-test-settings>=2.0.0",
+    "faker>=37.4.2",
+    "model-bakery>=1.20.5",
+    "time-machine>=2.16.0",
+    "tox-uv>=1.26.2",
+]
+
+notebook = [
+    "dj-notebook>=0.7.0",
+    "great-tables>=0.18.0",
+    "matplotlib>=3.10.3",
+    "matplotlib-venn>=1.1.2",
+    "numpy>=2.3.2",
+    "pandas>=2.3.1",
+    "pdfkit>=1.0.0",
+    "scikit-learn>=1.7.1",
+    "scipy>=1.16.0",
+    "selenium>=4.34.2",
+    "tabulate>=0.9.0",
+]
+
+develop = [
+    "clinicedc",
+    "clinicedc-tests",
+    'argon2-cffi',
+    'python-memcached',
+    'django-environ',
+    'django-storages',
+    'fontawesomefree',
+    "django-audit-fields",
+    'django-crypto-fields',
+    'django-revision',
+    'django-multisite2',
+    'django-simple-history',
+    'django-pandas',
+    'django-logentry-admin',
+    'django-admin-rangefilter',
+    'django-db-views',
+    "model-bakery>=1.20.5",
+    "faker>=37.5.3",
+    "time-machine>=2.17.0",
+    "ipython>=9.5.0",
+]
+
+[tool.uv.sources]
+clinicedc = { workspace = true }
+clinicedc-tests = { path = "../clinicedc-tests", editable = true }
+django-audit-fields = { path = "../django-audit-fields", editable = true }
+django-crypto-fields = { path = "../django-crypto-fields", editable = true }
+django-revision = { path = "../django-revision", editable = true }
+# django-multisite2 = { path = "../django-multisite2", editable = true }
+edc-test-settings = { path = "../edc-test-settings", editable = true }