meta-edc 1.1.10__tar.gz → 1.1.13__tar.gz

meta_edc-1.1.13/PKG-INFO

@@ -0,0 +1,175 @@
+Metadata-Version: 2.4
+Name: meta-edc
+Version: 1.1.13
+Summary: META Trial EDC (https://www.isrctn.com/ISRCTN76157257)
+Keywords: django,clinicedc,META EDC,EDC,clinical trials,META Trial,ISRCTN76157257
+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: Environment :: Web Environment
+Classifier: Framework :: Django
+Classifier: Framework :: Django :: 5.2
+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: clinicedc>=2.0.13
+Requires-Dist: edc-he>=1.1.0
+Requires-Dist: edc-microscopy>=1.1.1
+Requires-Dist: edc-mnsi>=1.1.3
+Requires-Dist: edc-phq9>=1.0.1
+Requires-Dist: edc-qol>=1.1.2
+Requires-Dist: psycopg2>=2.9.10
+Requires-Python: >=3.12, <3.14
+Description-Content-Type: text/x-rst
+
+|pypi| |actions| |codecov| |downloads| |clinicedc|
+
+META EDC
+========
+
+Metformin treatment in Africa - META
+
+* https://www.ucl.ac.uk/global-health/research/z-research/respond-africa/metformin-treatment-africa-meta
+* https://www.inteafrica.org/related-projects/meta-trial/
+* https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
+* http://www.isrctn.com/ISRCTN76157257
+
+py 3.12+ / DJ 5.2 using the `Clinic EDC <https://github.com/clinicedc/edc>`_ framework
+
+This codebase is used for two randomized clinical trials:
+
+____
+
+META PHASE II:
+
+(final version `0.1.77 <https://github.com/meta-trial/meta-edc/tree/0.1.77>`_)
+
+Metformin Treatment for Diabetes Prevention in Africa: META Trial
+TASO, MRC/UVRI/LSHTM, NIMR – TZ and Liverpool School of Tropical Medicine (ISRCTN76157257)
+http://www.isrctn.com/ISRCTN76157257
+
+____
+
+META 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.
+
+Liverpool School of Tropical Medicine
+
+EDCTP grant number: RIA2018CO-2513
+
+Trial registration: ISCRTN 77382043
+
+https://ico.org.uk/ESDWebPages/Entry/Z4763134
+
+____
+
+See also https://github.com/clinicedc/edc
+
+|django|
+
+Installation
+------------
+
+As of version 1.1.10, we are building and deploying with `uv <https://docs.astral.sh/uv>`_.
+
+Here we assume you have your DB setup and already have your ``.env`` file.
+
+First-time install
+++++++++++++++++++
+
+Assuming you are logged into the account ``myaccount``:
+
+.. code-block:: bash
+
+    mkdir -p ~/.etc/meta && \
+    mkdir ~/edc && \
+    cd ~/edc && \
+    uv venv && \
+    uv pip install -U meta-edc==1.1.12 && \
+    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.12/manage.py && \
+    uv pip freeze | grep meta-edc
+
+Copy your ``.env`` file to ``~/.etc``.
+
+Place this at or near the end of your ``.bashrc``:
+
+.. code-block:: bash
+
+    # >>> EDC using uv >>>
+    export DJANGO_SETTINGS_MODULE=meta_edc.settings.uat
+    export META_PHASE=3
+    export DJANGO_BASE_DIR=/home/myaccount/edc
+    export DJANGO_ENV_DIR=/home/myaccount/.etc/
+    cd ~/edc
+    source .venv/bin/activate
+    export PATH="/home/myaccount/edc:$PATH"
+    # <<< EDC using uv <<<
+
+Source ``.bashrc`` and run ``manage.py check``.
+
+.. code-block:: bash
+
+    source ~/.bashrc && \
+    cd ~/edc && \
+    python manage.py check
+
+If all is OK, run ``migrate``:
+
+    Explicitly specify the settings file when using ``migrate``.
+
+    * live: ``--settings=meta_edc.settings.live``
+    * uat: ``--settings=meta_edc.settings.uat``
+    * debug:  ``--settings=meta_edc.settings.debug``
+
+
+.. code-block:: bash
+
+    cd ~/edc && \
+    python manage.py migrate --settings=meta_edc.settings.live
+
+Update an existing install
+++++++++++++++++++++++++++
+
+From the above example:
+
+.. code-block:: bash
+
+    cd ~/edc && \
+    uv venv --clear && \
+    uv pip install -U meta-edc==1.1.12 && \
+    wget -O manage.py https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.10/manage.py && \
+    uv pip freeze | grep meta-edc && \
+    python manage.py check
+
+If all is OK, run ``migrate``
+
+.. code-block:: bash
+
+    cd ~/edc && \
+    python manage.py migrate --settings=meta_edc.settings.live
+
+
+
+.. |pypi| image:: https://img.shields.io/pypi/v/meta-edc.svg
+    :target: https://pypi.python.org/pypi/meta-edc
+
+.. |actions| image:: https://github.com/meta-trial/meta-edc/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/meta-trial/meta-edc/actions/workflows/build.yml
+
+.. |codecov| image:: https://codecov.io/gh/meta-trial/meta-edc/branch/develop/graph/badge.svg
+  :target: https://codecov.io/gh/meta-trial/meta-edc
+
+.. |downloads| image:: https://pepy.tech/badge/meta-edc
+   :target: https://pepy.tech/project/meta-edc
+
+.. |django| image:: https://www.djangoproject.com/m/img/badges/djangomade124x25.gif
+   :target: http://www.djangoproject.com/
+   :alt: Made with Django
+
+.. |clinicedc| image:: https://img.shields.io/badge/framework-Clinic_EDC-green
+   :alt:Made with clinicedc
+   :target: https://github.com/clinicedc

meta_edc-1.1.13/README.rst

@@ -0,0 +1,148 @@
+|pypi| |actions| |codecov| |downloads| |clinicedc|
+
+META EDC
+========
+
+Metformin treatment in Africa - META
+
+* https://www.ucl.ac.uk/global-health/research/z-research/respond-africa/metformin-treatment-africa-meta
+* https://www.inteafrica.org/related-projects/meta-trial/
+* https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
+* http://www.isrctn.com/ISRCTN76157257
+
+py 3.12+ / DJ 5.2 using the `Clinic EDC <https://github.com/clinicedc/edc>`_ framework
+
+This codebase is used for two randomized clinical trials:
+
+____
+
+META PHASE II:
+
+(final version `0.1.77 <https://github.com/meta-trial/meta-edc/tree/0.1.77>`_)
+
+Metformin Treatment for Diabetes Prevention in Africa: META Trial
+TASO, MRC/UVRI/LSHTM, NIMR – TZ and Liverpool School of Tropical Medicine (ISRCTN76157257)
+http://www.isrctn.com/ISRCTN76157257
+
+____
+
+META 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.
+
+Liverpool School of Tropical Medicine
+
+EDCTP grant number: RIA2018CO-2513
+
+Trial registration: ISCRTN 77382043
+
+https://ico.org.uk/ESDWebPages/Entry/Z4763134
+
+____
+
+See also https://github.com/clinicedc/edc
+
+|django|
+
+Installation
+------------
+
+As of version 1.1.10, we are building and deploying with `uv <https://docs.astral.sh/uv>`_.
+
+Here we assume you have your DB setup and already have your ``.env`` file.
+
+First-time install
+++++++++++++++++++
+
+Assuming you are logged into the account ``myaccount``:
+
+.. code-block:: bash
+
+    mkdir -p ~/.etc/meta && \
+    mkdir ~/edc && \
+    cd ~/edc && \
+    uv venv && \
+    uv pip install -U meta-edc==1.1.12 && \
+    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.12/manage.py && \
+    uv pip freeze | grep meta-edc
+
+Copy your ``.env`` file to ``~/.etc``.
+
+Place this at or near the end of your ``.bashrc``:
+
+.. code-block:: bash
+
+    # >>> EDC using uv >>>
+    export DJANGO_SETTINGS_MODULE=meta_edc.settings.uat
+    export META_PHASE=3
+    export DJANGO_BASE_DIR=/home/myaccount/edc
+    export DJANGO_ENV_DIR=/home/myaccount/.etc/
+    cd ~/edc
+    source .venv/bin/activate
+    export PATH="/home/myaccount/edc:$PATH"
+    # <<< EDC using uv <<<
+
+Source ``.bashrc`` and run ``manage.py check``.
+
+.. code-block:: bash
+
+    source ~/.bashrc && \
+    cd ~/edc && \
+    python manage.py check
+
+If all is OK, run ``migrate``:
+
+    Explicitly specify the settings file when using ``migrate``.
+
+    * live: ``--settings=meta_edc.settings.live``
+    * uat: ``--settings=meta_edc.settings.uat``
+    * debug:  ``--settings=meta_edc.settings.debug``
+
+
+.. code-block:: bash
+
+    cd ~/edc && \
+    python manage.py migrate --settings=meta_edc.settings.live
+
+Update an existing install
+++++++++++++++++++++++++++
+
+From the above example:
+
+.. code-block:: bash
+
+    cd ~/edc && \
+    uv venv --clear && \
+    uv pip install -U meta-edc==1.1.12 && \
+    wget -O manage.py https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.10/manage.py && \
+    uv pip freeze | grep meta-edc && \
+    python manage.py check
+
+If all is OK, run ``migrate``
+
+.. code-block:: bash
+
+    cd ~/edc && \
+    python manage.py migrate --settings=meta_edc.settings.live
+
+
+
+.. |pypi| image:: https://img.shields.io/pypi/v/meta-edc.svg
+    :target: https://pypi.python.org/pypi/meta-edc
+
+.. |actions| image:: https://github.com/meta-trial/meta-edc/actions/workflows/build.yml/badge.svg
+  :target: https://github.com/meta-trial/meta-edc/actions/workflows/build.yml
+
+.. |codecov| image:: https://codecov.io/gh/meta-trial/meta-edc/branch/develop/graph/badge.svg
+  :target: https://codecov.io/gh/meta-trial/meta-edc
+
+.. |downloads| image:: https://pepy.tech/badge/meta-edc
+   :target: https://pepy.tech/project/meta-edc
+
+.. |django| image:: https://www.djangoproject.com/m/img/badges/djangomade124x25.gif
+   :target: http://www.djangoproject.com/
+   :alt: Made with Django
+
+.. |clinicedc| image:: https://img.shields.io/badge/framework-Clinic_EDC-green
+   :alt:Made with clinicedc
+   :target: https://github.com/clinicedc

meta_edc-1.1.13/pyproject.toml

@@ -0,0 +1,198 @@
+[project]
+name = "meta-edc"
+version = "1.1.13"
+description = "META Trial EDC (https://www.isrctn.com/ISRCTN76157257)"
+readme = "README.rst"
+keywords = [
+    "django",
+    "clinicedc",
+    "META EDC",
+    "EDC",
+    "clinical trials",
+    "META Trial",
+    "ISRCTN76157257",
+]
+authors = [
+    { name = "Erik van Widenfelt", email = "ew2789@gmail.com" },
+    { name = "Jonathan Willitts", email = "j.willitts@ucl.ac.uk" }
+]
+classifiers = [
+    "Environment :: Web Environment",
+    "Framework :: Django",
+    "Framework :: Django :: 5.2",
+    "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 = [
+    "clinicedc>=2.0.13",
+    "edc-he>=1.1.0",
+    "edc-microscopy>=1.1.1",
+    "edc-mnsi>=1.1.3",
+    "edc-phq9>=1.0.1",
+    "edc-qol>=1.1.2",
+    "psycopg2>=2.9.10",
+]
+
+[build-system]
+requires = ["uv_build>=0.8.2,<0.9.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-root = "src"
+module-name = [
+    "meta_ae",
+    "meta_analytics",
+    "meta_auth",
+    "meta_consent",
+    "meta_dashboard",
+    "meta_data_manager",
+    "meta_edc",
+    "meta_export",
+    "meta_labs",
+    "meta_lists",
+    "meta_pharmacy",
+    "meta_prn",
+    "meta_rando",
+    "meta_reports",
+    "meta_screening",
+    "meta_sites",
+    "meta_subject",
+    "meta_visit_schedule",
+]
+source-include = ["meta_*/templates/**", "meta_*/locale/**", "locale/**"]
+source-exclude = ["meta_*/tests/**", "meta_*/notebooks/**", "tests/**"]
+namespace = false
+
+[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", "PLR2004", "TRY003"]
+
+[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 = ["meta_edc"]
+
+[tool.coverage.paths]
+source = ["meta_edc"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+omit = ["*.txt", "*/migrations/*"]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+]
+
+[dependency-groups]
+lint = [
+    "ruff>=0.12.5",
+]
+
+test = [
+    "clinicedc-tests>=0.1.6",
+    "django-webtest>=1.9.13",
+    "edc-test-settings>=1.1.2",
+    "faker>=37.4.2",
+    "model-bakery>=1.20.5",
+    "time-machine>=2.16.0",
+]
+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 = [
+    'django>=5.2.4,<5.3',
+    "clinicedc>=2.0.10",
+    "time-machine>=2.16.0",
+    'edc-he',
+    'edc-microscopy',
+    'edc-mnsi',
+    # 'edc-next-appointment',
+    'edc-phq9',
+    'edc-qol',
+    'edc-test-settings',
+    "django-redis>=6.0.0",
+    "ipython>=9.4.0",
+]
+
+[tool.uv.sources]
+meta-edc = { workspace = true }
+clinicedc = { path = "../clinicedc", editable = true }
+django-audit-fields = { path = "../django-audit-fields", editable = true }
+django-crypto-fields = { path = "../django-crypto-fields", editable = true }
+django-logentry-admin = { path = "../django-logentry-admin", editable = true }
+django-multisite2 = { path = "../django-multisite2", editable = true }
+django-revision = { path = "../django-revision", editable = true }
+django-simple-history = { path = "../django-simple-history", editable = true }
+edc-microbiology = { path = "../edc-microbiology", editable = true }
+edc-microscopy = { path = "../edc-microscopy", editable = true }
+edc-mnsi = { path = "../edc-mnsi", editable = true }
+edc-next-appointment = { path = "../edc-next-appointment", editable = true }
+edc-phq9 = { path = "../edc-phq9", editable = true }
+edc-qol = { path = "../edc-qol", editable = true }
+edc-he = { path = "../edc-he", editable = true }
+edc-test-settings = { path = "../edc-test-settings", editable = true }
+