Merge pull request #3 from gyorilab/refactor_who

Refactor WHO

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# PyCharm
+.idea/
+
+# Docs
+doc/_build/
+
+.DS_Store

.readthedocs.yml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+    install:
+    - requirements: doc/requirements.txt
+

doc/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+import sys
+
+sys.path.insert(0, os.path.join(os.path.abspath('..'), 'src'))
+
+project = 'trialsynth'
+copyright = '2024, Gyori lab'
+author = 'Gyori lab'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.autodoc"]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

doc/index.rst

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+.. trialsynth documentation master file, created by
+   sphinx-quickstart on Thu Jun  6 14:55:48 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to trialsynth's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules/index
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/modules/index.rst

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+Trialsynth modules reference
+============================
+
+ClinicalTrials.gov
+------------------
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.config
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.fetch
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.process
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.rest_api_response_models
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.store
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.transform
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.util
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.clinical_trials_dot_gov.validate
+    :members:
+    :show-inheritance:
+
+WHO-ICTRP
+---------
+
+.. automodule:: trial_synth.who.config
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.fetch
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.process
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.trial_model
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.store
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.transform
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.util
+    :members:
+    :show-inheritance:
+
+.. automodule:: trial_synth.who.validate
+    :members:
+    :show-inheritance:

doc/requirements.txt

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+sphinx-rtd-theme