From 9754f87546b7b90816696fe8efc4e8448f26c48b Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:04:38 +0100 Subject: [PATCH 01/26] fix license --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index 32c9863..de18f5d 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2023 AI2MS +Copyright (c) 2023 AIDH MS Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From 6c337b7949ea1fb50652dcb37b84f141231ac89d Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:04:53 +0100 Subject: [PATCH 02/26] add devcontainer --- .devcontainer/Dockerfile | 6 ++++ .devcontainer/devcontainer.json | 47 ++++++++++++++++++++++++++++ .devcontainer/docker-compose.yml | 18 +++++++++++ .devcontainer/scripts/initialize.sh | 1 + .devcontainer/scripts/post-create.sh | 5 +++ .devcontainer/scripts/post-start.sh | 1 + 6 files changed, 78 insertions(+) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/docker-compose.yml create mode 100644 .devcontainer/scripts/initialize.sh create mode 100644 .devcontainer/scripts/post-create.sh create mode 100644 .devcontainer/scripts/post-start.sh diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 0000000..42061f0 --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,6 @@ +FROM mcr.microsoft.com/devcontainers/python:3.13 + +ENV PYTHONUNBUFFERED 1 + +# Install Python Deps +RUN pip install --upgrade pip pre-commit poetry diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..678f055 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,47 @@ +{ + "name": "pyAKI", + "dockerComposeFile": "docker-compose.yml", + "service": "pyaki", + "workspaceFolder": "/workspaces", + "remoteUser": "vscode", + "postCreateCommand": "bash .devcontainer/scripts/post-create.sh", + "postStartCommand": "bash .devcontainer/scripts/post-start.sh", + "customizations": { + "vscode": { + "extensions": [ + "ms-python.python", + "ms-python.mypy-type-checker", + "tamasfe.even-better-toml", + "charliermarsh.ruff", + "ryanluker.vscode-coverage-gutters", + "GitHub.copilot", + "GitHub.copilot-chat", + "ms-vsliveshare.vsliveshare", + "GitHub.vscode-pull-request-github", + "github.vscode-github-actions", + "ms-toolsai.jupyter" + ], + "settings": { + "[python]": { + "editor.defaultFormatter": "charliermarsh.ruff", + "editor.codeActionsOnSave": { + "source.fixAll": true, + "source.organizeImports": true + }, + "files.eol": "\n" + }, + "mypy-type-checker.importStrategy": "fromEnvironment", + "mypy-type-checker.args": [ + "--config-file=${workspaceFolder}/pyproject.toml" + ], + "python.analysis.typeCheckingMode": "basic", + "coverage-gutters.coverageBaseDir": "/workspaces/pyAKI", + "coverage-gutters.coverageFileNames": [ + "coverage.xml" + ] + } + } + }, + "forwardPorts": [], + "initializeCommand": "bash .devcontainer/scripts/initialize.sh" +} diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml new file mode 100644 index 0000000..b37703e --- /dev/null +++ b/.devcontainer/docker-compose.yml @@ -0,0 +1,18 @@ +version: '3.8' + +services: + pyaki: + container_name: pyaki + + init: true + build: + context: .. + dockerfile: .devcontainer/Dockerfile + environment: + - no_proxy="127.0.0.1,localhost" + - NO_PROXY="127.0.0.1,localhost" + volumes: + - ..:/workspaces:cached + - type: bind + # Overrides default command so things don't shut down after the process ends. + command: sleep infinity diff --git a/.devcontainer/scripts/initialize.sh b/.devcontainer/scripts/initialize.sh new file mode 100644 index 0000000..3a5f924 --- /dev/null +++ b/.devcontainer/scripts/initialize.sh @@ -0,0 +1 @@ +docker pull mcr.microsoft.com/devcontainers/python:3.13 diff --git a/.devcontainer/scripts/post-create.sh b/.devcontainer/scripts/post-create.sh new file mode 100644 index 0000000..02c269c --- /dev/null +++ b/.devcontainer/scripts/post-create.sh @@ -0,0 +1,5 @@ +# Add bash-completion's +echo "source /usr/share/bash-completion/completions/git" >> ~/.bashrc + +# install deps +pre-commit install diff --git a/.devcontainer/scripts/post-start.sh b/.devcontainer/scripts/post-start.sh new file mode 100644 index 0000000..3ea6d40 --- /dev/null +++ b/.devcontainer/scripts/post-start.sh @@ -0,0 +1 @@ +poetry install --with dev From 0d7f27b330729011b8877770ed43269cc8431958 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:06:00 +0100 Subject: [PATCH 03/26] add vscode settings --- .vscode/settings.json | 4 ++++ .vscode/tasks.json | 17 +++++++++++++++++ 2 files changed, 21 insertions(+) create mode 100644 .vscode/settings.json create mode 100644 .vscode/tasks.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..0cd2911 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,4 @@ +{ + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true +} diff --git a/.vscode/tasks.json b/.vscode/tasks.json new file mode 100644 index 0000000..cc1c093 --- /dev/null +++ b/.vscode/tasks.json @@ -0,0 +1,17 @@ +{ + "version": "2.0.0", + "tasks": [ + { + "label": "run pre-commit", + "type": "shell", + "command": "pre-commit run --all-files", + "problemMatcher": [] + }, + { + "label": "update pre-commit", + "type": "shell", + "command": "pre-commit autoupdate", + "problemMatcher": [] + } + ] +} From aaae15027515bada8cbaaca4b98cdc5c9bb6612d Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:07:16 +0100 Subject: [PATCH 04/26] fix authors --- AUTHORS | 1 - 1 file changed, 1 deletion(-) diff --git a/AUTHORS b/AUTHORS index 3e33ecb..e71ccc1 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,6 +1,5 @@ Christian Porschen <57251443+aegis301@users.noreply.github.com> Jan Ernsting -Paul <115164840+Paul-B98@users.noreply.github.com> Paul-B98 <115164840+Paul-B98@users.noreply.github.com> aegis301 <57251443+aegis301@users.noreply.github.com> dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> From ae8c945a889d0bd9394862684bb00e174e043b4b Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:25:15 +0100 Subject: [PATCH 05/26] clean up gitignore --- .gitignore | 3 --- 1 file changed, 3 deletions(-) diff --git a/.gitignore b/.gitignore index 5c0cf17..87765c7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,4 @@ # env -.vscode results paper .DS_Store @@ -164,5 +163,3 @@ cython_debug/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ - -/tests/data/* \ No newline at end of file From ad0f74b0e1ebc7cb3a8eefe97db873a53c9fcc72 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:25:33 +0100 Subject: [PATCH 06/26] fix devcontainer --- .devcontainer/docker-compose.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml index b37703e..1484820 100644 --- a/.devcontainer/docker-compose.yml +++ b/.devcontainer/docker-compose.yml @@ -13,6 +13,5 @@ services: - NO_PROXY="127.0.0.1,localhost" volumes: - ..:/workspaces:cached - - type: bind # Overrides default command so things don't shut down after the process ends. command: sleep infinity From 1754007e8f320886eb040129fd93f6322509049d Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:25:59 +0100 Subject: [PATCH 07/26] add tool configs --- .pre-commit-config.yaml | 26 ++++++++++++++ .ruff.toml | 76 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 .pre-commit-config.yaml create mode 100644 .ruff.toml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..68206b8 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,26 @@ +# https://pre-commit.com/ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + hooks: + - id: fix-byte-order-marker + - id: trailing-whitespace + - id: end-of-file-fixer + - id: detect-private-key + - id: check-case-conflict + - id: check-toml + - id: check-json + - id: check-yaml + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.2.1 + hooks: + - id: ruff + args: [ --fix ] + - id: ruff-format + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.8.0 + hooks: + - id: mypy + additional_dependencies: + - pandera[mypy] + - types-PyYAML diff --git a/.ruff.toml b/.ruff.toml new file mode 100644 index 0000000..2515b48 --- /dev/null +++ b/.ruff.toml @@ -0,0 +1,76 @@ +# Exclude a variety of commonly ignored directories. +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".git-rewrite", + ".hg", + ".ipynb_checkpoints", + ".mypy_cache", + ".nox", + ".pants.d", + ".pyenv", + ".pytest_cache", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + ".vscode", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "site-packages", + "venv", +] + +line-length = 120 +indent-width = 4 + +# Assume Python 3.12 +target-version = "py312" + +[lint] +# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default. +# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or +# McCabe complexity (`C901`) by default. +select = ["E4", "E7", "E9", "F"] +ignore = [] + +# Allow fix for all enabled rules (when `--fix`) is provided. +fixable = ["ALL"] +unfixable = [] + +# Allow unused variables when underscore-prefixed. +dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" + +[format] +# Like Black, use double quotes for strings. +quote-style = "double" + +# Like Black, indent with spaces, rather than tabs. +indent-style = "space" + +# Like Black, respect magic trailing commas. +skip-magic-trailing-comma = false + +# Like Black, automatically detect the appropriate line ending. +line-ending = "auto" + +# Enable auto-formatting of code examples in docstrings. Markdown, +# reStructuredText code/literal blocks and doctests are all supported. +# +# This is currently disabled by default, but it is planned for this +# to be opt-out in the future. +docstring-code-format = false + +# Set the line length limit used when formatting code snippets in +# docstrings. +# +# This only has an effect when the `docstring-code-format` setting is +# enabled. +docstring-code-line-length = "dynamic" From 69271353eb4d7ae1e54178f7b1a1e67f19182e52 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:26:26 +0100 Subject: [PATCH 08/26] add project config --- poetry.lock | 3110 ++++++++++++++++++++++++++++++++++++++++++++++++ poetry.toml | 2 + pyproject.toml | 63 + 3 files changed, 3175 insertions(+) create mode 100644 poetry.lock create mode 100644 poetry.toml create mode 100644 pyproject.toml diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..7b6b4c8 --- /dev/null +++ b/poetry.lock @@ 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"https://github.com/AI2MS/pyAKI" +keywords = ["AKI", "Data", "ICU", "Healthcare", "Analysis"] +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Intended Audience :: Science/Research", + "Intended Audience :: Developers", +] + +[tool.poetry.urls] +Changelog = "https://github.com/AI2MS/pyAKI/releases" +Bugtracker = "https://github.com/AI2MS/pyAKI/issues" + +[tool.poetry.dependencies] +python = "^3.13" +pandas = "^2.2.3" +pandas-stubs = "^2.2.3.241126" +scipy = "^1.15.0" +typer = {extras = ["all"], version = "^0.9.0"} + +[tool.poetry.group.dev.dependencies] +mypy = "^1.14.1" +pytest = "^8.0.2" +coverage = "^7.6.10" +pytest-cov = "^6.0.0" +ruff = "^0.8.6" +pytest-recording = "^0.13.1" +pytest-random-order = "^1.1.1" +jupyterlab = "^4.3.4" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.mypy] +python_version = "3.13" +warn_return_any = true +warn_unused_configs = true +disallow_untyped_defs = true +strict_optional = true + +[tool.pytest.ini_options] +python_files = ["test_*.py", "*_test.py"] +filterwarnings = ["ignore::DeprecationWarning"] +asyncio_mode = "auto" +addopts = [ + "--cov", + "--cov-branch", + "--cov=src", + "--cov-report=xml", + "--import-mode=importlib", + "--random-order", +] From b5f65db6a30081cbb4143b3b6144fa53086a3cda Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:29:41 +0100 Subject: [PATCH 09/26] move tests --- .pre-commit-config.yaml | 4 +- {test => tests}/__init__.py | 0 {test => tests}/data/validation_data.csv | 0 {test => tests}/preprocessors/__init__.py | 0 .../test_creatinie_preprocessor.py | 0 .../test_demographics_preprocessor.py | 4 +- .../preprocessors/test_rrt_preprocessor.py | 0 .../test_time_index_preprocessor.py | 0 .../test_urineoutput_preprocessor.py | 0 {test => tests}/probes/__init__.py | 0 .../probes/test_creatinine_probes.py | 95 +++++-------------- {test => tests}/probes/test_rrt_probe.py | 8 +- .../probes/test_urineoutput_probes.py | 27 ++---- {test => tests}/set_up.py | 0 {test => tests}/test_analyser.py | 16 +--- 15 files changed, 40 insertions(+), 114 deletions(-) rename {test => tests}/__init__.py (100%) rename {test => tests}/data/validation_data.csv (100%) rename {test => tests}/preprocessors/__init__.py (100%) rename {test => tests}/preprocessors/test_creatinie_preprocessor.py (100%) rename {test => tests}/preprocessors/test_demographics_preprocessor.py (93%) rename {test => tests}/preprocessors/test_rrt_preprocessor.py (100%) rename {test => tests}/preprocessors/test_time_index_preprocessor.py (100%) rename {test => tests}/preprocessors/test_urineoutput_preprocessor.py (100%) rename {test => tests}/probes/__init__.py (100%) rename {test => tests}/probes/test_creatinine_probes.py (66%) rename {test => tests}/probes/test_rrt_probe.py (84%) rename {test => tests}/probes/test_urineoutput_probes.py (90%) rename {test => tests}/set_up.py (100%) rename {test => tests}/test_analyser.py (87%) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 68206b8..2e2f93d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -21,6 +21,4 @@ repos: rev: v1.8.0 hooks: - id: mypy - additional_dependencies: - - pandera[mypy] - - types-PyYAML + exclude: "^tests/.*" diff --git a/test/__init__.py b/tests/__init__.py similarity index 100% rename from test/__init__.py rename to tests/__init__.py diff --git a/test/data/validation_data.csv b/tests/data/validation_data.csv similarity index 100% rename from test/data/validation_data.csv rename to tests/data/validation_data.csv diff --git a/test/preprocessors/__init__.py b/tests/preprocessors/__init__.py similarity index 100% rename from test/preprocessors/__init__.py rename to tests/preprocessors/__init__.py diff --git a/test/preprocessors/test_creatinie_preprocessor.py b/tests/preprocessors/test_creatinie_preprocessor.py similarity index 100% rename from test/preprocessors/test_creatinie_preprocessor.py rename to tests/preprocessors/test_creatinie_preprocessor.py diff --git a/test/preprocessors/test_demographics_preprocessor.py b/tests/preprocessors/test_demographics_preprocessor.py similarity index 93% rename from test/preprocessors/test_demographics_preprocessor.py rename to tests/preprocessors/test_demographics_preprocessor.py index afb190c..5a8363b 100644 --- a/test/preprocessors/test_demographics_preprocessor.py +++ b/tests/preprocessors/test_demographics_preprocessor.py @@ -17,9 +17,7 @@ def test_preprocessor(self): }, ) - _, df = self.preprocessor.process([Dataset(DatasetType.DEMOGRAPHICS, demo_df)])[ - 0 - ] + _, df = self.preprocessor.process([Dataset(DatasetType.DEMOGRAPHICS, demo_df)])[0] pd.testing.assert_series_equal( df["weight"], diff --git a/test/preprocessors/test_rrt_preprocessor.py b/tests/preprocessors/test_rrt_preprocessor.py similarity index 100% rename from test/preprocessors/test_rrt_preprocessor.py rename to tests/preprocessors/test_rrt_preprocessor.py diff --git a/test/preprocessors/test_time_index_preprocessor.py b/tests/preprocessors/test_time_index_preprocessor.py similarity index 100% rename from test/preprocessors/test_time_index_preprocessor.py rename to tests/preprocessors/test_time_index_preprocessor.py diff --git a/test/preprocessors/test_urineoutput_preprocessor.py b/tests/preprocessors/test_urineoutput_preprocessor.py similarity index 100% rename from test/preprocessors/test_urineoutput_preprocessor.py rename to tests/preprocessors/test_urineoutput_preprocessor.py diff --git a/test/probes/__init__.py b/tests/probes/__init__.py similarity index 100% rename from test/probes/__init__.py rename to tests/probes/__init__.py diff --git a/test/probes/test_creatinine_probes.py b/tests/probes/test_creatinine_probes.py similarity index 66% rename from test/probes/test_creatinine_probes.py rename to tests/probes/test_creatinine_probes.py index 56fe7f9..f31a877 100644 --- a/test/probes/test_creatinine_probes.py +++ b/tests/probes/test_creatinine_probes.py @@ -23,9 +23,7 @@ def setUp(self) -> None: def test_abs_creatinine_aki(self): creatinine_df = pd.DataFrame( data={"creat": [1] * 24 + [1.3] * 23 + [6] * 23}, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-03 21:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-03 21:00:00", freq="h"), ) _type, df = self.probe.probe( @@ -40,9 +38,7 @@ def test_abs_creatinine_aki(self): pd.Series( data=[0.0] * 24 + [1.0] * 23 + [3.0] * 23, name="abs_creatinine_stage", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-03 21:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-03 21:00:00", freq="h"), ), check_index=False, ) @@ -80,9 +76,7 @@ def setUp(self) -> None: def test_rel_creatinine_aki(self): creatinine_df = pd.DataFrame( data={"creat": [1] * 24 + [1.5] * 23 + [3] * 23 + [9] * 23}, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) _type, df = self.probe.probe( @@ -97,9 +91,7 @@ def test_rel_creatinine_aki(self): pd.Series( data=[0.0] * 24 + [1.0] * 23 + [2.0] * 23 + [3.0] * 23, name="rel_creatinine_stage", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ), check_index=False, ) @@ -131,148 +123,113 @@ def test_validation_data(self): class TestBaselineCreatinine(TestCase): def test_rolling_min_baseline(self): - probe = AbstractCreatinineProbe( - baseline_timeframe="1d", method=CreatinineBaselineMethod.ROLLING_MIN - ) + probe = AbstractCreatinineProbe(baseline_timeframe="1d", method=CreatinineBaselineMethod.ROLLING_MIN) series = pd.Series( data=[1.0] * 47 + [1.5] * 23 + [2.0] * 23, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_rolling_first_baseline(self): - probe = AbstractCreatinineProbe( - baseline_timeframe="1d", method=CreatinineBaselineMethod.ROLLING_FIRST - ) + probe = AbstractCreatinineProbe(baseline_timeframe="1d", method=CreatinineBaselineMethod.ROLLING_FIRST) series = pd.Series( data=[1.0] * 47 + [1.5] * 23 + [2.0] * 23, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_rolling_mean_baseline(self): - probe = AbstractCreatinineProbe( - baseline_timeframe="1d", method=CreatinineBaselineMethod.ROLLING_MEAN - ) + probe = AbstractCreatinineProbe(baseline_timeframe="1d", method=CreatinineBaselineMethod.ROLLING_MEAN) series = pd.Series( data=[1] * 24 + [1.5] * 23 + [2] * 23 + [3] * 23, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) series = series.rolling(24).mean() # rolling window of 24 hours series = series.bfill() # backwards fill self._test_helper(probe, series) def test_fixed_min_baseline(self): - probe = AbstractCreatinineProbe( - baseline_timeframe="1d", method=CreatinineBaselineMethod.FIXED_MIN - ) + probe = AbstractCreatinineProbe(baseline_timeframe="1d", method=CreatinineBaselineMethod.FIXED_MIN) series = pd.Series( data=[1.0] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_fixed_mean_baseline(self): - probe = AbstractCreatinineProbe( - baseline_timeframe="2d", method=CreatinineBaselineMethod.FIXED_MEAN - ) + probe = AbstractCreatinineProbe(baseline_timeframe="2d", method=CreatinineBaselineMethod.FIXED_MEAN) data_list = [1] * 24 + [1.5] * 23 + [2] * 23 + [3] * 23 mean_value = np.mean(data_list[:49]) series = pd.Series( data=[mean_value] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_overall_first_baseline(self): - probe = AbstractCreatinineProbe( - method=CreatinineBaselineMethod.OVERALL_FIRST) + probe = AbstractCreatinineProbe(method=CreatinineBaselineMethod.OVERALL_FIRST) series = pd.Series( data=[1.0] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_overall_min_baseline(self): - probe = AbstractCreatinineProbe( - method=CreatinineBaselineMethod.OVERALL_MIN) + probe = AbstractCreatinineProbe(method=CreatinineBaselineMethod.OVERALL_MIN) series = pd.Series( data=[1.0] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_overall_mean_baseline(self): - probe = AbstractCreatinineProbe( - method=CreatinineBaselineMethod.OVERALL_MEAN) + probe = AbstractCreatinineProbe(method=CreatinineBaselineMethod.OVERALL_MEAN) data = [1] * 24 + [1.5] * 23 + [2] * 23 + [3] * 23 mean_value = np.mean(data) series = pd.Series( data=[mean_value] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_constant_baseline(self): - probe = AbstractCreatinineProbe( - method=CreatinineBaselineMethod.CONSTANT) + probe = AbstractCreatinineProbe(method=CreatinineBaselineMethod.CONSTANT) series = pd.Series( data=[1.0] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) def test_calculated_baseline(self): - probe = AbstractCreatinineProbe( - method=CreatinineBaselineMethod.CALCULATED) + probe = AbstractCreatinineProbe(method=CreatinineBaselineMethod.CALCULATED) series = pd.Series( data=[2.9159636295463067] * 93, name="creat", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) self._test_helper(probe, series) @@ -280,9 +237,7 @@ def test_calculated_baseline(self): def _test_helper(self, probe, series): creatinine_df = pd.DataFrame( data={"creat": [1] * 24 + [1.5] * 23 + [2] * 23 + [3] * 23}, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) patient_df = pd.Series( diff --git a/test/probes/test_rrt_probe.py b/tests/probes/test_rrt_probe.py similarity index 84% rename from test/probes/test_rrt_probe.py rename to tests/probes/test_rrt_probe.py index e8e24ee..ca84f7c 100644 --- a/test/probes/test_rrt_probe.py +++ b/tests/probes/test_rrt_probe.py @@ -17,9 +17,7 @@ def test_rrt_probe(self): data={ "rrt_status": [0] * 24 + [1] * 23 + [0] * 23 + [1] * 23, }, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) _, df = self.probe.probe([Dataset(DatasetType.RRT, rrt_df)])[0] @@ -29,9 +27,7 @@ def test_rrt_probe(self): pd.Series( data=[0] * 24 + [3] * 23 + [0] * 23 + [3] * 23, name="rrt_stage", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), dtype=float, ), check_index=False, diff --git a/test/probes/test_urineoutput_probes.py b/tests/probes/test_urineoutput_probes.py similarity index 90% rename from test/probes/test_urineoutput_probes.py rename to tests/probes/test_urineoutput_probes.py index 8deaa9f..51aa22e 100644 --- a/test/probes/test_urineoutput_probes.py +++ b/tests/probes/test_urineoutput_probes.py @@ -48,8 +48,7 @@ def test_anuria(self): pd.testing.assert_series_equal( df["urineoutput_stage"], pd.Series( - data=[np.nan, np.nan, np.nan, np.nan, - np.nan, 1, 1, 1, 1, 1, 1, 3], + data=[np.nan, np.nan, np.nan, np.nan, np.nan, 1, 1, 1, 1, 1, 1, 3], name="urineoutput_stage", index=pd.DatetimeIndex( data=[ @@ -187,9 +186,7 @@ def test_validation_data(self): ), Dataset( DatasetType.DEMOGRAPHICS, - self.validation_data_unlabelled[["weight"]] - .groupby("stay_id") - .first(), + self.validation_data_unlabelled[["weight"]].groupby("stay_id").first(), ), ], probes=[UrineOutputProbe()], @@ -206,9 +203,7 @@ def test_validation_data(self): def test_aki_strict(self): urine_output_df = pd.DataFrame( data={"urineoutput": [100] + [25] * 24}, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-02 00:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-02 00:00:00", freq="h"), ) demographics = pd.Series(data={"weight": 100}) @@ -225,9 +220,7 @@ def test_aki_strict(self): pd.Series( data=[np.nan] * 5 + [0] + [1] * 6 + [2] * 12 + [3], name="urineoutput_stage", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-02 00:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-02 00:00:00", freq="h"), dtype=float, ), check_index=False, @@ -236,9 +229,7 @@ def test_aki_strict(self): def test_nan_values(self): urine_output_df = pd.DataFrame( data={"urineoutput": [100] * 6 + [np.nan] * 6 + [100] * 6}, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h"), ) demographics = pd.Series(data={"weight": 100}) @@ -262,9 +253,7 @@ def test_nan_values(self): pd.Series( data=[np.nan] * 5 + [0] + [np.nan] * 11 + [0], name="urineoutput_stage", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h"), dtype=float, ), check_index=False, @@ -275,9 +264,7 @@ def test_nan_values(self): pd.Series( data=[np.nan] * 5 + [0] + [np.nan] * 11 + [0], name="urineoutput_stage", - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h"), dtype=float, ), check_index=False, diff --git a/test/set_up.py b/tests/set_up.py similarity index 100% rename from test/set_up.py rename to tests/set_up.py diff --git a/test/test_analyser.py b/tests/test_analyser.py similarity index 87% rename from test/test_analyser.py rename to tests/test_analyser.py index 5af512f..07c82b9 100644 --- a/test/test_analyser.py +++ b/tests/test_analyser.py @@ -25,9 +25,7 @@ def test_validation_data(self): data={ "rrt_status": [0] * 24 + [1] * 23 + [0] * 23 + [1] * 22 + [-1], }, - index=pd.period_range( - start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h" - ), + index=pd.period_range(start="2023-01-01 00:00:00", end="2023-01-04 20:00:00", freq="h"), ) with self.assertRaises(ValueError): @@ -84,18 +82,12 @@ def test_creatinine_settings(self): DatasetType.URINEOUTPUT, self.validation_data_unlabelled[["urineoutput"]], ), - Dataset( - DatasetType.CREATININE, self.validation_data_unlabelled[["creat"]] - ), + Dataset(DatasetType.CREATININE, self.validation_data_unlabelled[["creat"]]), Dataset( DatasetType.DEMOGRAPHICS, - self.validation_data_unlabelled[["weight"]] - .groupby("stay_id") - .first(), - ), - Dataset( - DatasetType.RRT, self.validation_data_unlabelled[["rrt_status"]] + self.validation_data_unlabelled[["weight"]].groupby("stay_id").first(), ), + Dataset(DatasetType.RRT, self.validation_data_unlabelled[["rrt_status"]]), ], preprocessors=[], ).process_stays() From 90466fb38a77e50e86a037f2dbe5915e9f4ce069 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:30:59 +0100 Subject: [PATCH 10/26] fix tests --- tests/probes/test_creatinine_probes.py | 12 ++++++------ tests/probes/test_rrt_probe.py | 6 +++--- tests/probes/test_urineoutput_probes.py | 7 +++---- tests/test_analyser.py | 4 ++-- 4 files changed, 14 insertions(+), 15 deletions(-) diff --git a/tests/probes/test_creatinine_probes.py b/tests/probes/test_creatinine_probes.py index f31a877..2c61cda 100644 --- a/tests/probes/test_creatinine_probes.py +++ b/tests/probes/test_creatinine_probes.py @@ -1,18 +1,18 @@ from unittest import TestCase -import pandas as pd import numpy as np +import pandas as pd + +from pyAKI.kdigo import Analyser from pyAKI.probes import ( - RelativeCreatinineProbe, AbsoluteCreatinineProbe, - CreatinineBaselineMethod, AbstractCreatinineProbe, + CreatinineBaselineMethod, Dataset, DatasetType, + RelativeCreatinineProbe, ) -from pyAKI.kdigo import Analyser - -from test.set_up import setup_validation_data +from tests.set_up import setup_validation_data class TestAbsCreatinineProbe(TestCase): diff --git a/tests/probes/test_rrt_probe.py b/tests/probes/test_rrt_probe.py index ca84f7c..8ed0e80 100644 --- a/tests/probes/test_rrt_probe.py +++ b/tests/probes/test_rrt_probe.py @@ -1,10 +1,10 @@ from unittest import TestCase + import pandas as pd -from pyAKI.probes import RRTProbe, Dataset, DatasetType from pyAKI.kdigo import Analyser - -from test.set_up import setup_validation_data +from pyAKI.probes import Dataset, DatasetType, RRTProbe +from tests.set_up import setup_validation_data class TestRRTProbe(TestCase): diff --git a/tests/probes/test_urineoutput_probes.py b/tests/probes/test_urineoutput_probes.py index 51aa22e..48e6856 100644 --- a/tests/probes/test_urineoutput_probes.py +++ b/tests/probes/test_urineoutput_probes.py @@ -1,12 +1,11 @@ from unittest import TestCase -import pandas as pd import numpy as np +import pandas as pd -from pyAKI.probes import UrineOutputProbe, Dataset, DatasetType, UrineOutputMethod from pyAKI.kdigo import Analyser - -from test.set_up import setup_validation_data +from pyAKI.probes import Dataset, DatasetType, UrineOutputMethod, UrineOutputProbe +from tests.set_up import setup_validation_data class TestUrineOutputProbe(TestCase): diff --git a/tests/test_analyser.py b/tests/test_analyser.py index 07c82b9..13c6391 100644 --- a/tests/test_analyser.py +++ b/tests/test_analyser.py @@ -2,9 +2,9 @@ import pandas as pd -from pyAKI.probes import Dataset, DatasetType from pyAKI.kdigo import Analyser -from test.set_up import setup_validation_data +from pyAKI.probes import Dataset, DatasetType +from tests.set_up import setup_validation_data class TestAnalyser(TestCase): From fa8b38c6dc7585ae695635d7f91d6c9bfcaadfba Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:37:37 +0100 Subject: [PATCH 11/26] set version to 3.12 --- .devcontainer/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 42061f0..8075d4c 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -1,4 +1,4 @@ -FROM mcr.microsoft.com/devcontainers/python:3.13 +FROM mcr.microsoft.com/devcontainers/python:3.12 ENV PYTHONUNBUFFERED 1 From aae7aeb4b33d9ff1271ffdc1e5a683b047d17caa Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:37:56 +0100 Subject: [PATCH 12/26] update deps --- poetry.lock | 152 +++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 3 +- 2 files changed, 148 insertions(+), 7 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7b6b4c8..685126a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -15,6 +15,7 @@ files = [ [package.dependencies] idna = ">=2.8" sniffio = ">=1.1" +typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] @@ -411,18 +412,33 @@ files = [ {file = "charset_normalizer-3.4.1.tar.gz", hash = "sha256:44251f18cd68a75b56585dd00dae26183e102cd5e0f9f1466e6df5da2ed64ea3"}, ] +[[package]] +name = "click" +version = "8.1.8" +description = "Composable command line interface toolkit" +optional = false +python-versions = ">=3.7" +groups = ["main"] +files = [ + {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"}, + {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + [[package]] name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" -groups = ["dev"] -markers = "sys_platform == \"win32\"" +groups = ["main", "dev"] files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, ] +markers = {dev = "sys_platform == \"win32\""} [[package]] name = "comm" @@ -517,6 +533,26 @@ files = [ [package.extras] toml = ["tomli"] +[[package]] +name = "coveralls" +version = "4.0.1" +description = "Show coverage stats online via coveralls.io" +optional = false +python-versions = "<3.13,>=3.8" +groups = ["dev"] +files = [ + {file = "coveralls-4.0.1-py3-none-any.whl", hash = "sha256:7a6b1fa9848332c7b2221afb20f3df90272ac0167060f41b5fe90429b30b1809"}, + {file = "coveralls-4.0.1.tar.gz", hash = "sha256:7b2a0a2bcef94f295e3cf28dcc55ca40b71c77d1c2446b538e85f0f7bc21aa69"}, +] + +[package.dependencies] +coverage = {version = ">=5.0,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<8.0", extras = ["toml"]} +docopt = ">=0.6.1,<0.7.0" +requests = ">=1.0.0,<3.0.0" + +[package.extras] +yaml = ["pyyaml (>=3.10,<7.0)"] + [[package]] name = "debugpy" version = "1.8.11" @@ -577,6 +613,17 @@ files = [ {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, ] +[[package]] +name = "docopt" +version = "0.6.2" +description = "Pythonic argument parser, that will make you smile" +optional = false +python-versions = "*" +groups = ["dev"] +files = [ + {file = "docopt-0.6.2.tar.gz", hash = "sha256:49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491"}, +] + [[package]] name = "executing" version = "2.1.0" @@ -1115,6 +1162,31 @@ docs = ["autodoc-traits", "jinja2 (<3.2.0)", "mistune (<4)", "myst-parser", "pyd openapi = ["openapi-core (>=0.18.0,<0.19.0)", "ruamel-yaml"] test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-validator (>=0.6.0,<0.8.0)", "pytest (>=7.0,<8)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "ruamel-yaml", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"] +[[package]] +name = "markdown-it-py" +version = "3.0.0" +description = "Python port of markdown-it. Markdown parsing, done right!" +optional = false +python-versions = ">=3.8" +groups = ["main"] +files = [ + {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"}, + {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"}, +] + +[package.dependencies] +mdurl = ">=0.1,<1.0" + +[package.extras] +benchmarking = ["psutil", "pytest", "pytest-benchmark"] +code-style = ["pre-commit (>=3.0,<4.0)"] +compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"] +linkify = ["linkify-it-py (>=1,<3)"] +plugins = ["mdit-py-plugins"] +profiling = ["gprof2dot"] +rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] +testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] + [[package]] name = "markupsafe" version = "3.0.2" @@ -1201,6 +1273,18 @@ files = [ [package.dependencies] traitlets = "*" +[[package]] +name = "mdurl" +version = "0.1.2" +description = "Markdown URL utilities" +optional = false +python-versions = ">=3.7" +groups = ["main"] +files = [ + {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"}, + {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"}, +] + [[package]] name = "mistune" version = "3.1.0" @@ -1962,7 +2046,7 @@ version = "2.19.1" description = "Pygments is a syntax highlighting package written in Python." optional = false python-versions = ">=3.8" -groups = ["dev"] +groups = ["main", "dev"] files = [ {file = "pygments-2.19.1-py3-none-any.whl", hash = "sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c"}, {file = "pygments-2.19.1.tar.gz", hash = "sha256:61c16d2a8576dc0649d9f39e089b5f02bcd27fba10d8fb4dcc28173f7a45151f"}, @@ -2384,6 +2468,25 @@ files = [ {file = "rfc3986_validator-0.1.1.tar.gz", hash = "sha256:3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055"}, ] +[[package]] +name = "rich" +version = "13.9.4" +description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" +optional = false +python-versions = ">=3.8.0" +groups = ["main"] +files = [ + {file = "rich-13.9.4-py3-none-any.whl", hash = "sha256:6049d5e6ec054bf2779ab3358186963bac2ea89175919d699e378b99738c2a90"}, + {file = "rich-13.9.4.tar.gz", hash = "sha256:439594978a49a09530cff7ebc4b5c7103ef57baf48d5ea3184f21d9a2befa098"}, +] + +[package.dependencies] +markdown-it-py = ">=2.2.0" +pygments = ">=2.13.0,<3.0.0" + +[package.extras] +jupyter = ["ipywidgets (>=7.5.1,<9)"] + [[package]] name = "rpds-py" version = "0.22.3" @@ -2621,6 +2724,18 @@ enabler = ["pytest-enabler (>=2.2)"] test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.14.*)", "pytest-mypy"] +[[package]] +name = "shellingham" +version = "1.5.4" +description = "Tool to Detect Surrounding Shell" +optional = false +python-versions = ">=3.7" +groups = ["main"] +files = [ + {file = "shellingham-1.5.4-py2.py3-none-any.whl", hash = "sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686"}, + {file = "shellingham-1.5.4.tar.gz", hash = "sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de"}, +] + [[package]] name = "six" version = "1.17.0" @@ -2755,6 +2870,31 @@ files = [ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"] +[[package]] +name = "typer" +version = "0.9.4" +description = "Typer, build great CLIs. Easy to code. Based on Python type hints." +optional = false +python-versions = ">=3.6" +groups = ["main"] +files = [ + {file = "typer-0.9.4-py3-none-any.whl", hash = "sha256:aa6c4a4e2329d868b80ecbaf16f807f2b54e192209d7ac9dd42691d63f7a54eb"}, + {file = "typer-0.9.4.tar.gz", hash = "sha256:f714c2d90afae3a7929fcd72a3abb08df305e1ff61719381384211c4070af57f"}, +] + +[package.dependencies] +click = ">=7.1.1,<9.0.0" +colorama = {version = ">=0.4.3,<0.5.0", optional = true, markers = "extra == \"all\""} +rich = {version = ">=10.11.0,<14.0.0", optional = true, markers = "extra == \"all\""} +shellingham = {version = ">=1.3.0,<2.0.0", optional = true, markers = "extra == \"all\""} +typing-extensions = ">=3.7.4.3" + +[package.extras] +all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<14.0.0)", "shellingham (>=1.3.0,<2.0.0)"] +dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] +doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"] +test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.971)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<14.0.0)", "shellingham (>=1.3.0,<2.0.0)"] + [[package]] name = "types-python-dateutil" version = "2.9.0.20241206" @@ -2785,7 +2925,7 @@ version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" -groups = ["dev"] +groups = ["main", "dev"] files = [ {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, @@ -3106,5 +3246,5 @@ propcache = ">=0.2.0" [metadata] lock-version = "2.1" -python-versions = "^3.13" -content-hash = "1c43346179ebf9032800c1fd2b9bdcfe60400b5d74f4c38606eb206292690a48" +python-versions = "~3.12" +content-hash = "e43cd3b73142d988685d65dfd07785f53eabc4046bee814ed2573245148dab06" diff --git a/pyproject.toml b/pyproject.toml index 245561b..5e8760f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ Changelog = "https://github.com/AI2MS/pyAKI/releases" Bugtracker = "https://github.com/AI2MS/pyAKI/issues" [tool.poetry.dependencies] -python = "^3.13" +python = "~3.12" pandas = "^2.2.3" pandas-stubs = "^2.2.3.241126" scipy = "^1.15.0" @@ -37,6 +37,7 @@ ruff = "^0.8.6" pytest-recording = "^0.13.1" pytest-random-order = "^1.1.1" jupyterlab = "^4.3.4" +coveralls = "^4.0.1" [build-system] requires = ["poetry-core"] From 22fd47d77b6164257bd6271d6051b7a04d494cc6 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:38:37 +0100 Subject: [PATCH 13/26] update dependabot --- .github/dependabot.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ea49867..183285c 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -5,6 +5,14 @@ version: 2 updates: + - package-ecosystem: "docker" + directory: "/" + schedule: + interval: "daily" + - package-ecosystem: "devcontainers" + directory: "/" + schedule: + interval: "daily" - package-ecosystem: "github-actions" # See documentation for possible values directory: "/" # Location of package manifests schedule: @@ -12,4 +20,4 @@ updates: - package-ecosystem: "pip" directory: "/" schedule: - interval: "daily" \ No newline at end of file + interval: "daily" From b9e80fb7aaa5c2628a65861db8d8c1bdb7d3032d Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:38:57 +0100 Subject: [PATCH 14/26] python ci --- .github/workflows/python_ci.yml | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 .github/workflows/python_ci.yml diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml new file mode 100644 index 0000000..f535ff0 --- /dev/null +++ b/.github/workflows/python_ci.yml @@ -0,0 +1,43 @@ +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Continuous Integration (Python) +on: push + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.12"] # Add more Python versions to test here + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Cache Virtual Environment + uses: actions/cache@v4 + with: + path: | + .venv + ~/.cache/pip + ~/.cache/pypoetry + key: ${{ runner.os }}-venv-${{ hashFiles('poetry.lock') }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install poetry + poetry install --with dev + + - name: Lint with ruff + run: poetry run ruff check . + - name: Check types with mypy + run: poetry run mypy . + - name: Test with pytest + run: poetry run pytest . From 69929670159d86fb4da5383c9e83acebf21d9537 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:39:15 +0100 Subject: [PATCH 15/26] clean up --- requirements.txt | 6 ------ setup.cfg | 26 -------------------------- setup.py | 7 ------- 3 files changed, 39 deletions(-) delete mode 100644 requirements.txt delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 08d6220..0000000 --- a/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -pandas==2.2.2 -pandas-stubs==2.2.2.240514 -numpy==1.26.4 -scipy==1.13.1 -pbr==6.0.0 -typer[all]==0.9.0 \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index f544e71..0000000 --- a/setup.cfg +++ /dev/null @@ -1,26 +0,0 @@ -[metadata] -metadata-version = 2.1 -name = pyAKI -description_file = README.md -version = 0.0.2 -long_description_content_type = text/markdown -summary = pyAKI allows calculation of Acute Kidney Injury from urine output and creatinine based on KDIGO criteria. -author = 'Jan Ernsting, Christian Porschen, Paul Brauckmann' -url = https://github.com/AI2MS/pyAKI -project_urls= - Source Code = https://github.com/AI2MS/pyAKI - Documentation = https://github.com/AI2MS/pyAKI - Bug Tracker = https://github.com/AI2MS/pyAKI/issues - -download_url=https://github.com/AI2MS/pyAKI -keywords= - AKI -classifier= - Programming Language :: Python :: 3 - Operating System :: OS Independent - Intended Audience :: Science/Research - Intended Audience :: Developers -decription-file = README.md - -[files] -packages=pyAKI diff --git a/setup.py b/setup.py deleted file mode 100644 index ca808e8..0000000 --- a/setup.py +++ /dev/null @@ -1,7 +0,0 @@ -from setuptools import setup, find_packages - -setup( - pbr=True, - packages=find_packages(), - scripts=["bin/process_aki_stages.py"], -) From aedbe8c7896ba01c88ab4927ceb75f6fd398aadb Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:57:55 +0100 Subject: [PATCH 16/26] fix tests --- tests/preprocessors/test_creatinie_preprocessor.py | 7 ++++--- tests/preprocessors/test_demographics_preprocessor.py | 5 +++-- tests/preprocessors/test_rrt_preprocessor.py | 8 ++++---- tests/preprocessors/test_time_index_preprocessor.py | 5 +++-- tests/preprocessors/test_urineoutput_preprocessor.py | 7 ++++--- tests/probes/test_creatinine_probes.py | 4 ++-- tests/probes/test_rrt_probe.py | 4 ++-- tests/probes/test_urineoutput_probes.py | 4 ++-- tests/set_up.py | 2 +- tests/test_analyser.py | 4 ++-- 10 files changed, 27 insertions(+), 23 deletions(-) diff --git a/tests/preprocessors/test_creatinie_preprocessor.py b/tests/preprocessors/test_creatinie_preprocessor.py index ea7c6f9..81d4528 100644 --- a/tests/preprocessors/test_creatinie_preprocessor.py +++ b/tests/preprocessors/test_creatinie_preprocessor.py @@ -1,9 +1,10 @@ from unittest import TestCase -import pandas as pd + import numpy as np +import pandas as pd -from pyAKI.preprocessors import CreatininePreProcessor -from pyAKI.utils import Dataset, DatasetType +from pyaki.preprocessors import CreatininePreProcessor +from pyaki.utils import Dataset, DatasetType class TestCreatininePreProcessor(TestCase): diff --git a/tests/preprocessors/test_demographics_preprocessor.py b/tests/preprocessors/test_demographics_preprocessor.py index 5a8363b..dd9c074 100644 --- a/tests/preprocessors/test_demographics_preprocessor.py +++ b/tests/preprocessors/test_demographics_preprocessor.py @@ -1,8 +1,9 @@ from unittest import TestCase + import pandas as pd -from pyAKI.preprocessors import DemographicsPreProcessor -from pyAKI.utils import Dataset, DatasetType +from pyaki.preprocessors import DemographicsPreProcessor +from pyaki.utils import Dataset, DatasetType class TestDemographicsPreProcessor(TestCase): diff --git a/tests/preprocessors/test_rrt_preprocessor.py b/tests/preprocessors/test_rrt_preprocessor.py index e50520f..08a243d 100644 --- a/tests/preprocessors/test_rrt_preprocessor.py +++ b/tests/preprocessors/test_rrt_preprocessor.py @@ -1,10 +1,10 @@ from unittest import TestCase -import pandas as pd -import numpy as np +import numpy as np +import pandas as pd -from pyAKI.preprocessors import RRTPreProcessor -from pyAKI.utils import Dataset, DatasetType +from pyaki.preprocessors import RRTPreProcessor +from pyaki.utils import Dataset, DatasetType class TestRRTPreProcessor(TestCase): diff --git a/tests/preprocessors/test_time_index_preprocessor.py b/tests/preprocessors/test_time_index_preprocessor.py index ab81987..682cd5e 100644 --- a/tests/preprocessors/test_time_index_preprocessor.py +++ b/tests/preprocessors/test_time_index_preprocessor.py @@ -1,8 +1,9 @@ from unittest import TestCase + import pandas as pd -from pyAKI.preprocessors import TimeIndexCreator -from pyAKI.utils import Dataset, DatasetType +from pyaki.preprocessors import TimeIndexCreator +from pyaki.utils import Dataset, DatasetType class TestTimeIndexCreator(TestCase): diff --git a/tests/preprocessors/test_urineoutput_preprocessor.py b/tests/preprocessors/test_urineoutput_preprocessor.py index 9004caf..b912df3 100644 --- a/tests/preprocessors/test_urineoutput_preprocessor.py +++ b/tests/preprocessors/test_urineoutput_preprocessor.py @@ -1,9 +1,10 @@ from unittest import TestCase -import pandas as pd + import numpy as np +import pandas as pd -from pyAKI.preprocessors import UrineOutputPreProcessor -from pyAKI.utils import Dataset, DatasetType +from pyaki.preprocessors import UrineOutputPreProcessor +from pyaki.utils import Dataset, DatasetType class TestUrineOutputPreProcessor(TestCase): diff --git a/tests/probes/test_creatinine_probes.py b/tests/probes/test_creatinine_probes.py index 2c61cda..21806cd 100644 --- a/tests/probes/test_creatinine_probes.py +++ b/tests/probes/test_creatinine_probes.py @@ -3,8 +3,8 @@ import numpy as np import pandas as pd -from pyAKI.kdigo import Analyser -from pyAKI.probes import ( +from pyaki.kdigo import Analyser +from pyaki.probes import ( AbsoluteCreatinineProbe, AbstractCreatinineProbe, CreatinineBaselineMethod, diff --git a/tests/probes/test_rrt_probe.py b/tests/probes/test_rrt_probe.py index 8ed0e80..0f8095d 100644 --- a/tests/probes/test_rrt_probe.py +++ b/tests/probes/test_rrt_probe.py @@ -2,8 +2,8 @@ import pandas as pd -from pyAKI.kdigo import Analyser -from pyAKI.probes import Dataset, DatasetType, RRTProbe +from pyaki.kdigo import Analyser +from pyaki.probes import Dataset, DatasetType, RRTProbe from tests.set_up import setup_validation_data diff --git a/tests/probes/test_urineoutput_probes.py b/tests/probes/test_urineoutput_probes.py index 48e6856..75805ac 100644 --- a/tests/probes/test_urineoutput_probes.py +++ b/tests/probes/test_urineoutput_probes.py @@ -3,8 +3,8 @@ import numpy as np import pandas as pd -from pyAKI.kdigo import Analyser -from pyAKI.probes import Dataset, DatasetType, UrineOutputMethod, UrineOutputProbe +from pyaki.kdigo import Analyser +from pyaki.probes import Dataset, DatasetType, UrineOutputMethod, UrineOutputProbe from tests.set_up import setup_validation_data diff --git a/tests/set_up.py b/tests/set_up.py index 7db40db..ff3ffd9 100644 --- a/tests/set_up.py +++ b/tests/set_up.py @@ -2,7 +2,7 @@ def setup_validation_data(): - validation_data = pd.read_csv("test/data/validation_data.csv") + validation_data = pd.read_csv("tests/data/validation_data.csv") # coerce stay_id to int validation_data["stay_id"] = validation_data["stay_id"].astype(int) # convert charttime to datetime diff --git a/tests/test_analyser.py b/tests/test_analyser.py index 13c6391..e89e5aa 100644 --- a/tests/test_analyser.py +++ b/tests/test_analyser.py @@ -2,8 +2,8 @@ import pandas as pd -from pyAKI.kdigo import Analyser -from pyAKI.probes import Dataset, DatasetType +from pyaki.kdigo import Analyser +from pyaki.probes import Dataset, DatasetType from tests.set_up import setup_validation_data From d04d9cce76ad2c2487b9d7c30992f5e037337e40 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 21:58:29 +0100 Subject: [PATCH 17/26] add script --- pyproject.toml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5e8760f..d138b80 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "pyAKI" +name = "pyaki" description = "pyAKI allows calculation of Acute Kidney Injury from urine output and creatinine based on KDIGO criteria." version = "1.0.0" license = "MIT" @@ -43,6 +43,9 @@ coveralls = "^4.0.1" requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" +[tool.poetry.scripts] +pyaki-cli = "pyaki.bin.process_aki_stages:run" + [tool.mypy] python_version = "3.13" warn_return_any = true From 398e489436cfef6c60fc177615c61cae3b0d13d4 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 22:05:00 +0100 Subject: [PATCH 18/26] umpdate pyaki --- pyAKI/__init__.py | 6 ---- pyaki/__init__.py | 0 {bin => pyaki/bin}/process_aki_stages.py | 22 +++++++----- {pyAKI => pyaki}/kdigo.py | 46 +++++++++--------------- {pyAKI => pyaki}/preprocessors.py | 6 ++-- {pyAKI => pyaki}/probes.py | 24 ++++++------- {pyAKI => pyaki}/utils.py | 23 +++++------- 7 files changed, 51 insertions(+), 76 deletions(-) delete mode 100644 pyAKI/__init__.py create mode 100644 pyaki/__init__.py rename {bin => pyaki/bin}/process_aki_stages.py (85%) rename {pyAKI => pyaki}/kdigo.py (88%) rename {pyAKI => pyaki}/preprocessors.py (97%) rename {pyAKI => pyaki}/probes.py (97%) rename {pyAKI => pyaki}/utils.py (88%) diff --git a/pyAKI/__init__.py b/pyAKI/__init__.py deleted file mode 100644 index 7e76fa7..0000000 --- a/pyAKI/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -from pyAKI.kdigo import Analyser - -from pbr.version import VersionInfo # type: ignore - -# Check the PBR version module docs for other options than release_string() -__version__ = VersionInfo("pyAKI").release_string() diff --git a/pyaki/__init__.py b/pyaki/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/bin/process_aki_stages.py b/pyaki/bin/process_aki_stages.py similarity index 85% rename from bin/process_aki_stages.py rename to pyaki/bin/process_aki_stages.py index 3eb6455..7bd5816 100755 --- a/bin/process_aki_stages.py +++ b/pyaki/bin/process_aki_stages.py @@ -1,14 +1,13 @@ #! /usr/bin/env python3 -"""pyAKI CLI tool""" - -import typer +"""pyaki CLI tool""" from pathlib import Path import pandas as pd +import typer -from pyAKI.kdigo import Analyser -from pyAKI.utils import Dataset, DatasetType +from pyaki.kdigo import Analyser +from pyaki.utils import Dataset, DatasetType def main( @@ -17,7 +16,7 @@ def main( creatinine_file: str = "creatinine.csv", rrt_file: str = "rrt.csv", demographics_file: str = "demographics.csv", -): +) -> None: """ CLI tool to process AKI stages from time series data. @@ -46,8 +45,8 @@ def main( if (scr_file := root_dir / creatinine_file).is_file(): datasets.append(Dataset(DatasetType.CREATININE, pd.read_csv(scr_file))) - if (rrt_file := root_dir / rrt_file).is_file(): - datasets.append(Dataset(DatasetType.RRT, pd.read_csv(rrt_file))) + if (_rrt_file := root_dir / rrt_file).is_file(): + datasets.append(Dataset(DatasetType.RRT, pd.read_csv(_rrt_file))) if (demo_file := root_dir / demographics_file).is_file(): datasets.append(Dataset(DatasetType.DEMOGRAPHICS, pd.read_csv(demo_file))) @@ -56,5 +55,10 @@ def main( ana.process_stays().to_csv(root_dir / "aki.csv") -if __name__ == "__main__": +def run() -> None: + """Run the CLI tool""" typer.run(main) + + +if __name__ == "__main__": + run() diff --git a/pyAKI/kdigo.py b/pyaki/kdigo.py similarity index 88% rename from pyAKI/kdigo.py rename to pyaki/kdigo.py index 89288bb..92eaa14 100644 --- a/pyAKI/kdigo.py +++ b/pyaki/kdigo.py @@ -1,26 +1,24 @@ import logging - from typing import Optional import pandas as pd -from pyAKI.probes import ( - Probe, - UrineOutputProbe, - AbsoluteCreatinineProbe, - RelativeCreatinineProbe, - RRTProbe, -) -from pyAKI.preprocessors import ( - Preprocessor, - TimeIndexCreator, - UrineOutputPreProcessor, +from pyaki.preprocessors import ( CreatininePreProcessor, DemographicsPreProcessor, + Preprocessor, RRTPreProcessor, + TimeIndexCreator, + UrineOutputPreProcessor, ) - -from pyAKI.utils import Dataset +from pyaki.probes import ( + AbsoluteCreatinineProbe, + Probe, + RelativeCreatinineProbe, + RRTProbe, + UrineOutputProbe, +) +from pyaki.utils import Dataset logger = logging.getLogger(__name__) @@ -74,19 +72,11 @@ def __init__( ] if preprocessors is None: # apply default preprocessors if not provided preprocessors = [ - TimeIndexCreator( - stay_identifier=stay_identifier, time_identifier=time_identifier - ), - UrineOutputPreProcessor( - stay_identifier=stay_identifier, time_identifier=time_identifier - ), - CreatininePreProcessor( - stay_identifier=stay_identifier, time_identifier=time_identifier - ), + TimeIndexCreator(stay_identifier=stay_identifier, time_identifier=time_identifier), + UrineOutputPreProcessor(stay_identifier=stay_identifier, time_identifier=time_identifier), + CreatininePreProcessor(stay_identifier=stay_identifier, time_identifier=time_identifier), DemographicsPreProcessor(stay_identifier=stay_identifier), - RRTPreProcessor( - stay_identifier=stay_identifier, time_identifier=time_identifier - ), + RRTPreProcessor(stay_identifier=stay_identifier, time_identifier=time_identifier), ] # validate datasets @@ -164,9 +154,7 @@ def process_stay(self, stay_id: str) -> pd.DataFrame: if isinstance(_df, pd.Series): _df = pd.DataFrame([_df], index=df.index) columns = set(_df.columns) - set(df.columns) - df = df.merge( - _df[[*columns]], how="outer", left_index=True, right_index=True - ) + df = df.merge(_df[[*columns]], how="outer", left_index=True, right_index=True) df["stage"] = df.filter(like="stage").max(axis=1) return df.set_index( diff --git a/pyAKI/preprocessors.py b/pyaki/preprocessors.py similarity index 97% rename from pyAKI/preprocessors.py rename to pyaki/preprocessors.py index 04e4b51..16b6d94 100644 --- a/pyAKI/preprocessors.py +++ b/pyaki/preprocessors.py @@ -4,15 +4,13 @@ import pandas as pd from pandas.api.types import is_datetime64_any_dtype -from pyAKI.utils import dataset_as_df, df_to_dataset, Dataset, DatasetType +from pyaki.utils import Dataset, DatasetType, dataset_as_df, df_to_dataset class Preprocessor(ABC): """Abstract base class for preprocessors.""" - def __init__( - self, stay_identifier: str = "stay_id", time_identifier: str = "charttime" - ) -> None: + def __init__(self, stay_identifier: str = "stay_id", time_identifier: str = "charttime") -> None: """ Initialize a new instance of the Preprocessor class. diff --git a/pyAKI/probes.py b/pyaki/probes.py similarity index 97% rename from pyAKI/probes.py rename to pyaki/probes.py index 9184a00..7b50f9f 100644 --- a/pyAKI/probes.py +++ b/pyaki/probes.py @@ -3,12 +3,12 @@ from abc import ABC, ABCMeta from enum import StrEnum, auto +from typing import Any -import pandas as pd import numpy as np +import pandas as pd -import logging -from pyAKI.utils import dataset_as_df, df_to_dataset, approx_gte, Dataset, DatasetType +from pyaki.utils import Dataset, DatasetType, approx_gte, dataset_as_df, df_to_dataset class Probe(ABC): @@ -42,7 +42,7 @@ def probe(self, datasets: list[Dataset], **kwargs) -> pd.DataFrame: RESNAME: str = "" # name of the column that will be added to the dataframe - def probe(self, datasets: list[Dataset], **kwargs) -> list[Dataset]: + def probe(self, datasets: list[Dataset], **kwargs: Any) -> list[Dataset]: """ Abstract method to be implemented by subclasses. @@ -127,7 +127,7 @@ def probe( self, df: pd.DataFrame, patient: pd.DataFrame, - **kwargs, + **kwargs: Any, ) -> pd.DataFrame: """ Perform urine output analysis on the provided DataFrame. @@ -303,12 +303,10 @@ def creatinine_baseline(self, df: pd.DataFrame, patient: pd.DataFrame) -> pd.Ser .ffill()[self._column] ) min_value: pd.DatetimeIndex = values[ - values.index - <= (values.index[0] + pd.Timedelta(self._baseline_timeframe)) + values.index <= (values.index[0] + pd.Timedelta(self._baseline_timeframe)) ].min() # calculate min value for first 7 days values[ - values.index - > (values.index[0] + pd.Timedelta(self._baseline_timeframe)) + values.index > (values.index[0] + pd.Timedelta(self._baseline_timeframe)) ] = min_value # set all values after first 7 days to min value return values @@ -436,7 +434,7 @@ def probe( self, df: pd.DataFrame, patient: pd.DataFrame, - **kwargs, + **kwargs: Any, ) -> pd.DataFrame: """ Perform KDIGO stage calculation based on absolute creatinine elevations on the provided DataFrame. @@ -480,7 +478,7 @@ class RelativeCreatinineProbe(AbstractCreatinineProbe): @dataset_as_df(df=DatasetType.CREATININE, patient=DatasetType.DEMOGRAPHICS) @df_to_dataset(DatasetType.CREATININE) - def probe(self, df: pd.DataFrame, patient: pd.DataFrame, **kwargs) -> pd.DataFrame: + def probe(self, df: pd.DataFrame, patient: pd.DataFrame, **kwargs: Any) -> pd.DataFrame: """ Perform calculation of relative creatinine elevations on the provided DataFrame. @@ -498,9 +496,7 @@ def probe(self, df: pd.DataFrame, patient: pd.DataFrame, **kwargs) -> pd.DataFra baseline_values: pd.Series = self.creatinine_baseline(df, patient) df.loc[:, self.RESNAME] = 0 - df.loc[ - approx_gte((df[self._column] / baseline_values), 1.5), self.RESNAME - ] = 1.0 + df.loc[approx_gte((df[self._column] / baseline_values), 1.5), self.RESNAME] = 1.0 df.loc[approx_gte((df[self._column] / baseline_values), 2), self.RESNAME] = 2 df.loc[approx_gte((df[self._column] / baseline_values), 3), self.RESNAME] = 3 diff --git a/pyAKI/utils.py b/pyaki/utils.py similarity index 88% rename from pyAKI/utils.py rename to pyaki/utils.py index 405dc69..9fdba5b 100644 --- a/pyAKI/utils.py +++ b/pyaki/utils.py @@ -1,8 +1,7 @@ import logging - -from typing import NamedTuple, cast from enum import StrEnum, auto from functools import wraps +from typing import Any, Callable, NamedTuple, cast import numpy as np import pandas as pd @@ -41,7 +40,7 @@ class Dataset(NamedTuple): df: pd.DataFrame -def dataset_as_df(**mapping: DatasetType): +def dataset_as_df(**mapping: DatasetType) -> Callable: """ Decorator factory for methods that process datasets with dataframes. @@ -82,14 +81,12 @@ def process_data(self, data: pd.DataFrame, labels: pd.DataFrame): # in_mapping: Dict[DatasetType, str] = {v: k for k, v in mapping.items()} - def decorator(func): + def decorator(func: Callable) -> Callable: @wraps(func) - def wrapper(self, datasets: list[Dataset], *args, **kwargs) -> list[Dataset]: + def wrapper(self: Any, datasets: list[Dataset], *args: Any, **kwargs: Any) -> list[Dataset]: # map the dataset types to corresponding DataFrames _mapping: dict[str, pd.DataFrame] = { - in_mapping[dtype]: df - for dtype, df in datasets - if dtype in in_mapping.keys() + in_mapping[dtype]: df for dtype, df in datasets if dtype in in_mapping.keys() } # check if all datasets are mapped, otherwise return the original datasets if len(in_mapping) != len(_mapping): @@ -103,16 +100,14 @@ def wrapper(self, datasets: list[Dataset], *args, **kwargs) -> list[Dataset]: _dtype, _df = func(self, *args, **_mapping, **kwargs) # return the updated datasets - return [ - Dataset(dtype, _df if dtype == _dtype else df) for dtype, df in datasets - ] + return [Dataset(dtype, _df if dtype == _dtype else df) for dtype, df in datasets] return wrapper return decorator -def df_to_dataset(dtype: DatasetType): +def df_to_dataset(dtype: DatasetType) -> Callable: """ Decorator that converts a DataFrame into a dataset with the specified type. @@ -135,9 +130,9 @@ def process_dataframe(self, *args: list, **kwargs: dict) -> pd.DataFrame: ... """ - def decorator(func): + def decorator(func: Callable) -> Callable: @wraps(func) - def wrapper(self, *args: list, **kwargs: dict) -> Dataset: + def wrapper(self: Any, *args: Any, **kwargs: Any) -> Dataset: return Dataset(dtype, func(self, *args, **kwargs)) return wrapper From cbe779cd2ae020d9119331730f70f0ab8444304a Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 22:07:50 +0100 Subject: [PATCH 19/26] update pipeline --- .github/workflows/lint_and_test.yml | 38 ----------------------------- .github/workflows/python_ci.yml | 5 ++++ 2 files changed, 5 insertions(+), 38 deletions(-) delete mode 100644 .github/workflows/lint_and_test.yml diff --git a/.github/workflows/lint_and_test.yml b/.github/workflows/lint_and_test.yml deleted file mode 100644 index 9d28d81..0000000 --- a/.github/workflows/lint_and_test.yml +++ /dev/null @@ -1,38 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a single version of Python -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Python application -on: push - -jobs: - build: - name: Test pyAKI - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest_cov coveralls mypy - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest - run: | - pytest --cov=. test/ - - name: Coveralls - run: coveralls - env: - COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} - - name: Run mypy - run: | - mypy ./pyAKI/ \ No newline at end of file diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index f535ff0..a3844f2 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -41,3 +41,8 @@ jobs: run: poetry run mypy . - name: Test with pytest run: poetry run pytest . + + - name: Coveralls + run: poetry run coveralls + env: + COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} From c8d99029a4b81f7dded770d0e180c0f3d90c0f20 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 22:09:16 +0100 Subject: [PATCH 20/26] update pipeline --- .github/workflows/python_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index a3844f2..5996936 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -6,7 +6,7 @@ on: push jobs: build: - + environment: pyaki runs-on: ubuntu-latest strategy: matrix: From 19e7e8336d366749fd13f80d5e82b644f1ad87f2 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Tue, 7 Jan 2025 22:25:32 +0100 Subject: [PATCH 21/26] fix mypy --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index d138b80..bfcb1db 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,6 +52,7 @@ warn_return_any = true warn_unused_configs = true disallow_untyped_defs = true strict_optional = true +exclude = ["^tests/.*", ] [tool.pytest.ini_options] python_files = ["test_*.py", "*_test.py"] From 85ee21430997d356752eb1beeb1330b853fad259 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:15:03 +0100 Subject: [PATCH 22/26] update github actions --- .github/workflows/python_cd.yml | 45 +++++++++++++++++++++++++++++++++ .github/workflows/python_ci.yml | 6 ++++- pyproject.toml | 2 +- 3 files changed, 51 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/python_cd.yml diff --git a/.github/workflows/python_cd.yml b/.github/workflows/python_cd.yml new file mode 100644 index 0000000..095e455 --- /dev/null +++ b/.github/workflows/python_cd.yml @@ -0,0 +1,45 @@ +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Continuous Delivery (Python) +on: + release: + types: [published] + +jobs: + build: + environment: pyaki + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.12"] # Add more Python versions to test here + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Cache Virtual Environment + uses: actions/cache@v4 + with: + path: | + .venv + ~/.cache/pip + ~/.cache/pypoetry + key: ${{ runner.os }}-venv-${{ hashFiles('poetry.lock') }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install poetry + poetry install --with dev + + - name: Build and publish Package + run: | + poetry version ${{ github.ref_name }} + poetry publish --skip-existing --build + env: + POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }} diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index 5996936..c8ad338 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -2,7 +2,11 @@ # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions name: Continuous Integration (Python) -on: push +on: + push: + branches: [ main, develop ] + pull_request: + branches: [ main, develop ] jobs: build: diff --git a/pyproject.toml b/pyproject.toml index bfcb1db..5064c13 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "pyaki" description = "pyAKI allows calculation of Acute Kidney Injury from urine output and creatinine based on KDIGO criteria." -version = "1.0.0" +version = "0.0.0" # Placeholder license = "MIT" authors = ["ADIH MS"] readme = "README.md" From 5fd8116ce5dd03eccc6ca981efa901ff47fcfdec Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:29:17 +0100 Subject: [PATCH 23/26] update readme --- README.md | 43 ++++++++++++++++++++++++++++++++++++++----- 1 file changed, 38 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index efd7a51..7f44402 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,14 @@ The goal of this package is to establish well tested, comprehensive functions fo ## Installation +You can install the pyAKI package from PyPI or from source. + +Frm PyPI: +```shell +pip install pyAKI +``` + +From source: ```shell pip install git+https://github.com/aidh-ms/pyAKI ``` @@ -18,8 +26,8 @@ pip install git+https://github.com/aidh-ms/pyAKI ```python import pandas as pd -from pyAKI.probes import Dataset, DatasetType -from pyAKI.kdigo import Analyser +from pyaki.probes import Dataset, DatasetType +from pyaki.kdigo import Analyser data = [ Dataset(DatasetType.URINEOUTPUT, pd.DataFrame()), @@ -32,15 +40,40 @@ analyser = Analyser(data) results: pd.Dataframe = analyser.process_stays() ``` +## Contributing + +### Getting Started + +> [!NOTE] +> Use the included dev container to automatically install all the necessary dev tools and dependencies. To use this you first need to install docker under Linux or WSL2 under windows. + +1. **Clone the repository:** + ```bash + git clone https://github.com/aidh-ms/pyAKI + cd pyAKI + ``` + +2. **Open the project in Visual Studio Code:** + ```bash + code . + ``` + +3. **Reopen in Container:** + - Press `F1` to open the command palette. + - Type `Remote-Containers: Reopen in Container` and select it. + - VS Code will build the Docker container defined in the `.devcontainer` folder and open the project inside the container. + ### Tests +To test your contribution, you can use the testing tap in the VS code or utilise the following command to run the unit tests for this project: + ```shell -pytest --cov=. test/ +poetry run pytest . ``` ### Acknowledgement -We encourage all users to use pyAKI in their scientific work. Doing so, please use the following citation: +We encourage all users to use pyAKI in their scientific work. Doing so, please use the following citation. Our paper can be found on [PLOS One](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315325). ``` @article{10.1371/journal.pone.0315325, doi = {10.1371/journal.pone.0315325}, @@ -58,5 +91,5 @@ We encourage all users to use pyAKI in their scientific work. Doing so, please u } ``` -Our paper can be found on [PLOS One](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315325). + [^kdigo]: Improving Global Outcomes (KDIGO) Acute Kidney Injury Work Group. KDIGO Clinical Practice Guideline for Acute Kidney Injury. Kidney inter., Suppl. 2012; 2: 1–138. From 1d65f3b622cdb3410e10f1805f02ec79d7b3c5ae Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:41:58 +0100 Subject: [PATCH 24/26] clean up --- ChangeLog | 235 ------------------------------------------------------ 1 file changed, 235 deletions(-) delete mode 100644 ChangeLog diff --git a/ChangeLog b/ChangeLog deleted file mode 100644 index 5902053..0000000 --- a/ChangeLog +++ /dev/null @@ -1,235 +0,0 @@ -CHANGES -======= - -0.0.2 ------ - -* Update setup.cfg -* Update README.md -* build(deps): bump pandas-stubs from 2.1.4.231227 to 2.2.0.240218 -* build(deps): bump numpy from 1.26.3 to 1.26.4 -* Update README.md -* clean up -* update README -* build(deps): bump scipy from 1.11.4 to 1.12.0 -* build(deps): bump pandas from 2.1.4 to 2.2.0 -* build(deps): bump pandas-stubs from 2.1.4.231218 to 2.1.4.231227 -* build(deps): bump numpy from 1.26.2 to 1.26.3 -* fix: nan defaults -* Update README.md -* test: fix rel crea -* test: fix abs crea -* test: fix val data -* test: fix test rel creat -* update default timeframe forabs creat probe -* feat: change default probe -* build(deps): bump pandas-stubs from 2.1.1.230928 to 2.1.4.231218 -* build(deps): bump pandas from 2.1.3 to 2.1.4 -* Remove unneccessary columns -* build(deps): bump actions/setup-python from 4 to 5 -* fix typing -* fix minor issue -* test: fix analyser test -* test: fix test with old threshold -* feat: change threshold -* test: fix test for analyser pipeline -* feat: add test for complete analyser -* doc: add docstrings for new baseline methods -* feat: unify df augmentation method -* feat: tests for new baseline methods -* feat: implement new baseline methods with tests -* chore: add citation.cff file -* Update README.md -* Update README.md -* Update README.md -* Update README.md -* merge -* fix test -* add calc method for creat -* fix constant method -* feature: implement calculated baseline method -* fix: remove test -* feature: implement constant creatinine baseline -* build(deps): bump scipy from 1.11.3 to 1.11.4 -* fix pandas warnings -* minor fixes after feedback -* fix nan values -* update github actions -* update github actions -* update github actions -* update github actions -* add mypy to github actions -* fx typing of utils -* types: fix some type errors by hardening programn flow -* types: change variable name to fix pylance warning -* types: fix types in utils.py -* types: fix types in approx\_gte -* add logging for analyser -* add waringn when probe is skipped -* add test case for negative input -* handle negative data -* fix type hints -* add test for urine output strict probe -* build(deps): bump pandas from 2.1.2 to 2.1.3 -* build(deps): bump numpy from 1.26.1 to 1.26.2 -* minor fixes -* add urine output preprocessor test -* add creatinie preprocessor test -* add time preprocessor test -* add demographics preprocessor test -* add rrt preprocessor test -* add test structure -* clean up tests -* minor fix -* chore: adjust metadata version -* chore: Remove author email from setup.cfg -* chore: Add metadata version and package version, update author list -* Added coverage badge -* Added coverage calculation -* build(deps): bump pbr from 5.11.1 to 6.0.0 -* chore: add paper to gitignore -* chore: add results folder to keep locally -* doc: add docstrings for CLI -* add typer as dep -* build(deps): bump pandas from 2.1.1 to 2.1.2 -* fix: fill empty row -* chore: remove unnecessary files -* fixes -* fix urine output test -* fix: fix error in uo stage -* fix urine output tests -* fix crrt test -* chore: Update lint\_and\_test.yml -* fix data -* fix abs creat test -* fix: correct validation data with nans for creat -* update creat tests -* update creat tests -* fix test -* doc: add some documentation to decorators -* feat: fix crrt probe nan bug -* test: add validation data -* test: add tests on validation data -* chore: first cleanup of test folder -* rename crt to rrt -* build(deps): bump numpy from 1.26.0 to 1.26.1 -* fix for floating point errors -* clean up -* add time index creator -* fix minor issues -* fix minor issues -* build(deps): bump scipy from 1.11.2 to 1.11.3 - -v0.1.0 ------- - -* fix bug -* build(deps): bump numpy from 1.25.2 to 1.26.0 -* build(deps): bump pandas from 2.0.3 to 2.1.1 -* fix abs value for stage 3 from 4mg/dl increase over baseline to 4mg/dl -* build(deps): bump actions/checkout from 3 to 4 -* update setup file -* initiation for human testing -* build(deps): bump scipy from 1.11.1 to 1.11.2 -* remove prints -* generation of experiment data -* build(deps): bump numpy from 1.25.1 to 1.25.2 -* new testing notebook -* add unittest for creatinine baseline -* clean up -* fix unittests -* doc: add module docstring -* fix: Default creatinine baseline method is fixed 7d -* doc: add documentation for FIXED method -* test generation -* feat: add fixed creatinine baseline method -* fix: change baseline creatinie to correct method -* fix: add resilience when data is missing -* build(deps): bump numpy from 1.25.0 to 1.25.1 -* feature: add enum for urineoutputprobe -* feature: mean method for urine output -* feature: crrt probe working with tests -* build(deps): bump scipy from 1.10.1 to 1.11.1 -* build(deps): bump pandas from 2.0.2 to 2.0.3 -* build(deps): bump numpy from 1.24.3 to 1.25.0 -* feature: adjust for new dataframes -* fix: fix settingwithcopywarning in pandas -* add typing imports -* fix: remove additional stay\_id column -* chore: fix spelling in tests -* clean up and fixes -* add rel creatinine test -* add abs creatinine test -* set python version to 3.11 for ci -* fix imports -* merge -* clean up -* add test for urineoutput probe -* fix imports for mimic test -* fix imports -* feature: add crrt to analyser class -* feature: crrt probe -* feature: time series preprocessor for crrt -* fix: add environment to gitignore -* fix: resolve comments -* doc: use optional type hints -* chore: fix some imports and configs -* doc: add documentation for preprocessors -* chore: fix style -* chore: add data folder to .gitignore -* doc: add type annotation -* update mimic test -* chore: format style test\_kdigo -* doc: add type annotations in kdigo -* doc: add documentation for process stays -* chore: remove duplicate documentation -* add test script for mimic data -* add method for processing multiple stays -* chore: fix spelling -* chore: remove unnecessary import -* doc: add documentation to analyser -* chore: fix spelling in Analyzer class -* chore: formatting -* doc: finish docstrings for probes -* fix: pull the calculation of baseline crea into abstract class -* chore: rename timeframe to baseline\_timeframe -* chore: rename creatininemethod to CreatinineBaselineMethod -* chore: fix spelling in AbstracCreatinineProbe -* doc: add documentation for urineoutput probe -* chore: fix typo in Resampler Class -* doc: add type annotation and docstrings to probe -* docs: add type annotations to preprocessor -* docs: add docstrings and type annotations to utils.py -* doc: add docstrings to utils.py -* clean up -* update to new decorator -* add preprocessor for demograhics dataset -* add preprocessor for creatinine dataset -* add preprocessor for urineoutput dataset -* fix readme -* add DEMOGRAPHICS dataset to types -* refactor propes -* add abs serum creatinie probe -* correct urineoutput in docs -* add tests to readme -* refactor probes -* create analysis services -* add probes for urine output and relative serum creatinine -* add proprocessor for data -* add util methods -* Update .gitignore -* Remove pyaki from .gitignore -* Updated testing -* Updated workflows -* Initial version of pyAKI. [WIP] -* Create dependabot.yml -* init tests -* update requirements -* add vscode stuff -* add vscode stuff -* init requirements file -* fix readme -* init kdigo file -* add env -* update readme file -* Initial commit From ed9eec6026bfeb500780b8d39346de74b4fe7562 Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:55:01 +0100 Subject: [PATCH 25/26] update readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7f44402..d5af596 100644 --- a/README.md +++ b/README.md @@ -71,7 +71,7 @@ To test your contribution, you can use the testing tap in the VS code or utilise poetry run pytest . ``` -### Acknowledgement +## Acknowledgement We encourage all users to use pyAKI in their scientific work. Doing so, please use the following citation. Our paper can be found on [PLOS One](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315325). ``` From 71678c49c50880f6436bd7c4ef45d1c9a927ceeb Mon Sep 17 00:00:00 2001 From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com> Date: Wed, 8 Jan 2025 20:43:08 +0100 Subject: [PATCH 26/26] fix install from source in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d5af596..ad0025b 100644 --- a/README.md +++ b/README.md @@ -49,7 +49,7 @@ results: pd.Dataframe = analyser.process_stays() 1. **Clone the repository:** ```bash - git clone https://github.com/aidh-ms/pyAKI + git clone git+https://github.com/aidh-ms/pyAKI cd pyAKI ```