diff --git a/.github/workflows/docs_pages.yaml b/.github/workflows/docs_pages.yaml index 2ad27dfa..c2c9df4a 100644 --- a/.github/workflows/docs_pages.yaml +++ b/.github/workflows/docs_pages.yaml @@ -1,42 +1,44 @@ name: Docs2Pages on: - pull_request: - branches: - - master + workflow_run: + workflows: ["CI"] + types: + - completed permissions: contents: write jobs: build-docs: runs-on: ubuntu-latest steps: - - name: Checkout - uses: actions/checkout@master - with: - fetch-depth: 0 - - uses: actions/setup-python@v2 - with: - python-version: 3.8 - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - version: latest - virtualenvs-create: true - virtualenvs-in-project: true - installer-parallel: true - - name: Install package - run: poetry install - - name: Build documentation - run: | - mkdir gh-pages - touch gh-pages/.nojekyll - cd docs/ - poetry run make html - cp -r build/* ../gh-pages/ - cd ../gh-pages/ - cp -r html/* . - rm -rf html/ - - name: Deploy documentation - uses: JamesIves/github-pages-deploy-action@4.1.4 - with: - branch: gh-pages - folder: gh-pages + - name: Checkout + uses: actions/checkout@master + with: + fetch-depth: 0 + - uses: actions/setup-python@v2 + with: + python-version: 3.8 + + - uses: pdm-project/setup-pdm@v3 + with: + prerelease: false + enable-pep582: false + allow-python-prereleases: false + + - name: Install package + run: pdm install + + - name: Build documentation + run: | + mkdir gh-pages + touch gh-pages/.nojekyll + cd docs/ + pdm run make html + cp -r build/* ../gh-pages/ + cd ../gh-pages/ + cp -r html/* . + rm -rf html/ + - name: Deploy documentation + uses: JamesIves/github-pages-deploy-action@4.1.4 + with: + branch: gh-pages + folder: gh-pages diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index ade0a8d0..ba189ab6 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -6,9 +6,9 @@ name: CI on: # Triggers the workflow on push or pull request events but only for the master branch push: - branches: [ master, develop ] + branches: [master, develop] pull_request: - branches: [ master, develop ] + branches: [master, develop] # Allows you to run this workflow manually from the Actions tab workflow_dispatch: @@ -21,29 +21,30 @@ jobs: timeout-minutes: 60 strategy: matrix: - python-version: ['3.10'] + python-version: ["3.10"] steps: - - uses: conda-incubator/setup-miniconda@v2 - with: - auto-activate-base: true - activate-environment: "" - - - uses: actions/checkout@v3 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - version: latest - installer-parallel: true - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install nox nox-poetry - - run: nox + - uses: conda-incubator/setup-miniconda@v2 + with: + auto-activate-base: true + activate-environment: "" + + - uses: actions/checkout@v3 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Setup PDM + uses: pdm-project/setup-pdm@v3 + with: + prerelease: false + enable-pep582: false + allow-python-prereleases: false + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install nox + - run: nox diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml new file mode 100644 index 00000000..cdb5fb63 --- /dev/null +++ b/.github/workflows/publish-to-test-pypi.yml @@ -0,0 +1,52 @@ +name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI + +on: + push: + branches: [master] + pull_request: + branches: [master] + +jobs: + build-n-publish: + name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.x" + - name: Setup PDM + uses: pdm-project/setup-pdm@v3 + with: + prerelease: false + enable-pep582: false + allow-python-prereleases: false + # - name: Install pypa/build + # run: >- + # python3 -m + # pip install + # build + # --user + # - name: Build a binary wheel and a source tarball + # run: >- + # python3 -m + # build + # --sdist + # --wheel + # --outdir dist/ + # . + - name: Build a binary wheel and a source tarball + run: >- + pdm build + - name: Publish distribution 📦 to Test PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + password: ${{ secrets.TEST_PYPI_API_TOKEN }} + repository-url: https://test.pypi.org/legacy/ + - name: Publish distribution 📦 to PyPI + if: startsWith(github.ref, 'refs/tags') + uses: pypa/gh-action-pypi-publish@release/v1 + with: + password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.gitignore b/.gitignore index 88d7808c..623dda17 100644 --- a/.gitignore +++ b/.gitignore @@ -288,4 +288,5 @@ results_July2021_gpu scripts/automorf.ipynb debug.ipynb -dask-worker-space/ \ No newline at end of file +dask-worker-space/ +.pdm-python diff --git a/README.md b/README.md index d6343b96..4ac4331e 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction -Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction +Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction ## Setup @@ -10,26 +10,26 @@ To install the `drexml` package use the following: ``` conda create -n drexml python=3.10 -conda run -n drexml pip install git+https://github.com/loucerac/drexml.git@master +conda activate drexml +pip install drexml ``` -If a CUDA~11 compatible device is available use: +If a CUDA~10.2/11.x (< 12) compatible device is available use: ``` conda create -n drexml --override-channels -c "nvidia/label/cuda-11.8.0" -c conda-forge cuda cuda-nvcc cuda-toolkit gxx=11.2 python=3.10 -conda run -n drexml pip install git+https://github.com/loucerac/drexml.git@master +conda activate drexml +pip install --no-cache-dir --no-binary=shap drexml ``` To install `drexml` in an existing environment, activate it and use: ``` -pip install git+https://github.com/loucerac/drexml.git@master +pip install drexml ``` Note that by default the `setup` will try to compile the `CUDA` modules, if not possible it will use the `CPU` modules. -To install the development version use `@develop` instead of `@master`. - ## Run To run the program for a disease map that uses circuits from the preprocessed `KEGG` pathways and the `KDT` standard list, construct an environment file (e.g. `disease.env`): @@ -47,6 +47,7 @@ circuits=circuits.tsv.gz ``` The `TSV` file `circuits.tsv` has the following format (tab delimited): + ``` index in_disease P-hsa03320-37 0 @@ -69,8 +70,9 @@ P-hsa03320-28 1 ``` where: -* `index`: Hipathia circuit id -* `in_disease`: (boolean) True/1 if a given circuit is part of the disease + +- `index`: Hipathia circuit id +- `in_disease`: (boolean) True/1 if a given circuit is part of the disease Note that in all cases you can restrict the circuits to the physiological list by setting `use_physio=true` in the `env` file. @@ -81,9 +83,10 @@ drexml run --n-gpus 0 --n-cpus 10 $DISEASE_PATH ``` where: -* `--n-gpus` indicates the number of gpu devices to use in parallel (-1 -> all) (0 -> None) -* `--n-cpus` indicates the number of cpu devices to use in parallel (-1 -> all) 8 -* `DISEASE_PATH` indicates the path to the disease env file (e.g. `/path/to/disease/folder/disease.env`) + +- `--n-gpus` indicates the number of gpu devices to use in parallel (-1 -> all) (0 -> None) +- `--n-cpus` indicates the number of cpu devices to use in parallel (-1 -> all) 8 +- `DISEASE_PATH` indicates the path to the disease env file (e.g. `/path/to/disease/folder/disease.env`) Use the `--debug` option for testing that everything works using a few iterations. @@ -91,17 +94,19 @@ Note that the first time that the full program is run, it will take longer as it https://doi.org/10.5281/zenodo.6020480 - ## Contribute to development The recommended setup is: + - setup `pipx` - setup `miniforge` -- use `pipx` to install `poetry` -- use `pipx` to install `nox` and inject `nox-poetry` into `nox` +- use `pipx` to install `pdm` +- use `pipx` to inject pd-bump into `pdm` +- use `pipx` to install `nox` - run `make`, if you want to use a CUDA enabled GPU, use `make gpu=1` ## Documentation + The documentation can be found here: https://loucerac.github.io/drexml/ diff --git a/drexml/cli/cli.py b/drexml/cli/cli.py index 67b44832..0032ac75 100644 --- a/drexml/cli/cli.py +++ b/drexml/cli/cli.py @@ -200,7 +200,11 @@ def run_cmd(ctx): cmd = build_cmd(ctx) # Unpythonic, update with dasks's LocalCudaCluster (currently unreliable). print(" ".join(cmd)) - output = subprocess.run(cmd, capture_output=True, text=True, check=True) + try: + output = subprocess.run(cmd, capture_output=True, text=True, check=True) + except subprocess.CalledProcessError as err: # pragma: no cover + click.echo("Ping stdout output:\n", err.output) + if ctx["verbosity"]: click.echo(output.stderr) click.echo(output.stdout) diff --git a/drexml/cli/stab_explainer.py b/drexml/cli/stab_explainer.py index c9eabb99..90f903e4 100644 --- a/drexml/cli/stab_explainer.py +++ b/drexml/cli/stab_explainer.py @@ -99,7 +99,6 @@ print(f"{add=}") def runner(model, bkg, new, check_add, use_gpu): - gpu_id = queue.get() if use_gpu: explainer = shap.GPUTreeExplainer(model, bkg) diff --git a/drexml/config.py b/drexml/config.py index d4f9c3ee..23cc170e 100644 --- a/drexml/config.py +++ b/drexml/config.py @@ -15,6 +15,7 @@ "circuits_zenodo": False, "genes": None, "genes_zenodo": False, + "activity_normalizer": "false", "circuits_column": "in_disease", "genes_column": "drugbank_approved_targets", "GTEX_VERSION": "v8", diff --git a/drexml/datasets.py b/drexml/datasets.py index bd2fd3ad..748aa7a5 100644 --- a/drexml/datasets.py +++ b/drexml/datasets.py @@ -52,13 +52,12 @@ def fetch_file(key, env, version="latest"): try: zenodo = Zenodo() path = zenodo.download_latest(RECORD_ID, env[key], force=False) - except (ConnectTimeout) as err: + except ConnectTimeout as err: print(err) path = pathlib.Path.home().joinpath( ".data", "zenodo", RECORD_ID, "20230612" ) else: - path = env[key] print(key, path) diff --git a/drexml/utils.py b/drexml/utils.py index aba2fa48..4baf741b 100644 --- a/drexml/utils.py +++ b/drexml/utils.py @@ -348,7 +348,7 @@ def read_seed_genes(config): def read_use_physio(config): - """Read use_physio from config file. It expect a boolean. + """Read use_physio from config file. It expects a boolean. Parameters ---------- @@ -376,6 +376,37 @@ def read_use_physio(config): return config +def read_activity_normalizer(config): + """Read activity_normalizer from config file. It expects a boolean. + + Parameters + ---------- + config : dict + Parsed config dict. + + Returns + ------- + dict + Updated config dict. + + Raises + ------ + ValueError + Raise error if format is unsupported. + """ + + try: + config["activity_normalizer"] = check_cli_arg_is_bool( + config["activity_normalizer"] + ) + except ValueError as err: + print(err) + print("activity_normalizer should be a boolean.") + raise + + return config + + def read_path_based(config, key, data_path): """Read path based. @@ -507,6 +538,7 @@ def read_disease_config(disease): config = read_seed_genes(config) config = read_use_physio(config) + config = read_activity_normalizer(config) config = read_path_based(config, key="gene_exp", data_path=env_parent_path) config = read_path_based(config, key="pathvals", data_path=env_parent_path) config = read_path_based(config, key="genes", data_path=env_parent_path) @@ -571,13 +603,20 @@ def build_pathvals_fname(config): Filename. """ + if config["activity_normalizer"]: + hipathia_str = f"hipathia-norm-{config['HIPATHIA_VERSION']}" + else: + hipathia_str = f"hipathia-{config['HIPATHIA_VERSION']}" + + print(hipathia_str) + return ( "_".join( [ "pathvals", f"gtex-{config['GTEX_VERSION']}", f"edger-{config['EDGER_VERSION']}", - f"hipathia-{config['HIPATHIA_VERSION']}", + hipathia_str, ] ) + ".feather" diff --git a/makefile b/makefile index e974011e..aafe59b8 100644 --- a/makefile +++ b/makefile @@ -14,17 +14,19 @@ else conda create -y -p ./.venv --override-channels -c conda-forge python=3.10 endif $(CONDA_ACTIVATE) ./.venv - poetry install - poetry run pytest + + PDM_NO_BINARY=shap pdm install + pdm run pytest + python -c 'import shap; shap.utils.assert_import("cext_gpu")' format: $(CONDA_ACTIVATE) ./.venv autoflake --remove-all-unused-imports --ignore-init-module-imports \ --remove-unused-variables -i drexml/*.py autoflake --remove-all-unused-imports --ignore-init-module-imports \ --remove-unused-variables -i tests/*.py - poetry run isort drexml tests noxfile.py - poetry run black drexml tests noxfile.py - (cd docs && poetry run make html) + pdm run isort drexml tests noxfile.py + pdm run black drexml tests noxfile.py + (cd docs && pdm run make html) test: ifeq ($(use_gpu),1) nox -- "gpu" @@ -33,4 +35,25 @@ else endif cover: $(CONDA_ACTIVATE) ./.venv - poetry run coverage run -m pytest tests/ -v && poetry run coverage report -m + pdm run coverage run -m pytest tests/ -v && pdm run coverage report -m +build: + rm -rf dist + rm -rf ./.venv +ifeq ($(use_gpu),1) + conda create -y -p ./.venv --override-channels -c "nvidia/label/cuda-11.8.0" \ + -c conda-forge cuda cuda-nvcc cuda-toolkit gxx=11.2 python=3.10 +else + conda create -y -p ./.venv --override-channels -c conda-forge python=3.10 +endif + $(CONDA_ACTIVATE) ./.venv + + PDM_NO_BINARY=shap pdm install + pdm publish --repository testpypi + wait + sleep 60 + pip install --no-cache-dir --no-binary=shap -i https://test.pypi.org/simple/ \ + drexml==0.11.2 --extra-index-url=https://pypi.org/simple +ifeq ($(use_gpu),1) + python -c 'import shap; shap.utils.assert_import("cext_gpu")' +endif + python -c 'import drexml' diff --git a/noxfile.py b/noxfile.py index b694a2a9..a4d6f83f 100644 --- a/noxfile.py +++ b/noxfile.py @@ -1,16 +1,16 @@ # -*- coding: utf-8 -*- """ -Test suite. +Nox test suite. """ import nox -from nox_poetry import session -@session(venv_backend="conda") +@nox.session(venv_backend="conda") @nox.parametrize("python", ["3.10", "3.9", "3.8"]) def tests(session): """Test with conda.""" + pdm_env = {"PDM_IGNORE_SAVED_PYTHON": "1"} if session.posargs: if any(("gpu" in arg for arg in session.posargs)): session.conda_install( @@ -25,5 +25,7 @@ def tests(session): "--override-channels", ) - session.install("pytest", ".") + pdm_env["PDM_NO_BINARY"] = "shap" + + session.run("pdm", "install", "-vd", external=True, env=pdm_env) session.run("pytest") diff --git a/pdm.lock b/pdm.lock new file mode 100644 index 00000000..b9c3e514 --- /dev/null +++ b/pdm.lock @@ -0,0 +1,1733 @@ +# This file is @generated by PDM. +# It is not intended for manual editing. + +[[package]] +name = "alabaster" +version = "0.7.13" +requires_python = ">=3.6" +summary = "A configurable sidebar-enabled Sphinx theme" + +[[package]] +name = "astroid" +version = "2.15.5" +requires_python = ">=3.7.2" +summary = "An abstract syntax tree for Python with inference support." +dependencies = [ + "lazy-object-proxy>=1.4.0", + "typing-extensions>=4.0.0; python_version < \"3.11\"", + "wrapt<2,>=1.11; python_version < \"3.11\"", +] + +[[package]] +name = "babel" +version = "2.12.1" +requires_python = ">=3.7" +summary = "Internationalization utilities" +dependencies = [ + "pytz>=2015.7; python_version < \"3.9\"", +] + +[[package]] +name = "black" +version = "22.12.0" +requires_python = ">=3.7" +summary = "The uncompromising code formatter." +dependencies = [ + "click>=8.0.0", + "mypy-extensions>=0.4.3", + "pathspec>=0.9.0", + "platformdirs>=2", + "tomli>=1.1.0; python_full_version < \"3.11.0a7\"", + "typing-extensions>=3.10.0.0; python_version < \"3.10\"", +] + +[[package]] +name = "certifi" +version = "2023.5.7" +requires_python = ">=3.6" +summary = "Python package for providing Mozilla's CA Bundle." + +[[package]] +name = "charset-normalizer" +version = "3.1.0" +requires_python = ">=3.7.0" +summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." + +[[package]] +name = "click" +version = "8.1.4" +requires_python = ">=3.7" +summary = "Composable command line interface toolkit" +dependencies = [ + "colorama; platform_system == \"Windows\"", +] + +[[package]] +name = "cloudpickle" +version = "2.2.1" +requires_python = ">=3.6" +summary = "Extended pickling support for Python objects" + +[[package]] +name = "colorama" +version = "0.4.6" +requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +summary = "Cross-platform colored terminal text." + +[[package]] +name = "contourpy" +version = "1.1.0" +requires_python = ">=3.8" +summary = "Python library for calculating contours of 2D quadrilateral grids" +dependencies = [ + "numpy>=1.16", +] + +[[package]] +name = "coverage" +version = "7.2.7" +requires_python = ">=3.7" +summary = "Code coverage measurement for Python" + +[[package]] +name = "cycler" +version = "0.11.0" +requires_python = ">=3.6" +summary = "Composable style cycles" + +[[package]] +name = "dataclasses-json" +version = "0.5.9" +requires_python = ">=3.6" +summary = "Easily serialize dataclasses to and from JSON" +dependencies = [ + "marshmallow-enum<2.0.0,>=1.5.1", + "marshmallow<4.0.0,>=3.3.0", + "typing-inspect>=0.4.0", +] + +[[package]] +name = "dill" +version = "0.3.6" +requires_python = ">=3.7" +summary = "serialize all of python" + +[[package]] +name = "docutils" +version = "0.18.1" +requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +summary = "Docutils -- Python Documentation Utilities" + +[[package]] +name = "exceptiongroup" +version = "1.1.2" +requires_python = ">=3.7" +summary = "Backport of PEP 654 (exception groups)" + +[[package]] +name = "flake8" +version = "4.0.1" +requires_python = ">=3.6" +summary = "the modular source code checker: pep8 pyflakes and co" +dependencies = [ + "mccabe<0.7.0,>=0.6.0", + "pycodestyle<2.9.0,>=2.8.0", + "pyflakes<2.5.0,>=2.4.0", +] + +[[package]] +name = "flake8-black" +version = "0.3.6" +requires_python = ">=3.7" +summary = "flake8 plugin to call black as a code style validator" +dependencies = [ + "black>=22.1.0", + "flake8>=3", + "tomli; python_version < \"3.11\"", +] + +[[package]] +name = "fonttools" +version = "4.40.0" +requires_python = ">=3.8" +summary = "Tools to manipulate font files" + +[[package]] +name = "idna" +version = "3.4" +requires_python = ">=3.5" +summary = "Internationalized Domain Names in Applications (IDNA)" + +[[package]] +name = "imagesize" +version = "1.4.1" +requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +summary = "Getting image size from png/jpeg/jpeg2000/gif file" + +[[package]] +name = "importlib-metadata" +version = "6.7.0" +requires_python = ">=3.7" +summary = "Read metadata from Python packages" +dependencies = [ + "zipp>=0.5", +] + +[[package]] +name = "importlib-resources" +version = "5.12.0" +requires_python = ">=3.7" +summary = "Read resources from Python packages" +dependencies = [ + "zipp>=3.1.0; python_version < \"3.10\"", +] + +[[package]] +name = "iniconfig" +version = "2.0.0" +requires_python = ">=3.7" +summary = "brain-dead simple config-ini parsing" + +[[package]] +name = "isort" +version = "5.12.0" +requires_python = ">=3.8.0" +summary = "A Python utility / library to sort Python imports." + +[[package]] +name = "jinja2" +version = "3.1.2" +requires_python = ">=3.7" +summary = "A very fast and expressive template engine." +dependencies = [ + "MarkupSafe>=2.0", +] + +[[package]] +name = "joblib" +version = "1.3.1" +requires_python = ">=3.7" +summary = "Lightweight pipelining with Python functions" + +[[package]] +name = "kiwisolver" +version = "1.4.4" +requires_python = ">=3.7" +summary = "A fast implementation of the Cassowary constraint solver" + +[[package]] +name = "lazy-object-proxy" +version = "1.9.0" +requires_python = ">=3.7" +summary = "A fast and thorough lazy object proxy." + +[[package]] +name = "llvmlite" +version = "0.40.1" +requires_python = ">=3.8" +summary = "lightweight wrapper around basic LLVM functionality" + +[[package]] +name = "markupsafe" +version = "2.1.3" +requires_python = ">=3.7" +summary = "Safely add untrusted strings to HTML/XML markup." + +[[package]] +name = "marshmallow" +version = "3.19.0" +requires_python = ">=3.7" +summary = "A lightweight library for converting complex datatypes to and from native Python datatypes." +dependencies = [ + "packaging>=17.0", +] + +[[package]] +name = "marshmallow-enum" +version = "1.5.1" +summary = "Enum field for Marshmallow" +dependencies = [ + "marshmallow>=2.0.0", +] + +[[package]] +name = "matplotlib" +version = "3.7.2" +requires_python = ">=3.8" +summary = "Python plotting package" +dependencies = [ + "contourpy>=1.0.1", + "cycler>=0.10", + "fonttools>=4.22.0", + "importlib-resources>=3.2.0; python_version < \"3.10\"", + "kiwisolver>=1.0.1", + "numpy>=1.20", + "packaging>=20.0", + "pillow>=6.2.0", + "pyparsing<3.1,>=2.3.1", + 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-[installer] -no-binary = ["shap"] diff --git a/pyproject.toml b/pyproject.toml index ee34af71..2a1eec78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,48 +1,52 @@ -[tool.poetry] +[project] +authors = [ + { name = "Carlos Loucera", email = "carlos.loucera@juntadeandalucia.es" }, + { name = "Marina Esteban-Medina", email = "marina.esteban@juntadeandalucia.es" }, + { name = "Maria Pena-Chilet", email = "maria.pena.chilet.ext@juntadeandalucia.es.com" }, +] +requires-python = ">=3.8,<3.11" +dependencies = [ + "scikit-learn>=1.3.0", + "numpy>=1.24.4", + "scipy>=1.10.1", + "pandas>=2.0.3", + "seaborn>=0.12.2", + "shap==0.42.0", + "matplotlib>=3.7.2", + "python-dotenv>=1.0.0", + "pyarrow>=12.0.1", + "zenodo-client<0.3", +] name = "drexml" -version = "0.9.12" +version = "0.11.6" description = "(DRExM³L) Drug REpurposing using and eXplainable Machine Learning and Mechanistic Models of signal transduction\"" -authors = [ - "Carlos Loucera ", - "Marina Esteban-Medina ", - "Maria Pena-Chilet " - ] -license = "MIT" +readme = "README.md" -[tool.poetry.dependencies] -python = ">=3.8, <3.11" -scikit-learn = "1.1.1" -numpy = "<1.22" -scipy = "^1.8.1" -pandas = "^1.4.2" -seaborn = "^0.11.2" -python-dotenv = "^0.20.0" -click = "^8" -zenodo-client = "^0.2.0" -pyarrow = "^8.0.0" -shap = {git = "https://github.com/slundberg/shap", rev = "v0.41.0"} -matplotlib = "~3.6" +[project.license] +text = "MIT" -[tool.poetry.dev-dependencies] -black = "^22.3.0" -isort = "^5.10.1" -pylint = "^2.14.0" -pytest = "^7.1.2" -Sphinx = "^5.0.1" -sphinx-click = "^4.1.0" -sphinx-rtd-theme = "^1.0.0" -flake8 = "^4.0.1" -flake8-black = "^0.3.3" - -[tool.poetry.group.dev.dependencies] -coverage = {extras = ["toml"], version = "^7.2.7"} +[project.group.dev.dependencies.coverage] +extras = [ + "toml", +] +version = "^7.2.7" -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +[project.scripts] +drexml = "drexml.cli.cli:main" -[tool.poetry.scripts] -drexml = 'drexml.cli.cli:main' +[tool.pdm.dev-dependencies] +dev = [ + "black<23.0.0,>=22.3.0", + "isort<6.0.0,>=5.10.1", + "pylint<3.0.0,>=2.14.0", + "pytest<8.0.0,>=7.1.2", + "Sphinx<6.0.0,>=5.0.1", + "sphinx-click<5.0.0,>=4.1.0", + "sphinx-rtd-theme<2.0.0,>=1.0.0", + "flake8<5.0.0,>=4.0.1", + "flake8-black<1.0.0,>=0.3.3", + "coverage>=7.2.7", +] [tool.pytest.ini_options] minversion = "6.0" @@ -60,8 +64,18 @@ profile = "black" [tool.black] line-length = 88 - [tool.coverage.run] -omit = [".*", "*/site-packages/*", "./tests/*"] +omit = [ + ".*", + "*/site-packages/*", + "./tests/*", +] + [tool.coverage.report] fail_under = 100 + +[build-system] +requires = [ + "pdm-backend", +] +build-backend = "pdm.backend" diff --git a/tests/example.env b/tests/example.env new file mode 100644 index 00000000..da72fb31 --- /dev/null +++ b/tests/example.env @@ -0,0 +1,3 @@ +seed_genes=9901 +use_physio=true +activity_normalizer=true \ No newline at end of file diff --git a/tests/test_utils.py b/tests/test_utils.py index ce4e2ca4..2bea47ce 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -272,7 +272,7 @@ def test_convert_names_axisnotok(): utils.convert_names(data, keys=("circuits",), axis=(2,)) -@pytest.mark.parametrize("seeds", ["11.2", "hola, 12"]) +@pytest.mark.parametrize("seeds", ["11.2", "Vader, 12"]) @pytest.mark.xfail(raises=ValueError) def test_read_seed_genes_fails(seeds): """Unit test that read_seed_genes raises an error.""" @@ -280,7 +280,7 @@ def test_read_seed_genes_fails(seeds): utils.read_seed_genes(config) -@pytest.mark.parametrize("value", ["hola"]) +@pytest.mark.parametrize("value", ["Vader"]) @pytest.mark.xfail(raises=ValueError) def test_read_use_physio_fails(value): """Unit test that read_use_physio raises an error.""" @@ -288,6 +288,23 @@ def test_read_use_physio_fails(value): utils.read_use_physio(config) +@pytest.mark.parametrize("value", ["Vader"]) +@pytest.mark.xfail(raises=ValueError) +def test_read_activity_normalizer(value): + """Unit test that read_use_physio raises an error.""" + config = {"activity_normalizer": value} + utils.read_activity_normalizer(config) + + +def test_build_pathvals_fname(): + """Test that build_pathvals-fname produces a valid string.""" + + config = DEFAULT_DICT.copy() + config["activity_normalizer"] = True + fname = utils.build_pathvals_fname(config) + assert "norm" in fname + + @pytest.mark.xfail(raises=(ValueError, FileNotFoundError)) def test_read_path_based_fails(): """Unit test that read_path_based raises an error."""