From f5564254bc5508e0815327d2fce98a879bb0cec7 Mon Sep 17 00:00:00 2001 From: "Huska, Matthew" Date: Fri, 15 Nov 2024 12:35:31 +0100 Subject: [PATCH] Bump version --- CONTRIBUTING.md | 6 +- README.md | 6 +- envs/breakfast-dev.yml | 12 + noxfile.py | 22 +- poetry.lock | 498 ++++++++++++++++++++++++++++------------- pyproject.toml | 4 +- 6 files changed, 377 insertions(+), 171 deletions(-) create mode 100644 envs/breakfast-dev.yml diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index f4dc7b8..3f0ae67 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -14,16 +14,16 @@ breakfast is written in Python and tries to follow the excellent packaging guide ### Setting up your development tools -Some tooling needs to be set up before you can work on breakfast. To install this we use mamba, a faster replacement for the conda package manager, and place them in their own environment: +Some tooling needs to be set up before you can work on breakfast. To install this we use conda, and place them in their own environment: ```sh -mamba create -n breakfast-dev python=3 poetry fortran-compiler nox pre-commit +conda env create -n breakfast-dev -f envs/breakfast-dev.yml ``` Then when you want to work on the project, or at the very least if you want to use poetry commands or run tests, you need to switch to this environment: ```sh -mamba activate breakfast-dev +conda activate breakfast-dev ``` The rest of this document assumes that you have the breakfast-dev environment active. diff --git a/README.md b/README.md index 03020dc..8527ffe 100644 --- a/README.md +++ b/README.md @@ -15,9 +15,9 @@ Breakfast is available in [bioconda](http://bioconda.github.io/recipes/breakfast/README.html). You can install it using either the conda command, or if you've installed [mamba](https://github.com/mamba-org/mamba) you can use that: ``` -$ conda install breakfast +$ conda install -c bioconda breakfast # or -$ mamba install breakfast +$ mamba install -c bioconda breakfast ``` ### Installation using pip @@ -43,7 +43,7 @@ You will find your results in `test-run/cluster.tsv`, which should be identical ### Using breakfast with input from covsonar -breakfast uses pre-calculated sequence features (= mutations) as input rather than raw sequences. These features can be calculated with several different programs, but the one we mainly use is [covSonar](https://github.com/rki-mf1/covsonar). It can be used to maintain a database of mutations for a large number of sequences, which can then be easily queried. +breakfast uses pre-calculated sequence features (= mutations) as input rather than raw sequences. These features can be calculated with several different programs, but the one we mainly use is [covsonar](https://github.com/rki-mf1/covsonar). It can be used to maintain a database of mutations for a large number of sequences, which can then be easily queried. ``` conda activate sonar diff --git a/envs/breakfast-dev.yml b/envs/breakfast-dev.yml new file mode 100644 index 0000000..28fa515 --- /dev/null +++ b/envs/breakfast-dev.yml @@ -0,0 +1,12 @@ +name: breakfast-dev +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - python>=3.9,<3.10 + - poetry + - poetry-plugin-export + - fortran-compiler + - nox + - pre-commit diff --git a/noxfile.py b/noxfile.py index 2cf5d53..295dffb 100644 --- a/noxfile.py +++ b/noxfile.py @@ -8,7 +8,8 @@ package = "breakfast" nox.options.sessions = "lint", "tests" -locations = "src", "tests", "noxfile.py" +nox.options.default_venv_backend = "conda" +locations = "src", "tests", "./noxfile.py" def install_with_constraints(session: Session, *args: str, **kwargs: Any) -> None: @@ -25,23 +26,32 @@ def install_with_constraints(session: Session, *args: str, **kwargs: Any) -> Non kwargs: Additional keyword arguments for Session.install. """ with tempfile.NamedTemporaryFile() as requirements: + # Hide a warning that I have already handled + session.run( + "poetry", + "config", + "warnings.export", + "false", + external=True, + ) session.run( "poetry", "export", - "--dev", + "--with", + "dev", "--format=requirements.txt", "--without-hashes", f"--output={requirements.name}", external=True, ) - session.install(f"--constraint={requirements.name}", *args, **kwargs) + session.install("-r", requirements.name, *args, **kwargs) @nox.session(python="3.9") def black(session: Session) -> None: """Run black code formatter.""" args = session.posargs or locations - install_with_constraints(session, "black") + install_with_constraints(session) session.run("black", *args) @@ -66,6 +76,6 @@ def lint(session: Session) -> None: @nox.session(python=["3.10", "3.9"]) def tests(session): args = session.posargs or ["--cov"] - session.run("poetry", "install", "--no-dev", external=True) - install_with_constraints(session, "coverage[toml]", "pytest", "pytest-cov") + session.run("poetry", "install", "--without", "dev", external=True) + install_with_constraints(session) session.run("pytest", *args) diff --git a/poetry.lock b/poetry.lock index 3830618..4cf629b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,24 +1,42 @@ +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. + [[package]] name = "attrs" version = "22.1.0" description = "Classes Without Boilerplate" -category = "dev" optional = false python-versions = ">=3.5" +files = [ + {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"}, + {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"}, +] [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", 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