Merge pull request #23 from rki-mf1/22-update-dependencies-resolve-de…

…pendabot-alerts

Bump dependabot mentioned deps, bump version

.github/workflows/release.yml

@@ -6,13 +6,13 @@ jobs:
   release:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.10'
         architecture: x64
-    - run: pip install nox==2022.1.7
-    - run: pip install poetry==1.1.13
+    - run: pip install nox==2024.10.9
+    - run: pip install poetry==1.8.4
     - run: nox
     - run: poetry build
     - run: poetry publish --username=__token__ --password=${{ secrets.PYPI_TOKEN }}

.github/workflows/test-pypi.yml

@@ -7,13 +7,13 @@ jobs:
   release:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.10'
         architecture: x64
-    - run: pip install nox==2022.1.7
-    - run: pip install poetry==1.1.13
+    - run: pip install nox==2024.10.9
+    - run: pip install poetry==1.8.4
     - run: nox
     - run: version=$(poetry version --short) && poetry version $version.dev.$(date +%s)
     - run: poetry build

.github/workflows/tests.yml

@@ -8,11 +8,11 @@ jobs:
         python-version: ['3.10']
     name: Python ${{ matrix.python-version }}
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
-    - run: pip install nox==2022.1.7
-    - run: pip install poetry==1.1.13
+    - run: pip install nox==2024.10.9
+    - run: pip install poetry==1.8.4
     - run: nox

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.

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

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

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)