Release 1.0.0.rc2

.chglog/config.yml

@@ -2,7 +2,7 @@ style: github
 template: CHANGELOG.tpl.md
 info:
   title: CHANGELOG
-  repository_url: https://github.com/rmnldwg/lyscripts
+  repository_url: https://github.com/lycosystem/lyscripts
 options:
   commits:
     filters:

.github/workflows/release.yml

@@ -1,4 +1,4 @@
-name: Build and release Python package on PyPI
+name: Build
 
 on:
   release:

.github/workflows/testpypi.yml

@@ -1,4 +1,4 @@
-name: Build and release Python package on TestPyPI
+name: Test Build
 
 on:
   push:

.github/workflows/tests.yml

@@ -1,38 +1,56 @@
-# This is a workflow that runs test on the package
-name: Tests
+name: tests
 
-# Controls when the action will run.
 on:
-  # Triggers the workflow on push or pull request events but only for the main branch
   push:
     branches: [ main ]
   pull_request:
     branches: [ main ]
 
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
+  tests:
+    name: Run tests & report coverage
     runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
+    permissions:
+      pull-requests: write
+      contents: write
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Install python 3
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-      - name: install dependencies
-        run: |
-          python3 -m pip install -U pip setuptools setuptools-scm wheel
-          python3 -m pip install .[test]
-      - name: Run tests
+          python-version: "3.10"
+
+      - name: Install dependencies
         run: |
-          python3 -m pytest --doctest-modules
+          python -m pip install --upgrade pip
+          python -m pip install .[tests]
+
+      # Below, we first run pytest in the `tests/` folder. Because we use a `src`
+      # layout, this will fail if the package is not installed correctly.
+      - name: Test package is installable
+        run: pytest --cov=lyscripts --cov-config=pyproject.toml tests
+        env:
+          COVERAGE_FILE: .coverage.is_installable
+
+      # Now, we execute all doctests in the `src` tree. This will NOT run with
+      # the installed code, but it doesn't matter, because we already know it is
+      # installable from the step above.
+      - name: Run doctests
+        if: success() || failure()   # run these even if previous step fails
+        run: pytest --cov=lyscripts --cov-config=pyproject.toml --doctest-modules src
+        env:
+          COVERAGE_FILE: .coverage.doctests
+          GITHUB_TOKEN: ${{ secrets.LYCOSYSTEM_READALL }}
+
+      # Lastly, we collect all files that start with `.coverage` into one file and
+      # create a report either as a comment on the PR or in a separate branch if its
+      # a commit to the main branch. From that branch we can put badges and coverage
+      # reports into e.g. our main README.md
+      - name: Add coverage comment
+        if: success() || failure()   # run these even if previous step fails
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+          MERGE_COVERAGE_FILES: true

.pre-commit-config.yaml

@@ -1,17 +1,22 @@
+default_install_hook_types: [pre-commit, commit-msg]
+
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
+  - id: check-toml
+  - id: check-yaml
+  - id: check-json
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.4
+  rev: v0.12.0
   hooks:
     - id: ruff
       args: [ --fix ]
     - id: ruff-format
 - repo: https://github.com/compilerla/conventional-pre-commit
-  rev: v3.3.0
+  rev: v4.2.0
   hooks:
   - id: conventional-pre-commit
     stages: [commit-msg]

CHANGELOG.md

@@ -2,6 +2,35 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.0.0rc2] - 2025-06-26
+
+### Bug Fixes
+
+- Divide by midext prevalence. Fixes [#72].\
+  This fixes a bug we reintroduced where we didn't compute observed and
+  model prevalence in an analogous and comparable way.
+
+### Documentation
+
+- Fix build badge in README.
+- Fix outdated links to rmnldwg.
+
+### Miscellaneous Tasks
+
+- Update pre-commit & ruff rules.
+
+### Testing
+
+- Fix the dataset used for testing prevalences.
+
+### Build
+
+- Switch to `src` layout. Fixes [#74].
+
+### Ci
+
+- Use tests action with coverage.
+
 ## [1.0.0rc1] - 2025-05-27
 
 ### Bug Fixes
@@ -819,63 +848,66 @@ returns `None` instead. Fixes [#11]
 ## [0.5.3] - 2022-08-22
 
 <!-- markdownlint-disable-file MD024 -->
-[1.0.0rc1]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a7...1.0.0rc1
-[1.0.0.a7]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a6...1.0.0.a7
-[1.0.0.a6]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a5...1.0.0.a6
-[1.0.0.a5]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a4...1.0.0.a5
-[1.0.0.a4]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a3...1.0.0.a4
-[1.0.0.a3]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a2...1.0.0.a3
-[1.0.0.a2]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a1...1.0.0.a2
-[1.0.0.a1]: https://github.com/rmnldwg/lyscripts/compare/1.0.0.a0...1.0.0.a1
-[1.0.0.a0]: https://github.com/rmnldwg/lyscripts/compare/0.7.3...1.0.0.a0
-[0.7.3]: https://github.com/rmnldwg/lyscripts/compare/0.7.2...0.7.3
-[0.7.2]: https://github.com/rmnldwg/lyscripts/compare/0.7.1...0.7.2
-[0.7.1]: https://github.com/rmnldwg/lyscripts/compare/0.7.0...0.7.1
-[0.7.0]: https://github.com/rmnldwg/lyscripts/compare/0.6.9...0.7.0
-[0.6.9]: https://github.com/rmnldwg/lyscripts/compare/0.6.8...0.6.9
-[0.6.8]: https://github.com/rmnldwg/lyscripts/compare/0.6.7...0.6.8
-[0.6.7]: https://github.com/rmnldwg/lyscripts/compare/0.6.6...0.6.7
-[0.6.6]: https://github.com/rmnldwg/lyscripts/compare/0.6.5...0.6.6
-[0.6.5]: https://github.com/rmnldwg/lyscripts/compare/0.6.4...0.6.5
-[0.6.4]: https://github.com/rmnldwg/lyscripts/compare/0.6.3...0.6.4
-[0.6.3]: https://github.com/rmnldwg/lyscripts/compare/0.6.2...0.6.3
-[0.6.2]: https://github.com/rmnldwg/lyscripts/compare/0.6.1...0.6.2
-[0.6.1]: https://github.com/rmnldwg/lyscripts/compare/0.6.0...0.6.1
-[0.6.0]: https://github.com/rmnldwg/lyscripts/compare/0.5.11...0.6.0
-[0.5.11]: https://github.com/rmnldwg/lyscripts/compare/0.5.10...0.5.11
-[0.5.10]: https://github.com/rmnldwg/lyscripts/compare/0.5.9...0.5.10
-[0.5.9]: https://github.com/rmnldwg/lyscripts/compare/0.5.8...0.5.9
-[0.5.8]: https://github.com/rmnldwg/lyscripts/compare/0.5.7...0.5.8
-[0.5.7]: https://github.com/rmnldwg/lyscripts/compare/0.5.6...0.5.7
-[0.5.6]: https://github.com/rmnldwg/lyscripts/compare/0.5.5...0.5.6
-[0.5.5]: https://github.com/rmnldwg/lyscripts/compare/0.5.4...0.5.5
-[0.5.4]: https://github.com/rmnldwg/lyscripts/compare/0.5.3...0.5.4
-[0.5.3]: https://github.com/rmnldwg/lyscripts/compare/0.5.2...0.5.3
-
-[#2]: https://github.com/rmnldwg/lyscripts/issues/2
-[#5]: https://github.com/rmnldwg/lyscripts/issues/5
-[#8]: https://github.com/rmnldwg/lyscripts/issues/8
-[#11]: https://github.com/rmnldwg/lyscripts/issues/11
-[#13]: https://github.com/rmnldwg/lyscripts/issues/13
-[#15]: https://github.com/rmnldwg/lyscripts/issues/15
-[#16]: https://github.com/rmnldwg/lyscripts/issues/16
-[#17]: https://github.com/rmnldwg/lyscripts/issues/17
-[#20]: https://github.com/rmnldwg/lyscripts/issues/20
-[#21]: https://github.com/rmnldwg/lyscripts/issues/21
-[#23]: https://github.com/rmnldwg/lyscripts/issues/23
-[#25]: https://github.com/rmnldwg/lyscripts/issues/25
-[#30]: https://github.com/rmnldwg/lyscripts/issues/30
-[#31]: https://github.com/rmnldwg/lyscripts/issues/31
-[#33]: https://github.com/rmnldwg/lyscripts/issues/33
-[#40]: https://github.com/rmnldwg/lyscripts/issues/40
-[#41]: https://github.com/rmnldwg/lyscripts/issues/41
-[#44]: https://github.com/rmnldwg/lyscripts/issues/44
-[#45]: https://github.com/rmnldwg/lyscripts/issues/45
-[#51]: https://github.com/rmnldwg/lyscripts/issues/51
-[#53]: https://github.com/rmnldwg/lyscripts/issues/53
-[#54]: https://github.com/rmnldwg/lyscripts/issues/54
-[#57]: https://github.com/rmnldwg/lyscripts/issues/57
-[#70]: https://github.com/rmnldwg/lyscripts/issues/70
+[1.0.0rc2]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc1...1.0.0rc2
+[1.0.0rc1]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a7...1.0.0rc1
+[1.0.0.a7]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a6...1.0.0.a7
+[1.0.0.a6]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a5...1.0.0.a6
+[1.0.0.a5]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a4...1.0.0.a5
+[1.0.0.a4]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a3...1.0.0.a4
+[1.0.0.a3]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a2...1.0.0.a3
+[1.0.0.a2]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a1...1.0.0.a2
+[1.0.0.a1]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a0...1.0.0.a1
+[1.0.0.a0]: https://github.com/lycosystem/lyscripts/compare/0.7.3...1.0.0.a0
+[0.7.3]: https://github.com/lycosystem/lyscripts/compare/0.7.2...0.7.3
+[0.7.2]: https://github.com/lycosystem/lyscripts/compare/0.7.1...0.7.2
+[0.7.1]: https://github.com/lycosystem/lyscripts/compare/0.7.0...0.7.1
+[0.7.0]: https://github.com/lycosystem/lyscripts/compare/0.6.9...0.7.0
+[0.6.9]: https://github.com/lycosystem/lyscripts/compare/0.6.8...0.6.9
+[0.6.8]: https://github.com/lycosystem/lyscripts/compare/0.6.7...0.6.8
+[0.6.7]: https://github.com/lycosystem/lyscripts/compare/0.6.6...0.6.7
+[0.6.6]: https://github.com/lycosystem/lyscripts/compare/0.6.5...0.6.6
+[0.6.5]: https://github.com/lycosystem/lyscripts/compare/0.6.4...0.6.5
+[0.6.4]: https://github.com/lycosystem/lyscripts/compare/0.6.3...0.6.4
+[0.6.3]: https://github.com/lycosystem/lyscripts/compare/0.6.2...0.6.3
+[0.6.2]: https://github.com/lycosystem/lyscripts/compare/0.6.1...0.6.2
+[0.6.1]: https://github.com/lycosystem/lyscripts/compare/0.6.0...0.6.1
+[0.6.0]: https://github.com/lycosystem/lyscripts/compare/0.5.11...0.6.0
+[0.5.11]: https://github.com/lycosystem/lyscripts/compare/0.5.10...0.5.11
+[0.5.10]: https://github.com/lycosystem/lyscripts/compare/0.5.9...0.5.10
+[0.5.9]: https://github.com/lycosystem/lyscripts/compare/0.5.8...0.5.9
+[0.5.8]: https://github.com/lycosystem/lyscripts/compare/0.5.7...0.5.8
+[0.5.7]: https://github.com/lycosystem/lyscripts/compare/0.5.6...0.5.7
+[0.5.6]: https://github.com/lycosystem/lyscripts/compare/0.5.5...0.5.6
+[0.5.5]: https://github.com/lycosystem/lyscripts/compare/0.5.4...0.5.5
+[0.5.4]: https://github.com/lycosystem/lyscripts/compare/0.5.3...0.5.4
+[0.5.3]: https://github.com/lycosystem/lyscripts/compare/0.5.2...0.5.3
+
+[#2]: https://github.com/lycosystem/lyscripts/issues/2
+[#5]: https://github.com/lycosystem/lyscripts/issues/5
+[#8]: https://github.com/lycosystem/lyscripts/issues/8
+[#11]: https://github.com/lycosystem/lyscripts/issues/11
+[#13]: https://github.com/lycosystem/lyscripts/issues/13
+[#15]: https://github.com/lycosystem/lyscripts/issues/15
+[#16]: https://github.com/lycosystem/lyscripts/issues/16
+[#17]: https://github.com/lycosystem/lyscripts/issues/17
+[#20]: https://github.com/lycosystem/lyscripts/issues/20
+[#21]: https://github.com/lycosystem/lyscripts/issues/21
+[#23]: https://github.com/lycosystem/lyscripts/issues/23
+[#25]: https://github.com/lycosystem/lyscripts/issues/25
+[#30]: https://github.com/lycosystem/lyscripts/issues/30
+[#31]: https://github.com/lycosystem/lyscripts/issues/31
+[#33]: https://github.com/lycosystem/lyscripts/issues/33
+[#40]: https://github.com/lycosystem/lyscripts/issues/40
+[#41]: https://github.com/lycosystem/lyscripts/issues/41
+[#44]: https://github.com/lycosystem/lyscripts/issues/44
+[#45]: https://github.com/lycosystem/lyscripts/issues/45
+[#51]: https://github.com/lycosystem/lyscripts/issues/51
+[#53]: https://github.com/lycosystem/lyscripts/issues/53
+[#54]: https://github.com/lycosystem/lyscripts/issues/54
+[#57]: https://github.com/lycosystem/lyscripts/issues/57
+[#70]: https://github.com/lycosystem/lyscripts/issues/70
+[#72]: https://github.com/lycosystem/lyscripts/issues/72
+[#74]: https://github.com/lycosystem/lyscripts/issues/74
 
 [`emcee`]: https://emcee.readthedocs.io/en/stable/
 [`rich`]: https://rich.readthedocs.io/en/latest/

README.md

@@ -1,16 +1,17 @@
-<img src="https://raw.githubusercontent.com/rmnldwg/lyscripts/main/github-social-card.png" alt="social card" style="width:830px;"/>
+<img src="https://raw.githubusercontent.com/lycosystem/lyscripts/main/github-social-card.png" alt="social card" style="width:830px;"/>
 
-[![MIT license](https://img.shields.io/badge/license-MIT-blue.svg?style=flat)](https://github.com/rmnldwg/lyscripts/blob/main/LICENSE)
-[![GitHub repo](https://img.shields.io/badge/rmnldwg%2Flymph-grey.svg?style=flat&logo=github)](https://github.com/rmnldwg/lyscripts)
-[![build badge](https://github.com/rmnldwg/lyscripts/actions/workflows/build.yml/badge.svg?style=flat)](https://pypi.org/project/lyscripts/)
+[![MIT license](https://img.shields.io/badge/license-MIT-blue.svg?style=flat)](https://github.com/lycosystem/lyscripts/blob/main/LICENSE)
+[![GitHub repo](https://img.shields.io/badge/lycosystem%2Flymph-grey.svg?style=flat&logo=github)](https://github.com/lycosystem/lyscripts)
+[![build badge](https://github.com/lycosystem/lyscripts/actions/workflows/release.yml/badge.svg?style=flat)](https://pypi.org/project/lyscripts/)
 [![docs badge](https://readthedocs.org/projects/lyscripts/badge/?version=latest)](https://lyscripts.readthedocs.io/en/latest/?badge=latest)
-[![tests badge](https://github.com/rmnldwg/lyscripts/actions/workflows/tests.yml/badge.svg?style=flat)](https://lyscripts.readthedocs.io/en/latest/?badge=latest)
+[![tests badge](https://github.com/lycosystem/lyscripts/actions/workflows/tests.yml/badge.svg?style=flat)](https://lyscripts.readthedocs.io/en/latest/?badge=latest)
+[![Coverage badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/lycosystem/lyscripts/python-coverage-comment-action-data/endpoint.json)](https://htmlpreview.github.io/?https://github.com/lycosystem/lyscripts/blob/python-coverage-comment-action-data/htmlcov/index.html)
 
 ## What are these `lyscripts`?
 
-This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a *command line interface* (CLI) to the [lymph](https://github.com/rmnldwg/lymph) library and the [lydata](https://github.com/rmnldwg/lydata) repository that stores lymphatic progression data.
+This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a *command line interface* (CLI) to the [lymph](https://github.com/lycosystem/lymph) library and the [lydata](https://github.com/rmnldwg/lydata) repository that stores lymphatic progression data.
 
-We are making these "convenience" scripts public, because doing so is one necessary requirement to making our research easily and fully reproducible. There exists another repository, [lynference](https://github.com/rmnldwg/lynference), where we stored the pipelines that produced our published results in a persistent way.
+We are making these "convenience" scripts public, because doing so is one necessary requirement to making our research easily and fully reproducible. There exists another repository, [lynference](https://github.com/lycosystem/lynference), where we stored the pipelines that produced our published results in a persistent way.
 
 ## Installation
 
@@ -23,7 +24,7 @@ pip install lyscripts
 or installed from source by cloning this repo
 
 ```bash
-git clone https://github.com/rmnldwg/lyscripts.git
+git clone https://github.com/lycosystem/lyscripts.git
 cd lyscripts
 pip install .
 ```
@@ -59,7 +60,7 @@ For these YAML files we provide a unified schema containing all possible fields
 ```json
 {
     "yaml.schemas": {
-        "https://raw.githubusercontent.com/rmnldwg/lyscripts/main/schemas/ly.json": "*.ly.yaml"
+        "https://raw.githubusercontent.com/lycosystem/lyscripts/main/schemas/ly.json": "*.ly.yaml"
     }
 }
 ```

pyproject.toml

@@ -56,7 +56,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.urls]
-source = "https://github.com/rmnldwg/lyscripts"
+source = "https://github.com/lycosystem/lyscripts"
 documentation = "https://lyscripts.readthedocs.io"
 
 [project.optional-dependencies]
@@ -68,41 +68,51 @@ docs = [
     "myst_parser",
     "autodoc_pydantic",
 ]
-test = [
+tests = [
     "pytest",
+    "pytest-cov",
     "pytest-mpl",
 ]
+dev = [
+    "pre-commit",
+    "git-cliff",
+]
 
 [project.scripts]
 lyscripts = "lyscripts:main"
 
 [tool.setuptools.packages.find]
-include = ["lyscripts"]
+where = ["src"]
 
 [tool.setuptools_scm]
-write_to = "lyscripts/_version.py"
+write_to = "src/lyscripts/_version.py"
 local_scheme = "no-local-version"
 
-[tool.setuptools.dynamic]
-version = {attr = "lyscripts._version.version"}
-
 [tool.pytest.ini_options]
 testpaths = "."
 
 [tool.ruff.lint]
-select = ["E", "F", "W", "B", "C", "R", "U", "D", "I", "S", "T", "A", "N"]
+select = ["E", "F", "W", "B", "C", "R", "U", "D", "I", "S", "T", "A", "N", "COM", "FURB", "NPY", "UP"]
 ignore = ["D409"]
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["E402"]
-"**/{tests,docs}/*" = [
+"{tests,docs}/*" = [
     "D103",
     "E402",
     "S101",
     "S603",
     "S607",
 ]
 
+[tool.coverage.paths]
+source = [
+    "src/",
+    "**/site-packages/",
+]
+
+[tool.coverage.run]
+relative_files = true
 
 # git-cliff ~ default configuration file
 # https://git-cliff.org/docs/configuration