ENH: add action to collate fastp reports (#1)

* ENH: add action to collate JSON reports

* Add tests

* Migrate to pyproject.toml

* Reformat with black

* Update black to 24.10

* Fix the ci.yaml workflow

* Assert calls in any order

* Black again

* Add visualization test

* More tests

* Black again

* Corrections to conda recipe

.coveragerc

@@ -6,7 +6,6 @@ omit =
     **/__init__.py
     **/_version.py
     versioneer.py
-    **/_examples.py
 
 [report]
 fail_under = 90

.gitattributes

@@ -1 +1 @@
-q2_fastp/_version.py export-subst
+pyproject.toml export-subst

.github/workflows/black.yaml

@@ -0,0 +1,17 @@
+name: Black
+
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        with:
+          version: "24.10.0"
+          options: ". --check --extend-exclude '.*_version\\.py$' --verbose"

.github/workflows/ci-dev.yaml

@@ -9,25 +9,5 @@ jobs:
   ci:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
-      distro: metagenome
-      additional-reports-path: ./coverage.xml
-      additional-reports-name: coverage
-
-  coverage:
-    needs: [ci]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/download-artifact@v3
-        name: 'Fetch coverage from builds'
-        with:
-          name: ${{ needs.ci.outputs.additional-reports-name }}
-          path: ${{ needs.ci.outputs.additional-reports-path }}
-
-      - uses: codecov/codecov-action@v4
-        name: 'Upload coverage'
-        with:
-          fail_ci_if_error: true
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      distro: moshpit
+      recipe-path: 'conda-recipe'

.github/workflows/ci.yaml

@@ -5,7 +5,7 @@ on:
   push:
     branches: ["main"]
 env:
-    DISTRO: metagenome
+    DISTRO: moshpit
 
 jobs:
   test:
@@ -28,8 +28,8 @@ jobs:
       - name: Get last commit
         id: get-commit-msg
         run: |
-          echo "$(git log --pretty=%B -n 1 --skip 1)"
-          echo "commit-msg=$(git log --pretty=%B -n 1 --skip 1)" >> $GITHUB_OUTPUT
+          commit_msg=$(git log --pretty=%B -n 1 --skip 1 2>/dev/null)
+          echo "commit-msg=$commit_msg" >> $GITHUB_OUTPUT
 
       - name: Install dependencies
         run: python -m pip install requests yq
@@ -58,8 +58,8 @@ jobs:
       - name: Setup miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: 3.9
-          mamba-version: 1.5.10
+          python-version: "3.10"
+          mamba-version: "*"
           channels: conda-forge,defaults
           channel-priority: true
           activate-environment: conda-env

.gitignore

@@ -130,3 +130,5 @@ dmypy.json
 
 # PyCharm configuration
 .idea/
+
+_version.py

Makefile

@@ -15,7 +15,7 @@ test-cov: all
 	python -m coverage run -m pytest && coverage xml -o coverage.xml
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install pre-commit

ci/recipe/meta.yaml → conda-recipe/meta.yaml

@@ -1,12 +1,9 @@
-{% set data = load_setup_py_data() %}
-{% set version = data.get('version') or 'placehold' %}
-
 package:
   name: q2-fastp
-  version: {{ version }}
+  version: {{ PLUGIN_VERSION }}
 
 source:
-  path: ../..
+  path: ..
 
 build:
   script: make install
@@ -15,6 +12,13 @@ requirements:
   host:
     - python {{ python }}
     - setuptools
+    - versioningit
+    - wheel
+
+  build:
+    - python {{ python }}
+    - setuptools
+    - versioningit
 
   run:
     - fastp
@@ -26,12 +30,11 @@ requirements:
 test:
   requires:
     - coverage
-    - parameterized
   imports:
     - q2_fastp
     - qiime2.plugins.fastp
   commands:
-    - coverage run --rcfile ./repo/.coveragerc -m pytest && coverage xml -o coverage.xml
+    - pytest --pyargs q2_fastp
 
 about:
   home: https://github.com/bokulich-lab/q2-fastp

pyproject.toml

@@ -0,0 +1,50 @@
+[project]
+name = "q2-fastp"
+authors = [
+    { name = "Michal Ziemski", email = "[email protected]" }
+]
+description = "QIIME 2 plugin for metagenome analysis."
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/bokulich-lab/q2-fastp"
+Repository = "https://github.com/bokulich-lab/q2-fastp"
+
+[project.entry-points.'qiime2.plugins']
+"q2-fastp" = "q2_fastp.plugin_setup:plugin"
+
+[build-system]
+requires = [
+    "setuptools",
+    "versioningit",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.versioningit.vcs]
+method = "git-archive"
+describe-subst = "$Format:%(describe)$"
+default-tag = "0.0.1"
+
+[tool.versioningit.next-version]
+method = "minor"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.write]
+file = "q2_fastp/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_fastp*"]
+
+[tool.setuptools.package-data]
+q2_fastp = ["**/*"]

q2_fastp/__init__.py

@@ -5,9 +5,13 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-from . import _version
 from .fastp import process_seqs
+from .utils import collate_fastp_reports
 from .visualization import visualize
 
-__version__ = _version.get_versions()["version"]
-__all__ = ["process_seqs", "visualize"]
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = "0.0.0+notfound"
+
+__all__ = ["collate_fastp_reports", "process_seqs", "visualize"]