Merge branch 'main' into update_install_instr

.github/workflows/ci-dev.yaml

@@ -0,0 +1,33 @@
+name: CI
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+
+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@v3
+        name: 'Upload coverage'
+        with:
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/join-release.yaml

@@ -0,0 +1,6 @@
+name: join-release
+on:
+  workflow_dispatch: {}
+jobs:
+  release:
+    uses: qiime2/distributions/.github/workflows/lib-join-release.yaml@dev

.github/workflows/tag-release.yaml

@@ -0,0 +1,7 @@
+name: tag-release
+on:
+  push:
+    branches: ["Release-*"]
+jobs:
+  tag:
+    uses: qiime2/distributions/.github/workflows/lib-tag-release.yaml@dev

Makefile

@@ -16,13 +16,11 @@ test-cov: all
 
 install: all
 	bash install-sra-tools.sh
-	maturin build --release -m fastq_writer/Cargo.toml
 	$(PYTHON) setup.py install
-	$(PYTHON) -m pip install --no-deps fastq_writer --find-links fastq_writer/target/wheels/
 
 dev: all
 	bash install-sra-tools.sh
-	pip install coverage parameterized maturin==0.10.3
+	pip install coverage parameterized
 	pip install -e .
 
 clean: distclean

README.md

@@ -1,5 +1,5 @@
 # q2-fondue
-![CI](https://github.com/bokulich-lab/q2-fondue/actions/workflows/ci.yml/badge.svg)
+![CI](https://github.com/bokulich-lab/q2-fondue/actions/workflows/ci-dev.yaml/badge.svg)
 [![codecov](https://codecov.io/gh/bokulich-lab/q2-fondue/branch/main/graph/badge.svg?token=UTM4W4B1KW)](https://codecov.io/gh/bokulich-lab/q2-fondue)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6388476.svg)](https://doi.org/10.5281/zenodo.6388476)
 [![DOI](http://img.shields.io/badge/DOI-10.1093/bioinformatics/btac639-B31B1B.svg)](https://doi.org/10.1093/bioinformatics/btac639)

ci/recipe/meta.yaml

@@ -14,35 +14,30 @@ build:
     make install
 
 requirements:
-  build:
-    - maturin ==0.10.3
-    - rust ==1.58.1
-
   host:
     - python {{ python }}
     - setuptools
 
   run:
-    - python {{ python }}
+    - entrezpy >=2.1.2
     - xmltodict
-    - pyzotero
+    - python {{ python }}
     - python-dotenv
-    - tqdm >=4.62.3
-    - entrezpy >=2.1.2
+    - pyzotero
     - q2-types {{ qiime2_epoch }}.*
     - qiime2 {{ qiime2_epoch }}.*
+    - tqdm >=4.62.3
 
 test:
   imports:
     - q2_fondue
     - qiime2.plugins.fondue
-    - fastq_writer
   requires:
     - parameterized
     - coverage
     - pytest-cov
   commands:
-    - pytest --cov q2_fondue --pyargs q2_fondue
+    - pytest --cov q2_fondue --cov-report xml:coverage.xml --pyargs q2_fondue
 
 about:
   home: https://github.com/bokulich-lab/q2-fondue