Merge branch 'main' into feature_data_prodigal_iss_101

.github/PULL_REQUEST_TEMPLATE/PR_template.md

@@ -0,0 +1,38 @@
+### What's new
+- Describe what was changed in the code and why it is useful or necessary
+- Closes #<issue_number>
+
+```[tasklist]
+### Blocked by...
+- [ ] merge after user/repo_name#PR_number
+- [ ] depends on #PR_number
+```
+
+### Run it locally 
+1. Checkout the PR branch.
+
+> Assuming 1) you already have a local copy of `q2-moshpit` that is installed in editable mode in your activated virtual environment and 2) the working directory is `q2-moshpit`; run the following. 
+
+```bash
+PR=<PR_number>
+git fetch origin pull/${PR}/head:pr-${PR}
+git checkout pr-${PR}
+```
+
+2. Let's get you some data to play with: 
+```bash
+<your code here>
+```
+
+3. Test it out!
+```bash
+<your code here>
+```
+
+### TODO
+- [ ] Fill in *Whats new* section. Erase any bullet points that are not used.
+- [ ] Erase *Blocked by...* task list if not used.
+- [ ] In *Run it locally*, **step 1**, make sure to write the PR number after you have submitted the PR.
+- [ ] In *Run it locally*, **step 2**, fill in the code to fetch the inputs to test the code.
+- [ ] In *Run it locally*, **step 3**, fill in the code to test the changes. 
+- [ ] Erase the *TODO* section.

.github/workflows/ci-dev.yaml

@@ -9,7 +9,7 @@ jobs:
   ci:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
-      distro: shotgun
+      distro: metagenome
       additional-reports-path: ./coverage.xml
       additional-reports-name: coverage
 
@@ -25,7 +25,9 @@ jobs:
           name: ${{ needs.ci.outputs.additional-reports-name }}
           path: ${{ needs.ci.outputs.additional-reports-path }}
 
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         name: 'Upload coverage'
         with:
           fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

q2_moshpit/kraken2/database.py

@@ -41,6 +41,7 @@
     "pluspfp8": "pluspfp_08gb",
     "pluspfp16": "pluspfp_16gb",
     "eupathdb": "eupathdb48",
+    "nt": "nt",
     "greengenes": "Greengenes13.5",
     "rdp": "RDP11.5",
     "silva132": "Silva132",

q2_moshpit/plugin_setup.py

@@ -310,7 +310,7 @@
             ['viral', 'minusb', 'standard', 'standard8',
              'standard16', 'pluspf', 'pluspf8', 'pluspf16',
              'pluspfp', 'pluspfp8', 'pluspfp16', 'eupathdb',
-             "greengenes", "rdp", "silva132", "silva138"],
+             'nt', 'greengenes', 'rdp', 'silva132', 'silva138'],
         ),
         'threads': Int % Range(1, None),
         'kmer_len': Int % Range(1, None),