Address review: CopraRNA2, IntaRNAsTar, compressed genomes and vector reports

.github/workflows/python.yml

@@ -1,4 +1,4 @@
-name: Python migration
+name: CopraRNA 3
 on:
   push:
   pull_request:
@@ -17,9 +17,9 @@ jobs:
           - python: '3.11'
             biopython: '1.84'
           - python: '3.12'
-            biopython: '1.86'
+            biopython: '1.88'
           - python: '3.13'
-            biopython: '1.86'
+            biopython: '1.88'
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -35,7 +35,7 @@ jobs:
           /tmp/coprarna-wheel/bin/python -m pip install --force-reinstall --no-deps dist/*.whl
           cd /tmp
           /tmp/coprarna-wheel/bin/coprarna --version
-          /tmp/coprarna-wheel/bin/coprarna status
+          /tmp/coprarna-wheel/bin/coprarna helpers
           /tmp/coprarna-wheel/bin/coprarna helper archive-readme
 
   scientific:
@@ -50,10 +50,12 @@ jobs:
         shell: bash -el {0}
         run: |
           python -m pip install --no-deps .
+          python -m pip install ".[web]"
           python -m playwright install chromium --only-shell
       - name: Native scientific workflow and browser integration
         shell: bash -el {0}
         env:
           COPRARNA_PIPELINE_TESTS: '1'
           COPRARNA_BROWSER_TESTS: '1'
+          COPRARNA_REFERENCE_TESTS: '1'
         run: python -m pytest -q

.gitignore

@@ -1 +1,9 @@
 /.project
+
+__pycache__/
+*.py[cod]
+.pytest_cache/
+build/
+dist/
+*.egg-info/
+core_genome_archive/metadata/*.lock

MANIFEST.in

@@ -1,9 +1,7 @@
-include AGENTS.md README.2.md README.md LICENSE environment*.yml CopraRNA2.pl CopraRNA2.pl.md .gitignore copra_sRNA.jpg
-recursive-include coprarna *.py *.json *.txt *.gz
-recursive-include coprarna_aux *.pl *.R *.py *.js *.html *.txt *.csv *.md
-recursive-include core_genome_archive *.bz2
-recursive-include update_kegg2refseq *.pl *.sh *.txt *.csv *.md
+include AGENTS.md ChangeLog.md README.md LICENSE environment.yml .gitignore
+recursive-include coprarna *.py *.txt *.html
+recursive-include core_genome_archive *.gz *.json
 recursive-include tests *.py
 recursive-include tests/fixtures *
 recursive-include tools *.py
-global-exclude __pycache__ *.py[cod]
+global-exclude __pycache__ *.py[cod] *.lock